With the proven success of the e-BioGrid project, life science e-infrastructure support and development is continued within SURFsara with a coordinating team and life science specific support.
Within the e-BioGrid project (2010-2012) e-infrastructure for life sciences was developed in the main and dedicated support projects: Frequently used algorithms or software can be run on high-performance computing facilities, and multidisciplinary collaborations have been set up. The tools that have been developed so far are listed below. See also our show cases.
The results of each of the main e-BioGrid projects can be found at the technology area project pages: biobanking, mass spectrometry, micro array technology, nanoscopy and imaging, next generation sequencing (WUR), next generation sequencing (VLPB), medical imaging. Results of other ad-hoc support projects are found at the project pages.
Within the e-BioGrid project several tools have been developed and available below:
|ArrayDesigner||a tool to design tiled multistrain micro-array probes|
|Genbank Blast||A Cloud Image with a Genbank release 182 is available and can be used with BLAST (you'll need to have access to the HPC Cloud)|
|Life Science Grid Portal||The Life Science Grid Portal provides an easy interface to run several selected jobs on the grid. It enables users to start an application through a HTTPS REST interface. With minimal knowledge of the grid, researchers and scientific programmers can start these applications on the grid, even with just a browser. The portal contains several applications, such as BlastP, BlastN, BWA and Maq, and other applications can be added on request. Besides this, it is also possible to upload and share databases.|
|NBIC Galaxy on Cloud||In collaboration with NBIC, the e-BioGrid team developed NBIC Galaxy on Cloud. It allows bioinformaticians and biologists to run their Galaxy tools and workflows, e.g. genomics and proteomics data analysis, on the SARA High Performance Computing (HPC) cloud. The application scales dynamically with increasing workload. Having access to the HPC Cloud enables processing of big data volumes, and high speed network connection provides rapid data transfers.|
A number of e-science tools have been submitted at the EGI repository.
Publications and presentationsThis list includes publications and presentations using the infrastructure of Big Grid / e-BioGrid in the field of life sciences.
Doreleijers, J. F., Vranken, W. F., Schulte, C., Markley, J. L., Ulrich, E. L., Vriend, G., & Vuister, G. W. (2011). NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Research. doi:10.1093/nar/gkr1134
M. Krzeminski, T. Singh, S. Andre, M. Lensch, A.M. Wu, A.M.J.J. Bonvin and H.-J. Gabius, Human galectin-3 (Mac-2 antigen): defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region." Biochimica et Biophysica Acta 1810, 150-161 (2010)
E. Karaca, A.S.J. Melquiond, S.J. de Vries, P.L. Kastritis and A.M.J.J. Bonvin, Building macromolecular assemblies by information-driven docking: Introducing the HADDOCK multibody docking server.
Mol. Cell.Proteomics 9, 1784-1794 (2010)
M. van Dijk and A.M.J.J. Bonvin, Pushing the limits of what is achievable in protein-DNA docking. Benchmarking HADDOCK's performance. Nucl. Acid Res. 38, 5634-5647 (2010)
A.M.J.J. Bonvin, A. Rosato and T.A.Wassenaar.
The eNMR platform for structural biology. J. Struct.Funct.Genomics 11, 1-8 (2010)
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin, The HADDOCK web server for datadriven biomolecular docking. Nature Protocols 5, 883-897 (2010)
N. Loureiro-Ferreira, T.A. Wassenaar, S. J. De Vries, M. van Dijk, G. van der Schot, J. van der Zwan, R. Boelens, A. Giachetti, D.Carotenuto, A.Rosato, I. Bertini, T. Herrmann, A.Bagaria, V.Zharavin, H.R.A., Jonker, P.Guentert. e-NMR gLite grid enabled infrastructure IBERGRID: 4th Iberian grid infrastructure conference proceedings. A. Proenca A,A. Pina , J.G. Tobio, L. Ribeiro Eds 368-380 (2010)
Schwalbe, W.F. Vranken, S. Dal, Pra, M. Mazzucato, E. Frizziero, S.Traldi, M. Verlato, A.M.J.J. Bonvin A.M.J.J. Bonvin Overview of the WeNMR project, EGI technical forum, Amsterdam, September 14-17, 2010
A.M.J.J. Bonvin. Overview of the WeNMR project. BigGRid userday,Amsterdam, September 13, 2010
A.M.J.J. Bonvin. WeNMR 8th e-Infrastructure concertation meeting, CERN Geneva November 4-5, 2010
A.M.J.J. Bonvin. eNMR ICTDelta2010: "Simuleren Voor Gezondheid", Rotterdam, March 18, 2010
H Sontrop, W Verhaegh, R van den Ham, MJT Reinders, PD Moerland. Subtype specific breast cancer event prediction, GENSIPS 2010: 9th IEEE International Workshop Genomic Signal Processing and Statistics, Cold Spring Harbor Laboratory, NY, USA 10-12 November 2010.
