Structural biology research demands high performance computing facilities for the analysis of spectra and especially for the molecular modelling of protein structures. The main project involves the development of an e-infrastructure for the NMR and SAXS spectroscopy community in collaboration with the e-NMR community. Access to the infrastructure is provided through a portal integrating commonly used software and GRID technology.
e-BioGrid program is open for dedicated NMR, SAXS and modeling projects. Contact us
if you are involved in Structural Biology research and you
have a need for support in software of hardware infrastructure.
The objective of WeNMR, a EU funded project, is to optimize and extend the use of the NMR and SAXS research infrastructures through the implementation of an e-infrastructure in order to provide the user community with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the e-NMR infrastructure is provided through a portal integrating commonly used software and GRID technology.
Alexander Bonvin, Bijvoet Centre for Biomolecular Research
A portal with NMR and SAXS data analysis and modelling tools is available on the we-NMR website. The project team is currently working with the US OSG to enable support for our enmr.eu VO. We have already successfully deployed software and run test jobs on OSG sites, demonstrating interoperability of EU and US grids.
This is an educational project aiming at introducing CLOUD computing into the chemistry teaching at the bachelor level within the chemistry curriculum of Utrecht University. In the second year of the chemistry curriculum students can choose for a 'molecular modelling and mathematics' course in which the principles of molecular simulation techniques and force fields are introduced in parallel with all the necessary mathematical background. The course contains a practical part in which students learn the basics of molecular dynamics simulations by performing simulations of a protein using Gromacs and studying the effect of mutations on structure and dynamics. In this project CLOUD computers are used for students to perform the entire work (setup, production, analysis), on a single and dedicated system. In that way we introduce e-Science into teaching so that students can get acquainted with CLOUD computing. 'Education in the clouds' should be a novel and attractive concept for students.
Alexandre Bonvin, Utrecht University
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Alexandre Bonvin, Adrien Melquiond, Alain van Hoof
This project, called NMR_REDO, aims to recalculate 5,000 Biomolecular structures the Protein DataBank (PDB) on the basis of experimental NMR data. For this large-scale project we implemented this setup onto virtual machines (VMs) in a cloud environment. The VM contains all necessary software components (about 25 diverse types of programs) for the computation and validation that would be very hard, if not impossible to configure on a traditional grid node. The VM, called VirtualCin has recently been reconfigured as an 32 bit Ubuntu 11.04 server edition and measures 11 Gb in .tgz format. VC slave threads take their instructions from a Sara-hosted job server called Topos. Data is exchanged by scp with a storage unit at the CMBI data center in Nijmegen.
Jurgen Doreleijers, Radboud University Nijmegen Medical Centre