JISC

Project title

Integrative Biology Virtual Research Environment

Start date

01-04-2005

End date

31-03-2007

Lead institution

University of Oxford

Partner institutions

Project manager & contact details

Matthew Mascord, Research Technologies Service, OUCS, 13 Banbury Road, Oxford, OX2 6NN, matthew.mascord@oucs.ox.ac.uk

Project web URL

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

Overall description

Name of VRE solution/s

Integrative Biology Virtual Research Environment

Description of VRE solution/s

The project is focusing on designing and developing a common, centralised online collaboration environment for integrative biology.

Primary user group/s

Integrative Biology Research Consortium: Mathematical and Computational Biologists

Functionality

• VRE Portal based on uPortal
• Tools integrated into the VRE portal:
• • In silico experiment repository
  • Paper notification tool
• Third-party tools:
• • Collaborative visualisation tool
  • