eScience Center holds inspiring workshop on Machine Learning for Research

January 23rd, 2020

Advancing research through machine learning: an applied coding workshop

From 20 -24 January, the Netherlands eScience Center held a workshop on Machine Learning for Research at its offices at Amsterdam Science Park. 

During the workshop, which took place in a collaborative workspace, six teams from different disciplines and research institutions spent a week of hands-on work with machine learning experts from the eScience Center. Each team came equipped with their own data and went on to an intensive one-week collaboration with machine-learning experts from the eScience Center and SURF to explore the best machine learning strategy to tackle their research question.

The core focus of the workshop was on writing and developing code to analyze the data and apply suitable machine-learning techniques. This hands-on machine-learning experience was complemented by inspiring talks by the Director of the Netherlands eScience Center, Joris van Eijnatten, Maxwell Cai (SURF) on machine and deep learning, Vincent Warmerdam (GoDataDriven) on artificial stupidity, Jakub Tomczak (VU) on deep generative modeling and Florian Huber (eScience Center) on machine learning in research – dealing with the non-ideal.

“The workshop was a great experience. Together with my team, I got to actually focus on the research for 5 days without any interruption. The experts gave us enough time to work with our own data, providing us with good set of starting models we can refine. The talks were inspiring and informative. The trainers didn’t just explore the possibilities of machine Learning but also discussed its pitfalls.” – Eduard Klapwijk

“The best thing is we get to use our own data and work on our own problem instead of a hypothetical problem. It feels like we are actually getting somewhere instead of leaving the workshop with a very abstract view on machine learning tackling research problems” – Niala den Braber

“I was amazed by how motivated, persistent, and curious all teams were in exploring machine-learning options on all the great datasets they brought. Many participants started from a fairly basic understanding of machine-learning, but I really felt that their good knowledge about research and data allowed them to super quickly get a very good intuition about what machine-learning can and cannot do. I hadn’t expected that we would come that far in only one week.” – Florian Huber 

Textual analysis provides insight into development of conservative rhetoric

January 15th, 2020

How has conservative rhetoric evolved over the past two centuries? And what kind of language have writers consciously used to express a moral opinion that might be qualified as conservative? In a new research paper, historian Joris van Eijnatten employs textual analysis tools to explore the nature of conservative rhetoric in the London-based Times newspaper between 1785 and 2010. Among other things, his findings throw light on the confluence of right-wing and left-wing rhetoric over time. The paper was recently published in Digital Scholarship, Digital Classrooms - New International Perspectives in Research and Teaching.

For his research, Van Eijnatten, director of the Netherlands eScience Center, employs two text mining techniques: n-grams (especially bigrams) and word embeddings. He traces a number of bigram phrases during the period in question, the most important of which are “conservative principles”, “conservative values”, “traditional values” and “permissive society”.

On principles and values

Van Eijnatten starts by exploring the term ‘conservative principles’, arguably the first instance of conservative rhetoric. His analysis reveals the popularity of this term and how its usage, both in parliament and in the Times, peaked in the 1840s before declining from the 1850s onwards. While the term was mostly political in nature, its usage can be classified into three distinct phases. During the first phase, pre-1830, it reflected the counterrevolutionary sentiment of early conservative thought. In phase two, between 1830 to 1950, it continued to be used in opposition to reform and the reform movement. The third and final phase (1950-2010) was characterised by a decline in its use.

Using bigram embeddings, the author then demonstrates several phrases that came to have the same meaning as conservative principles, the most popular being ‘conservative values’. "The use of the term values grew towards the end of the 19th century, when principles were on the wane", Eijnatten explains. "In its original sense, it referred to the economy, finances and trade. Its ethical connotation and political connotation originally emerged in the US before being widely adopted in British English.”

The moralising turn

But could the linguistic popularity of the term ‘conservative values’ have arisen in another context than principles? To answer this, Van Eijnatten selected nine words that continued to have stabled meanings in the periods 1901-1905, 1951-1955, and 2001-2005. For each of these words, he generated the top fifty most similar words, and for each of these words another top fifty most similar words. This resulted in 22,500 words in total (9 x 50 x 50), with the number of unique words ranging from 5,000 to 7,500.

By forcing the network to cluster automatically into three groups, a linguistic pattern emerges, one that seems to indicate what Van Eijnatten refers to as the ‘historical moralisation’ of politics. "Between 1955 and 2001, the semantic relations between the political and the civilisational became stronger, as illustrated by the transition from 'conservative principles' to 'conservative values'. This led me to examine value-laden phrases in which the political qualifier 'conservative' was omitted, in particular the phrase 'traditional values'."

The phrase 'traditional values' can be traced to the early part of the 20th century, a time of rising tension between tradition and modernity, says Van Eijnatten. Initially, the debate largely centred on socio-cultural change and allowed for various opinions and positions. This tension evolved into conflict in the early 1960s, when tradition was used in an explicitly oppositional sense to what become known as the permissive society. “The term eventually took on clear political significance and, as its use in The Times shows, became part of the rhetoric on the right in the UK.”

Conservativism as moral language

By tracking several strands of conservative rhetoric, from conservative principles through conservative values to traditional values, Van Eijnatten’s findings demonstrate how these phrases followed specific historical trajectories and, just as interestingly, how conservative rhetoric became assimilated into popular discourse in the UK in the 1980s.

Van Eijnatten: "We tend to categorise moral languages as ideologies, as enlightened, liberal, Christian, nationalist or conservative, but these simple labels often do more justice to ordering the present than to understanding the past and vice versa. Digital history techniques help us to identify the changing clusters of words that come together in moral languages. As my research shows, these techniques open up new avenues for research and paint us a different, more complex, ambiguous, and varied past, and help us conceive of different futures in a present that seems to have lost its bearings.”

Publication details

J. van Eijnatten, ‘On Principles and Values: Mining for Conservative Rhetoric in the London Times, 1785-2010’ in Digital Scholarship, Digital Classrooms - New International Perspectives in Research and Teaching pp. 1-26 (Farmington Hills, MI: Gale, 2020).

Read the full paper

Four projects awarded funding in the ESiWACE2 Service 1 call

January 8th, 2020

The Netherlands eScience Center and Atos-Bull have granted four proposals within the EU-funded project ‘Center of Excellence in Simulation of Weather and Climate in Europe’ (ESiWACE2). The selected projects will receive consultancy, advice and engineering from the research software engineers at the eScience Center and Atos-Bull. These collaborative projects will allow experts in high-performance computing (HPC) and accelerated computing to work together with model developers to advance the software in order that (parts of) the model can be executed efficiently on modern CPU processor or modern computing accelerators such as Graphics Processing Units (GPUs).

The ESiWACE and ESiWACE2 projects aim to improve model efficiency and prepare the software to enable model execution on existing and near-future hardware architectures and simulate experiments at unprecedented grid resolutions or ensemble sizes. In addition, it will include computationally expensive physical processes that were previously unfeasible.

The proposals

Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany - Natalja Rakowsky

Finite-volumE Sea ice-Ocean Model, Version 2.0 (FESOM2)

FESOM2 is a global sea-ice ocean circulation model based on unstructured meshes. It allows one to simulate the global ice-ocean system at extremely high resolution in the regions of interest at an affordable computational cost. The broad spectra of FESOM2 applications include several climate models and standalone sea ice-ocean configurations. The earth system components that have been successfully coupled to FESOM2 include: ECHAM6.3, OpenIFS, REMO, PISM and ReCOM.

Two aspects will be addressed:

1) Profile FESOM2 with GPUs in mind and port the best suited numerical kernels to GPUs.

2) Get a fresh view on FESOM2 optimization in general.

Cyprus Institute - Theo Christoudias

EMAC (ECHAM-MESSy Atmosphere Climate) model

The ECHAM/MESSy Atmospheric Chemistry (EMAC) model is a numerical chemistry and climate simulation system that includes sub-models describing tropospheric and middle atmosphere processes and their interaction with oceans, land and human influences.

Within the "Earth System Chemistry Integrated Modelling (ESCIMo)" initiative, chemistry-climate-simulations are conducted by the MESSy Consortium with the ECHAM/MESSy Atmospheric Chemistry (EMAC) model for special topics related to the national project of the DFG-Forschergruppe SHARP (Stratospheric Change and its Role for Climate Prediction) and the international IGAC/SPARC Chemistry-Climate Model Initiative (CCMI). These simulations will be carried out in support of upcoming WMO/UNEP ozone and IPCC climate assessments and will help to answer emerging scientific questions as well as improve process understanding. Acceleration of the chemistry mechanism can reduce required CPU-nodes and time-to-solution by a factor 5, with an order of magnitude more complex atmospheric chemical mechanism (in terms of number of species and reactions) than current state-of-the-art.

Delft University of Technology, Centrum Wiskunde & Informatica - Fredrik Jansson, Pier Siebesma

DALES - the Dutch Atmospheric Large Eddy Simulation

DALES is a large-eddy simulation code designed for studies of the physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers. DALES can also be used for studying more specific cases, such as flow over sloping or heterogeneous terrain, and dispersion of inert and chemically active species.

The main goals of this new collaboration are 1) improving the scaling of DALES to many nodes and 2) improved single-threaded performance through more cache-friendly data-access patterns, potentially switching from double to single precision calculations, and improved numerical algorithms.

The aim is to merge the optimizations into the official DALES version, so as to be easily accessible for all users.

Royal Netherlands Meteorological Institute (KNMI) - Thomas Reerink

OBLIMAP 2.0

Ice caps are part of the climate system and interact with the atmosphere and the ocean via various feedback mechanisms. Ice sheet models need to be coupled with general circulation models (GCMs) in order to simulate the interactions between ice sheets, atmosphere and ocean. Due to the type of the ice dynamic equations, ice sheet models use coordinate systems different from GCMs, requiring a projection and regridding or interpolation step. These and other specific GCM-ISM coupling issues are addressed by OBLIMAP.

This collaboration aims to develop a parallel implementation of OBLIMAP’s fast scan method and will serve the near-future demand of being capable to couple ice sheet modes, which are based on adaptive grids with GCMs. A parallel implementation of OBLIMAP’s fast mapping will improve the on-line mapping performance, which is interesting for high resolution (< 1km) applications. While OBLIMAP is ready for the major step to achieve on-line coupling of an ISM within an ESM which has been a scientific goal for about 15 years now, the proposed parallel OBLIMAP release will significantly extend the number of more complex or high-resolution applications.

Read more about ESiWACE2

Netherlands eScience Center co-develops portable workflow for structural variant detection

January 8th, 2020

Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. Despite advances in whole genome sequencing, however, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. To address this problem, a team of scientists and research software engineers from the Netherlands eScience Center has developed a new portable open-source workflow called sv-callers that enables improved detection of SVs in cancer genomes using multiple tools. Their work was recently published in PeerJ – the Journal of Life and Environmental Sciences.

Structural variants such as deletions, insertions and duplications, account for a large part of the genomic diversity among individuals and have been implicated in many diseases, including cancer. With the advent of novel DNA sequencing technologies, whole genome sequencing (WGS) is becoming an integral part of cancer diagnostics and can potentially enable tailored treatments of individual patients. However, despite advances in large-scale cancer genomics projects, the detection of SVs in genomes remains challenging due to computational and algorithmic limitations.

The ensemble approach

“Recent tools for somatic and germline SV detection exploit more than just one type of information present in WGS data”, says Dr Arnold Kuzniar, eScience Engineer and first author. “A promising way to obtain more accurate and comprehensive results is by using what is known as the ensemble approach, which has been shown to improve the detection of SVs. Nevertheless, running multiple SV tools efficiently on a user’s computational infrastructure or adding new SV callers as they become available has been difficult.”

According to Kuzniar, a common practice is to couple multiple tools, or “callers”, together with monolithic wrapper scripts and, to a lesser extent, by a workflow system. Such a workflow is recommended as a way to improve the extensibility, portability and reproducibility of data-intensive analyses, but is usually developed to run on one computer system and therefore not necessarily portable to or reusable on another system.

SV callers tied together

To address these problems, the team developed “sv-callers, a user-friendly, portable and scalable workflow based on the Snakemake and Xenon (middleware) software. The workflow includes state-of-the-art somatic and germline SV callers, which can easily be extended, and runs on high performance computing clusters or clouds with minimal effort. It supports all the major SV types as detected by the individual callers.

“The workflow was developed incrementally based on requirements in the context of the Googling the cancer genome project, which is led by Dr Jeroen de Ridder from the University Medical Center Utrecht and supported by the eScience Center”, says Kuzniar. “We have extensively tested the workflow with [human] WGS datasets on different HPC systems as well as performed a number of production runs on the genomes of cancer patients. The workflow readily automated parallel execution of the tools across compute nodes and enabled streamlined data analyses in a Jupyter Notebook.”

Kuzniar credits the workflow’s results to the wide-ranging expertise of the individual project partners. “Developing this workflow was truly a collective endeavor. Without the in-depth knowledge of and experience with short read sequencing data and SV detection in particular, the workflow would have been computationally efficient but the results incomplete or inaccurate from a biological point of view. I am really happy to be part of what we’ve achieved together.”

The team has already made the workflow freely available and moving forward intends to maintain the software.

Publication details

Kuzniar A, Maassen J, Verhoeven S, Santuari L, Shneider C, Kloosterman WP, de Ridder J. “SV-Callers: A Highly Portable Parallel Workflow for Structural Variant Detection on Whole-Genome Sequence Data” in PeerJ (6 January 2020). https://doi.org/10.7717/peerj.8214

Challenges in Machine Learning (CiML) 2019: A Look Back

December 23rd, 2019

On 13 December, the 6th edition of the Challenges in Machine Learning (CiML) workshop took place in Vancouver, Canada. This event, which is held annually, acts as a discussion platform for stakeholders involved in challenges in machine learning and data science – open online competitions that address problems by providing datasets or simulated environments. The aim of CiML is to allow participants to share their experience with challenge organization and to discuss best practices in challenge design.

This year’s edition was co-organized by Dr Adriënne Mendrik, eScience Coordinator at the Netherlands eScience Center. In the following interview, Adriënne looks back on the event and her involvement in it.

Can you briefly explain what the workshop is about?

The workshop is mostly focused on challenge design and provides the opportunity for challenge organizers to share lessons learned, what worked and what didn't. Organizing challenges is a complex task and a huge amount of work, that involves both social and technical aspects. Therefore, it is important to learn from each other and gain new insights. In general, challenges in machine learning and data science are open online competitions that address problems by providing datasets or simulated environments. They measure the performance of machine learning algorithms with respect to a given problem, resulting in a leaderboard. The playful nature of challenges naturally attracts students, making challenges a great teaching resource. However, in addition to the use of challenges as educational tools, challenges have a role to play towards a better democratization of AI and machine learning. They function as cost effective problem-solving tools and a means of encouraging the development of re-usable problem templates and open-sourced solutions.

How did the idea for this year’s workshop come about?

Last year, I submitted an abstract to the CiML workshop at the Conference on Neural Information Processing Systems (NeurIPS). During this workshop, the organizer Isabelle Guyon asked participants whether they would be interested in organizing the 2019 edition of CiML. I volunteered, since challenge design is one of my research interests – I recently submitted a joint paper on the topic of challenge design in medical image analysis to arXiv.

CiML is one of the few workshops I know of that focuses on challenge design, so it presented a great opportunity to get together with other experts in the field and discuss challenge design.

What were the main goals?

This years' topic was “Machine Learning Competitions for All”. I think challenges or machine learning competitions are a great way to bring people with different expertise together to work on relevant problems, and to gain insight into the strengths and weaknesses of algorithms. However, I also think there is a lot to gain in terms of challenge design and also in terms of diversity and awareness.

If challenges are about bringing people together to work on relevant problems and gain insight, it is good to think about how we can increase diversity in order to get better and more interesting results. This means that we should carefully consider the topics that we choose for challenges, but also think about how to for example include people with less experience in data science, people from different countries and people who are not competitive in nature, by for example emphasizing collaboration.

Our objective was twofold:one, to enlarge the challenge design community and foster greater diversity among participants and organizers;and two, to promote the organization of challenges for the benefit of more diverse communities.

Do you think you achieved these?

We are not there yet, but I think we made a great start and brought some great people together with various backgrounds. I especially loved the talks by Dina, Tara, Emily, Isabell and Frank. Dr. Dina Machuve is lecturer and researcher at the Nelson Mandela African Institution of Science and Technology (NM-AIST) in Arusha, Tanzania. She talked about her outlook from Africa, all the great work that is being done there, but also the hurdles that still need to be overcome. As a result of her talk, Kaggle (Google) reached out to Dina to discuss what they could do to overcome some of the hurdles. Dr. Tara Chklovski (CEO and founder of Technovation) was invited by Amir Banifatemi (XPrize). She talked about applying challenges to democratize AI, and the wonderful work she is doing to empower girls and families to be leaders and problem solvers in their lives and communities. Professor Emily M. Bender is the director of the Computational Linguistics Laboratory at the University of Washington (USA). She made us aware that we should consider how challenges impact direct and indirect stakeholders, for example a challenge (shared task) organized in her field on “Prediction of Intellectual Ability”. She proposed to include feedback from stakeholders in challenge design. Dr. Isabell Kiral (data scientist and blockchain researcher at IBM, Australia) talked about the epilepsy detection challenge she organized within IBM, where she tried to make it as easy as possible for people to participate, which resulted in people with various backgrounds being able to participate. Professor Frank Hutter is head of the machine learning lab at the University of Freiburg (Germany) and shared his thoughts about how we could make challenges less about engineering and give computer scientists the opportunity to benchmark their latest methodologies. At the end of the workshop we had open space sessions in which we discussed the organization of challenges for the benefit of more diverse communities.

Why are workshops like CiML important?

At present, the geographic and sociological repartition of challenge participants and organizers is very biased. While recent successes in machine learning have raised much hopes, there is a growing concern that the societal and economic benefits might increasingly be in the power and under control of a few. Therefore, it is absolutely crucial that organizers and practitioners regularly come together to discuss the ways to increase diversity and design challenges for the benefit of more diverse communities.

Is this workshop related to your work at the eScience Center?

Yes, at the eScience center I'm leading the EYRA benchmark project together with Annette Langedijk from SURF. It is important to keep up-to-date with the latest developments in challenge design so as to be able to advise researchers on how to design good benchmarks for science.

Are you planning to organize a similar workshop or event in 2020?

Yes, many people were enthusiastic about this years’ workshop. As a result we had many people who were interested in co-organizing the workshop next year. Isabelle Guyon (UPSud/INRIA, U. Paris-Saclay and ChaLearn) and Evelyne Viegas (Microsoft Research) are going to step down, because they have been organizing this workshop since 2014. I will continue next year together with Wei-Wei Tu (4Paradigm Inc. and ChaLearn), Tara Chklovski, Max Cappellari (XPrize), Justin Guinney (Sage Bionetworks), Isabell Kiral, Amir Banifatemi, and Gustavo Stolovitzky (IBM). 

Read more about CiML

Read more about Adriënne Mendrik

Winning proposals announced for eTEC-BIG call

December 12th, 2019

The Netherlands eScience Center and SURFsara have announced the winning proposals for the Innovative eScience Technologies for ‘Big Science’ (eTEC-BIG) call. The three winning projects will seek to accelerate the search for dark matter, improve an all-sky radio telescope and transient detection facility, and scale up a promising pangenome approach to plant genome sequencing.

The eTEC-BIG call aims to support research and development of innovative eScience technologies and software associated with big data handling, big data analytics and related computational methods, driven by a direct demand from any research area that can be identified broadly by the term ‘Big Science’. 

The proposals are classified into one of three technological research directions: Scalable Machine Learning & AI; Processing of Streaming Data; Large Scale (Distributed) Data Organization, Management & Semantics.

Each of the winning projects will receive a grant consisting of funds and in-kind support by research engineers from the eScience Center and technology and e-Infrastructure experts from SURFsara.

The awarded projects

DarkGenerators – Interpretable Large Scale Deep Generative Models for Dark Matter Searches
Dr. Christoph Weniger (University of Amsterdam)

Dark matter is five times more abundant in the universe than visible matter. Yet, its nature remains unknown and constitutes one of the most exciting and complex research questions today. This project will use advanced data science methods to enhance and accelerate the interpretation of astrophysical and collider data in the search for signals of dark matter. As such, deep generative models and differentiable probabilistic programming will be used to construct a framework for the fast and precise inference of high-dimensional data models.

Technological research direction: Scalable Machine Learning & AI

The PetaFLOP AARTFAAC Data-Reduction Engine
Dr. John Romein (Netherlands Institute for Radio Astronomy)

AARTFAAC is an all-sky radio telescope and transient-detection facility. It piggybacks on raw data from a limited number of antennas of the LOFAR telescope. Last year, the AARTFAAC 2.0 program started, which combines a planned telescope upgrade with better transient-detection capabilities and new science cases. The project will improve the AARTFAAC processing pipeline in order to:

  • incorporate algorithmic improvements and new GPU technologies to permit scaling to larger collecting area, larger bandwidth and higher resolution;
  • detect transients well within 7 seconds to allow triggering of the TBBs and alert other instruments;
  • provide near real-time calibrated data/images for space-weather and ionospheric monitoring;
  • facilitate other science cases by providing intermediate data products.

Technological research direction: Processing of Streaming Data

Scaling up Pangenomics for Plant Breeding
Dr. Sandra Smit (Wageningen University)

Modern plant research is being transformed to a data-driven endeavor. A main driver of this development is the continuous reduction in DNA sequencing costs – reconstructing the complete genome of a plant from short DNA sequences or finding genetic variants with respect to a reference genome are applications where large amounts of sequencing data are generated and applied to study plants and to accelerate and improve breeding. Traditional approaches to compare genomes, centered on a single reference, no longer suffice and therefore the field of genomics is switching to so-called pangenome approaches. Several novel graph-based data structures and algorithms are under development, but none of these can handle the numbers of large plant genomes required in modern research and in applications in plant breeding. This project will improve the scalability of a promising pangenome approach, called PanTools, using eScience technologies.

Technological research direction: Large-Scale (Distributed) Data Organization, Management & Semantics

Netherlands eScience Center and DANS launch new FAIR Software website

November 21st, 2019

The Netherlands eScience Center and Data Archiving and Networked Services (DANS) have developed a new FAIR Software website for researchers. The website, which was officially launched during the National eScience Symposium on 21 November 2019, provides recommendations to researchers on ways to improve the quality and reproducibility of their software.

Research software has become a fundamental part of current research practice and is also considered an increasingly important research output. As such, there is a growing awareness of the importance of improving the quality of research software as well as the recognition research software engineers receive from producing such software.

FAIR software principles

The FAIR principles are meant to help researchers and developers improve the reusability and reproducibility of software by providing a set of guiding principles to make research software findable, accessible, interoperable and reusable (FAIR). The principles, which are increasingly viewed as a hallmark of excellent research, originated in the field of data management. Their applicability to software is currently a topic of active research.

The new FAIR Software website aims to encourage the greater adoption of FAIR principles by providing a set of starting recommendations that researchers can use to improve the quality, reach and reproducibility of their software. The website is a joint initiative between the eScience Center and DANS.

“Together with our partners at DANS, we as the eScience Center are proud to have been involved in making this website a reality”, says Rob van Nieuwpoort, acting director. “The website answers a growing need among researchers for a set of good practices that can guide them in developing software that is of excellent quality, is reproducible and can be widely reused by other researchers, potentially in different disciplines. I have no doubt the FAIR Software site will become a vital go-to reference for the research community.”

“It was wonderful to work with such a diverse group of people”, says Dr Carlos Martinez-Ortiz, eScience Research Engineer and closely involved in the development of the website. “FAIR is a very important trend in science and has mostly been applied to data. But software is also extremely important for science and how the FAIR principles can be applied to software is an important step in improving the quality of research software.”

Visit fair-software.nl

Towards FAIR principles for research software

The launch of the website coincides with a recent position paper authored by a group of international researchers that summarizes the current status of the debate around FAIR and software as a basis for the development of community-agreed principles for FAIR research software. The authors discuss the differences between software and data with regard to the application of the FAIR principles. In addition, they present an analysis of where the existing principles can be applied to software directly, where they need to be adapted or reinterpreted, and where the definition of additional principles is required.

Read the full paper.

eScience Center holds National eScience Symposium on open science

November 21st, 2019

The Netherlands eScience Center held its 6th National eScience Symposium at the Johan Cruijff ArenA in Amsterdam on 21 November 2019. Titled ‘Digital Challenges in Open Science’, this year’s edition included interdisciplinary sessions on various topics on open science, the launch of a new FAIR Software website and the announcement of the Young eScientist Award 2019.

The symposium was kicked off by Prof. Rob van Nieuwpoort, acting director of the eScience Center, who briefly spoke about the growing influence of the open science movement and the irreversible transition to open science. However, while open science represents the future of research and reflects the fundamental values of the scientific process, it still faces major hurdles, according to Van Nieuwpoort. This is why it is imperative that researchers, policymakers and industry stakeholders come together to discuss these challenges and together find meaningful answers.

Prof. Frank Miedema, Vice Rector for Research at Utrecht University, then delivered the keynote address on the promise of open science. According to Miedema, there is much more to open science than only open access and FAIR open data. It also seeks to connect research more directly and continuously with societal stakeholders, who comprise a broad range of public groups with a diverse set of problems. “This open relation at all stages of knowledge production has been shown to improve the research agenda and to enhance the potential impact, use and adoption of new knowledge”, said Miedema.

The plenary session was followed by morning and afternoon sessions on the challenges and opportunities of open science in various domains, including health and life sciences, the humanities and social sciences.

See a recap of the full program.

FAIR Software and Young eScientist Award

The closing plenary included two highlights of the symposium – the announcement of the Young eScientist Award 2019 and the launch of the FAIR Software website.

First, the winner of the Young eScientist Award was announced. This year’s winning proposal was submitted by Lise Stork, a PhD researcher at the Leiden Institute of Advanced Computer Science (LIACS) at Leiden University. Stork, one of three finalists, received the award for her proposal to make historical biodiversity data directly available to researchers. As this year’s winner, Stork will receive 50,000 euros worth of expertise from the eScience Center to develop her proposal.

Read more about the Young eScientist Award 2019

Next up was the launch of a new FAIR Software website, a joint initiative between the Netherlands eScience Center and Data Archiving and Networked Services (DANS). The website provides recommendations to researchers on ways to improve the quality and reproducibility of their software.

Read more about the FAIR Software website

The symposium was concluded with an exhibition of a number of software tools and methodologies produced by the Netherlands eScience Center.

Lise Stork wins Young eScientist Award 2019

November 21st, 2019

Lise Stork was announced winner of the Young eScientist Award 2019 during the 6th National eScience Symposium on 21 November. Stork, a PhD researcher at Leiden University's Institute of Advanced Computer Science (LIACS), received the award for her project proposal to make historical biodiversity data directly available to researchers. As winner, Stork will receive 50,000 euros worth of expertise from the Netherlands eScience Center to develop her proposal.

For her project, Stork aims to enable researchers to access historical biodiversity data. Such data is present in various types of historical sources, commonly collected during expeditions to biodiverse areas. Although there are millions of such resources stored in museum archives worldwide, these are currently inaccessible to researchers and include handwritten organism descriptions, physical specimens and detailed organism illustrations. To this end, Stork has developed a workflow that allows biodiversity researchers to semantically annotate and access the data present in these diverse types of observational data. Together with the eScience Center, Stork will take the next crucial step to create a scalable and sustainable integrated web environment based on this workflow, which will allow researchers to disclose the contents of their archives.

“Receiving this award is an immense honor and gives me the opportunity to develop my project further”, says Stork. “My main objective is to create methods that will enable greater understanding and reuse of the rich archives of data that have been previously underused and therefore undervalued. By accessing these, biodiversity researchers will gain new insights into the changing picture of global biodiversity over several hundred years. These insights are crucial now that we are faced with growing biodiversity depletion. With the expertise and experience of the eScience Center, I will be able to embed my proof-of-concept solutions into scalable and sustainable services for the biodiversity research community.”

Great potential

“Lise's work is a prime example of how digital technologies can enhance and accelerate scientific progress in a research domain – in Lise's case in the area of global biodiversity”, says Dr. Frank Seinstra, program director of the Netherlands eScience Center. “The aim to facilitate and enhance access to a wealth of historical biodiversity resources is part of a larger aim to develop services for the domain as a whole. The Young eScientist Award is specifically intended to stimulate research endeavors of this type, as these have the potential to have a very broad impact - even far beyond that of the work of one individual researcher. The eScience Center is looking forward to partnering with Lise to help make her research idea a reality.”

