Six new projects enabling scientific discovery to start in 2015

17 Dec 2014 - 6 min

The projects, scheduled to start in 2015, are collaborations with research teams from multiple Dutch academic groups and represent the latest step in the continued development of NLeSC’s project portfolio.

The six projects result from two recent calls. Two projects will be funded in the areas of Humanities and Social Sciences. Project leaders Dr. Loro Aroyo and Prof. Piek Vossen will each receive funding to the value of 125K euro. Four more projects will receive funding to the value of 500K euro to address challenges in climate research, eChemistry and green genetics. NLeSC funds projects by the direct provision of cash and the in kind provision of eScience Research Engineers.

For more information, please contact Dr. Frank Seinstra  or Dr. Scott Lusher 

DIVE+: Interacting with Historical Events in Linked Cultural Heritage
Dr. L. Aroyo
VU University Amsterdam

This project provides a basis for interpretation support in searching and browsing of heritage objects, where semantic information from existing collections plus open linked data vocabularies are linking collection objects to the events, people, locations and concepts that are depicted or associated with those objects. An innovative interface paradigm allows for browsing this network of data in an intuitive fashion supporting both digital humanities scholars and general audiences in their online explorations.

Visualizing uncertainty and perspectives
Prof. dr. P. Vossen
VU University Amsterdam

This project aims to develop a tool that visualizes subjectivity, perspective and uncertainty to make them controllable variables in Humanities research. The tool should allow users to compare information from different sources representing alternative perspectives and visualize subjectivity and uncertainty. Such a visualization enables improved and comprehensive source criticism, provides new directions of research and strengthens the methodology of digital humanities.

Environmental Re-Analysis of Urban areas: Quantifying high-resolution energy and water budgets of European cities (ERA-URBAN) 
Prof. dr. A.A.M. Holtslag
Wageningen University

Ongoing world-wide climate change and urbanization illustrate the need to understand urban hydrometeorology and its consequences for human thermal comfort and water management.

Limited availability of long-term geographical and hydrometeorological observations and limited computational capacity for urban scale simulations have so far hampered answering related scientific research questions. This project will develop an urban hydrometeorological archive that combines all available, rich and heterogeneous observations with multi-scale atmospheric and hydrological model results. Our challenge is to make the data in the archive meaningful, insightful and useful for scientists, local-scale urban planners, policy makers, (local) companies and individual citizens.

3D-e-Chem: Integrated eScience workflow to translate biological and chemical data into structure-based protein-ligand polypharmacology prediction
Dr. C. de Graaf
VU University Amsterdam

Many new protein targets have been discovered recently and it has been shown that clinical efficacy is often the result of polypharmacologicalaction of drug molecules (i.e. the interaction with more than one protein target). Efficient exploitation of chemical and biological information is hampered however, because a good approach to efficiently integrate large volumes of heterogeneous data from different disciplines is still missing. The data needs to be properly integrated in order to extract useful information that is manageable and applicable in various life science disciplines. This project will develop technologies to improve the integration of ligand and protein data for structure-based prediction of protein-ligand selectivity and polypharmacology.

Computational chemistry made easy
Prof. dr. L. Visscher
VU University Amsterdam

This project concerns the construction and efficient execution of computational chemistry workflows. This allows computational chemists to use the emerging massively parallel computing environments in an easy manner and focus on interpretation of scientific data rather than on tedious job submission procedures and manual data processing. This makes entirely new approaches possible in which a single researcher can model and analyze thousands of compounds with high-level quantum chemistry methods. This yields a wealth of detailed data (molecular structures, transition states, charge distributions, electronic excitation energies) to rationally design solar cells, reduce solvent losses in organic synthesis, tune catalysts, or develop better LEDs, to name just a few applications. The project goal will be realized by bringing concepts from distributed computing (efficient parallelization in heterogeneous environments) and bioinformatics (data management and workflow construction) to the field of computational chemistry.

Prediction of Candidate Genes for Traits Using Interoperable Genome Annotations and Literature
Prof. dr. R.G.F. Visser
Wageningen University

Plant breeding companies are facing a paradigm shift. From traditional quantitative trait loci (QTL) studies, breeders got an insight which region(s) to introgress in their elite germplasm, with the aim to improve traits of interest. However, genome annotations are becoming available for more and more (crop) species and we observe that a QTL region could easily include 1000 genes, positively or negatively affecting the desired phenotype. This project addresses the scientific challenge to utilize genome annotations and semantic interoperability with other databases, such as literature, for computer-assisted prioritization to determine which gene(s) is a candidate explaining the QTL. The application of the project results will be utilized in a better choice of parents for crossing in plant breeding, and as a perspective in the longer term, to enable precision breeding (genomics-assisted in silico design of an optimal genotype with a set of defined traits (e.g. quality and/or resistance), for production in a given environment and the subsequent strategy to breed for such a genotype), but are applicable in (animal, human and plant) genetics research in general.