JISC

Start date: 1 April 2005

End date: 31 March 2007

Funding programme: Virtual Research Environments programme (phase 1)

Project website: http://www.vre.ox.ac.uk/ibvre

JISC theme(s): e-Research

Context

The JISC-funded IBVRE project is developing a large-scale Virtual Research Environment demonstrator to investigate the use of existing collaboration frameworks to support the entire research process of a large-scale, international research consortium, namely that of the Integrative Biology (IB) project. IB is a second-round EPSRC e-Science Pilot project developing a Grid infrastructure to support post-genomic research in Integrative Biology.

Integrative approaches to biology are rapidly evolving and characterised by the attempt to understand biological systems through the construction of large-scale software systems that simulate biological behaviour at a variety of spatial and temporal scales. These in silico experiments, as they are known, increasingly demand larger and more powerful resources, both in terms of data storage and computation; the primary aim of the IB project is to meet these needs by constructing a Grid infrastructure to provide tailored, seamless access to these vital facilities.

Aims and Objectives

The overall aim of the IBVRE project is to extend the IB infrastructure to become a VRE for computational biology.  This single, integrated environment will support the entire research process in its widest sense, including identification of research area, building and managing projects and consortia, disseminating results, experimental and simulated data generation acquisition, analysis and curation, access to IT, HPC and experimental resources, administration, and provision of training to new researchers entering the field (learning and teaching support tools).

Project Methodology

A VRE must seamlessly integrate and support the pattern of work demanded by the domain and which is familiar to the users, in other words, it must support the “research process” in which the user is engaged.  In order to ensure that the IBVRE does this, the initial focus of the project will be to carefully analyse a selection of IB research processes, identifying areas where enhancement is possible within an integrated environment.  The project will then concentrate on:

1. collecting tools relevant to these processes
2. ensuring the tools can be co-located within a portal framework and inter-operate
3. providing a tool management (or process support) layer

It is the process support layer that provides the interactions between the tools in the VRE to explicitly support the research process, distinguishing the IBVRE from a standard portal.

Implications/ Deliverables/ Stakeholders

The deliverables of the IBVRE project are:

• Reports on existing IB research processes with recommendations for areas where improvement is possible within the IBVRE.
• IBVRE infrastructure that allows third-party and bespoke IBVRE tools to be co-located and inter-operate.
• Survey of third-party tools and their integration into the IBVRE e.g. calendar, access grid, email, instant messaging, RSS feeds from blogs/groups/wikis/IRs, VLE, data & software repositories, KOS, peer-review, programme/project
• management, meeting management, collaboration management.
• Bespoke IBVRE tools (portlets and optionally rich clients) that wrap the IB base services e.g. computational workflow management, visualisation
• Process support layer implementing interactions between the IBVRE tools to support the selected IB research processes.
• Detailed reports on the requirements, specification, design and implementation stages of the development of the IBVRE.
• Recommendations and feedback to relevant standards committees and developer groups e.g. WSRP 2.0, Sakai, uPortal, JSR-168, OGCE.
• Evaluation reports on the use and extension of existing VRE middleware to support large-scale collaborative research.

The IBVRE project is expected to improve the pace, impact, and efficiency of integrative biology research in two of the most important problems in clinical medicine today.  It is hoped that the outputs of the project will be of interest to computational biologists outside the IB research consortium and will point to other research areas where the technologies developed could be equally applicable.  The IBVRE software will be released to the community under an open source licence and the results of the evaluation of VRE middleware will be fed back to the applicable standards and developer groups.