Dr. Meiert Grootes, eScience Engineer and part of the selection committee, adds: “We are very pleased to honor Lise Stork with this year’s Young eScientistAward. Her proposal perfectly highlights the potential inherent in applying eScience techniques, principles and technologies such as linked data, the FAIR paradigm and web technologies. We look forward to collaborating with Lise to unlock the potential of underused biodiversity data, as well as to rechanneling the developed eScience tooling and research software back to the community across scientific domains.”

Lise Stork is a fourth year PhD researcher at the Leiden Institute of Advanced Computer Science (LIACS). Her work is at the intersection of computer science, biodiversity and digital humanities research. It involves using and developing semantic web and computer vision methods for analyzing the content of historical biodiversity archives.

Read more about Lise Stork

About the Young eScientist Award

The Young eScientist Award is an annual prize awarded by the Netherlands eScience Center to a young and ambitious researcher with a novel research idea. The prize consists of 50,000 euros worth of expertise. The winner, who is always announced during the National eScience Symposium, receives support from a team of eScience Research Engineers to develop his or her proposal. Winners are selected on the basis of demonstrated previous success in the development or application of data-driven or compute-intensive research, the quality of a new project idea, and the contribution to scientific research beyond the project. 

Vacancy: eScience Research Engineers specialized in web application development

November 19th, 2019

The Netherlands eScience Center is the Dutch national expertise center for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology.

We are looking for enthusiastic 

eScience Research Engineers specialized in web application development.

The position:

As an eScience Research Engineer, you will operate in an agile team focused on developing high-quality web applications for science. In this position, you will work on several projects that deal with scientific data dissemination and visualization, with a strong focus on the communication aspects of research.

Our projects deal with many aspects of science. Currently, the team is developing a platform for the open comparison of scientific algorithms, developing a web-based system for the comparison of segmentation techniques in medical imaging, making a system for tracking and displaying human interaction in visual analytics, and starting on a project to dive into visual storytelling for the remote effects of climate change and their impact on Europe.

eScience is intrinsically a team effort. Your primary role within this team will be of technical expert, developing the required software together with our other developers.Additionally, there will be opportunities to work closely with both researchers in academia and other eScience research engineers in- and outside the team and facilitate knowledge transfer between scientific disciplines.

If you are an enthusiastic team player with:

  • A Bachelor or Master degree.
  • Strong and demonstrable experience developing software. Preferably in the form of web applications and/or scientific or information visualization(s).
  • Expertise with different programming languages (preferably Python, Javascript, Typescript, WebGL, D3.js).
  • Expertise with Web frameworks is a bonus.
  • Good communication and writing skills in English.

Working conditions:

We offer a position at theeScience Center for a fixed period of 2 years within the collective agreement for Dutch Research Institutes (cao-OI). The candidate will be based at the Netherlands eScience Center in Amsterdam. Compensation is based on education and experience, starting from € 2.736- up to € 5.064,- gross per month, with a 38-hour working week (salary scales9-11). Holiday pay amounts to an additional 8% of the gross salary, and we also offer a 13th month of salary as an end-of-year payment. Working part time is possible, but because of the focus on teamwork we have set the minimum for this position to 32 hours a week.

The eScience Center offers flexible working conditions and an interesting and challenging position with additional options for personal development. You will work in an international team with an informal but creative and ambitious working environment. The main location is Amsterdam (Science Park). The eScience Center has an active diversity policy and seeks to hire persons with a background that is underrepresented at the eScience Center. We therefore especially encourage women and minorities to apply.

Interested in this position?

Are you interested in joining the eScience Center’s team? Please send your application to vacancy@esciencecenter.nl before January 1st, 2020.

Your application must include:

  • A recent CV
  • A motivation letter
  • A code sample, preferably in a GitHub repository
  • Any applicable references

For more information about this opportunity, please contact Maarten van Meersbergen, Senior eScience Research Engineer at m.vanmeersbergen@esciencecenter.nl. Additional information can be found at www.esciencecenter.nl.

Joris van Eijnatten appointed director of Netherlands eScience Center

October 31st, 2019

The Supervisory Board of the Netherlands eScience Center has appointed Professor Joris van Eijnatten as general director of the eScience Center, effective 1 January 2020. Van Eijnatten, who is currently professor of Cultural History at Utrecht University, succeeds Wilco Hazeleger.

As director of the Netherlands eScience Center, Van Eijnatten will provide strategic leadership to the Center’s approximately 70 research engineers and support staff. He will be responsible for the preparation, development and implementation of the Center’s policy and strategy, and will ensure that its strategic and operational objectives are achieved. In addition, Van Eijnatten will be tasked with further positioning the eScience Center as the Dutch national center of excellence for the development and application of research software and methodologies. As such, he will stimulate greater collaboration with Dutch academia and researchers and seek to intensify the Center’s links with other digital research initiatives in the Netherlands and elsewhere.

“We are extremely pleased that Joris van Eijnatten has agreed to lead the eScience Center”, says Jan de Jeu, chair of the eScience Center Supervisory Board. “Besides his impressive research and teaching credentials, Joris brings a wealth of senior administrative experience. He has extensive knowledge of the Dutch research landscape and a clear vision on the increasing importance of eScience in driving new research outcomes.”

“The Netherlands eScience Center will benefit greatly from Joris’ expertise and experience”, says Prof. Rob van Nieuwpoort, director of Technology. “We as the board of directors look forward to working with him to ensure that we execute our core mandate: to accelerate and enhance research through the application of eScience.”

The appointment of Joris van Eijnatten has the unanimous support of the eScience Center Works Council, says Maarten van Meersbergen, chair. “We are pleased and excited that the vacancy was filled by a very established and well-liked professor with a background in a discipline with such potential and complexity. We are confident thathis leadership will bring renewed stability to the Center and ensure we continue to grow sustainably.”

Van Eijnatten: “Over the past six or seven years, it has been my mission in life to encourage interest in the application of digital methodologies and technologies in the Humanities, both in research and teaching. The position of general director at the Netherlands eScience Center will enable me to continue this work on a wholly different level: nationally, internationally and across all disciplines. I am especially looking forward to working with the people at the Center, who are key to both continuity and change in the rapidly evolving world of eScience research."

About Joris van Eijnatten

Joris van Eijnatten has served as full professor of Cultural History at Utrecht University since 2009. Prior to this, he was, among other things, full professor of Cultural History at VU University Amsterdam and a research fellow at the Royal Netherlands Academy of Arts and Sciences, the Institut für europäische Geschichte (Mainz, Germany) and the Netherlands Institute for Advanced Studies (NIAS).

In addition to his research and teaching duties, Van Eijnatten has held various substantial administrative posts. From 2013 to 2018, he was head of Utrecht University’s department of History and Art History, and chaired UU’s section of History of Culture, Mentalities and Ideas between 2009 and 2018. Previously, he was director of the Research Institute for Language, Culture and History at VU Amsterdam’s Faculty of Arts.

Van Eijnatten has been the recipient of various grants, including a Humanities in the European Research Area (HERA) grant and an NWO Horizon grant. He was awarded the Hendrik Casimir-Karl Ziegler Research Prize in 1999 and a Fellowship for digital humanities at the National Library of the Netherlands in 2016. He is the author of several books and numerous journal and book articles and is a founder of the open-access International Journal for History, Culture and Modernity. He has published extensively in leading international peer-reviewed media, including Journal for the History of Ideas, International Journal of Intangible Heritage, Low Countries Historical Review and the Journal of Religious Ethics

Read more about Joris Van Eijnatten

A platform to better predict Alzheimer’s disease

October 17th, 2019

In 2018 Dr Esther Bron, assistant professor of Neuroimage Analysis and Machine Learning at the Erasmus Medical Center (Erasmus MC), was named the winner of the Young eScientist Award. Bron received this prize, which is annually awarded by the Netherlands eScience Center, for her proposal to build a platform for developing and sharing prediction methods for Alzheimer’s disease.

In this interview, Bron talks about the project and her research and shares her experience working with the eScience Center.

What is your main motivation for doing research? And what is the primary goal of the TADPOLE project?

My primary motivation is curiosity ­– I enjoy learning new things and being challenged. But I also find it important to do work that is useful and will eventually benefit other people. This is why I carry out research in the field of medicine. I like the combination of medical problems and technical solutions. At the moment I am developing a new methodology for the analysis of brain MRI scans, using mostly machine learning techniques.

The main goal of my collaboration with the Netherlands eScience Center is to build a platform for sharing prediction algorithms for Alzheimer’s disease with the scientific community. The platform will enable the further development and improvement of these prediction methods as well as their further validation on other datasets of patients with Alzheimer’s disease. The project is called TADPOLE-SHARE and builds on the TADPOLE challenge that I recently organized with fellow researchers from University College London. In this challenge, we objectively compared 62 prediction models developed by 34 international research teams.

What is are your aims with your research and the project? And what are some of the challenges you face?

My research is mostly focused on developing novel MRI analysis and disease prediction methods for Alzheimer’s disease. Currently, no curative treatment for Alzheimer’s disease is available. It is therefore essential to establish an accurate prediction of the disease progression in the early stage of the disease in individual patients. This would enable clinical trials to include the patients in which the treatment is expected to be most effective. The main challenges for accurate diagnosis and prediction are the complexity of disease, the difference in the disease pattern between different patients and the differences in datasets between different hospitals.

How did the project take shape?

I submitted a project proposal to the eScience Center and eventually won the Young eScientist Award 2018. I was pleased to hear that the Center liked my proposal and were keen to collaborate with me. In January 2019, I met with Dr Adriënne Mendrik (eScience Coordinator, ed.) and the EYRA team to start our collaboration and prepare a project plan.

Did the project differ from the original proposal?

The original proposal was quite short, so we had to make the project more specific and develop a detailed execution plan. The project consists of two main components. First, we collaborate with researchers from different countries who developed a prediction method for the TADPOLE challenge in order to rewrite their code and make it available to and usable by other researchers. Second, we work with SURFsara to explore whether we can use the ‘Research Cloud’ that they are currently developing as the platform for our project.

What role does collaboration play in the way you do research?

An increasingly important one. Collaboration with clinical researchers and clinicians is essential for developing a methodology that can eventually be used in clinical practice. Moreover, I believe it is essential to combine different methodologies as a way to produce a better, more effective methodology. This is also one of the reasons why we originally organized the TADPOLE challenge. The challenge is set up as a competition to find the method that can best predict which patients are developing Alzheimer’s disease. The primary aim is to share knowledge between methodology researchers and to objectively compare prediction methods. With the TADPOLE-SHARE project and the collaboration with the eScience Center, I am taking this a step further and making the developed methods available in a standardized and user-friendly way to other researchers.

What has the collaboration with the eScience Center been like so far?

Excellent. The atmosphere at the eScience Center is very welcoming and friendly, and there is a lot of expert knowledge on software development in the context of research projects. For this project, I collaborate with the EYRA team, whose members use the Scrum method to plan and carry out their work. The work is planned in two-week sprints, with some members fully dedicated to working on TADPOLE-SHARE. During the sprints, I usually work at the eScience Center to ease collaboration.

The EYRA team brings essential skills to the project, not only on a programming level but also with respect to the planning and focus of the project and the collaboration with other initiatives such the SURFsara Research Cloud.

What long-term impact on your domain and society do you hope your project will have?

I hope this project will make a twofold contribution. First, by allowing researchers to improve the comparison between the algorithms from the TADPOLE challenge and ultimately deliver better algorithms. And second, by increasing the sustainability and re-use of algorithms, thereby making them available for future research.

I should also mention that our motivation for using the Research Cloud is to create a sustainable platform and a proof-of-concept that can later be adopted by other challenges.

Read more about TADPOLE-SHARE.

New call for proposals launched in area of Energy System Integration

October 10th, 2019

In the call ‘Energy System Integration: Towards a Future-Proof, Affordable and Reliable Energy System’, researchers of NWO-acknowledged knowledge institutes, TO2-institutes and universities of applied science can submit proposals in the area of Energy System Integration. A budget of 4,7 – 5,0 million euros is made available, provided by NWO-ENW, NWO-SGW,Topsector Energy, and Taskforce for Applied Research (SIA). Additionally, the Netherlands eScience Center will provide eScience Research Engineers worth 1,2 million euros.

Energy System Integration

The call ‘Energy System Integration’ focuses on the integration issues of energy systems on various scales, such as coupling and optimizing the infrastructures for production, transport and storage of energy, and on finding optimal transition paths. The system as a whole is central here, not specific parts. The aim of the call is also to make digital technologies for energy system integration widely available.

This demands multidisciplinary approaches, including, among other things, mathematics, computer science, electrical engineering, economics, public administration, psychology, law, innovation sciences and ethics. The multidisciplinary approach is therefore included in the evaluation of the proposals. This approach can consist of combining disciplines within one domain (i.e. either natural/technical sciences, or humanities and social sciences), or by combining disciplines from two or all of the aforementioned domains.

For more information, see the eScience Center funding page. 

Submission and deadlines

For more information on the submissions procedure and deadlines, see here.

Promoting Open Science through the Research Software Directory

September 26th, 2019

Research Engineer Jurriaan Spaaks on how the eScience Center’s Software Directory presents another important step towards Open Science.

The value of the Research Software Directory and how it promotes Open Science

The road to Open Science faces many obstacles, one of which is to successfully generate and develop software that is reusable. To ease the findability, scientific referencing and reproducibility of research software, the Netherlands eScience Center developed the Research Software Directory (RSD). The RSD is an open-source content management system that makes it easier for researchers to promote and share their software with other parties.

In this interview, Jurriaan Spaaks, eScience Research Engineer and co-developer of the Research Software Directory, discusses the value of the RSD and how it promotes Open Science.

What exactly is a Research Software Directory?

The RSD is a content management system that has been specifically developed to present research software. It is set up in such a way as to avoid duplicating information that is already stored in other repositories such as GitHub, Zenodo and Zotero. Instead, we simply harvest information from these sources through their respective APIs, which means less work for whoever is filling the content management system with data.

How does the Research Software Directory promote Open Science?

Open Science has three pillars. First, public access to research papers is needed so that the description of a study and its outcomes are accessible to everyone. Second, the data underpinning the study should be available, thereby allowing others to assess whether the analysis outlined in the paper works as described. Software constitutes the third pillar, since that’s usually how published results are generated from data. All three pillars are needed to ensure the ideas, analyses and conclusions of a given study are exposed to critical review, and also to enable others to expand on previous work.

For the first two pillars, we have reasonably mature mechanisms in place. For example, we’ve always taken great care of collecting, storing and indexing research papers, and in recent years that care has been extended to also include data. However, compared to data and papers, it is more difficult to collect, store and index software – it requires constant maintenance.

The Research Software Directory promotes Open Science by bringing together the data, the software and the resulting papers in one place. Additionally, it nudges its users toward better software development practices by including software citation information and the use of persistent identifiers such as DOIs to uniquely identify various versions of the research software.

How does the Research Software Directory help increase re-use of research software?

What many people don’t realize about adopting someone else’s software is that it is actually preceded by a few steps, and that missing even one of these will prevent adoption from happening. Search engines are crucial for the findability of software, so we had to design the RSD in such a way that it uses Search Engine Optimization (SEO) techniques.

But even if you do your SEO perfectly, adoption will not happen if visitors to your web page can’t tell if the advertised research software will actually help them address their research questions. In other words, you have to make this clear to visitors. This is why we opted for a simple page layout, where we describe the research software at three levels of detail and present each piece of research software along with its scientific context.

The final and often overlooked step is to provide visitors with a good starting point for using the research software. This can be a tutorial or a video, or even a beginner API supporting only some simple use cases.

What has the response been to the Research Software Directory?

We received positive feedback. Most researchers see its value when we show them our own online portfolio, which is powered by the Research Software Directory. Researchers get frustrated when searching for software – the RSD presents relevant information clearly and concisely and as a result helps others to evaluate the usability and contribution of the software for their own research.

Can researchers also use the Research Software Directory to create their own software directories?

Yes, certainly. We went through quite a bit of effort to document the software to such a level that others can run their own copy of the RSD. If you’re a researcher and you want to run your own customized copy of the Research Software Directory, (e.g. to keep track of all the research software that’s written in a given department or research group) we can even help you get started.

How GGIR became the software of choice for analysing activity monitors

September 26th, 2019

Since 2008, wrist worn activity monitors that store high-resolution output have been increasingly employed to study human behaviour and movement. One of the most widely used methods to analyse modern activity monitors data is GGIR, an open source R software package developed by Dr Vincent van Hees, Senior Research Engineer at the eScience Center and independent consultant.

In the following interview, Van Hees explains the benefits of GGIR and how this software package became so successful.

What is GGIR?

The research softwareI, with the help of others, developed for health research to process and analyse data collected with wearable movement sensors (accelerometers).

How did this software package come about?

During my PhD in Cambridge, I developed a range of algorithms for processing wearable movement sensor data and I started to apply these algorithms todata sets collected under real lifeconditions.Initially, I did this with my own local R scripts, but this soon evolved into anopen source R package applicable to the wide diversity of study designsinvolving a variety of sensor brands.

GGIR loads the data form files, corrects for sensor calibration error, extracts signal features, provides estimates of daily sleep and activity patterns and generates detailed quantitative summaries.In addition, it provides a couple of simple visualisations to facilitate data-quality checks.

GGIR continues to be widely used by researchers across the world. How would you explain its popularity?

I think the popularity comes from a number of factors:

  • The software is broadly applicable within the research field.
  • Open source software is "free" (not development time of course)
  • The online resources to guide new users seem sufficient.
  • The software is writing in the R language, which makes it fit well with the typical user.
  • The software is used in various prestigious data sets and publications that act like a billboard for the software and add to the credibility of the software.
  • The software was the first of its kind in the field, which gives it a competitive advantage.
  • And the popularity fuels itself because the research community favors methodological consistency.

Would you say working at the eScience Center has benefited the development and maintenance of GGIR? Why?

Yes, at a personal level working at the eScience Center has helped me to strengthen my software development skills and broaden my understanding of data analysis techniques.Moreover, it has made me aware of the challenges across scientific domains in software development and sustainability, and about existing solutions. The software quality of GGIR has benefitted immensely from this. For example,by addingversion control, unit tests, and continuous integration it is much easier for others to make a contribution to the code and much easier for me to secure consistent functionality.Also, the eScience Center has acted as host organisation for three externally funded projects to work on new algorithms for GGIR. These projects have boosted the development of GGIR.

This popularity eventually led you to switch careers and become an Independent software consultant. What made you decide to do this?

In 2018 I started doing independent consultancy for half a day a week, which I later that year expanded to one full day per week. This exploratory phase provided me with the confidence to work as an independent consultant.I have been building expertise around movement sensor data analysis since 2003 and being able to keep usingall this experience feels good.

What are your plans with GGIR for the coming years? Any other projects you are working on?

Thousands of researchers around the world are using wearable movement sensorsin their research and need open source software solutions for a wide range of data challenges. Sofor the moment, there is enough workto do on software and algorithm developmentand on training software users.Additionally, I am collaborating with researchers at the Southern Danish Universityin Odenseon building aplatform for international pooling and analysisof wearable movement sensor and GPS data.

Also, I see an increasing demand for translating open source software solutions supported by academiato applicationswithin the health care industry. For that reason, I have partnered up with Shimmer and Nextbridge health (US) todevelop services around open source software in the health care industry.

Watch the GGIR tutorial

Download GGIR

Visit Vincent Van Hees' personal website

Vacancy: eScience Research Engineers for Big Data and Health

September 23rd, 2019

The Netherlands eScience Center is the Dutch national center of excellence for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general.

We are looking for enthusiastic:

eScience Research Engineers for projects in the areas of Big Data and Health

The position

As an eScience research engineer, you will operate in a team consisting of both eScience Research Engineers and researchers from partner institutions. Your goal will be to develop high-quality scientific software for collaborativeresearch projects.

You will work on several health-related projects, translate scientific challenges into effective and reusable ICT solutions that enable innovative (health) research. Important challenges include improving interoperability between, and reuse of, a variety of data resources, applying machine learning techniques in the context of distributed and privacy sensitive data, supporting user friendly, web-based interfaces aimed to support academic researchers as well as citizen science approaches.

eScience is intrinsically a team effort. You will therefore work closely with other eScience Research Engineers in- and outside the team and facilitate knowledge transfer between scientific disciplines. Good soft skills for communicating and collaborating with researchers and colleagues are important, as are the following technical skills.

We require

  • A completed Masters’ degree or PhD
  • Experience with complex data handling, preferably using linked data and semantic web technology
  • Experiencewith different programming languages (preferably Python and Java)
  • Good open source software engineering skills (version control, continuous integration, documentation).
  • Expertise in one or more of the following:
    • advanced data analytics, e.g. machine learning or statistical analysis
    • building API’s
    • containerization techniques such as Docker or Kubernetes
  • Good communication and writing skills in English

Job offer

We offer a position at the eScience Center initially for a period of 2 years within the collective agreement for Dutch Research Institutes (cao-OI). The candidate will be based at the Netherlands eScience Center in Amsterdam.Classification is based on education and experience with salary depending on qualifications and experience, starting from €2.736- up to €5.064,- gross per month, with a 38-hour working week (salary scale 10-11). Holiday pay amounts to 8% of the gross salary and we also offer a 13th month of salary as an end-of-year payment.

The eScience Center offers an interesting and challenging position with additional options for personal development. You will work in an international team with an informal but creative and ambitious working environment. The main location is Amsterdam (Science Park). The eScience Center has an active diversity policy. We therefore encourage women and minorities to apply.

Application deadline

Are you interested in joining the eScience Center’s team and work on exciting projects? Please send your application to vacancy@esciencecenter.nl by 24 November, 2019.

Your application must include

  • A recent CV
  • A motivation letter
  • A code sample
  • Any applicable references

If you would like more information about this opportunity you can contact l.ridder@esciencecenter.nl , eScience Research Coordinator at l.ridder@esciencecenter.nl. Additional information may also be found at www.esciencecenter.nl

A short description of the projects can be found in the following link: https://www.esciencecenter.nl/news/four-public-private-projects-on-big-data-and-health-have-been-awarded-grant

New call for proposals in support of EU weather and climate model communities

September 16th, 2019

The Netherlands eScience Center and Atos-Bull have announced a call for proposals for the EU-funded projects ‘Center of Excellence in Simulation of Weather and Climate in Europe’ (ESiWACE and ESiWACE2). The call aims to support the weather and climate model developing communities in Europe with preparing their simulation codes for (pre-)exascale computing platforms.

Large and complex applications

Weather and climate models are large and complex applications that experience a tension field between investments to enhance certain features, increasing fidelity, spatio-temporal resolutions or resolving more physical processes, and investments to adapt the software to the latest hardware architectures. Generally, these improvements go hand in hand, as higher accuracy can often only be achieved through increased resolution or by extending the ensemble size and thereby increasing the required computational resources. Where the modeling developments are driven by scientific expertise, the performance optimization is driven by the desire to use the compute resources efficiently and at sufficient scale.

However, after a long period of relative stability, the computing infrastructure is rapidly evolving and diversifying, with more change on the horizon. Adapting existing software to the latest computing platforms and exploiting the full capability of the architecture requires specific expertise and extensive changes at the source code level. As such, continued development of weather and climate models requires new collaborations between experts from different fields.

Preparing software for computing platforms and architecture

The ESiWACE and ESiWACE2 projects aim to improve model efficiency and prepare the software to enable model execution on existing and near-future hardware architectures and simulate experiments at unprecedented grid resolutions or ensemble sizes. In addition, it will include computationally expensive physical processes that were previously unfeasible.

The joint eScience Center/Atos-Bull call will support this objective by stimulating new collaborations that provide consultancy and engineering efforts in support of exascale preparations of weather and climate model developing communities. These collaborative projects will allow experts in high performance computing (HPC) and accelerated computing to work together with the model developers to advance the codebase in order that (parts of) the model can be executed efficiently on modern CPU processor or modern computing accelerators, such as Graphics Processing Units (GPUs).

Read the full call description

Funding

A total of four proposals will be granted as part of the call. Each grant will consist of in-kind support in the form of one or two skilled Research Software Engineers (RSEs) employed by either the Netherlands eScience Center or Atos-Bull. The RSEs will work remotely on the project for 6 person months (PMs) during 2020. The hours will be planned flexibly and in mutual agreement with the applicant.

Procedure and deadline

Following submission, a technical review will be carried out on the technical feasibility and state-of-the art technology. The proposals that pass the review will be sent to an external scientific review committee for a final selection based on scientific merit and impact. The accepted proposals will be announced in December 2019.

The submission deadline is 14:00 CET on 1 November 2019. Proposals sent after this deadline will no longer be considered.

Apply now

Read more about ESiWACE2

ESiWACE2 has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823988.

Scientists develop detailed representation of clouds in weather and climate models

September 16th, 2019

An interdisciplinary team of climate researchers and computational experts has developed an innovative method to study cloud dynamics in unprecedented detail in weather and climate models. The method employs comprehensive three-dimensional cloud simulations to replace the traditional approximations of cloud processes currently used in global climate models. The coupling of these simulations to global models is done with the help of software technology originally developed for astrophysical researchThe team’s method and initial findings are published in the Journal of Advances in Modeling Earth Systems.

Superparameterization as alternative approach

It is notoriously difficult for climate modelers to accurately depict cloud processes. Cloud dynamics act on scales from millimeters to several kilometers, but present-day global climate models typically operate on scales from 100 km and coarser. To overcome this scale gap in the models, researchers have traditionally used approximate formulae, known as parameterizations, to represent cloud physics. Parameterizations are simplified numerical representations of physical processes based on measurements and physical understanding.

In their paper, the team, comprising researchers from the Royal Netherlands Meteorological Institute (KNMI), Delft University of Technology (TU Delft), the Centrum Wiskunde & Informatica (CWI) and the Netherlands eScience Center, presents a computationally attractive alternative. They have replaced the parameterizations of clouds in a global-scale model developed by the European Centre for Medium-Range Weather Forecasts (ECMWF) with a turbulence-resolving model (in technical terms a large-eddy simulation) developed by the KNMI and Dutch universities.

A 3D rendering of simulated cloud data in an artistic setting, illustrating the power of high-resolution calculations of 3D cloud structure at chosen geographic locations in a global weather-modeling contextCredits: Johanna Grönqvist

This approach of replacing parameterizations by explicit simulations, called superparameterization, has the advantage that all the relevant processes for the formation and development of clouds are actually resolved and represented in the model. This will increase the reliability of the simulations by, for example, improved predictions of cloud cover, cloud amount and cloud top heights.

"It is incredible that we can now represent clouds so realistically in global weather and climate models", says lead author Dr Fredrik Jansson from CWI. “It is still a big computation to resolve clouds globally, but by applying our method to the regions where traditional approximations fail, I think we can gain a huge understanding of the role of clouds in the present and future climate."

The authors plan to apply their method to quantify the response of the global model to the changes in cloud representation, which will allow improvements in weather prediction with respect to rainfall and ultimately quantify the global role of clouds in the future warming earth climate.

A side-by side view of simulated cloud fields over the Netherlands and a satellite image. The blue squares show the detailed cloud-resolving simulations which are coupled to the global weather model shown in purple. The satellite image is from Terra MODIS, NASA/Goddard Space Flight Center Earth Science Data and Information System.

proud partner

"It is very exciting and satisfying to be able to take technologies that were developed to understand celestial bodies and interstellar clouds and apply these to better understand the weather on earth”, says Dr Inti Pelupessy, co-author and research engineer at the eScience Center.

Fellow author and research engineer Dr Gijs van den Oord agrees: "In many ways clouds on Earth are more complicated than interstellar clouds, and it was a big challenge to let the global model talk correctly to our cloud modelling code. I am extremely proud and satisfied that we as the Netherlands eScience Center were able to contribute our expertise to this project.”

Publication details

Fredrik Jansson, Gijs van den Oord, Inti Pelupessy, Johanna H. Grönqvist, A. Pier Siebesma, Daan Crommelin, 'Regional Superparameterization in a Global Circulation Model Using Large Eddy Simulations' in Journal of Advances in Modeling Earth Systems (12 July, 2019). DOI: 10.1029/2018MS001600.

The project is led by Daan Crommelin at CWI and Pier Siebesma at the Delft University of Technology and KNMI. Contact information: Daan.Crommelin@cwi.nlA.P.Siebesma@tudelft.nl.

Read the full article. 

Read more about the project.

Towards better e-mental health treatment through the use of text analysis

September 10th, 2019

eScience Research Engineer Dr Erik Tjong Kim Sang on 'What Works When for Whom', a joint interdisciplinary project on improving the effectiveness of e-mental health (EMH) interventions. 

