Projects in other technology areas

Mapping Protein Sequence Space: a High Performance workflow to compute the world's first protein sequence and structure map
description:The overall aim of this project is to systematically chart the vast space of all possible protein sequences of certain lengths and several structural properties, creating valuable roadmaps guiding any protein design or engineering effort, and research into protein sequences and their function. Creating maps of sequence space is a technically straightforward, though data-intensive, three-step process: (1) Generating the appropriate pseudo-random sequences that systematically transect sequence space using the perfect sampling method; (2) Predicting the structural properties associated with the sequences using various algorithms; (3) Analyzing these data for relevant trends. The process will be implemented as a VLAM workflow that dynamically submits appropriate numbers of parallel jobs to the grid. The process will be performed for sequences of 12, 40, 80, 160, or 320 amino acid residues. For a specific use case in phage display experiments, all possible 1.28 billion peptides of 7 amino acid positions will be enumerated and stored in the Sequenome database.
applicant:Marco Roos, LUMC Klinische genetica
team:Marco Roos, eBioGrid support team
type:This is a dedicated project.
High-throughput simulations of the metabolism of the human gut microbiota
description:The aim of this pilot-project at the core modeling group of the Netherlands Consortium for Systems Biology (NCSB) is to upscale existing simulations of populations of metabolizing bacteria, that we use to study behavior and evolution of gut microbiota. Recent advances in high-throughput meta-genomics have shown that the gut is home to a very complex microbial community, consisting of several hundreds different species, the gut microbiota, whose collective genome contains more than 100 times as many genes as our own genome. In close collaboration with experimental and theoretical groups in NCSB-member the Top Institute Food and Nutrition (TIFN) we have developed an in silico simulation model of the gut microbiota. The aim is to uncover fundamental principles of intestinal microbial organization and its relation to health and diet of the host. We will use this VO playground project to set up a WS-VLAM infrastructure supporting our simulation system and to perform some initial simulations with it. As a first goal we aim at identifying parameter regions that support the coexistence of multiple bacterial species.
applicant:Roeland Merks, CWI
team:Roeland Merks, Milan van Hoek, Margriet Palm, Bas Teusink, Zhao Zhiming en Adam Belloum
type:This is a dedicated project.
Effects of detritivores on litter microbial community
description:This is part of a project intitled 'Traits meet trophic interactions: predicting the effects of climate change on soil carbon cycling using functional traits' (NWO / 819.01.017). It investigates the role of detritivores on driving species composition of microbial communities. In a last experiment, we endeavour to characterize the bacterial community present in litter exposed to different species of terrestrial isopods under three distinct water regimes. To characterize the bacterial community of the litter samples we used the Illumina next-generation sequencing platform, which returned more than five thousand sequences per sample. The normal computers we have in our department do not match the computer power necessary to manage, align and analyse this data set. Therefore, I would like to have access to the HPC Cloud system to do the bioinformatics necessary to analyse this data.
applicant:André Tavares Corrêa Dias, Vrije Universiteit Amsterdam
results:will follow soon
team:André Tavares Corrêa Dias, e-BioGrid team
type:This is a dedicated project.

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