T. Glatard, R. S. Soleman, D. J. Veltman, A.J. Nederveen, S. D. Olabarriaga. Large scale functional MRI study on a production grid, Future Generation Computer Systems vol. 26, no. 4, pp. 685-692, 2010
Matthan W.A. Caan, Frans M. Vos, Lucas J. van Vliet, Antoine H.C. van Kampen, Silvia D. Olabarriaga. Gridifying a Diffusion Tensor Imaging Analysis PipelineCCGRID-Health2010 workshop. Proceeding of the 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing 17-May 20. IEEE Computer Society. pp. 733-738, 2010.
M.W.A. Caan, H.G., Khedoe, D.H.J. Poot, A.J. den Dekker, S.D., Olabarriaga, C.A., Grimbergen, L.J. van Vliet, F.M. Vos. Estimation of diffusion properties in crossing fiber bundles, IEEE Transactions on Medical Imaging 2010, vol 29, no. 8, p.1504-1515
M.W.A. Caan, H.G. Khedoe, D.H.J. Poot, A.J. den Dekker, S.D. Olabarriaga, C.A. Grimbergen, L.J. van Vliet, F.M. Vos. Adaptive noise filtering for accurate and precise diffusion estimation in fiber crossings, MICCAI 2010 Part I, LNCS 6361, pp.167–174, 2010.
M.W.A. Caan. Quantifying pathology in Diffusion Weighted MRI, PhD thesis, TU Delft, Sept 2010 THES
F. Gwadry-Sridhar, S.D. Olabarriaga, A. van Kampen, M.Bauer, T.Solomonides. Hitting the ground running: Healthgrid deployment and adoption, Proceedings of HealthGrid conference, 2010. Studies in Health Technolology and Informatics 2010;159:40-51
Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga. Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics 2010 Dec, 14;11:598
Katja Ritz, Barbera, DC van Schaik, Marja E Jakobs, Antoine HC, Van Kampen, Eleonora Aronica, Marina A Tijssen, Frank Baas. SGCE isoform characterization and expression in human brain: implications for myoclonusdystonia pathogenesis? Eur J Hum Genet, 19(4), 438-444, 2011.
S.D. Olabarriaga, T. Glatard, P.T. de Boer. A Virtual Laboratory for Medical Image Analysis. IEEE Transactions on Information Technology In Biomedicine, Aug;29(8):15, 04-15, 2010.
S.D. Olabarriaga, M.Caan, C. Byrman, T. Glatard, A. Luyf, A.H.C. van Kampen, F. Vos, L. van Vliet, J.J. Keijser. Grid-enabled Medical Image Analysis: From Jobs to Workflow-based Service. EGEE User Forum 2010, Uppsala, Sweden. Abstract +oral presentation. May 2010
B.D.C. van Schaik, A.C.M. Luyf, S.D., Olabarriaga, M. De Vries K. Ritz, F. Baas, A.H.C. van Kampen. Setup and usage of an e-BioScience infrastructure for high throughput DNA sequence analysis EGEE User Forum 2010, Uppsala, Sweden. Abstract +oral presentation, May 2010 OTH
E. Drenth, S.D.Olabarriaga, M. Santcroos, W. Mulder. Using agents to support grid users EGI Technical Forum,Amsterdam Oral presentation Sept 2010 OTH
M. Caan, Y. Mohammed, S. Shahand, M. Santcroos. Course "Systems Neuroscience" 3-session practical course, AMC Radiology 2 Nov – 3 Dec 2010
Bas E. Dutilh, Martijn A. Huynen and Marc Strous. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly Bioinformatics 25: 2878-2881
Katharina F. Ettwig, Margaret K. Butler, Denis Le Paslier, Eric Pelletier, Sophie Mangenot, Marcel M.M. Kuypers, Frank Schreiber, Bas E. Dutilh, Johannes Zedelius, Dirk de Beer, Jolein. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria, Nature 464: 543-548
Nooren IM, e-BioGrid. Enabling Life Science Research and Development. NBIC Conference, Lunteren, 19-20 April 2011
Bot JJ, Next-generation sequencing data management. EGI Technical Forum, Lyon, 19-23 September 2011
Jansen M, eBioGrid: Dealing with the sins of bioinformaticians, HPC Cloud Day, Amsterdam, 3 October 2011
Vrooman H, Customized Pipelines for the Processing of Medical Images in Large Population Studies, HPC Cloud Day, Amsterdam, 3 October 2011
Doreleijers J, Validating biomolecular NMR structures using Cloud computing, HPC Cloud Day, Amsterdam, 3 October 2011
Rauwerda H, Using the BiG Grid HPC Cloud Infrastructure in Transcriptomics, HPC Cloud Day, Amsterdam, 3 October 2011
de Hollander, M. The Cloud for Biologists, HPC Cloud Day, Amsterdam, 3 October 2011