Mental health issues like depression and anxiety are among the leading causes of the global burden of disease. To improve access to psychotherapy for a wider audience, health care professionals are increasingly using e-mental health interventions (EMH) such as web-based psychotherapy treatments. Whereas these treatments tend to be equally effective, the responsiveness to a specific treatment shows large differences. The personalization of treatments is seen as a major road for improvement.

In the interdisciplinary project ‘What Works When for Whom’, the Netherlands eScience Center has teamed up with Dr Anneke Sools from the University of Twente (UT) to use eScience methods and tools to analyse patterns in therapy-related textual features in email correspondence between counselor and client. By connecting patterns of known change indicators, the aim is to identify which therapy works best for whom and, ultimately, improve the effectiveness of EMH.

In the following interview, Dr Erik Tjong Kim Sang briefly talks about the project and the progress that’s been made. 

How far along is the project?

In September 2019 we entered the final year of this 4-year project.

What is the eScience Center’s exact contribution? 

The eScience Research Engineers are working on two topics: text analysis and data visualization. The project data consists of a collection of emails written by therapists and their patients. By performing an automatic text analysis, we hope to reveal patterns in the mails that can help the domain researchers to better understand the effects of the therapeutic process. We use data visualizations to find the patterns discovered by the text analysis.

What are the major technical challenges you’ve run up against?

Like many of our other projects involving textual data, the major challenge is how to deal with the available data. There is never enough data available to adequately deal with the plans of the domain researchers. Furthermore, the data weren’t immediately ready to use for the purposes of the project. Cleaning the data is a process that has taken years in this project and which still remains to be finished.

Two weeks ago, you held a hackathon with students at UT. What was the aim and outcome?

The hackathon had three aims:

1. Integration: collect four different text analysis tools in one environment.

2. Modularization: separate the text preprocessing and data visualization tasks from these analysis tools so that in future they can be used with other preprocessing and visualization software.

3. Training: learn to work with and to develop for Orange3, the platform system on which we will offer the tools.

Obviously, privacy is a major issue when dealing with personal data, especially in health care. How are you ensuring the data you work with remains secure and anonymous?

All personal information has been removed from the emails. We have agreed with the data provider on a protocol for dealing with possible misses of the automatic anonymization process. We have received the data on encrypted password-protected USB sticks. Making copies of the data is discouraged and may only be done to hardware which is also password-protected and encrypted. Every researcher and student who receives access to the data has to sign a form in which they pledge to deal with the data in a responsible way.

What will you do with the tools and methods you develop for this project?

Like our other projects, the tools we develop will be made available to the research community on Github. For this particular project, the management of the tools will be transferred to the BMS Lab, the software support department of the UT’s Faculty of Psychology. They will maintain the tools after the project has finished.

When will the project be completed?

The project will be completed on 31 August 2020. By that time, we want the domain researchers to have access to flexible text analysis tools that will enable them to study larger volumes of text than before. The researchers will definitely develop new ideas for automatic analysis once the project ends. We hope that in future the BMS Lab and their computer science students will be able to help the researchers to improve and expand the tools we’ve developed. 

Read more about the project

Read more about Anneke Sools

eScience Center takes part in hackathon to improve tools for analysis of internet therapies

September 3rd, 2019

On 29 and 30 August, the Netherlands eScience Center took part in a unique hackathon at the University of Twente (UT). The goal of the hackathon was to assess the usability of the Orange platform, which will run the data analysis for the project What Works When for Whom.

The hackathon brought together eScience research engineers, the Center’s project partners from UT’s department of Psychology, Health and Technology, the BMS Lab, students from University College Twente (ATLAS) and an expert from Tactus Verslavingszorg, the project’s data provider.

“The diverse backgrounds of those participating in the hackathon enabled everyone to see familiar topics from a new angle”, says Erik Tjong Kim Sang, eScience Research Engineer

The team examined four existing automatic methods for psychological analysis (CM, DAAP, LIWC and MLM) and built three of them in the platform. After a successful demonstration of DAAP in Orange at the end of the hackathon, it was concluded that the platform could be a great asset to the project. Using this platform, the research team should be able to analyze text automatically in a flexible way.

The project team will extend its application in the coming months. The ambition is to perform more analysis, to improve text analysis and to showcase the results in different ways in graphs. The ultimate goal is to help researchers get a better understanding of the effects of online psychotherapy sessions so they can adapt therapies to each patient.

Related links:

What Works When for Whom?:
https://www.esciencecenter.nl/project/what-works-when-for-whom
Psychology, Health and Technology:
https://www.utwente.nl/en/bms/pht/
ATLAS Twente:
https://www.utwente.nl/en/education/bachelor/programmes/university-college-twente/
BMS Lab:
https://bmslab.utwente.nl/
Tactus Verslavingszorg:
http://tactus.nl/
Orange:
http://orange.biolab.si/

Image: Drew Leavy (CC License) https://www.flickr.com/photos/drewleavy/4638947724

Kom bij ons programmeren tijdens het Weekend van de Wetenschap!

August 26th, 2019

Wil je leren programmeren? Dit is jouw kans! Het Netherlands eScience Center organiseert op zaterdag 5 oktober 3 workshops programmeren voor kinderen tijdens de Amsterdam Science Park Open Dag. De workshops zullen worden gegeven door vier eScience Research Engineers van het eScience Center. Spelenderwijs zullen zij de kinderen leren programmeren.

Let op: er is beperkt plek - scroll naar beneden om je aan te melden.

Doelgroep

Deze activiteit is geschikt voor kinderen van 8 t/m 12 jaar.

Tijdstippen workhops

Er starten programmeer-workshops om 12:00 uur, 14:00 uur en 16:00 uur.

Aanmelden

Voor deze activiteit dien je je aan te melden. Je kunt je aanmelden door te mailen naar Karima El Hadji (k.elhadji@esciencecenter.nl). Geef daarbij aan met hoeveel kinderen je wilt deelnemen aan de workshop en naar welk tijdstip je voorkeur uit gaat.

eScience Center and SURF to organize workshop on Machine Learning

August 20th, 2019

Machine learning has become a hugely popular topic in recent years. Everybody is talking about it and it has shown to be very helpful for different purposes. But what are the potential benefits of applying machine learning to research? And how can machine learning methods become an integral part of a software project? On 10 and 11 September, SURF and the Netherlands eScience Center will host a workshop in which these and other questions will be addressed.

In the following interview, eScience Tech Lead Carlos Martinez, who will conduct the workshop, briefly explains its aims and intended audience.

What is Machine Learning?

Machine Learning consists of programming a computer to perform specific tasks without giving it explicit instructions on how to so. This is usually done by feeding it large volumes of data from which it can learn.

How does it benefit research?

Machine Learning makes it possible to find patterns in data that would otherwise be difficult to identify by conventional methods.

What is the objective of the workshop?

The objective is to provide researchers with a basic introduction to some of the available tools for machine learning. Participants will learn how to develop their machine learning software by following good practices for scientific software development.

Why is it important/necessary?

Good practices are important because they allow other researchers to reuse the machine learning software you develop.

Who is it for?

PhD students, postdocs and researchers who develop software and would like to take advantage of Machine Learning algorithms.

What role does Machine Learning play in the work carried out by the eScience Center?

We help researchers to use machine learning to improve their research and to develop their software in such a way that other researchers can reuse and benefit from it.

I should mention that the eScience Center and SURF have extensive experience in helping researchers to fully benefit from Machine Learning by providing ICT infrastructure and high-quality research software. In addition, we are constantly looking for opportunities to share our expertise with researchers by organising symposiums, trainings, roadshows and workshops like this. So, don't wait, sign up today.

This workshop forms part of a series of computational skills workshops organized by the eScience Center and SURF. See here for more info. 

Vacancy: eScience Research Engineers for Climate and Hydrology Studies

August 15th, 2019

The Netherlands eScience Center is the Dutch national center of excellence for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general.

We are looking for enthusiastic:

eScience Research Engineers for Climate and Hydrology studies

The position

As an eScience research engineer, you will operate in a team consisting of both eScience Research Engineers and academic colleagues. Your goal will be to develop high-quality scientific software for ongoing research projects. Together with your team, you will be responsible for translating the scientific questions raised by these projects into dedicated solutions.

In this 2-year position, you will work on several climate related projects, and mainly on eWaterCycle II, where we study water movement on a global scale using local and global hydrological models.

eScience is intrinsically a team effort. You will therefore work closely with other eScience Research Engineers in- and outside the team and facilitate knowledge transfer between scientific disciplines. Good soft skills for communicating and collaborating with researchers and colleagues are important, as are the following technical skills.

We require

  • A completed Masters’ degree or PhD
  • Proficiency in Python, unit tests and continuous integration
  • Expertise with different programming languages (preferably Python and Bash)
  • Expertise in one or more of the following technological fields:
    • Machine learning
    • Optimized data handling
    • Efficient computing
  • Good communication skills (verbal and written) in English

Job offer

We offer a position at the eScience Center for a period of 2 years within the Collective Agreement for Dutch Research Institutes (cao-OI). The candidate will be based at the Netherlands eScience Center in Amsterdam.
Classification is based on education and experience with salary depending on qualifications and experience, starting from €2.736- up to €5.064,- gross per month, with a 38-hour working week (salary scale 10-11). Holiday pay amounts to 8% of the gross salary and we also offer a 13th month of salary as an end-of-year payment.

The eScience Center offers an interesting and challenging position with additional options for personal development. You will work in an international team with an informal but creative and ambitious working environment. The main location is Amsterdam (Science Park). The eScience Center has an active diversity policy and would like to hire persons with a background that is underrepresented at the Center. We therefore encourage women and minorities to apply.

Application deadline

Are you interested in joining the eScience Center’s team and working on exciting projects? Please send your application to vacancy@esciencecenter.nl by 30 September, 2019.

Your application must include

  • A recent CV
  • A motivation letter
  • A code sample
  • Any applicable references

For more information about this opportunity, please contact Yifat Dzigan, eScience Research Coordinator at y.dzigan@esciencecenter.nl

For a short description of the projects, please also see: eWaterCycle IIIS-ENES3


Vacancy: eScience Research Engineer for Earth Observations

August 13th, 2019

The Netherlands eScience Center is the Dutch national center of excellence for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general.

We are looking for enthusiastic:

eScience Research Engineers for projects in the area of Earth Observations

The position

As an eScience Research Engineer, you will operate in a team consisting of both eScience Research Engineers and academic colleagues. Your goal will be to develop high-quality scientific software for ongoing research projects. Together with your team, you will be responsible for translating the scientific questions raised by these projects into dedicated solutions.

In this 2-year position, you will work on several Geoscience projects analyzing Earth Observations to study different effects on climate, from glacier height change and Antarctica’s ice shelf damage and instability to the role of vegetation in the water, energy and carbon cycles.

eScience is intrinsically a team effort. You will therefore work closely with other eScience Research Engineers in- and outside the team and facilitate knowledge transfer between scientific disciplines. Good soft skills for communicating and collaborating with researchers and colleagues are important, as are the following technical skills.

We require

  • A completed Masters’ degree or PhD
  • Experience with handling and analyzing Earth Observations
  • Expertise with different programming languages (preferably Python and Bash)
  • Expertise in one or more of the following technological fields:
    • Machine learning
    • Optimized data handling (familiarity with Spark, Hadoop, docker,…)
    • Efficient computing (workflows, high-performance and distributed computing)
  • Experience with Data Assimilation is a bonus
  • Good communication skills (verbal and written) in English

Job offer

We offer a position at the eScience Center for a period of 2 years within the Collective Agreement for Dutch Research Institutes (cao-OI). The candidate will be based at the Netherlands eScience Center in Amsterdam.
Classification is based on education and experience with salary depending on qualifications and experience, starting from €2.736- up to €5.064,- gross per month, with a 38-hour working week (salary scale 10-11). Holiday pay amounts to 8% of the gross salary and we also offer a 13th month of salary as an end-of-year payment.

The eScience Center offers an interesting and challenging position with additional options for personal development. You will work in an international team with an informal but creative and ambitious working environment. The main location is Amsterdam (Science Park). The eScience Center has an active diversity policy and would like to hire persons with a background that is underrepresented at the Center. We therefore encourage women and minorities to apply.

Application deadline

Interested in joining the eScience Center? Please send your application to vacancy@esciencecenter.nl by September 30, 2019.

Your application must include

  • A recent CV
  • A motivation letter
  • A code sample
  • Any applicable references

For more information about this opportunity, please contact Yifat Dzigan, eScience Research Coordinator at y.dzigan@esciencecenter.nl. Additional information may also be found at www.esciencecenter.nl

For a short description of the projects, please see: https://www.esciencecenter.nl/news/we-are-pleased-to-announce-three-new-collaborations-in-the-area-of-earth-ob

Winner Lorentz-eScience competition 2020 announced

July 9th, 2019


The workshop ‘Hot but Habitable – Innovating to Adapt to Heat Waves of the Future’ has been named as the winner of the Lorentz-eScience Competition 2020. The winning proposal was submitted by Prof. H.A.M. Daanen (VU Amsterdam), Dr J. Shumake-Guillemot (World Meteorological Organization), Dr P. van den Hazel MD (Academic Collaborative Center Environment and Health) and Prof.H.M. Jones (US National Oceanic and Atmospheric Administration).

About the workshop

The goal of the workshop is to identify transdisciplinary digital systems-based solutions to minimize the impact of heat waves on the habitability of our cities, the enjoyment of the outdoors, and the health of our people.

This proposal was very well received by the evaluation panel: "This workshop targets a highly relevant topic - adapting to heatwaves - in a challenging, transdisciplinary and innovative manner. The format chosen is most likely to fuel creative thinking that is critical in meeting transdisciplinary challenges. We are pleased that we can include such a high quality and interesting workshop in our program.’

The workshop will be held in spring 2020 at the Lorentz Center in Leiden, the Netherlands.

About the Lorentz-eScience Competition

The Lorentz-eScience workshop competitions, organized by the Netherlands eScience Center and the Lorentz Center, sponsor leading-edge international workshops on the application of software to advance academic research. The workshops bring together researchers from the academic scientific community with those from the public/private sector.

For more information visit: Lorentzcenter

Job Opportunity: eScience Research Engineers for “Visual Storytelling for Climate Effects”

June 25th, 2019

The Netherlands eScience Center is the Dutch national expertise center for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general.

We are looking for enthusiastic:

eScience Research Engineers for “Visual Storytelling for Climate Effects”

The position

As an eScience research engineer, you will operate in a team consisting of both eScience Research Engineers and academic colleagues. Your goal will be to develop high-quality scientific software for ongoing research projects. Together with your team, you will be responsible for translating the scientific questions raised by this project into dedicated solutions.

In this 2-year position, you will work on several projects that deal with scientific data dissemination and visualization, with a strong focus on the communication aspects of research. The overarching goal of most of our team’s projects is to convince decision-makers to take scientific analyses seriously and to use that knowledge for future policy-making. To this end, you will mostly be making web-based software.

A significant part of your work will consist of working on the RECEIPT (REmote Climate Effects and their Impact on European sustainability, Policy and Trade) project. In this project, we will develop software with which to create and view visual stories based on the scientific data of multiple European institutes. This data will include economic-, financial-, risk-, weather-, agriculture-, infrastructure- and demographics forecasts and more.

eScience is intrinsically a team effort. You will therefore work closely with other eScience Research Engineers in- and outside the team and facilitate knowledge transfer between scientific disciplines. Good soft skills for communicating with researchers and colleagues are important, as are skills for accurate requirements engineering. In this position you will collaborate closely with researchers, present your work at conferences and workshops, and sometimes work on-site at our project partners, including those at European-level.

We require

  • A completed Masters’ degree or PhD
  • Some experience developing scientific or information visualization(s) and/or web applications
  • Expertise with different programming languages (preferably Javascript, Typescript, WebGL, D3.js)
  • Expertise with Angular, React or Vue is a bonus
  • Good communication and writing skills in English

Working conditions

We offer a position at the eScience Center for a fixed period of 2 years within the collective agreement for Dutch Research Institutes (cao-OI). The candidate will be based at the Netherlands eScience Center in Amsterdam. Classification is based on education and experience with salary depending on qualifications and experience, starting from € 2.672- up to € 4.945,- gross per month, with a 38-hour working week (salary scale 10-11). Holiday pay amounts to 8% of the gross salary and we also offer a 13th month of salary as an end-of-year payment.

The eScience Center offers an interesting and challenging position with additional options for personal development. You will work in an international team with an informal but creative and ambitious working environment. The main location is Amsterdam (Science Park). The eScience Center has an active diversity policy and seeks to hire persons with a background that is underrepresented at the eScience Center. We therefore encourage women and minorities to apply.

Interested in this position?

Are you interested in joining the eScience Center’s team and work on the RECEIPT project? Please send your application to vacancy@esciencecenter.nl before July 31, 2019.

Your application must include

  • A recent CV
  • A motivation letter
  • A code sample
  • Any applicable references

For more information about this opportunity, please contact m.vanmeersbergen@esciencecenter.nl, Senior eScience Research Engineer and project manager of the RECEIPT project, at www.esciencecenter.nl.

Four public-private projects on big data and health have been awarded grants

June 24th, 2019

In the Commit2Data round for Big Data & Health, four public-private research projects have been awarded grants for research into the early detection and prevention of cardiovascular diseases. The Top Sector Life Sciences & Health, NWO, ZonMW, the Heart Foundation and the Ministry of Health, Welfare and Sport have jointly made a total of €6.58 million available for these projects. The Netherlands eScience Center is also providing each project with support in the form of eScience Research Engineers.

Approved public-private research projects

Perfect Fit: Targeting key risk factors for cardiovascular disease in at-risk individuals using a personalized and adaptive approach
Smoking and lack of exercise increase the risk of cardiovascular disease. A consortium led by Prof. N.H. Chavannes (Leiden University Medical Center) will use big data to develop a personalized and flexible virtual coach that will help people to quit smoking.

Partners: TU Delft, University of Twente, Trimbos Institute, Leiden University, m, Sense Health, Virtuagym, Roessingh Research & Development, Stichting Pharos, Stichting Publiek Privaat Partnership Stop met Roken, GlaxoSmithKline and Stichting Zorg & Zekerheid.

CARRIER - Coronary ARtery disease: Risk estimations and Interventions for prevention and EaRly detection

– a Personal Health Train project
A consortium led by Prof. A.L.A.J. Dekker (Maastricht University) aims to identify groups with a high risk of cardiovascular diseases using existing datasets obtained from Statistics Netherlands, hospitals and general practitioners. The research group is also developing an electronic lifestyle coach to encourage people in this high-risk group to stay with their therapy programmes. Patients and caregivers will use the coach to develop a personalized lifestyle plan.

Partners: Maastricht University, Maastricht UMC+, Sananet Care BV, CBS, MAASTRO Clinic, HuisartsenOZL and Huis van de Zorg.

MyDigiTwin: Using Big-Data to put a cardiovascular digital twin into the hands of people
A consortium led by Prof. P. van der Harst (University of Groningen) will use MyDigiTwin to identify ‘personal digital twins’ using artificial intelligence algorithms. MyDigiTwin can predict the effects of lifestyle changes on the health of individuals. By comparing themselves with their digital twins, individuals can be made aware of the risk of cardiovascular disease and act accordingly.

Partners: UMC Groningen, UMC Utrecht, University of Twente, Erasmus MC, Siemens Healthineers Nederland N.V., HartKlinieken, Drimpy, Harteraad, HartNet Noord-Nederland, Huisartsenpraktijk Waardenburg, Mijnhuisarts BV, Hartstichting, NL Heart Registration, Heartlife Klinieken, Niped, Gezondheidsplein Middelstum, NL Healthcare Institute, The Story Network, RTRN, Menzis, Novartis Pharma B.V., Bayer B.V. and Sanofi-Aventis NL B.V.

STRAP: Self TRAcking for Prevention and diagnosis of heart disease
A consortium led by Prof. P. Markopoulos (Eindhoven University of Technology) is investigating opportunities, restrictions and successful case studies in the care of heart patients. The research group will examine how vulnerable groups and healthcare personnel can be involved in, and become more committed to, the care process. The research group will develop a platform where patients can enter healthcare data themselves based on questionnaires and digital sensors.

Partners: Eindhoven University of Technology, Erasmus MC, TU Delft, Cardiron BV, MyoVista, Sostark SME, Reinier de Graaf Gasthuis, Stethee, BOBO Tech, Game Solutions Lab SME, Smart Toilets and WCN.

More information on Big Data & Health

Source: NWO

Self-learning machines hunt for explosions in the universe

June 12th, 2019

And speed up innovations in industry and society

The National Science Agenda has awarded a 5 million euro grant to CORTEX – the Center for Optimal, Real-Time Machine Studies of the Explosive Universe. The CORTEX consortium of 12 partners from academia, industry and society will make self-learning machines faster, to figure out how massive cosmic explosions work, and to innovate wider applications.

Machine learning has rapidly become an integral part of society, in speech recognition or information retrieval. This is also the case in science, for detecting patterns in nature and the Universe. But the need is growing rapidly for such machines to respond quickly, in the application of self-driving cars and responsive manufacturing for example. On a more fundamental level, self-learning machines help us unveil a dynamical Universe we did not know existed up to recently. Bright explosions appear all over the radio and gravitational-wave sky. Many citizens and scientists are curious to understand where these come from.

“In CORTEX we aim to solve these open problems by bridging fundamental research to society,“ says Dr. Joeri van Leeuwen (ASTRON), the project lead. “We can only reach these ambitious goals if academic, applied, public and industry partners work together.”

Ben van Werkhoven (Netherlands eScience Center) explains the role of the Netherlands eScience center within the project (video in Dutch):

“Within CORTEX, The Netherlands eScience Center investigates how we can create software with the help of AI that can make optimal use of the computing power of modern computers. We then want to apply this technology to implement software with which we can observe explosive events in the universe.”


The Netherlands eScience Center has a central role in CORTEX. We will be extending Kernel Tuner, a tool by Ben van Werkhoven that uses machine learning algorithms to effectively speedup the optimization process of compute-intensive applications, with many new features and capabilities. We will then use this technology to automatically optimize the real-time machine learning pipelines for observing the explosive universe developed within CORTEX.


The 5 million Euro grant from the Nationale Wetenschapsagenda: Onderzoek op Routes door Consortia (NWA-ORC) program thus funds research at partners ASTRON, Nikhef, SURF, Netherlands eScience Center, Universiteit van Amsterdam, Radboud Universiteit Nijmegen, Centrum Wiskunde & Informatica, IBM Nederland B.V., BrainCreators B.V., ABN AMRO N.V., NVIDIA, NOVA, and Stichting ILT; in cooperation with Rijksmuseum, Thermo Fisher B.V., and Leiden University.

Job opportunities: eScience Research Engineers

June 4th, 2019

The Netherlands eScience Center is looking for eScience Research Engineers for Data Analytics, Optimized Data Handling and for Efficient Computing.

We are looking for enthusiastic team players who will contribute to a medium size, growing and flexible non-profit organization with many stakeholders. The eScience Center offers an interesting and challenging working environment with options for personal development. You will work in an international team with an informal but creative and ambitious atmosphere. More information about our organization can be found in the Annual Report.

For more details regarding each position check out the links below:

eScience Research Engineers for Data Analytics

eScience Research Engineers for Optimized Data Handling

eScience Research Engineers for Efficient Computing

We are pleased to announce three new collaborations in the area of Earth Observation

June 3rd, 2019

The projects are a result of the 2018/2019 GO Call for Proposals (User Support Programme Space Research), published in collaboration with the Netherlands Space Office (NSO) and the Netherlands Organisation for Scientific Research (NWO). The aim of the GO Call was to support researchers working in the Netherlands in the use of space infrastructure for the purpose of excellent studies in the areas of earth observation and planetary research.

Scheduled to start in 2019 the three awarded projects are collaborations with research teams from Utrecht University and TU Delft:

Eratosthenes - chasing shadows to investigate glacier change worldwide
Prof. dr. Michiel van den Broeke (Utrecht University)

This project will detect shadows casted by mountain tops in satellite imagery of glaciers. Changes in these shadows are used to estimate changes in glacier height. This new, unconventional approach provides unprecedented information about the health of small glaciers, and improves water discharge forecasting, sea level predictions and glacier models.

Remote sensing of damage feedbacks and ice shelf instability in Antarctica
Dr. Stef Lhermitte (TU Delft)

Antarctica is the largest uncertainty in sea level rise projections, with contributions ranging from -7.5 cm to >1 m by 2100. Ice shelf weakening due to damage plays an important role, although its impact is still poorly understood. Therefore, this project will combine remote sensing and big data approaches to assess this impact.

A new perspective on global vegetation water dynamics from radar satellite data
Prof. dr. ir. Susan Steele-Dunne (TU Delft)

The Advanced Scatterometer on the Metop series makes it possible to monitor radar backscatter as a function of incidence angle. For the first time, this information will be used to study global vegetation water dynamics to better understand the role of vegetation in the water, energy and carbon cycles.

National eScience Symposium 2019: Digital Challenges in Open Science

May 9th, 2019

The Netherlands eScience Center will host its 6th annual National eScience Symposium on on 21 November 2019 at the Johan Cruijff ArenA in Amsterdam. The theme of this year’s edition is ‘Digital Challenges in Open Science’ and will focus on the ways that innovative digital technologies can be used to advance Open Science. The Dutch National eScience Symposium is a one-day event where academic researchers, industry representatives and policy-makers from various disciplines come together to discuss and share views on the latest developments in eScience.

Register now

Using digital technologies to advance Open Science

According to the European Commission “Open Science represents a new approach to the scientific process based on cooperative work and new ways of diffusing knowledge by using digital technologies and new collaborative tools. The idea captures a systemic change to the way science and research have been carried out for the last fifty years: shifting from the standard practices of publishing research results in scientific publications towards sharing and using all available knowledge at an earlier stage in the research process.” The 2017 Coalition Agreement of the Dutch cabinet states that very soon “Open Science […] will be the norm in scientific research”.

The systematic change of the practice of science is made possible only by a close collaboration between practitioners, policy makers, and the designers and developers of new digital solutions and tools. In particular, the role of research software and support is essential. The 2019 National eScience Symposium is an opportunity for anyone working in academia, industry, research funding, research publishing, and research policy to engage in fruitful discussions with advanced technology experts. It is the place for knowledge exchange on these topics, and to help shape and define the future of Open Science.

Topics

The symposium will feature thematic sessions showcasing world-class research and digital developments around Open Science. Topics include digital challenges in open science, the role of open science in space and earth research, and the European Open Science Cloud. In addition, the symposium will showcase several demos of cutting-edge research software developed by the eScience Center and her partners, as well as the announcement of the Young eScientist Award 2019.

Visit the symposium website

The Young eScientist Award 2019

Each year young and ambitious researchers can participate in the Young eScientist Award competition. The award aims to stimulate a young scientist demonstrating excellence in eScience: the development or application of digital technology to address scientific challenges. The Netherlands eScience Center awards €50,000 worth of expertise to the winner. At the symposium the Young eScientist 2019 will be announced. Would you like to get motivated to participate this year? Read the winning research idea of 2018 by Esther Bron.

Program

09:00 – 09:45: Registration & Coffee
09:45 – 10-00: Welcome by director Netherlands eScience Center
10:00 – 10:30: Keynote Speech by Prof. Frank Miedema, Vice Rector for Research at Utrecht University
10:30 – 11:00: Coffee & networking – incl. information stands partners
11:00 – 12:30: Sessions on various Open Science topics, including keynote, lightning talks and discussions
12:30 – 13:30: Lunch & networking – incl. information stands partners
13:30 – 15:00: Sessions on various Open Science topics, including keynote, lightning talks and discussions
15:00 – 15:15: Young eScientist Award 2019
15:15 – 15:30: Closing + Young eScience Demo
15:45 – 18:00: Demo exhibition, networking, and drinks

Venue

Johan Cruijff ArenA
ArenA Boulevard 1
www.amsterdamarena.nl

Netherlands eScience Center labeled “Center of Excellence” by international review committee

May 7th, 2019

In February 2019, an international independent assessment committee reviewed the quality, impact, relevance and viability of the eScience Center over the period January 2014-June 2018. The committee was impressed with the technological expertise and concluded that the research is of excellent quality. According to the multidisciplinary committee of experts, the eScience Center has national leadership in its core areas of research. A number of recommendations was made to further improve the visibility and impact of the eScience Center's work.

The committee praised the fast progress since the inception of the center. The open calls and in-kind funding mechanism to select and conduct projects across the country were identified as unique and effective. The academic relevance and the leadership of the organization in terms of digitalization was highly appreciated. Besides the organization's involvement with a wide range of stakeholders and disciplines, the committee commended the eScience Center's involvement in training and workshops, conferences, advisory boards, the NWA, international research projects and joint research calls.

For the future, the committee recommends taking up a leading role in open science and the stimulation of software reuse. To further increase the impact of the eScience Center’s work, closer connections should be established with eScience initiatives within universities and with international eScience Centers. Also, possibilities for public-private partnerships should be more actively explored. The recommendations will be taken into account in the future strategy of the eScience Center.

The Evaluation Committee members were prof. Emmo Meijer (Topsector Chemistry, chair), prof. Dorret Boomsma (VU Amsterdam), prof. David De Roure (Oxford University), prof. Simone Hochgreb (Cambridge University), prof. Sverker Holmgren (Uppsala University) and prof. Maarten van Steen (University of Twente). The full report can be downloaded here.

New series of computational skills workshops

April 30th, 2019

The Netherlands eScience Center and SURF are joining forces to bring to the research community a new series of essential computational skills workshops. These workshops are aimed at researchers who would like to improve their computational skills to conduct research in our digital era.

Through these workshops, the eScience center and SURF inform and inspire researchers about the use of best practices in scientific software development as well as efficient use of cutting-edge computing systems.

Are you a researcher and looking at expanding your digital skills? Then these workshops are for you! Do you know someone who would benefit from improving their computational skills? Please encourage them to join!

The workshops

Good practices for High Performance Computing and Cloud
Good practices for machine learning
Good practices for research with Python
Make your research reproducible

You can participate in each workshop separately. It is not necessary to participate in the entire series.

Job Opportunity: Algemeen Directeur

April 25th, 2019

Het Netherlands eScience Center is een jonge en ambitieuze organisatie met een betrokken team. Wij zijn het nationale ‘Center of Excellence’ voor de ontwikkeling en toepassing van geavanceerde onderzoekssoftware. Wij zijn ervan overtuigd dat vrijwel elke wetenschappelijke discipline verbeterd en tot versnelde resultaten gebracht kan worden door gerichte toepassing van geavanceerde digitale technieken. Onze werkwijze is expliciet multidisciplinair, waarbij we onze kennis op het gebied van ICT, big data analytics, efficient computing, grootschalig datamanagement en kwaliteitssoftware combineren met diepgaande begrip van vele wetenschappelijke disciplines.

We zijn een stichting met meer dan 70, veelal internationale, werknemers met een omzet van 7 miljoen Euro op basis van verschillende geldstromen. De belangrijkste financiering komt van NWO en SURF, waar we nauw mee samenwerken.

Zeer recent heeft een onafhankelijke, internationale evaluatie van het Netherlands  eScience Center plaatsgevonden. De bevindingen van de evaluatiecommissie waren zeer positief en de aanbevelingen van de commissie bieden een uitstekende basis voor de verdere ontwikkeling van het Netherlands eScience Center in de komende jaren.

Wij zijn actieve pleitbezorgers van ‘Open Science’: we stellen onze kennis, ontwikkelde methodologieën en tools zo veel mogelijk publiek beschikbaar, zodat ze (her)bruikbaar zijn voor iedereen. Wij werken in onderzoeksprojecten samen met universiteiten en kennisinstellingen, zowel nationaal als internationaal. Door onze focus op generieke en herbruikbare kwaliteitssoftware beogen wij tegelijk een bijdrage te leveren aan de wetenschap als geheel.

Het Netherlands eScience Center is op zoek naar een

Algemeen Directeur 0,8-1,0 fte (m/v).

De positie

De algemeen directeur geeft leiding aan het Netherlands eScience Center, en is verantwoordelijk voor de voorbereiding, ontwikkeling, formulering en het tot uitvoer brengen van de missie en strategie van het Netherlands eScience Center, alsook het realiseren van haar inhoudelijke en bedrijfseconomische doelstellingen.

De directeur heeft grote affiniteit met en kennis van eScience in al haar verschijningsvormen. De directeur is een gepassioneerd verkondiger van de mogelijkheden van (nieuwe) digitale ontwikkelingen ter ondersteuning en voortstuwing van zowel bestaand als geheel nieuw wetenschappelijke onderzoek – in alle domeinen. De directeur is in staat zaken en situaties op een creatieve en pragmatische wijze te bekijken, en te komen tot strategieën en oplossingen die mogelijk onconventioneel of onorthodox zijn.

De directeur is een echte teamspeler, en coördineert en implementeert in nauwe samenwerking met het directieteam en alle andere collega’s het door het Bestuur vastgestelde beleid. De directeur legt daarbij verantwoording af aan het Bestuur. De directeur stuurt het Netherlands eScience Center zodanig aan dat alle medewerkers op een prettige en natuurlijke wijze tot maximale prestaties worden gebracht, en tot optimale uitwisseling van kennis en ervaring. De directeur heeft tevens een constructieve blik naar buiten, en ontwikkelt en onderhoudt nauwe relaties in het algehele eScience-landschap, met inbegrip van wetenschap, industrie, overheid en maatschappij.

Het takenpakket van de directeur bestaat uit de volgende onderdelen:

  • Het ontwikkelen van voorstellen aan het Bestuur ten aanzien van visie, strategie en beleid waarmee invulling gegeven kan worden aan de taken van het Netherlands eScience Center;
  • Voortbouwend op de succesvolle internationale evaluatie, en gebruikmakend van de aanbevelingen uit het evaluatierapport, leidinggeven aan de volgende fase in de ontwikkeling van het Netherlands eScience Center, specifiek op het gebied van personele, organisatorische en budgettaire aangelegenheden;
  • Het coördineren en bewaken van de voortgang en de samenhang van de implementatie van strategie en beleid;
  • Het signaleren, onderzoeken en benutten van kansen voor de verwerving van financiële middelen voor de intermediërende rol van het Netherlands eScience Center, en het opbouwen en onderhouden van een hiertoe relevant netwerk als onderdeel van het ecosysteem voor eScience;
  • Het vertegenwoordigen van het Netherlands eScience Center in de nationale en internationale onderzoeksgemeenschap;
  • Het zorgdragen voor een goede verstandhouding tussen het wetenschapsveld en het Netherlands eScience Center, alsmede voor een vooraanstaande positionering in het wetenschapsveld;
  • Verantwoordelijkheid dragen voor een groeiende organisatie van meer dan 70 werknemers, en een omzet van meer dan 7 miljoen Euro per jaar.

Een interessante kandidaat herkent zich in het volgende:

  • Ruime managementervaring; pragmaticus met een aantoonbaar streven tot samenwerking en teambuilding; oog voor een gezonde werkcultuur en ‘de menselijke maat’;
  • Ruime ervaring met academisch onderzoek; gepromoveerd in een voor het Netherlands eScience Center relevante discipline; kan worden beschouwd als een autoriteit in het eigen onderzoeksgebied, zowel nationaal als internationaal;
  • Aantoonbaar en meermaals succesvol in het zelfstandig verwerven van onderzoeksfinanciering;
  • Ruime ervaring met (inter)nationale samenwerking, op het terrein van tenminste twee disciplines anders dan het eigen onderzoeksgebied;
  • Succesvol trackrecord in de (mede-)ontwikkeling van multidisciplinaire data- en/of rekenintensieve eScience oplossingen en applicaties; ruime ervaring in het bereiken van wetenschappelijke doorbraken door toepassing van eScience tools en methodologieën;
  • Ruime ervaring met (wetenschaps)beleid; oog voor maatschappelijke ontwikkelingen en de relevantie daarvan voor beleid en strategie van het Netherlands eScience Center; in staat tot beleidsmatig en strategisch ‘out-of-the-box’ denken;
  • Beschikking over een sterk netwerk in het technologieveld, incl. ICT science, data science, en e-Infrastructuur;
  • Goede onderhandelingsvaardigheden en in staat om netwerken op te zetten en te onderhouden, zowel in het wetenschapsveld als in het bedrijfsleven.

Arbeidsvoorwaarden

Wij bieden een aanstelling van in eerste instantie een jaar met uitzicht op een vast dienstverband, voor 0,8-1,0 fte. De salariëring is, afhankelijk van opleiding en ervaring, conform de CAO-Onderzoekinstellingen en naar rato van het dienstverband.

Het Netherlands eScience Center kent gunstige secundaire arbeidsvoorwaarden waaronder een eindejaarsuitkering van 8,3% en 8% vakantietoeslag.

Informatie

Perrett Laver is gevraagd het Netherlands eScience Center en de benoemingsadviescommissie te ondersteunen bij het identificeren en beoordelen van mogelijke kandidaten.

Zoals gedefiniëerd in de Algemene verorderning gegevensbescherming (AVG) is Perrett Laver een gegevensbeheerder en een gegevensverwerker, en haar wettelijke basis voor de verwerking van uw persoonlijke gegevens is ‘legitiem belang’. Voor meer informatie hieover, uw rechten en de aanpak van Perrett Laver omtrent gegevensbescherming en privacy kunt u terecht op de website van Perrett Laver:

http://www.perrettlaver.com/information/privacy-policy/

Inlichtingen

Voor inlichtingen kunt u contact opnemen met Robert Prettner van Perrett Laver op +31(0)202404341. Sollicitaties kunnen worden geüpload op

www.perrettlaver.com/candidates onder vermelding van referentienummer 4151.

Interesse?

Belangstellenden kunnen solliciteren tot 12 mei 2019. U wordt verzocht uw cv en motivatiebrief te sturen naar robert.prettner@perrettlaver.com.
Sollicitatiegesprekken en een mogelijk assessment zullen plaatsvinden in de eerste drie weken van juni 2019.

Het Netherlands eScience Center hanteert een actief diversiteitsbeleid. Wij verzoeken belangstellenden met een achtergrond die ondervertegenwoordigd is in onze organisatie daarom nadrukkelijk hun interesse in de positie kenbaar te maken.We moedigen daarom vrouwen en minderheden aan om te reageren.

Acquisitie naar aanleiding van deze vacature wordt niet op prijs gesteld.

Uitnodiging Oratie: The e-scientist. Universal scientist or specialist?

April 23rd, 2019

Rob van Nieuwpoort geeft woensdag 8 mei zijn oratie over eScience: “The e-scientist. Universal scientist or specialist?” Heb je interesse in eScience & Efficient Computing, woon de oratie bij in the Aula van de UVA!

Wetenschap wordt steeds complexer en heeft meer en complexere ICT nodig. Het toepassen en onderzoeken van innovatieve complexe ICT in de wetenschappelijke disciplines noemen we eScience. Een echt kenmerk van eScience is dat het onderzoek plaatsvindt in nauwe samenwerkingsverbanden tussen informatici en wetenschappers in de disciplines. EScience bestrijkt alle wetenschapsgebieden, van archeologie tot levenswetenschappen en de astronomie. Ook technisch is eScience enorm breed. Afhankelijk van de wetenschappelijke vraag en het vakgebied kan het gaan om grootschalige simulaties, het koppelen van modellen, het integreren van observaties en modellen, het koppelen van verschillende databronnen, het zoeken in ongestructureerde data, visualisatie, machine learning en nog veel meer.

Het is enorm spannend en uitdagend om state-of-the-art informaticaonderzoek toe te passen om lastige wetenschappelijke problemen aan te pakken. Ook levert eScience een enorm veel inspiratie op voor nieuw en innovatief informaticaonderzoek. Een belangrijk aspect van eScience is het vergroten van impact van informaticaonderzoek. Dan gaat het niet alleen om impact in de wetenschap, maar ook maatschappelijke impact, bijvoorbeeld in de gezondheidszorg, of juist in industriële fabricageprocessen. Tegelijkertijd werkt het ook omgekeerd, en kunnen we als e-scientists met kennis van nieuwe technische mogelijkheden wetenschappers juist uitdagen om hun onderzoeksvragen aan te scherpen en nog groter te denken.

Rob's leerstoel heeft de titel “Efficient Computing for eScience”. Efficiënt rekenen heeft drie verschillende aspecten. Efficiëntie op grootschalige systemen, de schaalbaarheid dus; energie efficiëntie, en de efficiëntie van het programmeerproces zelf. Zijn onderzoek behandeld elk van deze thema’s, in verschillende toepassingsgebieden, met een focus op grootschalige gedistribueerde radio telescopen, zoals LOFAR en de Square Kilometre Array (SKA).

Oratie: The e-scientist. Universal scientist or specialist?
Datum - Tijd: 8 Mei, 16:00 uur
Locatie: Aula UvA
Spui, 1071 DN Amsterdam

Note: The lecture will be in Dutch

Job Opportunity: Human Capital Adviseur

April 23rd, 2019

Het Netherlands eScience Center is op zoek naar een part-time Human Capital Adviseur.

Bij het eScience Center zijn we ervan overtuigd dat wetenschappelijk onderzoek versterkt kan worden door de inzet van digitale technologie. Ons multidisciplinaire team, dat bestaat uit meer dan 70 medewerkers, heeft veel kennis van software ontwikkeling én van wetenschappelijk onderzoek in uiteenlopende disciplines. Sinds onze oprichting meer dan zes jaar geleden hebben we met meer dan honderd wetenschappelijke teams samengewerkt, van sociologen tot biologen en astronomen. Zulke samenwerkingen leiden niet alleen tot wetenschappelijke doorbraken, maar ook tot vernieuwende software die door andere wetenschappers kan worden ingezet. Naast onderzoek besteden we daarom ook veel aandacht aan het verspreiden van onze kennis en software om zo niet alleen onze projecten, maar ook de wetenschap als geheel vooruit te helpen.

Het eScience Center is een jonge, groeiende en ambitieuze organisatie zonder winstoogmerk met een betrokken team van veelal internationale werknemers. Er zijn veel mogelijkheden om kansen te pakken en jezelf te ontwikkelen. Daarnaast bieden wij een goed secundaire arbeidsvoorwaardenpakket aan met onder meer een eindejaarsuitkering, goede pensioenregeling en een ruime verlofregeling.

Human Capital Adviseur (m/f)
Part-time: 24 uur

Wat ga je doen?

Als Human Capital adviseur ben je verantwoordelijk voor Human Capital (HC). De waarde van de werknemer staat hoog in het vaandel bij ons Center en om dit te benadrukken hebben wij gekozen voor deze alternatieve benaming van Human Resources.

Je bent bij het Center de enige HC adviseur en je maakt deel uit van een klein Operations team. Je bent sparringpartner van het managementteam voor alle HC gerelateerde onderwerpen, rapporteert aan de Director Operations en via de Director Operations adviseer je ook het directieteam. Naast adviestaken, voer je zelf de HC administratie (o.a. in Loket), voer je recruitment uit, stel je zelf (arbeids)overeenkomsten op, en personele wijzigingen geef je door aan de externe salarisadministratie. Ook maak je rapportages en analyseer je HC gegevens ten behoeve van HC management informatie. We hebben regelmatig werknemers vanuit het buitenland waardoor je ook verantwoordelijk bent voor visumaanvragen en 30% regeling aanvragen.

Je bent empathisch, tactvol en houdt goed contact met zowel alle leidinggevenden als alle werknemers zodat je een goed beeld hebt wat er speelt en je tijdig kan benodigde acties kan afstemmen met de Director Operations. Je ondersteunt en begeleidt alle leidinggevenden bij o.a. het aanname proces, personeelsontwikkeling en verzuimdossiers.

Je krijgt energie van het leiden en implementeren van HC projecten (organisatie-breed), actualiseren van HC beleid en zorgen dat de werknemers van de wijzigingen op de hoogte zijn.

We zoeken een oplossings- en servicegericht persoon die meedenkt hoe we de organisatie professioneler maken, hoe processen efficiënter ingericht kunnen worden en iemand die in staat is deze inzichten pro-actief om te zetten in concrete acties en/of projecten.

Jouw werkuren kunnen over meerdere dagen, minimaal drie, in de week op kantoor verspreid worden. Het is de bedoeling dat je in elk geval de maandag en donderdag (deels) aanwezig bent.

In deze functie werk je nauw samen met de Director Operations. We zijn als organisatie hard aan het groeien. Daarom kijken we naar wat je kunt en spelen daar op in binnen de ontwikkeling van deze functie.

Wat is jouw profiel?

  • Je hebt een HBO/WO opleiding of equivalente werkervaring;
  • Een goede beheersing van de Engelse en de Nederlandse taal in woord en geschrift;
  • Minimaal 2 jaar ervaring als stand-alone HR adviseur in een groeiende organisatie;
  • Je hebt aantoonbare ervaring met het structureren van administratieve processen en het meedenken over organisatieontwikkeling en ontwikkeling van HC beleid;
  • Affiniteit met wetenschap, wat blijkt uit je cv;
  • Projectmanagement ervaring;
  • Je kan goed overweg met het Microsoft Office pakket;
  • Je hebt een pro-actieve werkhouding en durft op mensen af te stappen;
  • Samenwerken staat bij jou voorop en je bent in staat om met een grote verscheidenheid aan mensen te werken;
  • Je bent accuraat;
  • Ervaring met Loket is een pré;
  • Ervaring in samenwerking met een OR is een pré;
  • Ervaring met het schrijven van notities is een pré.

Wat bieden we jou?

Een aanstelling van vooralsnog één jaar, voor 24 uur per week. Salariëring, afhankelijk van opleiding en ervaring, van minimaal € 2.736,- tot maximaal € 4.339,- bruto per maand (schaal 10 van CAO-Onderzoekinstellingen 2019), bij een 38-urige werkweek. Het Netherlands eScience Center kent gunstige secundaire arbeidsvoorwaarden waaronder een eindejaarsuitkering van 8,3% en 8% vakantietoeslag.

Interesse?

Stuur je motivatie en CV uiterlijk 13 mei 2019 per email naar vacancy@esciencecenter.nl.

Wil je meer weten over het Netherlands eScience Center, bezoek dan onze website www.eScienceCenter.nl. Voor meer informatie over deze vacature kun je contact opnemen met de Mariska de Vogel, HC advisor a.i. (hc@esciencecenter.nl).

Bij het eScience Center hanteren we een actief diversiteitsbeleid. We zijn bewust op zoek naar nieuwe medewerkers met een achtergrond die ondervertegenwoordigd is in de organisatie. We moedigen daarom vrouwen en minderheden aan om te reageren.

Acquisitie naar aanleiding van deze vacature wordt niet op prijs gesteld.

New call & matchmaking meeting ‘Energy System Integration’

April 4th, 2019

NWO is organising a third call in the Energy System Integration programme in close collaboration with the System Integration Programme of the Top Sector Energy.

Researchers from knowledge institutions recognised by NWO, TO2 institutions and universities of applied sciences, can submit proposals in this call in the area of energy system integration and digitization. A total of 4.9 million euros has been reserved, funded by NWO Science, NWO Social Sciences and Humanities, the Top Sector Energy, the Taskforce for Applied Research (NPRO- SIA) and the Netherlands eScience Center. Interested parties can register for the information and matchmaking meeting to be held on May 23.

Energy system integration

The call 'Energy system integration' focuses on the integration issues of energy systems on various scales, such as coupling and optimizing the infrastructures for production, transport and storage of energy, finding optimal transition paths, etc. The system as a whole is central here, not specific parts. Another aim of the call is to make digital technologies for energy system integration widely available.

For whom?

The call is relevant for researchers in science and technology disciplines (such as mathematics, computer science, electrical engineering, physics and chemistry), as well as the disciplines in the social sciences and humanities. Researchers from knowledge institutions recognised by NWO can submit as a main applicant or a co-applicant, and can request funding for 2-3 PhDs or postdocs. Researchers from universities of applied sciences and TO2 institutions can also apply for salary costs. They can only act as co-applicants.

Conditions

An eScience Research Engineer will be added to each project awarded funding. Each proposal should therefore contain an approach for the eScience component of the research. Furthermore, proposals should have a design that is as multidisciplina as possible. There is a compulsory in-kind contribution (but no cash contribution) in addition to the project budget requested from NWO, which must be provided by public/private parties. The information about conditions for the call is subject to change. The final conditions will be stated in the call as soon as it is published in mid-May 2019.

Information and matchmaking meeting

On 23 May an information and matchmaking meeting will be held. You will receive more information about this call and its conditions during the meeting. You will also be able to pose questions to all partners involved and there will be the opportunity to find suitable consortium partners. You can now register for the information and matchmaking meeting via systeemintegratie@nwo.nl. In your mail please state your title, first name, surname, organisation, scientific discipline, and any dietary requirements. By registering you agree with your details being passed on to the other attendees for the purpose of matchmaking unless you explicitly state otherwise.

Contact and more information

Do you have questions or would you like to receive a specific advice about the suitability of your project idea or possible partners? Please do not hesitate to contact NWO via systeemintegratie@nwo.nl. In your mail please state whether the project idea can be shared with the funding partners of the call.

Source: NWO

New Call for Proposals: Innovative eScience Technologies for ‘Big Science’ (eTEC-BIG)

March 25th, 2019

New Call for Proposals & Information Event: Innovative eScience Technologies for ‘Big Science’ (eTEC-BIG)

The new call for proposals ‘Innovative eScience Technologies for Big Science (eTEC-BIG)’ is open. We invite ‘Big Science’ researchers and ICT researchers to apply for funding to address innovative compute-intensive and/or data-driven research problems.

Purpose

This call for proposals aims to support research and development of innovative eScience technologies and software associated with big data handling, big data analytics and related computational methods, driven by a direct demand from any research area that can be identified broadly by the term ‘Big Science’.

In the context of this call, ‘Big Science’ broadly indicates those scientific research directions 1) whose challenges in terms of complexity and 2) whose needs in terms of data analytics and data management capabilities, as well as processing power, far exceed that of other research endeavors today. Typically, technological developments in Big Science domains are expected to arrive in – and impact – other (non-Big Science) domains only years or even decades later.

Each project must focus on one of the following ‘Technological Research Directions’:

I. Scalable Machine Learning & AI
II. Processing of Streaming Data
III. Large-scale (Distributed) Data Organization, Management & Semantics

Projects awarded in this call for proposals typically will be led by either:

- a technology-oriented PI from the selected Big Science research area, or
- a domain-oriented PI from ICT Science (i.e. a technical discipline such as data science or computer science). In this case, it is required to include at least one co-applicant & team member from the selected Big Science research area.

When to apply?

The deadline for the submission of pre-proposals is Thursday 9 May 2019, 14:00 CET.
The deadline for submission of full proposals is Thursday 29 August 2019, 14:00 CET.

Information event

To further inform interested applicants of the specific aims of this call for proposals, the mission and approach of both the eScience Center and SURFsara, the role and expertise of the eScience Research Engineers and the SURFsara Technology & e-infrastructure Experts, the software technologies implemented and applied by the eScience Center and SURFsara, and the specific capabilities of the Dutch National e-Infrastructure, an information event will be organized at Amsterdam Science Park on April 9, 2019. Registration is required. Presence of at least one team member at the event is highly recommended, but not mandatory.

Program

13:30 – 14:00 Arrival & Coffee
14:00 – 14:20 General introduction: eTEC-BIG Call for Proposals
14:20 – 14:50 Netherlands eScience Center & Core Technological Competences
14:50 – 15:20 SURFsara, Technological Expertise & SURF e-Infrastructure
15:20 – 15:30 Break
15:30 – 16:00 Examples of ongoing eScience & SURFsara projects
16:00 – 16:30 Remaining questions
16:30 Drinks

Contact

Dr. Frank Seinstra (NLeSC): dtec-call@esciencecenter.nl of 020 – 460 4770
Dr. Axel Berg (SURFsara): axel.berg@surfsara.nl of 020 – 800 1300
Dr. Barbara van der Sar (NWO): e-science@nwo.nl of 070 – 349 4602

The Netherlands eScience Center is looking for a Community Officer Research

March 14th, 2019

The Netherlands eScience Center is the Dutch national expertise center for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general. Our activities are collaborative research projects with partners, dissemination of our expertise and coordination of eScience activities nationally and internationally. In this way we create an effective bridge between science and scholarly research and state-of-the-art digital technologies. We are looking for an enthusiastic:

eScience Community Officer Research 0.8 fte (m/f)

The position:
As ‘eScience community officer research’ you will stimulate data and compute intensive research in research communities nationally and internationally. You link the eScience Center’s expertise with different research communities in the Netherlands. That means that you will actively engage these communities with eScience activities. These communities are digital competence centers at university campuses and networks of researchers across the Netherlands and abroad. You will particularly focus on promoting and stimulating open science methodologies, with an emphasis on re-using and sustaining software. You like to make connections and can easily develop and maintain a network of external research partners. To enable the dissemination of eScience expertise and knowledge exchange, you are expected to initiate different activities such as organizing digital skills workshops. Also, you will stimulate the use of an important tool for sharing expertise develop by the eScience Center: the Research Software Directory. In this way you will stimulate our external stakeholders in academia to enhance scientific and scholarly research through efficient utilization of such tools. To make this happen you have a deep understanding and experience in research software development and usage and you combine this with strong communicating and networking skills.

Main components of the position:
• Develop and maintain a network with research institutions and research programs in the Netherlands relevant for the eScience Center, such as upcoming digital competence centers and domain research infrastructures;
• Organize activities with external research parties to stimulate (re)use of research software, stimulate software sustainability and strengthen digital skills in support of open science;
• Stimulate the (re)use of the Research Software Directory as a federated resource with external parties to find and share high quality research software;
• Engage in relevant activities on open science, with a focus on research software;
• Stimulate and facilitate external research parties to apply methodologies, applications and software developed by the eScience Center;
• Contribute and possibly initiate acquisition of research proposals.

We require:
• Academic level, with a PhD degree or equivalent experience;
• Experience in managing networks of partners;
• Experience in the use of scientific ICT;
• Proven expertise in research software (re)use and software sustainability;
• Experience with organizing events, such as teaching courses and workshops;
• Good software development skills, knowledge of software architectures and open source software communities.

Competences:
• Strong communication skills;
• Strong networking skills;
• A critical and constructive attitude to contribute actively to eScience developments;
• Motivated, flexible, creative, initiative taking, independent but also a real team player.

Working conditions:
We offer a position at the eScience Center within the collective agreement for Research Institutes (Cao-OI). Classification is based on education and experience, starting from € 2734 up to € 5064 gross per month, based on a 38-hour working week (salary scales 10-11). Holiday pay amounts to 8% of gross salary actually received and a full 13th month of salary as an end-of-year payment.

Information:
The eScience Center offers an interesting and challenging position at the interface of science and digital technologies. You will work in an international team with an informal but creative and ambitious working environment. The location is Amsterdam (Science Park), but site work at collaborating organizations is an important part of your work and this will involve travelling.

The eScience Center has an active diversity policy and would like to hire persons with a background that is underrepresented at the eScience Center. We therefore encourage women and minorities to apply.

For more information about this opportunity, you can contact Wilco Hazeleger, by emailing w.hazeleger@esciencecenter.nl or by calling +31(0)20-4604770. Please send your resume and application letter before May 1, 2019 to vacancy@esciencecenter.nl. Additional information may also be found at www.esciencecenter.nl.

Director eScience Center takes on new challenge

March 11th, 2019

Netherlands eScience Center director Wilco Hazeleger departs the organization. As of July 1st, 2019, prof. dr. ir. Wilco Hazeleger will be the new Dean of the Faculty of Geosciences of Utrecht University. Hazeleger served as the director of the eScience Center since 2014.

During Wilco’s time at the Netherlands eScience Center the organization grew from 25 to 60 people. In that period, digital methodologies and research software obtained a prominent position in most research practices and the eScience Center played a pivotal role in putting that on the agenda. Hazeleger feels it is the right time to hand over the eScience Center to a new director. I have had a great time at the eScience Center, primarily because of my dear colleagues. Together we have managed to position the eScience Center as an important expertise center in the Dutch academic landscape. I am very proud on the accomplishments of the past 5 years.”

Wilco Hazeleger is returning to his own research domain, taking on a position that fits his intrinsic interests in the Earth System and impact of environmental change. He will also be responsible for the strategic theme 'Pathways to Sustainability' of the university.

Utrecht University is an international research university of the highest quality and the alma mater of many leading names, academics and scientists who have made an important contribution to the quality of society. The Faculty of Geosciences studies the Earth: from the Earth's core to its surface, including man's spatial and material utilisation of the Earth – always with a focus on sustainability and innovation.

