BioAssist

Development of a programme for support and dissemination of bioinformatics tools and expertise

Introduction

Active dissemination of bioinformatics expertise and tools towards the end users in biology research is an important aspect of bioinformatics research. BioAssist is the bioinformatics support programme, set up by the Netherlands Bioinformatics Centre (NBIC) with bioinformaticians and expert groups in IT and e-science. The end users are represented by the genomics research consortia under the Netherland Genomics Initiative (NGI).

Background and context

Bioinformatics plays an essential role in capturing the knowledge contained in the increasingly complex data sets in life sciences. To this end, bioinformatics is an enabling science. Since bioinformatics forms the interface between life sciences, mathematics and informatics it is also a highly collaborative science.

Collaboration

BioAssist is a collaborative programme that brings adequate e-science approaches as well as ICT standards and infrastructures for the benefit of life sciences research in the Netherlands. Key to this e-bioscience approach is collaboration. BioAssist aims to realize effective bioinformatics support in which expertise and capacity are combined to make existing software and databases available to end-users. All is built on advanced ICT infra-structures that are currently being rolled out to interlink research institutes in the Netherlands.

Support platforms

BioAssist streamlines research support through implementing bioinformatics task forces for specific research approaches, such as in genomics, including integration of data sources and tools. The task forces are set up in close collaboration with bioinformatics groups with a link to genomics and other research consortia. With Virtual Laboratory for e-Science (VL-e) , BIG-GRID and with the national computing centre SARA to maintain and coordinate the implementation of necessary research infrastructures.

BioAssist has started the implementation of bioinformatics task forces for:

• Integrated analysis of functional genomics data
• Proteomics data management and analysis
• Metabolomics data management and analysis
• Biobanking
• High throughput sequencing
• System bioinformatics

Dutch Life Science Grid

In all platforms, positions for scientific software developers have been created close to the life science groups involved to realize solutions that will be meaningful and useful in their research. GRID nodes (i.e. computer clusters) of the Dutch Science GRID are located close to the participating groups. They provide access to the Life Science Grid and the VL-e Proof-of-Concept environment, which features a large body of tools to facilitate the implementation of the support platforms. Through the GRID, network storage and compute facilities are made available.

Questions regarding access to, use of or systems administration of the life-science grid can be addressed to lsgrid@grid.sara.nl

User information about using the Life Science Grid can be found here.

Data and technology exchange

Thus, end-users and developers jointly develop specific platforms that meet the needs of their specific domains and which provide a coherent approach in realizing support for a broader community. Adopting ‘de facto’ standards like, for example, VLe-PoC, the San Diego SRB, SOA (web-services), and Workflow Management (e.g. Taverna) ensures international data and technology exchange.

Repository

BioAssist facilitates a trac repository that can be used as centralized subversion repository, code exchange platform and mailing list hub. The repository is located at https://trac.nbic.nl/

There is an explanatory set of pages to teach developers how to use NBIC Trac

Framework document

More detailed information on the (technical) framework/structure of BioAssist can be found here.

Meetings

NBIC organizes programmer meetings to excange knowledge and ideas with the BioAssist programmer community. The agenda for these meetings and the presentations of previous meetings can be found at BioAssist:Meetings

More information

• Marc van Driel, marc.van.driel@nbic.nl

Netherlands Bioinformatics Centre
NBIC office, office@nbic.nl
+31 (0)24 3619500
http://www.nbic.nl/