What is e-BioGrid?

The e-BioGrid project (2010-2012) was funded by BiG Grid through NWO, led by partners NBIC and Nikhef, aiming to establish an e-Infrastructure for life science research in the Netherlands.[1] With the proven track record of success of e-BioGrid, life science e-Infrastructure support and development continued within SURFsara. See our Life Sciences Support and newsletter.

The e-BioGrid project supported life science researchers and programmers in using the infrastructure of the BiG Grid project that organized large computational infrastructure for scientific research. SURFsara’s e-Science & Cloud Services group participated actively in the e-BioGrid project. Together with life science experts an e-core team[2] coordinated the support projects. The project was initiated specifically for life scientists to get acquainted using the national advanced e-Infrastructure for data-intensive life sciences, e.g. omics experimentation, allowing innovative and more effective life science research.

Besides the support projects, e-BioGrid established a lively and agile life science e-Infrastructure community for exchanging ideas and expertise. Several trainings and workshops were organized. More information can be found on the e-BioGrid website.

e-Infrastructure via SURFsara

This infrastructure consists of compute clusters and data storage facilities, combined with specific middleware and software, to enable research that needs more than just raw computing power or data storage. As of 2013, this infrastructure is continued within SURFsara, in collaboration with its e-Infrastructure partners.

With e-BioGrid life scientists were able to make use of several facilities, such as the Life Science Grid, clusters and HPC Cloud Computing. Also the use of GPUs was facilitated. The support team helped life scientists in the Netherlands with the use of the e-Infrastructure, either by setting up their own work on the infrastructure, or by helping them to build special solutions.

e-BioGrid support projects

The e-BioGrid projects consisted of main support projects and dedicated support projects. The main projects involved relatively large efforts, e.g. the development of a pipeline software and hardware infrastructure for a particular analysis technology. These main projects required manpower from BiG Grid and took at least two years. In total we ran 7 main projects:

  • Next-generation sequencing – breeding (Richard Finkers, Wageningen University and Research Centre)
  • Next-generation sequencing - metagenomics (Sacha van Hijum, Center for Molecular and Biomolecular Informatics)
  • Micro-array technology (Timo Breit, University of Amsterdam)
  • Biobanking (Morris Swertz, University Medical Center Groningen)
  • Nanoscopy (Fons Verbeek, Leiden University)
  • Mass spectrometry (Theo Reijmers, Leiden University)
  • Medical imaging (Silvia Delgado Olabarriaga, Amsterdam Medical Centre)

In addition a large number of dedicated support projects were completed. The dedicated projects ran for a maximum of 3-4 months and enabled ad hoc support on demand.

e-BioGrid resulted in a high performance computing (HPC) deployed next-generation sequence analysis pipeline, the Life Science Grid Portal, micro-array design tools and many other solutions. Detailed information of the results can be found in the overview.

[1] Projectleaders: Maurice Bouwhuis (SURFsara), Joost Kok (Leiden University), Timo Breit (University of Amsterdam).
[2] e-core team: Machiel Janssen (SURFsara), Jan Bot (Leiden University), Irene Nooren (University of Amsterdam).