Job Opportunity: Technology Lead “optimized data handling”

March 8th, 2019

The Netherlands eScience Center is the Dutch national expertise center for the development and application of research software to advance academic research. We are convinced that research in every academic discipline can be improved by taking advantage of available digital technology. We take a multidisciplinary approach, combining our deep knowledge of both academic research and software development to help define and solve research challenges. We share our ideas and the tools we develop. Together with a wide range of partner organizations, we advance not just our research projects, but the state of academic research in general. Our activities are collaborative research projects with partners, dissemination of our expertise and coordination of eScience activities nationally and internationally. In this way we create an effective bridge between science and scholarly research and state-of-the-art digital technologies. We are looking for an enthusiastic: 

Technology Lead “optimized data handling” (m/f)

The position

The team of three Technology Leads are the eScience Center’s experts within their specific technological competence. They have a broad strategic view of their expertise and as such have an advisory role towards the director’s team of the eScience Center on related strategic topics. They develop and update the technological vision and strategy of the Center and promote this vision both internally and externally. They convert the technological strategy into a concrete work plan, and coordinate and oversee its execution. The Technology Leads are in close contact with the management team of the Center to be continuously aware of the expertise of the eScience research engineers and the technological needs within the various projects. Technology leads crucially also have an outside-in view. They recognize new developments in research and technologies, and they scout for digital technologies and methods outside the eScience Center. Also, they represent the eScience Center in (inter)national policy discussions. Finally, they take initiative and are involved in acquisition to strengthen the eScience Center expertise areas. The position of Technology Lead resorts under the Director of Technology.

The candidate holds a PhD and has shown experience in applying digital technologies in scientific and scholarly research. The technology lead can communicate easily and is interested in sharing knowledge and experience.

Main components of the position 

• Develop and update the technological vision and strategy of the Center and promote this vision both internally and externally.
• Convert the technological strategy into a concrete work plan, and coordinate and oversee its execution.
• Recognize the demand for technical solutions in our eScience project portfolio;
• Scout for and recognize new technical developments nationally and internationally;
• Ensure developed methodologies, applications and software in the eScience Center are applied and available for reuse or further development potentially in different domains;
• Contribute to and possibly initiate acquisition of research proposals for the eScience Center’s research;
• Build and maintain a relevant network in order to acquire new partnerships.

We require: 

• Academic level, with a PhD degree in computer or data science or equivalent experience;
• Broad experience with large-scale optimized data management;
• Excellence in one or more of the following topics: databases, data assimilation and integration, handling sensor data, linked data and semantics, real-time data analysis;
• Good software development skills, knowledge of software architecture;
• Technical project management experience;
• A drive to enthusiastically disseminate state-of-the-art digital technology to researchers and policy makers;
• Excellent research experience in academia or industry; 
• Experience with writing grant proposals;
• Excellent command of English and Dutch (both verbal and written);

Competences: 

• A critical and constructive attitude to contribute actively to eScience infrastructure improvements;
• Motivated, flexible, creative, initiative taking, independent but also a real team player;
• Strong communication skills with an external orientation;
• Innovative: translate scientific questions into unconventional (technological) solutions and new ideas and also able to realize them;
• Networking nationally and internationally;

Working conditions: 

We offer a position at the eScience Center within the collective agreement for Research Institutes (CAO WVOI). Classification is based on education and experience with salary depending on qualifications and experience, starting from € 4.478,- up to € 6.243, - gross per month, based on a 38-hour working week (salary scales 12-13). Holiday pay amounts to 8% of gross salary actually received and a full 13th month of salary as an end-of-year payment.

Information:

The eScience Center offers an interesting and challenging position at the interface of science and digital technologies. You will work in an international team with an informal but creative and ambitious working environment. The location is Amsterdam (Science Park), but site work at the eScience Center collaborating organizations is an important part of your work and will involve travelling. The eScience Center has an active diversity policy and would like to hire persons with a background that is underrepresented at the eScience Center. We therefore encourage women and minorities to apply. 

For more information about this opportunity, you can contact Rob van Nieuwpoort, Director of Technology, by emailing r.vannieuwpoort@esciencecenter.nl or by calling +31(0)20- 4604770. 

Please send your resume and application letter before May 13, 2019 to vacancy@esciencecenter.nl. Additional information may also be found at www.esciencecenter.nl.

Workshop Sustainable Software Sustainability 2019

February 21st, 2019

Organised by the Software Sustainability Institute (UK), DANS (NL) and the Netherlands eScience Center (NL), the Workshop on Sustainable Software Sustainability 2019 (WOSSS19) will bring together software creation, user, evaluation, and deposition groups from an array of disciplines, industry representatives, and cultural heritage organisations, to explore and discuss all aspects around Sustainable Software Sustainability (3S), from how to revive important legacy to preventing new legacy issues via training and guidelines.

3S focusses on long-term supported solutions for Software Sustainability. It addresses two forms of sustainability:

● How to cope with the existing legacy software (sharing insights and methodologies to revive old software and keep it maintainable for the future), and
● How to prevent new legacy to be created today (devising methods and principles that lead towards maintainable software with minimal technical debt).

At WOSSS19, we will explore the following 3S topics in relation to research software:

● FAIR principles for Software
● Software Legacy/Heritage
● Software Development: current and future best practice
● Software deposition routes
● Software Directories
● Resource acquisition & planning
● Software handover and succession

WOSSS19 will be an interactive workshop hosting talks from key organisations and long-term projects to discuss and establish the state-of-the-art in Sustainable Software Sustainability. The aim is to document the current state of 3S, publish a report, and help broadcast our findings to any relevant communities of practice.

Register for free and see the latest information about the program! Spaces are limited and allocated on a first come first serve basis. 

Date: April 24-26, 2019
Location:
NWO Den Haag
Laan van Nieuw Oost-Indië 300
NL-2593 CE The Hague
Registration fee: Free

Do you want to host a leading-edge workshop on digitally enhanced research?

February 19th, 2019

Lorentz-eScience competition 2020

The Netherlands eScience Center and the Lorentz Center are looking for researchers who want to join the Lorentz-eScience competition and organize a workshop at the Lorentz Center@Snellius, Leiden, the Netherlands.

The Lorentz-eScience competition aims to host a leading-edge workshop on digitally enhanced research (efficient utilization of data, software and e-infrastructure). The workshop should bring together researchers from the academic community and the public/private sector.

What we seek
• an innovative scientific programme, that takes us beyond our current boundaries
• an open and interactive format, with few lectures
• at least one scientific organizer based within and one outside the Netherlands
• at least one scientific organizer from the academic community and the public/private sector

What we offer
• a 5-day workshop for up to 25 people in the first half of 2020
• travel and accommodation reimbursements
• no registration fees or other organizational costs
• a professional support organization

Procedure
• a 1-page expression of interest by 15 April 2019
• a full application by 6 June 2019
• final decision end of June 2019
• submit applications to: proposal@lorentzcenter.nl

Information
• Wilco Hazeleger, director Netherlands eScience Center
w.hazeleger@esciencecenter.nl
• Arjen Doelman, director Lorentz Center
doelman@lorentzcenter.nl
• Henriette Jensenius, scientific manager Lorentz Center
jensenius@lorentzcenter.nl

Netherlands eScience Center contributes to new insights into the human body clock and health

January 31st, 2019

The study, published in Nature Communications, suggests that being genetically programmed to rise early may lead to greater wellbeing and a lower risk of schizophrenia and depression. The study was conducted by an international collaboration, led by the University of Exeter and Harvard Medical School and funded by the Medical Research Council.

An important aspect of this research is the data collection. 100,000 individuals from the UK were asked to wear a movement sensor for seven days during their daily life. The method to detect when individuals are sleeping was recently developed by dr. Vincent van Hees, Senior Research Engineer at Netherlands eScience Center. Sleep detection is not an easy task as inactivity during the evening and in the morning can easily be confused for extended bedtime and vice versa. In the absence of a reliable reference method to train such classifier with machine learning, a heuristic approach based on knowledge about the data was used to classify the data. You can find details of the method, released as open source software, in the following article: “Estimating Sleep Parameters using an Accelerometer without Sleep Diary”.

Dr. van Hees is a co-author of “ Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms”. Additional publications using Dr. van Hees’ method to gain better insights in sleep and health are expected soon.

Related news
NYT:Searching for the Genetic Underpinnings of Morning Persons and Night Owls
CNN:Hundreds of genes might decide whether you're an early bird or night owl
Daily Mail: Early risers less prone to mental health problems - study
The Conversation: Morning or night person? It depends on many more genes than we thought

Four new eScience collaborations to start in 2019

December 12th, 2018

We are pleased to announce the initiation of four new collaborative projects in the areas of Environment & Sustainability and Humanities & Social Sciences.

The projects are the result of the 2018 ASDI call for proposals. Scheduled to start in 2019, the projects are collaborations with research teams from multiple Dutch academic groups: VU University Amsterdam, Wageningen University, Tilburg University, and University Medical Center Utrecht.

1. MOSAIC
MOdelling Sea level And Inundation for Cyclones
Dr. P.J. Ward
Vrije Universiteit Amsterdam
Read more

2. Monitoring tropical forest recovery capacity using RADAR Sentinel satellite data
Demonstrating the potential of European Sentinel satellite data
Dr. ir. J. Verbesselt
Wageningen University
Read more

3. Understanding visually grounded spoken language via multi-tasking
An alternative approach for intelligent systems to understand human speech
Dr. G. Chrupala
Tilburg University
Read more

4. ePODIUM
Early Prediction of Dyslexia in Infants Using Machine learning
Dr. H.G. Schnack
University Medical Center Utrecht
Read more

Over 350 international participants for eScience Conference 2018

November 2nd, 2018

The winner of the Young eScientist Award 2018 is…

October 30th, 2018

Esther Bron (post-doc researcher at the Biomedical Imaging Group Rotterdam, Erasmus MC) has been awarded the Young eScientist Award 2018.

The prize aims to stimulate a young scientist demonstrating excellence in eScience: the development or application of digital technology to address scientific challenges. The prize will be used to undertake a joint research project, in which Esther will receive support by eScience Research Engineers (experts in the development and application of research software).

Her main research interest is advanced analysis of brain MRI for improving diagnostics. Currently, she is organizing a large international comparison study: The Alzheimer’s Disease Prediction Of Longitudinal Evolution challenge TADPOLE. This challenge objectively compares the performance of methods by international research groups that predict evolution of individuals at risk of Alzheimer’s disease. Her research idea is to develop a user-friendly web-based platform that allows users to apply TADPOLE methods to their own data. She would like to collaborate with the eScience Center to build a web-based platform, to integrate the prediction methods into the platform and to validate them. This will make a different state-of-the-art prediction methods publicly available and easily applicable which is in line with the definition of Open Science.

Esther impressed the reviewers with her track record and the impact she already created on a national and international level. Her proposal also fully embraces open science.

We hope Esther's research will inspire and encourage other young eScientists to enter next year’s competition!


Photo from left to right: Gennady Roshchupkin (Erasmus UMC), Esther Bron (Erasmus UMC), Meike Nauta (University of Twente) (Photography by Michiel Wijnbergh)

Making Open Science a reality: Rewards, Incentives & Support

October 15th, 2018

Date: 30 October 2018
Time: 16:30 - 17:30
Location: Mövenpick Hotel Amsterdam
Costs: Free of charge

We would like to invite you to join a conversation with Stan Gielen (NWO) & Erik Fledderus (SURF) on Open Science during the 14th International IEEE eScience Conference in Amsterdam. 

Open science is one of the hot topics across all scientific communities, and is seen as an important step towards making scientific research more sustainable. However, the current reward and incentive policy in academia and of research funders makes practicing full open science unrewarding for scientists. Also in order to fully embrace open science, scientific researchers should be able to rely on solid infrastructure and support without having to turn towards parties with a commercial interest.

In this interactive session, Stan Gielen, President of the Netherlands Organisation for Scientific Research will join up with Erik Fledderus, CEO of SURF to discuss the changes needed both in policy and practice in order to make open science the modus operandi in the research community. As policy shapers within the field of open science, they will share their visions and ideas on how to create a sustainable open science system that rewards and supports scientists for practicing open science. Furthermore, Stan and Erik will invite the session audience to join in on a discussion led by Marcel Brosens about the practical aspects of open science. Feedback from the research community on open science is highly appreciated in order to better connect policy and support to practice. 

We hope to welcome you to the Open Science session.

Date: 30 October 2018 Time: 16:30 - 17:30
Costs: Free of charge
Location: Mövenpick Hotel Amsterdam
Please confirm your attendance by sending an e-mail to communicatie@esciencecenter.nl

This session is part of the International IEEE eScience Conference 2018 The fourteenth IEEE eScience Conference will be held in Amsterdam, The Netherlands from October 29 - November 1, 2018. This conference brings together leading international researchers and offers a platform for digital technologies to advance research - from the humanities to the physical sciences. If you want to attend the full conference, please register here.


DAS-6 gets funding!

October 11th, 2018

The Dutch Science organization NWO has announced that the DAS-6 proposal submitted by the DAS steering committee, headed by prof. Henri Bal of Vrije Universiteit Amsterdam, will receive EUR 500.000 funding to build the next-generation high performance computing infrastructure. 

The Netherlands eScience Center is one of the 6 project partners. Together with VU, UvA, Leiden, Delft, ASTRON and SURFsara, the eScience Center will also invest over EUR 500.000.

The challenge of the new DAS-6 project is to study the feasibility of a next generation trusted ecosystem to face the proliferation of many developments in Computer Science, such as streaming applications, edge and fog computing, in-network processing, and complex security and trust policies. The DAS-6 research ecosystem will consist of 6 clusters with different functionalities, integrated into a coherent shared distributed system that is designed to fit the current research agenda of numerous Computer Science groups in The Netherlands. Over 60 funded research projects will use DAS-6 once it is operational, especially in systems areas like trust, security, blockchains, scheduling, big data, Internet-of-Things, and accelerators and in application areas like artificial intelligence (AI), deep learning (DL), and eScience.

The DAS steering committee will now work hard on starting the procurement procedure. DAS-6 is expected to become operational in the second half of 2019.

Congratulations to the winners of the IEEE eScience Conference Travel & Attendance Grants!

September 24th, 2018

After the announcement of the Travel & Attendance Grant, we received 46 applications from around the globe. Thank you to everyone who took the time to apply. Your applications have been truly inspiring and the variety we received show the vast array of eScience research happening across the globe. The grants are gratefully provided by the Moore Foundation, the World Meteorological Organization (WMO) and Philips. Without further ado, we are delighted to announce the winners of the Travel Grant competition. Congratulations go to:

Sponsored by Philips:
Mrs. Fagbola (Ladoke Akintola University of Technology, Ogbomoso, Nigeria)

Sponsored by the Moore Foundation:
Mrs. Adeleke (Bowen University, Iwo,Osun State,Nigeria)
Mr. Bogado (Universidad Nacional de La Plata, Argentina)
Mrs.Pule (Stellenbosch University, South Africa)
Mrs. Salamani(University of Geneva, Switzerland)

Sponsored by WMO:
Mrs. Mwenye(Department of Research and Specialist Services, Zimbabwe)
Mrs. Ogunrayi (Ondo State Ministry of Environment, Nigeria)
Mrs. Timsina (Sikkim University/Royal Thimphu College, Bhutan)

We are looking forward to meet the winners at the IEEE eScience Conference!

Draag bij aan onderzoek naar hart- en vaatziekten

September 20th, 2018

Draag bij aan onderzoek naar hart- en vaatziekten

Geef je mening op de onderzoeksplannen uit het programma Big Data & Gezondheid

Acivity trackers, zoals een Fitbit, zijn tegenwoordig immens populair. Mensen gebruiken deze apparaten om hun stappen te tellen, hartslag te meten, gewicht bij te houden en andere gezondheidsinformatie te verzamelen. De informatie, ook wel data, die deze apparaten oplevert biedt ondersteuning bij een gezonde leefstijl. In wetenschappelijk onderzoek wordt deze data gecombineerd met andere gegevens en biedt het inzicht in ziekte en gezondheid. Al deze data bij elkaar noemen we Big data. Omdat burgers steeds meer te zeggen hebben over hun eigen (medische) informatie roepen wij hen op om mee te denken.

Vroege opsporing en preventie van hart- en vaatziekten

Het programma Big Data & Gezondheid, vroege opsporing en preventie van hart- en vaatziekten, financiert onderzoek naar Big data. Heeft u ervaring met hart- en vaatziekten in uw naaste omgeving, bent u zelf patiënt of zorgverlener? Dan hebben wij uw hulp nodig om te zorgen dat de beoogde resultaten van deze onderzoeksplannen zo goed mogelijk aansluiten bij de wensen en behoeften van burgers, patiënten en zorgprofessionals. Wij nodigen u uit om uw mening te geven op de ingediende onderzoeksvoorstellen.

Bijeenkomst: Maandag 8 oktober 2018 organiseren wij een bijeenkomst waar zowel onderzoekers als geïnteresseerden voor zijn uitgenodigd. Op deze bijeenkomst lichten de onderzoekers kort hun onderzoeksplan toe (pitch) waarna de aanwezigen kunnen meedenken over het onderzoekplan. De aanvrager neemt deze feedback mee om zijn of haar onderzoeksplan te verbeteren.

Locatie: De bijeenkomst vindt plaats op een centrale plek in Utrecht. De ontvangst is vanaf 15:30 uur, de bijeenkomst start om 16:00 uur en duurt tot 19:30 uur. Voor een avondmaaltijd en afsluitende borrel wordt gezorgd. Uw inbreng wordt gewaardeerd met een attentie en uw reiskosten worden vergoed.

Aanmelden: Wilt u bijdragen aan onderzoek naar hart- en vaatziekten? Meldt u dan aan voor deze bijeenkomst door een e-mail te sturen naar data2person@nwo.nl. U ontvangt een bevestiging van uw deelname. 

WUR Scientific Symposium: FAIR Data Science for Green Life Sciences

September 19th, 2018

The Wageningen Data Competence Center – part of Wageningen University and Research – is organising a one-day scientific symposium on FAIR Data Science for Green Life Sciences. The symposium focuses on state-of-the-art knowledge in data science and data management, new applications in the green life sciences, and insights from other domains that could be transferred. The symposium aims to bring together researchers and domain experts for discussion and exchange of ideas of the latest developments in data science as well as on the best practices within the green life sciences.

Developments in data science offer enormous opportunities for the agri-food chain and life sciences. Advances in information science and technology, data science and analytics, applied to domain specific developments are expected to enable breakthroughs in the agri-food domain. Wageningen University & Research is building on current efforts of applied data science and actively surveying its research domain for new opportunities. Here, we adopt ‘green life sciences’ as a shorthand for this research domain.

For questions, please contact dr.ir. Chantal Hukkelhoven (Research Coordinator Wageningen Data Competence Center) at: chantal.hukkelhoven@wur.nl

Organised by: Wageningen Data Competence Center

Date: Wed 12 December 2018

Venue: Wageningen University & Research, Wageningen, the Netherlands

Price: Free

Online registration open soon

Job Opportunity: Postdoc Machine Learning

August 20th, 2018

The position

The post-doctoral researcher’s work will be part of a collaborative project, externally funded by the Lilly Research Award Program. The overarching objective of the position is to enhance sleep research by developing an innovative open analytical tool for quantifying human sleep from high resolution wearable movement sensor data. These data are now widely collected in population studies, which typically involve thousands of participants who are asked to wear the movement sensor on their wrist continuously for a week. The candidate will work in an international and inter-disciplinary team of health researchers in Europe and the United States, and data science and software engineering specialists at the Netherlands eScience Center in Amsterdam.

Enhancing sleep research by developing an open analytical tool for quantifying human sleep

Scientific background of the position

Sleep is fundamental for human health and wellbeing. Poor sleep may present a significant risk factor for the development of dementia and other illnesses. Existing research methods to quantify sleep under real life conditions are limited by their reliance on subjective self-reported data or use wearable movement sensors for whom only closed software is available. Additionally, little is known about how to best define and quantify the fragmentation (scattering) of sleep over time as an indicator of sleep quality. The post-doc will lead the development of a probabilistic classifier for sleep and sleep depth using existing ground truth datasets, explore how sleep fragmentation can best be defined and quantified, work with project partners to apply the newly developed tools to real-life large datasets, and lead on papers describing the new technology. The existing code base is in R (R package GGIR), which already includes a data cleaning pipeline and a heuristic binary sleep classification approach. Where possible, the candidate will use this as a starting point for their work. All code developed in the project will be released as open source software.

If the candidate accepts a full-time (38-hour) position, they will be expected to work for 15% of the time on other eScience projects to broaden their eScience experience and impact to other fields of science. If the candidate prefers a 32-hour work week, then this does not apply.

We require

  • Finished or close to finishing a PhD in an analytical discipline (Computer Science, Statistics, Mathematics, Bioinformatics, Physics, Computational biology, Epidemiology, etc.);
  • Experience with programming in R, Python, and/or C++;
  • Experience with advanced data analysis;
  • Demonstrated scientific writing skills.

We desire

  • Experience with machine learning techniques and/or probability theory;
  • Experience with wearable sensors, sleep assessment and/or health research.

Competences

  • Initiative taking;
  • Creative / Innovative problem solver;
  • Keen to learn about new technologies and ways of doing things;
  • Strong team player with excellent verbal and written communication skills.

Working conditions

We offer a position at the Netherlands eScience Center initially for 1 year within the collective agreement for Dutch Research Institutes (cao-OI) and, under the condition of sufficient progress can be extended to a two-year fixed period. When the candidate fits well with experience needed in other projects of the Center there will be other opportunities after the end of the Lilly project. The candidate will be based at the Netherlands eScience Center in Amsterdam.

The salary for the position is € 3.352,- gross per month growing to € 3.477,- in the second year, based on a 38 hour working week working week (salary scale 10). Holiday pay amounts to 8% of the gross salary and we also offer a 13th month of salary as an end-of-year payment.

Information

The eScience Center offers an interesting and challenging working environment with options for personal development. You will work in an international team with an informal but creative and ambitious atmosphere.

The eScience Center has an active diversity policy and would like to hire persons with a background that is underrepresented at the eScience Center. We therefore encourage women and minorities to apply.

For more information about this opportunity you can contact Vincent van Hees, eScience Research Engineer at the Netherlands eScience Center, by emailing v.vanhees@esciencecenter.nl. Please send your resume and application letter before the 11th of September 2018 to vacancy@esciencecenter.nl. Additional information may also be found at www.esciencecenter.nl.

The winner of the Lorentz - eScience competition 2018: Artificial Intelligence in Cybersecurity

July 25th, 2018

We congratulate Robbert Fokkink (TU Delft), Roy Lindelauf (Netherlands Defence Academy), Arnout van de Rijt (Universiteit Utrecht), Paulo Shakarian (Arizona State University) and V.S. Subrahmanian (Dartmouth College) on winning the competition for the Lorentz-eScience workshop with their proposal ‘Artificial Intelligence in Cybersecurity’. We are very pleased that we can continue this program with such a high quality and interesting workshop.

About the workshop

There is a growing community of computer scientists, mathematicians and computational sociologists conducting research in, and communicating ideas on:

  • Mining key-terrorists, criminals and hackers on Dark-web forums and markets
  • Game theoretic cyber threat mitigation
  • Identifying pathogenic social media accounts such as ‘fake news bots’
  • Identification of cyber threats from online discussions.

The central topic around which these researchers meet and conduct research is the analysis of phenomena related to cyber from different perspectives: mathematics (network science), computer science (cybersecurity) and computational sociology (social networks).

This workshop aims to get academic problem formulations related to cybersecurity more in sync with the practical end-goals of the practitioners in the field, and to have practitioners gain a wider understanding of state of the art practice in the academic field of cybersecurity research.

About the Lorentz-eScience competition

The Lorentz-eScience workshop competitions, organized by the Netherlands eScience Center and the Lorentz Center, sponsor leading-edge international workshops on the application of software to advance academic research. The workshops should bring together researchers from the academic scientific community with those from the public/private sector.

We Make The City Festival Workshop: “Audit the Algorithm”

July 5th, 2018

The VWData research programme hosted an interactive workshop (break-out session) during the “We Make The City” Festival in Amsterdam, on Thursday 21 June 2018. The workshop dealt with “Algorithm Auditing” and focused on a project that the City of Amsterdam, KPMG and the University of Amsterdam are conducting. The project will study the usage of algorithms by the City of Amsterdam, and will focus on algorithmic transparency, ethical auditing, and legislation. With: Tamas Erkelens (City of Amsterdam) and Sander Klous (KPMG and UvA). Approximately 20 people joined the workshop and there was a lively discussion. Topics mentioned included: ‘when is an algorithm good enough’, ‘who is responsible when things malfunction’, ‘how can you establish norms and criteria that an algorithm must meet’, and ‘what is a good role for the government in this domain’?

Research and software: perspectives from different communities

April 13th, 2018

Last week the Principal Investigators collaborating with the eScience Center’s team came together to share experiences on collaborative research projects.

Our work is driven by the challenges faced by academic researchers, which is why we want to deeply understand the needs and objectives of our principal investigators. We are convinced that by working together with researchers from different academic disciplines and technology areas we can advance the state of academic research. One of the goals of this day was therefore to jointly signal challenges and formulate opinions and solutions at the intersection of software and academic research.

Inspiring talks

The day started and ended with inspiring talks from eScience Prinicipal Investigators. In the morning, Christian Lange from Utrecht University presented his research on the Arabic-Islamic corpus. The ‘Bridging the Gap’ project is a collaboration with Christian Lange’s team and the eScience Center in which we develop and apply research software to gain more insight into the vast corpus of digitized Arabic texts that has become available in the last decade.

Talkshows

Christian Lange’s presentation was followed by a talkshow with two eScience Research Engineers collaborating on this project: Dafne van Kuppevelt and Janneke van der Zwaan. Dafne and Janneke talked about their experience on working in a discipline they were unfamiliar with before (Arabic literature), and the process of finding and re-using research software.

Finding and re-using software in different research communities was also the topic of the talkshow that followed. Joeri van Leeuwen (ASTRON), astronomer, Rolf Hut (TU Delft), hydrologist, and Martin Reynaert (Tilburg University), digital humanities, discussed how the practices of working with research software differ between their communities. The talkshow resulted in a lively discussion in which it was clear that there are different practices and opinions between communities around the use and sharing of software.

Break-out sessions on research & software

In the afternoon this discussion continued in smaller groups, in which different ways to stimulate to re-use of software were explored.

After lunch, Jurriaan Spaaks, eScience Research Engineer, presented the eScience Center’s Research Software Directory (RSD). The RSD is one of the vehicles by which the eScience Center aims to encourage the re-use of software. However, the success of any such directory depends on how well it fits the needs of Principal Investigators and different research communities. Jurriaan’s presentation was therefore followed by a break-out session in which Principal Investigators and the eScience Center’s team developed SWOT-analyses of the RSD — what are its strengths and weaknesses, and can we identify opportunities or threats?

After two energetic break-out sessions, Principal Investigator Frank Takes closed the day by presenting his exciting research on offshore finance in which he uses software to analyze complex relations and networks.

Valuable insights

The day provided valuable new input for the eScience Center on the needs of different research communities, which will guide the continued development of our activities in enabling digitally enhanced research, and specifically also the RSD. We are thankful for the contributions and inspirational insights of our collaborative partners in these discussions.

Photography: Elodie Burrillon

Werkbijeenkomst onderzoeksprogramma Big Data & gezondheid

April 11th, 2018

De Hartstichting, NWO, ZonMw, de Topsector LSH en het Netherlands eScience Center bundelen hun krachten en ontwikkelen samen een publiek-privaat onderzoeksprogramma onder de paraplu van het Big Data onderzoeksplatform Commit2Data. Voor de voorbereiding van projectvoorstellen wordt een werkbijeenkomst georganiseerd.

Doel onderzoeksprogramma Big Data & Gezondheid
Het doel van het programma is het benutten van (nieuwe) verbindingen tussen de gezondheid- en levenswetenschappen, data science en de creatieve industrie voor de ontwikkeling van nieuwe benaderingen in preventie en vroege opsporing van hart- en vaatziekten. Burgers en patiënten krijgen hierin een centrale rol. De Kennis en Innovatie Agenda ICT, LSH, en ClickNL en de principes van vitaal functioneren en positieve gezondheid zijn de inhoudelijke leidraad.

Doel projecten
Het programma zal bestaan uit 4 tot 6 verschillende publiek-private wetenschappelijke onderzoeksprojecten met een omvang van circa 1.5 M€ (per project). Ieder project is gericht op de beantwoording van belangrijke vraagstukken over preventie en vroege opsporing van hart- en vaatziekten en bevat wetenschappelijk onderzoek op het gebied van data science en de creatieve industrie. Deze projecten wordt voor een deel gefinancierd door een bedrijf of maatschappelijke organisaties (onder bepaalde voorwaarden).

Doel bijeenkomst
De werkbijeenkomst wordt georganiseerd om publiek-private consortia de gelegenheid te geven zich (verder) te vormen en stappen te zetten richting een projectvoorstel. Ook de kaders, planning en voorwaarden voor het onderzoeksprogramma zullen in deze bijeenkomst worden gepresenteerd. Deelname van potentiele aanvragers en van relevante consortia i.o. wordt ten sterkste aanbevolen. De werkbijeenkomst is maandag en dinsdag 2 en 3 juli 2018 (in principe met overnachting).

Voor wie is deze werkbijeenkomst?
Publiek-private consortia die in aanmerking komen voor subsidie bestaan minimaal uit twee verschillende universitaire vakgroepen, een bedrijf of maatschappelijke organisatie, burgers of patiënten en een of meer eScience Research Engineers aangesteld bij het Netherlands eScience Center. Om deze reden is de werkbijeenkomst bedoeld voor:

  • Wetenschappers o.a. uit de geneeskunde, gezondheidswetenschappen, levenswetenschappen, ICT, wiskunde, sociale en geesteswetenschappen
  • Bedrijven en maatschappelijke organisaties die zich in dit veld bewegen
  • Burgers en patiënten

Aanmelden
Doe mee aan deze interactieve bijeenkomst Big Data en Gezondheid. Aanmelden kan tot uiterlijk 15 mei 2018 via het aanmeldformulier.Stuur uw aanmelding naar: data2person@nwo.nl.
Niet aanwezig maar wel geïnteresseerd in de call? Laat het ons weten en stuur een mail!.
Voor vragen en meer informatie kunt u contact opnemen met onderstaande personen:

NWO Exacte en Natuurwetenschappen & Commit2Data
Astrid Zuurbier, coördinator van dit programma, A.Zuurbier@nwo.nl

Hartstichting
Deborah Alfarez, D.Alfarez@hartstichting.nl

ZonMw
Inge Valstar, Valstar@zonmw.nl

NWO Sociale en Geesteswetenschappen
Janneke van Kersen, J.vanKersen@nwo.nl

Topsector LSH
Jolande Zijlstra, Zijlstra@Health-Holland.com

Netherlands eScience Center
Frank Seinstra, F.Seinstra@esciencecenter.nl

Celebration and brainstorm with research partners on new collaborations

March 15th, 2018

On 12 and 15 February, the granting of fourteen new collaborative projects was celebrated at the Netherlands eScience Center. The new collaborations between the eScience Center and research teams from different Dutch universities will start in the first half of 2018.

During this day, several new collaborators of the eScience Center pitched their projects. Subsequently, the challenges and opportunities of the new collaborations were discussed in smaller groups together with eScience Research Engineers from the eScience Center.

The aim was to create an opportunity for the new Principal Investigators to benefit from the combined knowledge of the eScience Research Engineers at an early stage. eScience Research Engineers have knowledge of both academic research and software development, which can help define and solve research challenges.

We are looking forward to these new collaborations, through which we hope to advance not the just the projects itself but academic research in general.

Photography by Elodie Burrillon / HUCOPIX

Kabinet investeert extra in digitale infrastructuur voor onderzoekers

March 13th, 2018

Er wordt 20 miljoen euro per jaar extra geïnvesteerd in de Nederlandse digitale onderzoeksinfrastructuur. Ondersteuning bij data- en software-intensief onderzoek is hiervan een belangrijk onderdeel Dat heeft minister Van Engelshoven (OCW) afgelopen vrijdag laten weten in een brief aan de Kamer

In de kamerbrief wordt voor de invulling van de middelen verwezen naar het in 2017 verschenen adviesrapport van NWO, “Topwetenschap vereist topinfrastructuur. Hierin wordt gewezen op de sterk gestegen behoefte van de Nederlandse wetenschap aan hoogwaardige ondersteuning op het vlak van big data, onderzoekssoftware, snelle netwerken en supercomputers. Om de Nederlandse wetenschap op wereldniveau te laten blijven meedraaien, zijn volgens het rapport extra investeringen via de drie nationale partijen op het gebied van digitale infrastructuur - SURF, eScience Center en DANS - dan ook noodzakelijk.

The Second Information Universe Conference

February 26th, 2018

From 3 - 6 July the University of Groningen is organizing the Second Information Universe Conference.

The key topic of the IU conference series is: “What is the role of information in the Universe and its description?”. In an epoch where scientists need to handle Big Data and simulations, find highly organized systems in nature and grapple with the role of information in physics and other sciences, this appears to be one of the more fundamental questions that needs to be answered in order to understand the world around us. The Information Universe conference intends to unite various approaches, addressing the fundamental role of information both in nature (“in vivo”) and in data analysis, theory and computer modelling (“in vitro”).

The conference will approach the key role of information from the point of view of several disciplines: e.g. cosmology, physics, mathematics, life sciences, computer science (including quantum computing) and neuroscience. The deeper role of information is formulated in different ways by these various disciplines, leading to a multitude of fundamental questions such as:

  • Is there a deeper physical description of space-time based on information?
  • What are the consequences of quantum mechanics for cosmology?
  • Will quantum systems dominate the future of computing?
  • How do our numerical simulations and Big Data repositories (in vitro) differ from real natural system (in vivo)?
  • What is the role of information in highly organized complex life systems and genetics?
  • What will be the role of machine learning in the future of science?
  • How will information guide us in understanding fundamental cosmological problems: dark matter, dark energy, inflation and structure formation?
  • What is the deeper meaning of the information paradox at the Black hole horizon?
  • Is the universe one big information processing machine, a hologram, one of many?

To address these questions, the conference will host sessions on:

  • Emergent space-time and gravity
    Keynote speaker: Erik Verlinde
  • Euclid, cosmology and large-scale structure
    Keynote speaker: Alan Heavens, Invited speaker: Alessandra Silvestri
  • Quantum information & quantum computation
    Keynote speaker: Lieven Vandersypen
  • Machine learning (including industrial applications)
    Keynote speaker: Larry Wasserman
  • Information, complexity & handling big data (including applications)
    Keynote speaker: Peter Sloot, Invited speaker: Giuseppe Longo
  • Life science and biology
    Keynote speaker: Karlheinz Meier
  • Information and the Theory of Everything
    Keynote speaker: Thanu Padmanabhan

In addition there will be (at least) one public evening, and a panel discussion at the end of the conference.

The conference will be held in the 260 seater planetarium theatre in Groningen, which provides an immersive 3D full dome display. This enables speakers to show unique and inspiring visuals, e.g. numerical simulations of the formation of our Universe, the brain in 3D, and anything else that springs from the imagination of the presenters.

For more information and registration, please visit: www.informationuniverse.rug.nl.

Scientific Organizing Committee

  • Prof. Dr. Eric Bergshoeff (Van Swinderen Institute for Particle Physics and Gravity)
  • Prof. Dr. Konrad H. Kuijken (Leiden Observatory)
  • Prof. Dr. Edwin Valentijn (Kapteyn Astronomical Institute)
  • Prof. Dr. Rien van de Weijgaert (Kapteyn Astronomical Institute)

Local Organizing Committee

IEEE eScience 2018 Calls for Contributions

February 26th, 2018

The 14th IEEE Conference on eScience will take place in Amsterdam, the Netherlands from 29 Oct – 1 Nov 2018.
www.eScience2018.com

We are pleased to now invite contributions for inclusion in the conference program: Call for Papers Call for Workshops & Tutorials Call for Abstracts: Data Handling and Analytics for Health Call for Abstracts: Exascale Computing for High Energy Physics Call for Abstracts: Advances in eScience for the Humanities and Social Sciences Call for Abstracts: Weather and Climate Science in the Digital Era Please find all information regarding the calls and submission guidelines on our website.

Key Dates for Contributions

  • Abstract submission deadline: Friday 25 May 23:59 (AoE)
  • Full paper submission deadline: Friday 1 June 23:59 (AoE)
  • Notification of acceptance: Wednesday 15 August 2018
  • Camera-ready papers: Monday 17 September 2018

We look forward to receiving your submission and welcoming you to Amsterdam in October 2018. Visit www.eScience2018.com

About IEEE eScience 2018

The 14th IEEE Conference on eScience brings together leading international researchers and research software engineers from all disciplines to present and discuss how digital technology impacts scientific practice. eScience promotes innovation in collaborative, computationally- or data-intensive research across all disciplines, throughout the research lifecycle.

New this year: Multitrack day with focused sessions The three-day conference program consists of two single track days open for all eScience contributions. New this year is a multitrack day with focused sessions on Exascale Computing for High Energy Physics, Weather and Climate science in the digital era, Data Handling and Analytics for Health, Advances in eScience for the Humanities and Social Sciences, and Computer Science: Tools & Infrastructure.

On the day prior to the conference there will be workshops and tutorials.

Chair & Supervisory Committee

General chair
Wilco Hazeleger (Netherlands eScience Center, The Netherlands)

Program chairs
Adriënne Mendrik (Netherlands eScience Center, The Netherlands)
Rob van Nieuwpoort (Netherlands eScience Center, The Netherlands)

Supervisory committee 2018
Daniel S. Katz (National Center for Supercomputing Applications, University of Illinois, United States)
Franciska de Jong (CLARIN ERIC)
Jack Dongarra (University of Tennessee, United States)
Michelle Barker (Nectar, University of Melbourne, Australia)
Dan Henningson (KTH Royal Institute of Technology, Sweden)
Tony Hey (Science and Technology Facilities Council, United Kingdom)

Focussed session chairs

Computer Science: Tools & Infrastructure
Raül Sirvent Pardell (Barcelona Supercomputing Center)
Ben van Werkhoven (Netherlands eScience Center)

Weather & Climate science in the digital era
Peter Bauer (European Centre for Medium-Range Weather Forecasts)
Martine de Vos (Netherlands eScience Center)

Data Handling and Analytics for Health
Jaap Heringa (VU, Amsterdam)
Vincent van Hees (Netherlands eScience Center)

Advances in eScience for the Humanities and Social Sciences
Claes de Vreese (University of Amsterdam)
Carlos Martinez-Ortiz (Netherlands eScience Center)

Exascale Computing for High Energy Physics
Jeff Templon (Nikhef)
Yifat Dzigan (Netherlands eScience Center)

3D-e-Chem team develops building blocks and recipes for Computer-Aided Drug Discovery

February 16th, 2018

Following the development of a virtual machine (JCIM), the 3D-e-Chem team now published a series of building blocks (nodes) and recipes (workflows) that can support complex computer-aided drug discovery efforts. The 3D-e-Chem team consists of cheminformatics and bioinformatics researchers from Netherlands eScience Center, Vrije Universiteit Amsterdam, Radboudumc Nijmegen, and BioAxis Research, including Stefan Verhoeven (eScience) and Chris de Graaf (PI, VU Amsterdam).

These newly developed cheminformatics tools and workflows for KNIME (the leading open data analytics platform) integrate chemical, pharmacological, and structural information for the prediction of interactions between drug molecules and therapeutic protein targets. The modular setup of these computer-aided drug discovery workflows and the use of well-established standards enables researchers to re-use and customize these workflows for their own drug discovery projects.

The 3D-e-Chem software tools and applications thereof are described in a recent open access publication in ChemMedChem. All the building blocks (nodes) are readily available as a community contribution in KNIME. Moreover, the source code of the nodes is open and available on the 3D-e-Chem GitHub.

Karel Luyben appointed National Coordinator for Open Science

February 12th, 2018

Today, the steering group of the National Platform Open Science appointed former Delft University of Technology Rector Karel Luyben as the National Coordinator for Open Science. In this newly created role, Luyben will work to achieve the Netherlands' open science ambitions and to strengthen the country's pioneering role in this field. This will benefit everyone. Open access to publications, for example, allows lecturers to read up on the most recent developments in their field and to incorporate them into their courses. Furthermore, it allows doctors and nurses to apply the latest medical methods for better care.

Open science is about sharing research data and making scientific publications (digitally) available to a large audience. Publicly funded research must be publicly accessible. Dutch Minister of Science Van Engelshoven sees open science as an important priority of the Coalition Agreement.

The Netherlands is known as a pioneer in this field in Europe. This also became apparent during the Netherlands' EU presidency in 2016. They helped introduce the ambitions that by 2020 all scientific articles should be freely accessible, research data is to be optimally available for reuse and researchers must be valued and rewarded for sharing research data and results.

The Netherlands feels that open science should be encouraged and supported and has documented these ambitions in its National Plan Open Science, which was presented to the National Platform Open Science exactly one year ago today. A large number of organisations with a stake in this development are working together on this platform. Since its launch one year ago, the percentage of open-access publications has gone up and the sharing of research data has soared. The Netherlands has also taken the lead to create a European platform together with Germany and France to make all this possible: the GO FAIR initiative.

To interconnect the various Platform activities and monitor progress, it was decided to appoint a National Coordinator
for Open Science. Today it was announced that Karel Luyben will be filling this position. He was also given the specific task to make 'the scientist's voice' heard on the Platform. Karel Luyben was appointed by the National Platform Open Science, in which organisations such as VSNU, KNAW, NWO, VH, PNN, KB, SURF, NFU, ZonMW and GO-FAIR have joined forces.

Minister Van Engelshoven supports the appointment: "I am very pleased with this decision. Luyben is no stranger to the European networks and has a proven track record in the field of open science. I feel he has the expertise to set in motion and interconnect the national and international open science policies."

For more information, see www.openscience.nl.

Het VWData startimpulsprogramma is van start

February 1st, 2018

Zo’n 50 onderzoekers kwamen op 29 januari in Amersfoort bij elkaar voor de aftrap van het VWData startimpulsprogramma. Programmaleider Inald Lagendijk gaf aan hoe de uitvraag voor de Nationale Wetenschapsagenda resulteerde in 11700 vragen, die geclusterd zijn in 140 Grote Vragen, die op hun beurt weer in 25 ‘routes’ zijn gecombineerd, en hoe daaruit 8 routes zijn geselecteerd om middels een ‘Startimpuls’ hun bestaansrecht op de kaart te zetten. 

Het VWData startimpulsprogramma bestaat uit verschillende onderzoeksteams die zich richten op een gezamenlijk vraagstuk: Hoe kunnen we Big Data inzetten op een manier die juridisch en ethisch verantwoord en maatschappelijk acceptabel is? Fotografie: Elodie Burrillon / HUCOPIX

Een relevant thema voor zowel wetenschap als maatschappij

Het VWData programma, voluit “Verantwoorde Waardecreatie met Big Data”, komt voort uit de Big Data Route. Het programma concentreert zich op twee belangrijke concepten: FAIR (Findable, Accessible , Interoperable, Reusable) data, en FACT (Fair, Accurate, Confidential, Transparent) data science. Een buitengewoon relevant thema: het zal moeilijk zijn om een krant of een journaaluitzending te vinden waarin er niét “iets met data” aan de hand is.

Het programma zal niet alleen goede wetenschap bedrijven om zijn doelen waar te maken. Minstens zo belangrijk is dat ambassadeurs voor FACT en FAIR er voor zorgen dat zowel wetenschap als maatschappij verder bouwen op de VWData inzichten en resultaten. Daarom zal het programma óók contacten leggen met andere routes binnen de Nationale Wetenschapsagenda, maatschappelijke organisaties, nationale en internationale initiatieven linken.

Juridische, ethische en maatschappelijke vraagstukken

De kick-off startte natuurlijk met het presenteren van de projecten waaruit VWData opgebouwd is. Een korte greep uit die projecten (op de website www.vw-data.nl staat de volledige lijst met projecten en onderwerpen) geeft bijvoorbeeld aan dat bias één van de onderwerpen is: hoe percipiëren nieuwsconsumenten hun filter bubble? En is daar wat tegen te doen? Dicht daarbij ligt het onderwerp hoe je bias in nieuwsberichten zélf kunt opsporen; kun je bijvoorbeeld geautomatiseerd vaststellen hoe het met het diversiteitsgehalte in ons nieuws staat? Of de ‘toxiciteit’ van een bijdrage aan een forum bepalen?

Privacy is natuurlijk een ander belangrijk onderwerp. Het duurde niet lang voordat de GDPR genoemd werd, de General Data Protection Regulation die op 4 mei in Nederland van kracht gaat. Bijvoorbeeld bij het project dat netwerkdata wil analyseren – maar dan wél privacy-vriendelijk. Het verzamelen van data is überhaupt iets waarbij privacy altijd een rol speelt, en één van de projecten gaat dan ook expliciet in op de vraag of je daarvoor een ethisch afwegingskader kunt maken.

Opvallende observatie bij een project dat vooral op transparantie ingaat: soms is veel transparantie juist niét gunstig voor het vertrouwen dat gebruikers hebben in de geleverde dienst. Een mooie uitdaging voor het betreffende project…

Tot slot is het natuurlijk de vraag hoe al die data analyses kunnen worden uitgevoerd op zó’n manier dat er niet meer met de data gesleept hoeft te worden dan strikt nodig: van sommige gevoelige data (bijvoorbeeld medisch) wil je niet dat die het ziekenhuis verlaat. Het uitwerken van een aanpak waarbij het algoritme naar de data reist (en niet andersom) is een aanpak daarbij. Er werden mooie nieuwe woorden gebruikt als ‘FAIRification’ en ‘ FACTification’. Als je gedistribueerde data hebt, wil je ook wel weten of je data FAIR zijn. Heb je daar metrieken voor?

Meer dan een verzameling deliverables

Presenteren van de projecten is één; zorgen dat die projecten samen méér worden dan een verzameling deliverables is iets anders. Tijdens de kick-off is er daarom veel ruimte gereserveerd om te brainstormen over ‘overkoepelende demonstrators’ - hoe kunnen we de concepten van Verantwoorde Waardecreatie met Data laten zien op een aansprekende manier? Het zijn de verhalen die VWData gaat vertellen en de discussies die daardoor teweeggebracht worden, die er voor zorgen dat het programma met recht een Startimpuls genoemd kan worden.

In een vijftal groepen hebben de aanwezigen de eerste ideeën voor die verhalen geformuleerd. Er kwamen tools voorbij om mensen te helpen echte ‘FACT & FAIR services’ te ontwerpen, marktplaatsen, bijsluiters met stoplicht-indicatoren bij algoritmen, video’s waarin (een deel van) de 11700 vragen worden beantwoord, FACTathons, en nog veel meer. Opvallend was dat enerzijds de ‘schotjes’ tussen de projecten helemaal wegvielen bij de discussie, maar dat de ideeën ook nog wel wat generiek van aard waren. 

Op weg naar nieuwe en nóg betere vragen

De kick-off heeft gelukkig meer vragen opgeleverd dan antwoorden: de onderzoekers zullen hier de komende twee jaar hun handen meer dan vol aan hebben. Waarschijnlijk liggen er na die tijd naast een stapeltje antwoorden ook vooral weer nieuwe en nog betere vragen – zoals het een goede startimpuls betaamt!

De kick-off startte met de presentatie van de verschillende VWData projecten - Lora Aroyo presenteert het project ‘Capturing Bias’


Brainstormen over ‘overkoepelende demonstrators’

Programmaleider Inald Lagendijk

Pitches over ‘overkoepelende demonstrators’

Getekend verslag vatte de dag samen in een kunstwerk

Fotografie: Elodie Burrillon / HUCOPIX

Dynaslum research team publishes in Nature Scientific Data

January 26th, 2018

eScience Research Engineers from the eScience Center are collaborating in the research carried out within the projects DynaSlum and SIM-CITY. The projects are led by UvA researchers Peter Sloot and Michael Lees, and results of these projects were recently published in the journal Nature Scientific Data. 

New data yields deeper understanding of poverty in India

A new international study led by UvA researchers Peter Sloot and Michael Lees has yielded extensive data on slums in Bangalore and provides a detailed insight into the problem of poverty in India. The highly granular data, which was collected through a field survey of 36 slums, could lead to a better understanding of poverty and to more effective strategies for managing and improving conditions for slum dwellers. The results were recently published in the journal Nature Scientific Data.

In 2010, an estimated 860 million people were believed to be living in slums worldwide. In order to formulate effective slum development programs and poverty alleviation methods, more insight is needed into the characteristics and needs of slum dwelling communities. As part of their study, the researchers collected data to gain a more complete picture of the problem and developed predictive computer models. ‘Until now, the available data wasn’t sufficient enough to build the advanced computer models needed to calculate intervention scenarios’, says Sloot, who is professor of Computational Science and director of the UvA’s Institute for Advanced Study.

Fieldwork in 36 slums

Over the course of several years, the team conducted surveys and interviews in 36 slums across the city of Bangalore. The slums were chosen based on stratification criteria such as their location, population size, ethnicity and religious profile. By combining the fields of sociology, geography and computer science, the researchers studied the slums with geographical information systems and (agent-based) computer simulation. The collected data included approximately 267,894 data points spread over 242 questions for 1107 households. ‘With this data we are able to develop high-resolution computational models to gain a new understanding about the evolution of slums in India.’ says Michael Lees, assistant professor at the UvA’s Computational Science Lab.

Targeting horizontal inequality

The research team has used the dataset to conduct further research into the structure and dynamics of slums. ‘We have investigated group segregation and how it reinforces inequality within the slums of Bangalore’, adds Debraj Roy, a postdoctoral fellow closely involved in the project. ‘Our results show that we might be able to increase the rate of successful interventions in slums if we target so-called horizontal inequality – which is inequality between, for example, Indian ethnic and religious groups.’

The research team has used the insights from the unique dataset to develop an agent-based model called DynaSlum to identify the key social determinants that impact the behaviour of a slum household. Over the next three years, the researchers will evaluate other, wider aspects like water infrastructure, water management and sanitation practices. The ultimate objective is to create a computer system that will calculate the effects of interventions and allow policymakers to assess different policy strategies before implementation.

Publication details

Debraj Roy, Bharath Palavalli, Niveditha Menon, Robin King, Karin Pfeffer, Michael H. Lees & Peter M.A. Sloot: ‘Survey-based socio-economic data from slums in Bangalore, India’, in:Nature Scientific Data5 (9 januari 2018).https://www.nature.com/articles/sdata2017200

Source news item: http://www.uva.nl/en/disciplines/content/news/press-releases/2018/01/new-data-yields-deeper-understanding-of-poverty-in-india.html

Internship Digital Storytelling

December 22nd, 2017

Do you get excited about inspiring a broad audience with exciting scientific research? Do you think you have a knack for (online) stakeholder engagement, and a persistent attitude to successfully execute your ideas? And can you tell and show us how digital tools and social media can contribute to our overall communication strategy?

Then we should have a coffee. We are providing an internship for minimum 4 - 6 months in which you will learn what it’s like to work as a communications employee in a young and ambitious digital research organization. You’ll get freedom to suggest what you want to focus on in your internship. As long as you contribute to inspiring our broad set of stakeholders with the many hidden stories of the eScience Center.

With 50 digital scientists as your colleagues and many collaborations with researchers throughout the Netherlands, we have almost inexhaustible resources of inspiration for you.

What’s in it for you?

  • Get the freedom to express fresh and creative ideas to contribute to a fast-growing digital research organization
  • Develop and execute your own digital storytelling strategy
  • Meet researchers across a diverse range of disciplines, from Astronomy to the Humanities
  • Work within a fun, diverse and very ambitious team of digital researchers
  • Learn about the latest digital trends in academic research
  • Grow your network with leading academic organizations in the Netherlands
  • Gain knowledge about organizational communication
  • Learn how communication can contribute to organizational success
  • Learn and experience how to present your ideas to a Management Team
  • Unlimited high quality coffee! (according to academic standards)

You:

  • Are in your final year of a related HBO or university study
  • Speak and write English fluently
  • Like to think about impactful ways to get across stories
  • Are not afraid to dive into complex scientific subjects and turn these into stories that appeal to a broad audience
  • Are not afraid to express a different opinion
  • Want to get things done
  • Can handle freedom and take responsibility

What we ask from you:

Develop and execute a digital storytelling strategy that contributes to the eScience Center’s organizational success. This includes advice and assistance on growing our blog, social media and newsletter.

Monthly compensation:

You will receive a monthly compensation of 300-400 EUR (based on a 38 hour week) depending on your level of education. We also offer compensation for travel costs from home to work.

More information:

For more information about this internship you can contact Lode Kulik, Communications Advisor of the Netherlands eScience Center, by emailing l.kulik@esciencecenter.nl, or by calling +31(0)20 460 4770.

Please send your resume and motivation letter at the latest on January 28th 2018 to l.kulik@esciencecenter.nl. Additional information may also be found at www.eScienceCenter.nl.

Deadline:

28 January 2018

Fourteen new eScience collaborations to start in 2018

December 17th, 2017

We are pleased to announce the initiation of fourteen new collaborative projects in the areas of Environment & Sustainability, Life Sciences & eHealth, Physics & Beyond and Disruptive Computer & Data Science.

The projects are the result of the 2017 ASDI, JEDS and JCER calls. The 2017 JEDS call was organized in collaboration with the Netherlands Organisation for Scientific Research (NWO) Domain Science and Commit2Data. The 2017 JCER call was organized in collaboration with the NWO-Shell programme.   

Scheduled to start in 2018, the projects are collaborations with research teams from multiple Dutch academic groups.

2017 ASDI project call

The purpose of this Call for Proposals is to enable domain scientists to address compute-intensive and/or data-driven problems within their research.

Stochastic Multiscale Climate Models
Dr. ir. F.W. Wubs
University of Groningen
Read more about this project

Integrated omics analysis for small molecule-mediated host-microbiome interactions
Prof. dr. ir. D. de Ridder
Wageningen University
Read more about this project

2017 JCER project call

This call for project proposals aims for computational sciences for energy research, focused on developing eScience technologies.

Multiscale simulations of excitation dynamics in molecular materials for sustainable energy applications (MULTIXMAS)
Dr. A.V. Lyulin
Eindhoven University of Technology
Read more about this project

A phase field model to guide the development and design of next generation solid-state-batteries
Dr. ir. M. Wagemaker
Delft University of Technology
Read more about this project

Passing XSAMS
Dr. ir. J. van Dijk
Technische Universiteit Eindhoven
Read more about this project

A light in the dark: quantum Monte Carlo meets solar energy conversion
Prof. dr. C. Filippi
University of Twente
Read more about this project

eScience Technology to Boost Quantum Dot Energy Conversion
Dr. I.A.C. Infante
Vrije Universiteit Amsterdam
Read more about this project

Parallel-in-time methods for the propagation of uncertainties in wind-farm simulations
Prof. dr. ir. R.W.C.P. Verstappen
University of Groningen
Read more about this project

Accurate and Efficient Computation of the Optical Properties of Nanostructures for Improved Photovoltaics
Prof. dr. ir. J.J.W. van der Vegt
University of Twente
Read more about this project

Scalable high-fidelity simulations of reacting multiphase flows at transcritical pressure
Dr. ir. S. Hickel
Delft University of Technology
Read more about this project

2017 JEDS project call

This call for proposals aims at research and development of disruptive solutions associated with big data handling, big data analytics and related computational methods in order to be able to address the novel cross-sectoral scientific challenges described in the Commit2Data White Paper.

FAIR is as FAIR does: Integrating data publishing principles in scientific workflows M. Dumontier
Maastricht University
Read more about this project

FEDMix: Fusible Evolutionary Deep Neural Network Mixture Learning from Distributed Data for Robust Medical Image Analysis
Dr. P.A.N. Bosman
Centrum Wiskunde & Informatica (CWI)
Read more about this project

SecConNet: Smart, secure container networks for trusted Big Data Sharing
Dr. P. Grosso
University of Amsterdam
Read more about this project

Inside the filter bubble: A framework for deep semantic analysis of mobile news consumption traces
Dr. W.H. van Atteveldt
VU University Amsterdam
Read more about this project

Netherlands Research Software Engineer Survey 2017

December 5th, 2017

We would like to invite everyone working on research software in the Netherlands to participate in the RSE survey and spread the word.

The Netherlands Research Software Engineer community (NL-RSE) was started to gain insight into the various communities of RSEs in the Netherlands and increase the interaction between them. The RSE surveys in the UK in 2016 and 2017 [1, 2] have allowed to gain valuable insights and spread the word about the RSE movement. That is why the Netherlands eScience Center, ePLAN (Platform of eScience/Data Research Centres in the Netherlands), NL-RSE, and the UK RSE Association are organizing this survey for 2017 in the Netherlands.

The study is conducted by the University of Southampton on behalf of the Software Sustainability Institute and complies with University of Southampton ethics guidelines (reference no.: ERGO/FPSE/30610). The investigators are Simon Hettrick and Olivier Philippe. Contacts in the Netherlands are Ben van Werkhoven and Tom Bakker from the Netherlands eScience Center.

[1]: See RSE State of the Nation Report 2017, page 21.

[2]: See UK-RSE Survey 2017: Invitation to participate

Board members of The Finnish Union of University Professors visited the Netherlands eScience Center.

December 5th, 2017

Big Data and Research Methods

Higher education in the Netherlands is highly ranked. In the World Economic Forum’s Global Competitiveness Index 2016–2017, it was ranked third after Singapore and Finland.

Moreover, Dutch universities as a group have done very well in global university rankings. All thirteen publicly funded research universities made it to top 200 in THE World University Rankings 2018. Seven were ranked higher than the best-ranked Finnish university and twelve higher than the second bestranked Finnish university.

The board and office of the Finnish Union of University Professors visited the Netherlands to find out what there is to learn from the Dutch university system. They were hosted by Leiden University and Netherlands eScience Center. This article will focus on the eScience Center.

In the past, scientific disciplines worldwide had their own characteristic methods and research tools. In digital society, however, the most important tool in all scientific disciplines is the computer. Since researchers can have access to large amounts of data that must be managed, research projects are getting more and more complex and require new software, new methods and new practices.

The Dutch government seems to have understood what this means to Dutch universities. The “Wetenschapsvisie 2025” of the Dutch government calls for the strengthening of e-infrastructure and eScience in order to maintain the position of Netherlands as an attractive country for scientists and innovative industry. Modern e-infrastructure facilitates highperformance and distributed computing, networking, storage, and visualisation.

The eScience Center is a joint initiative of the Dutch national research council (NWO) and the Dutch organisation for ICT in education and research (SURF). The Center defines itself as “the national hub for the development and application of domain overarching software and methods for the scientific community”. The Center makes collaborative calls. The eScience Center funds and participates in multidisciplinary projects with data-handling, computing and big-data analytics at their core.

In other words, the eScience Center helps Dutch universities develop and apply digitally enhanced scientific tools and methods. The path from data to scientific breakthroughs consists of four steps:

Optimised data handling
1. Data: storage, access, privacy, metadata
2. Processing: annotation, integration

Big data analysis
3. Analysis: modelling, statistics, machine learning
4. Interpretation: visualisation, user interfaces

The Center prefers to develop a limited number of core technological competences where it can have a broad impact on research practices. To create an eScience platform, the Center tries to develop versatile tools and research software that can be generalised. Part of the work is to participate in international coordination within the confines of PLAN-E and EOSC.

The approach is problem-driven. The Center can collaborate with any research discipline. To increase the impact of its work, the Center nevertheless focuses on four broad discipline areas: Environment & Sustainability, Life Sciences & eHealth, Humanities & Social Sciences, and Physics & Beyond. While some of the disciplines within these discipline areas are early adopters of eScience methods, some may use eScience for the first time.

The benefits of Netherlands eScience Center are long term. For funding reasons, however, the Center has thought about ways to show even short-term benefits. Since eScience is the future of research, there are no past economic benefits. One may nevertheless signal research benefits in a quantitative way on the basis of research papers, downloads, or software IDs, or in a qualitative way by narratives. In the future, the Center might lead to spin-offs or consultancy work.

Although the eScience Center develops digital methods, the Center prefers face-to-face meetings with its partners. The staff of the eScience Center thus spend much time on the road visiting Dutch universities and talking directly to researchers and customers.

What lessons can one learn?

The first lesson is about ambition. The Dutch government seems to have understood that a country cannot be competitive in research unless its universities develop new digital research tools and practices that help to address questions that used to be beyond scientists’ reach.

In contrast, the Finnish government has chosen a different path. The Finnish government seems to focus on the digitalisation of education in the false belief that this will help to reduce the number of university lecturers and cut costs. This explains why the digitalisation of education tends to be mentioned — and the digitalisation of research not mentioned — in the new strategies of Finnish universities.

The second lesson relates to the structure of the university sector. It brings benefits to break the silo model of traditional universities. Innovative research increasingly is problem-driven. As a multidisciplinary platform for problem-driven cooperation and as a center that develops generally applicable research tools and practices and participates in multidisciplinary projects, Netherlands eScience Center contributes to a matrix organisation of university research.

University research that the eScience Center participates in is not organised along disciplinary lines. In the long run, this can contribute to new multidisciplinary structures at Dutch universities as well.

Third, one thinks about the number and spatial proximity of universities. The spatial proximity of many research universities in a rather small country seems to increase both cooperation and competition and the spreading of know-how. Cooperation and competition lift all boats and make the Dutch university sector more competitive and innovative as a whole.

The fourth lesson relates to collaboration. Netherlands eScience Center pays attention to being collaborative. It collaborates with researchers, start-ups and established firms. What it tries to avoid is focusing too much on its own research or technology. Shortly put, an eScience center should not be too lured towards its own infrastructure if it is to have an impact.

The fifth lesson is about proximity. Having many eScience specialists under the same roof increases the spreading of knowledge and innovation. So do face-to-face meetings between eScience specialists and scientists. There is no serious collaboration unless the parties meet in the same place.

Of course, university researchers could learn much more from the research projects of the eScience Center. You can use big data to study things ranging from the Big Bang to the human brain and from the weather to the use of case law by judges.

NWO advocates permanent funding for national digital infrastructure

November 28th, 2017

In a report entitled ‘Top science requires top infrastructure’, the Netherlands Organisation for Scientific Research (NWO) advises the new government to make an extra €27 million per year available for the Netherlands’ national digital infrastructure. According to the NWO Committee who produced the report, this is essential if the country is to remain among the best in the world in this area and if it is to meet Dutch researchers’ growing need for digital infrastructures.

Rationale behind the resources

The increasing digitization of science means that researchers have a growing need for digital infrastructures, such as advanced networks, supercomputers, research software and data facilities. Additional investments are also needed to meet the growing ambitions of the Dutch research community, as expressed in the Dutch National Research Agenda, the National Open Science Plan (OCW, 2017), The Digital Society (VSNU, 2016) and the National Roadmap (NWO, 2016). NWO’s Board of Directors has adopted the Committee’s advice, together with its recommendations, and has submitted these to the Ministry of Education, Culture and Science.

Investments provide a new boost

According to the report, additional investments are needed in terms of networks, data facilities and cybersecurity to facilitate the massive growth in data and digitization. This is in line with the Netherlands’ ambition to be a digital ‘mainport’ (hub). Additional investments in large computing facilities are also needed to keep pace with other leading knowledge economies in Europe. This will give researchers unprecedented opportunities to tackle major societal challenges. These issues include climate simulations in the context of global warming, research into specifications for new materials, and DNA analysis.

The Committee also considers that additional investments are needed to support the use of research software and big data. Researchers have an increasing need for specialist services and support of this kind. It also helps researchers to work in compliance with the principles of open science. This involves making scientific articles, research data, methods and software freely accessible to – and reusable for – researchers, companies and society at large.

Keeping up with the best in the world

Boosting investment in the country’s digital infrastructure will enable Dutch researchers to keep up with the best data-intensive research in the world. It will also give the Netherlands an opportunity to play a leading part in the development of open science.

More information

Kas Maessen, Science Division, Head Procedures and Quality
Telephone: +31 70 344 06 95 / 070 344 05 90
e-mail: k.maessen@nwo.nl

Download

Advisory report on the national digital infrastructure for scientific research June 2017

Source: NWO

eScience Center participates in new NWO Perspectief program

November 21st, 2017

In the coming years almost a hundred researchers are going to develop innovative technologies together with industry and social organisations. That will happen in six new Perspectief programmes, which have been given the green light by NWO, Netherlands Organisation for Scientific Research, on21 November 2017. The programmes should lead to a new 3D printer for large metal components, more efficient deep-learning systems, extreme microscopy, new bacteria for the chemical industry, injury-free exercise and wearable robotics for people suffering from muscular disorder.

The board of NWO Domain Applied and Engineering Sciences (AES) is providing 21 million euros for six large-scale research programmes within the Perspectief funding programme. The companies, civil society organisations and knowledge institutes involved in the programmes will supplement NWO’s funding with another 11 million euros. The overall budget will support 74 PhD candidates and 25 postdocs in their work for the coming five or six years.

With Perspectief, NWO is challenging scientists to establish a close partnership with industry and social organisations. It concerns multidisciplinary research with a special emphasis on application. Together the parties will develop new research lines linked to the top sectors.

View the selected 2017 Perspectiefprogramma's on YouTube.

The eScience Center will participate in the program called 'Efficient Deep Learning Systems'.

Efficient Deep Learning Systems

A computer that recognises dangerous situations on security footage: this is possible with deep-learning automated systems. But before this kind of system can operate independently, you have to design it and then train it with a huge number of examples. In addition, you need considerable computing power to let the system make decisions. At the Efficient Deep Learning programme, researchers are going to make deep learning much more efficient by using examples from daily life. They want to make it possible to use the technique (Of: They want to make the technique applicable) for other automatic visual inspections, tissue analysis, smart maintenance of equipment and intelligent hearing aids that can handle noisy environments.

Programme manager: Professor H. Corporaal (Eindhoven University of Technology)
Participants: AIIR Innovations, ASTRON, CWI, Cyclomedia, Cygnify, Donders Institute, FEI, 2getthere, GN Hearing, Holst Centre, ING, Intel, Irdeto, Lely, Mobiquity, Netherlands eScience Center, NXP, NVIDIA, Océ, Radboudumc, Schiphol, Scyfer, Sectra, Semiotic Labs, Siemens, Sightcorp, Sorama, SURFsara, TASS International, Tata Steel, TU Dresden, Delft University of Technology, Eindhoven University of Technology, Thales, TNO, TomTom, University of Twente, University of Amsterdam, 3DUniversum, VicarVision, ViNotion, VU Amsterdam, Wageningen University & Research

Link to NWO news item:
https://www.nwo.nl/en/news-and-events/news/2017/32...

Over 300 researchers visit National eScience Symposium 2017

October 18th, 2017

This year's edition of Science in a Digital World featured over 30 speakers and the announcement of the Young eScientist Award winner 2017: Frank Takes (read more).

The five thematic sessions, on Internet of Things, Energy Science, Natural Language Processing, Brain, Cognition and Behavior and The Future of Machine Learning were co-organized with SURFnet, Shell-NWO progamme, CLARIAH, NeuroLabNL and Commit2Data.

View a selection of photos below - for more photos visit our Flickr album.

The program, including all speakers and abstracts, can be viewed here.

Photography: Elodie Burrillon / http://hucopix.com


Wilco Hazeleger (Director Netherlands eScience Center) welcomes everyone at Science in a Digital World


Paul Rullmann (Chair of SURF) opens Science in a Digital World


Cecilia Aragon (University of Washington) gives her keynote presentation on 'The hearts and minds of data science'


Demo and poster exhibition


Discussion in the Brain, Cognition and Behavior session (with NeuroLabNL)


Discussion in the Internet of Things session (with SURFnet) 


Young eScientist Award 2017. From left to right: Maureen van Eijnatten (winner 2016), Frank Takes (winner 2017), Rob van Nieuwpoort (Director eScience Technology, Netherlands eScience Center)


Diederik Jekel delivers closing keynote on 'Living in a scientific revolution'

Young scientist wins award for platform to investigate corporate tax avoidance

October 12th, 2017

Frank Takes (31) from the University of Amsterdam has won the Young eScientist Award 2017. The prize aims to stimulate a young scientist demonstrating excellence in eScience: the development or application of digital technology to address scientific challenges. The prize will be used to undertake a joint research project, in which Takes will receive support by eScience Research Engineers (experts in the development and application of research software).

Investigating tax havens

Takes’ research focuses on corporate tax avoidance via offshore finance. This has been a hot topic in recent years, especially with large companies moving offshore from their ‘home’ nation for the purpose of tax avoidance. Together with the eScience Center, Takes’ wants to develop an interactive web-based platform to investigate the dynamics of this global network of offshore finance.

The platform, aimed at a non-technical audience, should serve both as a data hub and a yearly updated index of tax havens, and visualize value flows between hundreds of countries. This will enable researchers, journalists and policy makers to directly gain insight in the evolution of corporate tax avoidance across the globe – a topic with great relevance to society.

About the Netherlands eScience Center

For scientific researchers wanting to take full advantage of ever growing amounts of data and increasingly powerful digital technology, research software is essential. The Netherlands eScience Center is the Dutch national center of excellence for the development and application of research software.The eScience Center is a joint initiative of the Dutch national research council (NWO) and the Dutch organization for ICT in education and research (SURF).

More information about the Netherlands eScience Center: www.eScienceCenter.nl

More information about the Young eScientist Award: https://www.esciencecenter.nl/funding/young-escientist-award or contact r.vannnieuwpoort@esciencecenter.nl.

Photography: Elodie Burrillon / http://hucopix.com

Health-RI conference on 8 December 2017

October 12th, 2017

Health-RI 2017 will discuss the latest developments and opportunities in biobanking, FAIR data management, ethical and legal aspects, IT solutions, and exciting science, all centered around our collective quest for more and impactful personalized medicine and health solutions. Additionally, Health-RI 2017 will give you an update on how the Netherlands is gearing up for a collective biomedical research infrastructure that maximally supports research projects, and boosts the value of existing and newly generated research and healthcare data. 

This conference offers you an excellent opportunity to meet like-minded people from academia and industry, government, and health foundations to discuss your ideas and explore possible new collaborations.

This year's conference will take place on 8 December 2017 in Utrecht.

Visit the conference website here.

Adriënne Mendrik on Grand Challenges in Computer Vision Magazine

October 12th, 2017

Open science is supported by the eScience Center. One of our eScience Coordinators (Adriënne Mendrik) was co-organizer and presenter at a tutorial on designing benchmarks and challenges for measuring algorithm performance in biomedical image analysis at the 20th International Conference on Medical Image Computing and Computer Assisted Intervention (September 14th, 2017 in Quebec City, Quebec, Canada - view the article in Computer Vision Magazine).

Challenges are open online competitions, for which data and evaluation metrics are made publicly available to get insight into algorithm performance for a specific problem.

Adriënne Mendrik and Stephen Aylward presented a theoretical framework to help guide challenge design and redefine the objective of grand challenges, to either gain insight (insight challenge) or solve a problem (deployment challenge).

For more information see https://grand-challenge.org/.

There is to date no long-term solution that fully facilitates the sustainability of grand challenges in the biomedical image analysis field

NWA-routes conferentie

September 20th, 2017

Eén jaar na de presentatie van het Portfolio voor onderzoek en innovatie is er veel gebeurd binnen de 25 routes van de Nationale Wetenschapsagenda. Tijd om te reflecteren op het proces en de ontwikkeling van nieuwe samenwerkingsverbanden, resultaten te delen en nieuwe mogelijkheden voor co-creatie en kennisbenutting te verkennen. Dat doen we graag samen met de vertegenwoordigers van de routes en hun netwerken tijdens de NWA-routes conferentie op 31 oktober in Nieuwegein.

Workshops

Het programma is samengesteld op basis van de wensen die leven binnen de routes. We bieden ruimte voor ontmoeting en verdere verdieping, maar ook inhoudelijke themaworkshops, zoals over big data, living labs, sustainable development goals, kunst, kennis en innovatie én publiek-private samenwerking. Bekijk hier het complete aanbod van workshops.

Aanmelden

De conferentie is gericht op deelnemers vanuit de wetenschap, maatschappelijke organisaties, overheden en bedrijfsleven. Belangstellenden kunnen zich tot en met donderdag 19 oktober aanmelden.

Locatie

De conferentie vindt plaats in de Woonindustrie te Nieuwegein. De ontvangst is vanaf 9.30 uur. Het programma begint om 10.00 uur.

Contact

Mocht u nog vragen hebben over logistieke en/of organisatorische aspecten van de dag, dan kunt u ons per e-mail bereiken via congres@wetenschapsagenda.nl.

AA-ALERT project detects Fast Radio Burst

September 6th, 2017

Fast Radio Bursts, or FRBs, are one of the hottest topics in astronomy right now. These intense blasts of radio energy reach us from outside the galaxy, lasting only milliseconds before they disappear once more. Astronomers aren’t sure what causes them, and none of these bursts have ever repeated — except one, FRB 121102, which made headlines with the identification of its host galaxy, sitting nearly 3 billion light-years away.

ALERT, the Apertif Lofar Exploration of the Radio Transient Sky, is investigating the Northern Sky with unprecedented speed and precision, to determine the nature amongst others such Fast Radio Bursts. The Apertif Radio Transient System (ARTS) is the new, high-speed, wide-field radio camera for the Westerbork Synthesis Radio Telescope. It consists of the revolutionary new Apertif front ends (the "eyes") and an exceedingly powerful GPU supercomputer ("the brain"). The algorithms (the "thoughts") for this supercomputer were developed in a collaboration involving ASTRON, Universiteit van Amsterdam, and the Netherlands eScience Center.

The final ARTS GPU hardware was just installed in the Westerbork server room, in the last week of August. On 31 August the team started commissioning the system by observing FRB 121102. During this observation, ARTS detected a bright FRB, its first. The burst is very short (1.3 ms) and bright (24 Jy). The team reported the detection in ATel #10693. Further details and plots are available at http://www.alert.eu/FRB121102_20170831/

Read more about the project on our blog and on the project page.

Image source: Gemini Observatory/AURA/NRC/NSF/NRAO

“Crowdsourcing for Medical Image Analysis” wins Lorentz-eScience workshop competition

August 3rd, 2017

We congratulate professors Lora Aroyo (VU University Amsterdam), Alessandro Bozzon (Delft University of Technology), Veronika Cheplygina (Eindhoven University of Technology), Danna Gurari (University of Texas at Austin, USA) and Zoltán Szlavik (IBM Center for Advanced Studies Benelux) on winning the competition for the second Lorentz-eScience workshop with their proposal “Crowdsourcing for Medical Image Analysis”. We are very pleased that we can continue this program with such a high quality and interesting workshop.

Crowdsourcing for Medical Image Analysis

The vast amount of visual data collected at hospitals each year offers exciting opportunities for computer-aided diagnosis (CAD) of widespread diseases such as COPD or diabetes. However, progress in algorithms for CAD relies on annotated data, requiring costly annotation by medical experts. Crowdsourcing - outsourcing tasks to a crowd of internet users without any specific experience - has emerged in other communities, such as computer vision, to successfully offer a cost-effective, scalable alternative to extract meaningful information from images. However, medical images are still widely believed to be too difficult for untrained people to interpret.

Bringing together experts from academia and industry

This workshop will serve as an inter-disciplinary gathering for individuals in academia and industry interested in advancing this important, emerging field. The workshop will bring together experts from medical imaging (including clinical experts), machine learning (including computer vision) and crowdsourcing in order to identify key problems to tackle as a community, explore medical imaging datasets and crowdsourcing tools during hands-on sessions, and initiate projects to develop the community in the future.

The workshop will take place in the week of 9 – 13 July 2018 at the venue Lorentz Center@Snellius in Leiden, the Netherlands.

The Lorentz-eScience workshop competitions, organized by the Netherlands eScience Center and the Lorentz Center, sponsor leading-edge workshops on the application of digitally enhanced research. The workshops should bring together researchers from the academic scientific community with those from the public/private sector. More information: https://www.esciencecenter.nl/news/lorentz-escience-competition-2018

Prof. Jan de Boer joins Board of Directors eScience Center

July 24th, 2017

We are pleased to announce that Prof. Jan de Boer of the University of Amsterdam is joining the Board of Directors of the Netherlands eScience Center as of July 2017.

Jan de Boer has been associated with the University of Amsterdam since 2000 as Professor of Theoretical Physics. Between 2010 and 2015 he was education director of the Graduate School of Science. He also leads the Institute for Theoretical Physics Amsterdam (ITFA), part of the Institute of Physics. 

He was also one of the founders of GRAPPA research center. From 2015 until 2016, Jan de Boer was in the executive board of FOM and from 1 January 2017 in the board of NWO Domain Science (ENW). Jan de Boer is looking forward to strengthen the relation between the NWO Domain Science and the eScience Center.

An ambition for the global astronomical community

July 17th, 2017

Groen licht voor NWA Startimpulsprogramma VWData

July 7th, 2017

Op 5 juli heeft de NWA Route Big Data groen licht gekregen voor het uitvoeren van het Startimpulsprogramma VWData (Verantwoorde Waardecreatie met Big Data). Dit programma heeft een omvang van 2,5M Euro plus 0,5-1M Euro cofinanciering. In totaal heeft de Raad van Bestuur van NWO 20M Euro toegekend uit het Startimpulsbudget voor de Nationale Wetenschapsagenda aan acht verschillende Startimpulsprogramma’s.

Een succesvolle eerste stap
‘Dit is een succesvolle eerste stap in de implementatie van de NWA,’ aldus NWA-voorzitter Louise Gunning. ‘Zoals de NWA beoogt zijn er nieuwe samenwerkingsverbanden gecreëerd tussen wetenschappers van verschillende disciplines, maar ook tussen verschillende kennisinstellingen, ministeries, bedrijfsleven en maatschappelijke organisaties. Ook is geëxperimenteerd met een andere manier om geld aan partijen toe te delen en de krachten te bundelen. Hopelijk volgt er nu ook snel financiering voor de andere routes.’

VWData Startimpulsprogramma
De verantwoordelijkheid over het VWData Startimpulsprogramma programma is in handen van de aanvragers van dit programma. Het team van aanvragers bestrijkt de brede achterban van de route Big Data, en bestaat uit: Inald Lagendijk (route boegbeeld, hoofdaanvrager), Wilco Hazeleger (route trekker), Henk-Jan Vink (route trekker), Wil van der Aalst, Geleyn Meijer, Natali Helberger, en Wiro Niessen.

Het programma is tot stand gekomen door de selectie uit maar liefst 54 voorstellen. De grote en diverse set van ingeleverde voorstellen weerspiegelt het belang van verantwoorde waardecreatie met big data, en de grote betrokkenheid van partijen die zich met dit vraagstuk bezighouden.

Het programma bestaat momenteel uit zeven projecten (en projectteams) die zijn verdeeld over vijf inhoudelijke werkpakketten, met daarnaast een overstijgend werkpakket voor programmamanagement en kennisdisseminatie en voor onderzoek naar de betekenis en impact van FAIR en FACT ten behoeve van VWData-synergie en toekomstige programmering.

Werkpakket Fairness
FairNews: Nieuwsvoorziening in een Big Data Data tijdperk
Hoe ver kunnen en mogen algoritmes gaan in het filteren van informatie? Wanneer komen fundamentele rechten in het geding?
Claes de Vreese (UvA/CW), Claudia Hauff (TUD) en Joris Hoboken (UvA/IvIR)

Werkpakket Accuracy
Capturing Bias: Diversity-aware Computation for Accurate Big Media Data Analysis
The WP provides bias- and diversity-aware methods & tools to support accurate analysis and interpretation of big media data over time.
Lora Aroyo (VUA), Alessandro Bozzon (TUD), Alec Badenoch (UU) en Antoaneta Dimitrova (UL)

Werkpakket Confidentiality
Enabling of privacy-friendly analysis of network data and beyond
In dit project worden technieken ontwikkeld om big data op een privacy-vriendelijke wijze op te slaan, te delen en te analyseren.
Bart Jacobs (RUN), Joeri de Ruiter (RUN), Roland van Rijswijk-Deij (SURF) en Aiko Pras (UT)

Werkpakket Transparancy
Responsible Collection and Analysis of Personal Data in Law Enforcement
We will clarify how to balance transparency with other values, esp. accountability, confidentiality and fairness, in the collection and analysis of personal data in law enforcement.Ibo van de Poel (TUD), Nicolien Kop (Politieacademie) en Marc Steen (TNO)

Data-gedreven diensteninnovatie: compliancy en transparency 'by design'
By-design meenemen van en inzicht geven in verantwoorde verwerking van (big) data in innovatieve digitale diensten.
Gerard Schouten (Fontys), Johan Versendaal (HvU), Martijn Zoet (Zuyd Hogeschool) en Remko Helms (OU)

Werkpakket Accessibility & Operability
Distributed FAIR information systems to enable federated learning and reasoning
Enabling reliable, explainable federated learning and reasoning from distributed FAIR data assets with security enforcement mechanisms.
Cees de Laat (UvA), Henri Bal (VU), Barend Mons (LUMC, GO FAIR), Wessel Kraaij (UL/TNO) & team UU, VU, UL, KPMG, UvA, KLM, NLR, ASTRON

Analyzing partitioned FAIR health data responsibly
Combining and learning from access-restricted FAIR health and socioeconomic data across entities in a privacy-preserving manner.Michel Dumontier (UM), Andre Dekker (MUMC). David Townend (UM), Annemarie Koster (UM) en Bob van den Berg (CBS)

Over de Startimpuls
In september 2016 maakte het ministerie van OCW bekend 30 miljoen euro te investeren in de NWA. Het grootste deel hiervan, 20 miljoen euro, gaat naar de Startimpuls en is bestemd voor thematisch onderzoek binnen bepaalde thema’s. Daaronder vallen acht routes van de Nationale Wetenschapsagenda. Minister Bussemaker en staatssecretaris Dekker laten weten verheugd te zijn dat de toekenningen rond zijn. Minister Bussemaker geeft aan dat er nieuwe inzichten ontstaan door samenwerking die disciplines overstijgt, door nieuwe kenniscentra op te richten en broedplaatsen voor talent te ontwikkelen. ‘Met het thema veerkrachtige samenleving bijvoorbeeld, investeren we in nieuwe samenwerking tussen wetenschappers, bedrijfsleven én maatschappelijke organisaties. Samenwerking is cruciaal voor gelijke kansen voor iedereen, wat ik heel belangrijk vind,’ aldus minister Bussemaker. Staatssecretaris Dekker benadrukt de economische kansen: ‘De onderzoeken moeten leiden tot antwoorden op de maatschappelijke en economische vragen van vandaag en de nabije toekomst, tot nieuwe oplossingen en innovaties die zorgen voor economische groei en meer banen.’

ANDI project receives award for Amsterdam’s most innovative scientific idea

July 7th, 2017

The award for Amsterdam’s most innovative scientific idea

Nathalie de Vent and Joost Agelink van Rentergem of the University of Amsterdam are the winners of the Amsterdam Science & Innovation Award 2017, the annual award for the most innovative scientific idea of all Amsterdam knowledge and research institutes.

They received the award for the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), a new online infrastructure for the improvement of neuropsychological diagnostics. The eScience Center participated in this project, developing an interactive web application.

ANDI – a new online infrastructure for the improvement of neuropsychological diagnostics

Advanced Neuropsychological Diagnostics Infrastructure (ANDI) is a website for the analysis of neuropsychological test results to improve the diagnosis of brain trauma or brain disease. ANDI has a large database of representative standard data of healthy controls, which makes the comparison of a patient with the standard group more precise than when the traditional standard tables are used. Also, demographic background variables are taken into account in this equation. Nathalie: “This way, ANDI facilitates and improves neuropsychological diagnostics, which can also improve care for patients with brain diseases.”

Nathalie de Vent and Joost Agelink van Rentergem received the prize of € 10,000 from Mirjam van Praag, chairman of the jury. “ANDI can make the difference for thousands of people. The jury was initially surprised that such a platform did not already exist: it sounds like something that is practically possible and that serves a clear question. ANDI takes this up and uses big data and networks in an innovative way, “said Mirjam van Praag.

Amsterdam Science & Innovation Award

The Amsterdam Science & Innovation Award is the annual award for the most innovative idea with a social and/or commercial application, derived from scientific research. This year is the twelfth edition of this award. The Award is organized by IXA (Innovation Exchange Amsterdam). Partners of the Award are the City of Amsterdam, Amsterdam Science Park, Sanquin, NKI-AVL, Rabobank, Port of Amsterdam, Equinix, Surfsara and De Vries & Metman.

News item IXA: https://ixa.amsia.nl/winners/

DIVE+ receives the grand prize at the LODLAM Summit in Venice

July 4th, 2017

DIVE+ is a collaborative effort of the VU University Amsterdam (Victor de Boer, Oana Inel, Lora Aroyo, Chiel van den Akker, Susane Legene), Netherlands Institute for Sound and Vision (Jaap Blom, Liliana Melgar, Johan Oomen), Frontwise (Werner Helmich), University of Groningen (Berber Hagendoorn, Sabrina Sauer) and the Netherlands eScience Center (Carlos Martinez). It is supported by CLARIAH and NWO.

Beeld en Geluid is excited to announce that DIVE+ has been awarded the Grand Prize at the LODLAM Summit, held at the Fondazione Giorgio Cini this week. The summit brought together ~100 experts in the vibrant and global community of Linked Open Data in Libraries, Archives and Museums. It is organised bi-annually since 2011. Earlier editions were held in the US, Canada and Australia, making the 2017 edition the first in Europe.

The Grand Prize (USD$2,000) was awarded by the LODLAM community. It's a recognition of how DIVE+ demonstrates social, cultural and technical impact of linked data. The Open Data Prize (of USD$1,000) was awarded to WarSampo for its groundbreaking approach to publish open data.

Five finalists were invited to present their work, selected from a total of 21 submissions after an open call published earlier this year. Johan Oomen, head of research at the Netherlands Institute for Sound and Vision presented DIVE+ on day one of the summit. The slides of his pitch have been published, as well as the demo video that was submitted to the open call. Next to DIVE+ (Netherlands) and WarSampo (Finland) the finalists were Oslo public library (Norway), Fishing in the Data Ocean (Taiwan) and Genealogy Project (China). The diversity of the finalists is a clear indication that the use of linked data technology is gaining momentum. Throughout the summit, delegates have been capturing the outcomes of various breakout sessions. Please look at the overview of session notes and follow @lodlam on Twitter to keep track.

DIVE+ is an event-centric linked data digital collection browser aimed to provide an integrated and interactive access to multimedia objects from various heterogeneous online collections. It enriches the structured metadata of online collections with linked open data vocabularies with focus on events, people, locations and concepts that are depicted or associated with particular collection objects. DIVE+ is the result of a true interdisciplinary collaboration between computer scientists, humanities scholars, cultural heritage professionals and interaction designers. DIVE+ is integrated in the national CLARIAH (Common Lab Research Infrastructure for the Arts and Humanities) research infrastructure.

The LODLAM Challenge was generously sponsored by Synaptica. We would also like to thank the organisers, especially Valentine Charles and Antoine Isaac of Europeana and Ingrid Mason of Aarnet for all of their efforts. LODLAM 2017 has been a truly unforgettable experience for the DIVE+ team.

Photo credit: Enno Meijers

Are you our new Director Operations (Directeur Bedrijfsvoering)?

June 28th, 2017

eScience Center and CLARIAH grant four projects in the Arts and Humanities

June 26th, 2017

The eScience Center and CLARIAH are pleased to announce the initiation of four new projects in the Arts and Humanities. The four projects will pursue new scientific domain challenges and enhance and accelerate the process of scientific discovery within the Arts and Humanities using computer science, data science, and eScience technologies.

Scheduled to start in the second half of 2017, the projects are collaborations with research teams from multiple Dutch academic groups. The granted projects will use, adapt, and integrate existing methods and tools, as made available through the CLARIAH and eScience Center software infrastructures. Newly developed tools will be made available through the eScience Technology Platform of the Netherlands eScience Center and the CLARIAH Infrastructure for potential use in other studies.

The granted projects are:

Bridging the gap: Digital Humanities and the Arabic-Islamic corpus
Prof. dr. Christian Lange, Utrecht University

Despite some pioneering efforts in recent times, the longue durée analysis of conceptual history in the Islamic world remains a largely unexplored field of research. Researchers of Islamic intellectual history still tend to study a certain canon of texts, made available by previous Western researchers of the Islamic world largely based on considerations of the relevance of these texts for Western theories, concepts and ideas. Indigenous conceptual developments and innovations are therefore insufficiently understood, particularly as concerns the transition from premodern to modern thought in Islam.

This project seeks to harness state-of-the art Digital Humanities approaches and technologies to make pioneering forays into the vast corpus of digitised Arabic texts that has become available in the last decade. This is done along the lines of four case studies, each of which examines a separate genre of Arabic and Islamic literary history (jurisprudence, inter-faith literature, early modern and modern journalism, and Arabic poetry).

This project seeks to develop a web-based application that will (a) enable easy access to existing Arabic corpora on GitHub and other online repositories and offer the opportunity for researchers to upload their own corpus (b) offer a set of tools for Arabic text mining and computational analysis, and (c) provide opportunities to link search results to the datasets in Islamic and Middle Eastern Studies of Brill Publishers, Europe’s leading publisher in this area.

The project will be inserted into two ongoing ERC projects on Islamic intellectual history housed at the Department of Philosophy and Religious Studies at Utrecht University, and collaborate closely with international initiatives in the field of Arabic Digital Humanities.

TICCLAT: Text-Induced Corpus Correction and Lexical Assessment Tool
Dr. Martin Reynaert, Tilburg University

The Text-Induced Corpus Clean-up tool TICCL, integral part of the CLARIN infrastructure, is globally unique in utilizing the corpus-derived word form statistics to attempt to fully-automatically post-correct texts digitized by means of Optical Character Recognition.

The NWO 'Groot' project Nederlab will deliver by the end of 2017 a uniformly processed and linguistically enriched diachronic corpus of Dutch containing an estimated 5-6 billion word tokens. We aim to extend TICCL's correction capabilities with classification facilities based on specific data collected from the full Nederlab corpus: word statistics, document and time references and linguistic annotations, i.e. Part-of-Speech and Named-Entity labels. These data will complement a solid, renewed basis composed of the available validated lexicons and name lists for Dutch.

In this, TICCL as a post-correction tool will be transformed into TICCLAT, a lexical assessment tool capable of delivering not only correction candidates, but also e.g. more accurately dated diachronic Dutch word forms, more securely classified person and place names. To achieve this on scale, the TICCLAT project will seek a successful merger of TICCL's anagram hashing with bit-vectorization techniques. TICCLAT's capabilities will also be evaluated in comparison to human performance by an expert psycholinguist.

The data collected will be exportable for storage in a data repository, as RDF triples, for broad reuse. The project will greatly contribute to a more comprehensive overview of the lexicon of Dutch since its earliest days and of the person and place names that share its history. Its partners are the Dutch experts in Lexicology, Person Names and Toponyms.

News Genres: Advancing Media History by Transparent Automatic Genre Classification (NEWSGAC)
Prof. dr. Marcel J. Broersma, University of Groningen

This project studies how genres in newspapers and television news can be detected automatically using machine learning in a transparent manner. This will enable us to capture the often hypothesized but, due to the highly time consuming nature of manual content analysis, largely understudied shift from opinion-based to fact-centred reporting. Moreover, we will open the black box of machine learning by comparing, predicting and visualizing the effects of applying various algorithms on heterogeneous data with varying quality and genre features that shift over time. This will enable scholars to do large-scale analyses of historic texts and other media types as well as critically evaluate the methodological effects of various machine learning approaches.

This project brings together expertise of journalism history scholars (RUG), specialists in data modelling, integration and analysis (CWI), digital collection experts (KB & NISV) and e-science engineers (eScience Center). It will first use a big manually annotated dataset (VIDI-project PI) to develop a transparent and reproducible approach to train an automatic classifier. Building upon this, the project will generate three outcomes:

1. A study that revises our current understanding of the interrelated development of genre conventions in print and television journalism based upon large-scale automated content analysis via machine learning;

2. Metrics and guidelines for evaluating the bias and error of the different preprocessing and machine learning approaches and of-the-shelf software packages;

3. A dashboard that integrates, compares and visualises different algorithms and underlying machine learning approaches which can be integrated in the CLARIAH media suite.

EviDENce: Ego Documents Events modelliNg. How individuals recall mass violence
Dr. Susan Hogervorst, Open Universiteit Nederland

Much of our historical knowledge is based on oral or written accounts of eyewitnesses, particularly in cases of war and mass violence, when regular ways of documentation and record keeping are often absent. Although oral history and the study of ego documents both value these individual perspectives on history and its meaning, these research fields tend to operate separately. However, the digital revolution has shaken up the balance between spoken and written text. The paradigm emerging in the application of search technology to digitised oral history is characterised by a post-documentary sensibility: away from text and sensitive to other dimensions of human expression than language. Nonetheless, ‘mining’ of oral history accounts remains valuable in humanities research, especially considering the re-use of digital interview collections throughout the humanities.

EviDENce explores new ways of analysing and contextualising historical sources by applying event modelling and semantic web technologies. Our project suggests a systematic and integral content analysis of ‘ego-sources’ by applying state-of-the-art entity and event modelling methods and tools, in order to explore the nature and value of ego-sources and to disclose existing collections. We focus on representations of mass-violence in two case studies to generate and explore different kinds of events: 1) a synchronic analysis of WW2 events, centered around the oral history collection ‘Getuigenverhalen’ [1] and using the WW2 thesaurus [2], and 2) a diachronic analysis of ego-documents (1573-2012) from Nederlab [3]. In both cases, we use content-related contextual sources from Nederlab [4].

About the ADAH Call

The four projects result from the recent ADAH call (Accelerating Scientific Discovery in the Arts and Humanities). The purpose of the 2016 ADAH call is to enable researchers working in the Arts and Humanities to address compute-intensive and/or data-driven problems within their research and to contribute to a generic and sustainable research software infrastructure.

About the Netherlands eScience Center

The eScience Center is the national hub for the development and application of domain overarching software and methods for the scientific community. The eScience Center develops crucial bridges between increasingly complex modern e-infrastructures and the growing demands and ambitions of scientists from across all scientific disciplines.

About CLARIAH

CLARIAH is a national project that is designing, constructing and exploiting the Dutch parts of the European CLARIN and DARIAH infrastructures. CLARIAH covers the humanities as a whole but has three core discipline areas: linguistics, media studies, and socio-economic history.

Contact information

Prof. dr. Jan Odijk, Program Director CLARIAH
+31 (0)30 253 5745
j.odijk@uu.nl

Dr. Frank Seinstra, Director eScience Program, Netherlands eScience Center
+31 (0)20 4604770
f.seinstra@esciencecenter.nl

What is the impact of visualization on science?

June 21st, 2017

Call for proposals NWA-route Big Data

May 15th, 2017

De Nationale Wetenschapsagenda-route Big Data heeft een call for (verkorte) proposals uitgezet. Teams van onderzoekers worden uitgenodigd om een verkort voorstel in te dienen voor het uitvoeren van één van de vijf inhoudelijke werkpakketten binnen het voorgestelde programma Verantwoorde Waardecreatie met Big Data (VWData), dat vanaf januari 2018 van start moet gaan binnen als onderdeel van de NWA Startimpuls.

De Programmabeschrijving, de call-tekst en het template voor indiening vindt u hier.

De deadline is zaterdag 3 juni 2017.

DATA2PERSON - Big Data & Health

April 20th, 2017

Consortiums of academics and public/private parties can apply for funding for the development of effective, efficient, and responsible personal empowerment methods that promote a healthy society in the future.

Purpose

With this call for the COMMIT2DATA programme, NWO, ZonMW, and the Ministry of Economic Affairs stimulate big data Research (Data Science) to contribute to the development of effective, efficient, and responsible personal empowerment methods for a future healthy society in partnership with other scientific disciplines. The focus of this programme is on the way in which Data Science can make a contribution to a personalized offer and possibilities for the self/joint management of the individual health situation. Important questions relating to this call are: What works and what doesn't? Why? Or why not? For who does it work, and for who doesn't it?

Who can apply

Applications can be submitted on behalf of consortiums consisting of at least two academic departments from a research institute or institutes and one public or private partner that alone, or together with multiple private and public partners, meets the private/public matching criteria.

The principal applicant is an experienced researcher with a PhD who has a tenured or temporary appointment at a Dutch university or a research institute recognized by the NWO for the duration of the application process and the project.
The same standards apply to academic co-applicants. 

Private and public partners may be co-applicants and are not eligible to receive NWO funding, but contribute in cash and/or in kind to the research.

Researchers from universities of applied sciences, TO2 federation organizations, national institutes, and the non-university part of Wageningen University & Research may act as co-applicants as knowledge institutes but are not eligible to receive NWO funding.

More information can be found here.

How can network analysis lead to a new way of studying court decisions?

April 3rd, 2017

The eScience Center and NWO-Shell join forces for future energy

March 22nd, 2017

Future energy requires innovative solutions. Current energy developments are advanced by scientific research on geoscience, wind and solar energy, multiphase flows, computational chemistry and material sciences. The eScience Center and NWO-Shell’s Computational Sciences for Energy Research programme (CSER) are joining forces to support this research by opening a joint call for PhD project proposals with eScience support. This new joint call addresses research challenges in the computational sciences for future energy and develops sustainable software tools.

The CSER programme started in 2012 with the aim to strengthen the computational sciences in the Netherlands and to contribute to societal issues such as the Energy Challenge, as described by the Topsector Energy. The programme has not yet addressed the sustainability of the software tools and results of its research projects. The joint call with the eScience Center concentrates on both the scientific challenges and the sustainability of the software tools. The eScience Center is tasked to enhance science by working collaboratively in data and compute intensive research projects. It contributes to projects by providing eScience Research Engineer support to effectively use and develop modern digital tools and methodologies. The eScience Center also provides an online platform, the eScience Technology Platform, to sustain the developed tools and methodologies beyond the life time of the project.

About CSER

The Computational Sciences for Energy Research (CSER) programme is a joint large-scale public-private partnership in fundamental research in the energy domain between Shell and the Netherlands Organisation for Scientific Research (NWO). The goal of the programme is to strengthen the computational sciences in the Netherlands and to contribute to societal issues such as the Energy Challenge, as described by the Topsector Energy.

The programme has started in 2012 and a strong relationship between the partners is now established. The programme consists of 75 PhD projects spread over a range of computational sciences disciplines such as computational geoscience, wind and solar energy, multiphase flows, computational chemistry and material sciences for energy research. Besides developing top talented PhD students in the field of computational sciences, the programme also focuses on strengthening the knowledge infrastructure within the Netherlands through tenure track positions at various universities and research institutes.

About the Netherlands eScience Center

The eScience Center is the national hub for the development and application of domain overarching software and methods for the scientific community. The eScience Center develops crucial bridges between increasingly complex modern e-infrastructures and the growing demands and ambitions of scientists from across all scientific disciplines. The application of digitally enhanced scientific practices is nowadays fundamental toolbox for all researchers and is a prerequisite to ensure that the Dutch knowledge sector remains competitive and the greatest return can be achieved from scientific investments. In support of this goal, the eScience Center funds and participates in multidisciplinary projects with optimal data-handling, efficient computing and big-data analytics at their core.

3D-e-Chem team develops Virtual Machine for Computer-Aided Drug Discovery

February 24th, 2017

A team of cheminformatics and bioinformatics researchers from Netherlands eScience Center, Vrije Universiteit Amsterdam, Radboudumc Nijmegen, and BioAxis Research have developed a freely available virtual machine to enable computer-aided drug design.

The 3D-e-Chem consortium, including Stefan Verhoeven (Netherlands eScience Center), Ross McGuire (Radboudumc, BioAxis Research), and Chris de Graaf (PI, Vrije Universiteit Amsterdam), develop new cheminformatics technologies to improve the integration of chemical and biological data for the prediction of structural interactions between drug molecules and therapeutic protein targets. The computational drug discovery platform is currently applied to identify and optimize molecules that act on several proteins simultaneously (polypharmacology), while avoiding undesired side effects via interactions with off-target proteins.

The 3D-e-Chem software tools and virtual machine are described in a recent publication in the Journal of Chemical Modeling and Information and the computational building blocks (nodes) that enable researchers to design their own drug discovery workflows will soon be incorporated in KNIME, the leading open data analytics platform.

Lorentz-eScience competition 2018

February 20th, 2017

    Lorentz-eScience competition 2018

The Netherlands eScience Center and the Lorentz Center are looking for researchers who want to join the Lorentz-eScience competition and organize a workshop at the Lorentz Center@Snellius, Leiden, the Netherlands.

The Lorentz-eScience competition aims to host a leading-edge workshop on digitally enhanced research (efficient utilization of data, software and e-infrastructure). The workshop topic should bring together researchers from the academic scientific community and the public/private sector.

What we seek
• an innovative scientific programme, that takes us beyond our current boundaries
• an open and interactive format, with few lectures
• at least one scientific organizer based within and one outside the Netherlands
• at least one scientific organizer from the academic sector and one from the public/private sector

What we offer
• a 5-day workshop for up to 25 people in the first half of 2018
• travel and accommodation reimbursements
• no registration fees or other organizational costs
• a professional support organization

Procedure
• a 1-page expression of interest by 15 April 2017
• a full application by 6 June 2017
• final decision end of June 2017
• submit applications to: proposal@lorentzcenter.nl

Information
• Wilco Hazeleger, director Netherlands eScience Center;  w.hazeleger@esciencecenter.nl
• Arjen Doelman, director Lorentz Center; doelman@lorentzcenter.nl
• Henriette Jensenius, scientific manager Lorentz Center;  jensenius@lorentzcenter.nl

Ambities op terrein open science in stroomversnelling

February 9th, 2017

Vandaag overhandigt NWO, samen met 9 andere partijen, het Nationaal Plan Open Science aan staatssecretaris Sander Dekker van Onderwijs, Cultuur en Wetenschap. Het plan is een volgende stap in het realiseren van vrije toegang tot alle wetenschappelijke artikelen en optimaal hergebruik van onderzoeksdata.

NWO is al zeer actief op terrein van open access en datamanagement. Sinds 1 december 2015 moeten onderzoekers publicaties die voortkomen uit door NWO gefinancierd onderzoek direct openbaar toegankelijk – open access – maken. Ook onderzoeksdata die voortkomen uit NWO-onderzoek moeten optimaal vindbaar, toegankelijk, en herbruikbaar zijn voor andere onderzoekers. Daartoe heeft NWO vorig jaar in de gehele organisatie een datamanagementbeleid geïmplementeerd. NWO-voorzitter Stan Gielen: 'Open science leidt tot een duurzamer onderzoeksproces en uiteindelijk tot snellere kennisontwikkeling. NWO gaat nu onderzoeken hoe open science ook breder een plaats kan krijgen in de beoordeling van onderzoeksaanvragen. Daarbij zoeken we nadrukkelijk de aansluiting bij internationale ontwikkelingen.'

Tegelijkertijd met de presentatie van het plan door de tien partijen NWO, VSNU, KNAW, Vereniging Hogescholen, KB, SURF, NFU, ZonMw, Promovendi Netwerk Nederland en GO FAIR, wordt het Nationaal Platform Open Science gelanceerd. Dit platform moet de komende jaren zorgen voor een gecoördineerde inzet voor open science in dialoog met de gehele onderzoeksgemeenschap. Met deelname aan het platform kan NWO haar ambities op het gebied van open science versneld en in samenhang met de activiteiten van andere organisaties realiseren. 'Indien we open science echt mogelijk willen maken, dan vergt dat forse investeringen in infrastructuur om dit te kunnen realiseren. NWO wil graag een bijdrage leveren aan de strategische discussie hierover om daarmee haar missie waar te maken: het bevorderen van excellente wetenschap en het beschikbaar stellen van de resultaten hiervan aan de samenleving', aldus Stan Gielen.

Meer informatie

Bron: NWO

www.openscience.nl

Download Nationaal Plan Open Science

Credits: Tom Bakker

We have 3 new job opportunities

February 7th, 2017

We have 3 new job opportunities, if you are interested please click on the link.

Breaking jargon barriers at Talking eScience 2017

February 1st, 2017

Annual Report: Enabling digitally enhanced science in 2016

January 18th, 2017

Four new alliances and two new Path-Finding projects

December 21st, 2016

We are pleased to announce the initiation of four new alliances and two new Path-Finding projects.

The projects are collaborations with research teams from University of Twente, Centrum Wiskunde & Informatica, Delft University of Technology, University of Groningen and Wageningen University.

New alliances

High spatial resolution phenological modelling at continental scales
Dr. Raul Zurita-Milla
University of Twente
View project

IMPACT: Software Analytics for the monitoring and assessment of the global impact of eScience Software on eStep
Prof. dr. J. J. Vinju
Centrum Wiskunde & Informatica
View project

City Cloud: From the Things to the Cloud and back – Bridging the interoperability problem across IoT application segments
Dr. ir. Nirvana Meratnia
University of Twente
View project

AutoGraph: Automated multi-scale Graph manipulation with topological and flow-based methods
Prof.dr.ir. J.W.C. van Lint
Delft University of Technology
View project

New Path-Finding projects

Automated Analysis of Online Behaviour on Social Media
Prof.dr. Marcel J. Broersma
University of Groningen
View project

Data-mining tools for abrupt climate change
Sebastian Bathiany
Wageningen University
View project

Scientists take ‘blue-action’ to help society cope with the impacts of Arctic climate changes

December 6th, 2016

While the Arctic faces rapid warming and less sea ice currently covers the Arctic Ocean than ever before at this time of the year, an international partnership launches a major project to improve our detailed understanding of the processes and impacts of this changing climate and to construct better long-term forecast systems for the increasingly extreme weather of the Arctic and the wider northern hemisphere.

The Netherlands eScience Center will join Blue-Action - a four-year research and innovations project funded by the European Union’s Horizon 2020 programme with €7.5 million investment. It brings together 116 experts from 40 organisations in 17 countries on three continents working in academia, local authorities and maritime industries.

Pooling their expertise, skills, approaches and networks, the partners aim to improve how we describe, model and predict the weather and climate on seasonal to decadal time scales in the Arctic and over the northern hemisphere. This information will allow communities and businesses in Eurasia and North America to develop and plan their activities better.

“We will deliver this by synthesizing observations, assessing model performance, conducting coordinated multi-model sensitivity experiments, reducing and evaluating the uncertainty in prediction systems and developing new initialization techniques” explains Dr Daniela Matei from the Max-Planck Institute for Meteorology in Hamburg, one of two coordinators of the project.

“Working directly with local communities, businesses operating in the Arctic and industrial organisations, Blue-Action will demonstrate new opportunities for growth through tailored climate services. These will give users the information they need to live and work safely and successfully in the rapidly changing regions in and surrounding the Arctic” says project coordinator Dr Steffen M Olsen from the Danish Meteorological Institute in Copenhagen.

“We are starting today to reach out to the many communities and businesses in the far north to work with us to guide our research direction and to co-develop adaptation mechanisms that will allow them to not only sustain but to boost their performance,” says Steffen Olsen.

“We will collaborate with other modelling and observational climate projects funded within the JPI-Climate Belmont-Forum, EU-H2020 frameworks to maximise the synergy and efficiency of our research efforts,” adds Dr Matei.

While the project began its work on 1st December 2016, the Blue-Action kick-off meeting will be held 18-20 January 2017 at the Max Planck Society’s Harnack-Haus in Berlin.

Image: To thrive in the rapidly changing Arctic environment people - like polar bears - have to adapt swiftly. The new Blue-Action project will help empower Arctic communities and businesses to make informed choices through better forecast systems. (Photo copyright: Dirk Notz, Max-Planck Institute for Meteorology).

Eight new eScience projects to start in 2017

December 5th, 2016

We are pleased to announce the initiation of eight new projects in the areas of Environment & Sustainability, Life Sciences & eHealth, Humanities & Social Sciences, Physics & Beyond and Disruptive Computer & Data Science.

The projects are the result of the 2016 ASDI ( Accelerating Scientific Discovery) and DTEC (Disruptive Technologies) Calls. The 2016 DTEC call was organized in collaboration with the Netherlands Organisation for Scientific Research Physical Sciences (NWO) and Commit2Data.

Scheduled to start in 2017, the projects are collaborations with research teams from multiple Dutch academic groups and represent the latest step in the continued development of the eScience Center's project portfolio.

2016 ASDI project call (Accelerating Scientific Discovery):

1. eEcoLiDAR: eScience infrastructure for Ecological applications of LiDAR point clouds
Dr. rer. nat. W. Daniel Kissling
University of Amsterdam

2. Emotion Recognition in Dementia: Advancing technology for multimodal analysis of emotion expression in everyday life
Prof. dr. Gerben Westerhof
University of Twente, Enschede

3. DIRAC: DIstributed Radio Astronomical Computing
Dr. Sarod B. Yatawatta
ASTRON, Dwingeloo

4. Googling the cancer genome: Identification and prioritization of relevant structural variations in whole genome sequencing data of cancer patients
Dr. ir. Jeroen de Ridder
University Medical Center Utrecht

5. DeepRank: Scoring 3D protein-protein interaction models using deep learning
Prof. Dr. Alexandre M.J.J. Bonvin
Utrecht University

2016 DTEC project call (Disruptive Technologies):


6. A methodology and ecosystem for many-core programming
Prof. dr. ir. Henri E. Bal
VU University Amsterdam

7. Visual Storytelling of Big Imaging Data
Prof. dr. Jos Roerdink
University of Groningen (RUG)

8. Accelerating Astronomical Applications 2 (Triple-A 2)
Dr. John W. Romein
ASTRON, Dwingeloo

About our project calls

The Netherlands eScience Center receives an annual budget from NWO and SURF, the majority of which is provided to Dutch academics as subsidy in the form of cash and the in kind provision of eScience Research Engineers.

Cash & expertise

The awarding of both cash and expertise makes the eScience Center unique, balancing the role of both funder and collaborator. Large Projects are supported to the value of €500K (combined cash and in kind provision of eScience Research Engineers) and result from annual peer-reviewed project calls.

ASDI & DTEC Calls

The eight projects result from two recent calls (ASDI & DTEC).

The purpose of the 2016 ASDI call is to enable domain scientists, working in application fields of Environment & Sustainability, Humanities & Social Sciences, Life Sciences & eHealth, or Physics & Beyond, to address compute-intensive and/or data-driven problems within their research.

The purpose of the DTEC call is to support computer and data scientists in the research and development of novel eScience technologies and software.

Image: Sagar - Colony of Collared Sand Martins. The eEcoLiDAR project will reconstruct 3D ecosystem structures and apply these in species distribution models for breeding birds in forests and marshlands, for insect pollinators in agricultural landscapes, and songbirds at stopover sites during migration. This will allow novel insights into the hierarchical structure of animal-habitat associations, into why animal populations decline, and how they respond to habitat fragmentation and ongoing land use change.

C3S-MAGIC: Developing software for data from climate models

November 22nd, 2016

Om de gevolgen van klimaatverandering in kaart te brengen worden klimaatmodellen gebruikt. Dit zijn uitgebreide weermodellen die voor elke plek op de aarde, van hoog in de atmosfeer tot diep in de oceaan, onder andere de temperatuur, luchtvochtigheid en windsnelheid uitrekenen. In opdracht van het Europese milieuprogramma Copernicus zullen zeven Europese instituten onder leiding van het KNMI software ontwikkelen om de data uit verschillende klimaatmodellen op een gestandaardiseerde manier te ontsluiten.

Klimaatmodellen leveren gigantische hoeveelheden data op, wel honderden terabytes. Binnen de Copernicus Climate Change Service (C3S) wordt deze data beschikbaar gesteld en wordt er informatie uitgehaald voor schattingen van de stijging van de zeespiegel, veranderingen van windsnelheden en het aantal hittegolven.

Onder leiding van het KNMI wordt software ontwikkeld om de data uit verschillende klimaatmodellen op een gestandaardiseerde manier te ontsluiten.

Het project gaat voor Copernicus Climate Change Service (C3S) in een consortium software ontwikkelen, genaamd C3S-MAGIC. Een geïnteresseerde hoeft niet meer alle data op zijn eigen computer te hebben staan, maar kan alle berekeningen die nodig zijn laten uitvoeren op de plek waar de data gegenereerd en opgeslagen zijn. Via een webinterface wordt aangegeven welke berekeningen uitgevoerd moet worden en welke data er voor nodig zijn.

Verschillende modules

Omdat verschillende sectoren verschillende informatie nodig hebben, een waterbouwer is in andere dingen geïnteresseerd dan de ontwikkelaar van een windpark, ontwikkelt C3S-MAGIC modules die toegesneden zijn op de wensen van vier specifieke sectoren: kusten, hydrologie, energie en verzekeringen.

De betrokken partners hebben in de afgelopen jaren al veel voorbereidend werk gedaan, veelal in door de Europese Commissie betaalde samenwerkingsverbanden. Een voorbeeld is climate4impact.eu. Deze grotendeels door het KNMI ontwikkelde website gaat de basis vormen van de C3S-MAGIC software. climate4impact.eu maakt het al mogelijk om informatie van verschillende klimaatmodellen met elkaar te combineren en te visualiseren, maar een verdere bewerking is nog niet mogelijk. Dit wordt ondervangen door de nieuwe software C3S-MAGIC.

Consortiumpartners

In dit project werkt het KNMI samen met Netherlands eScience Center, Barcelona Supercomputing Center, Deutsches Zentrum für Luft- und Raumfahrt, Institute of Atmospheric Sciences and Climate – Consiglio Nazionale delle Ricerche, Swedish Meteorological and Hydrological Institute en University of Reading.

Visualisatie van software climate4impact.eu met luchttemperatuur ©KNMI

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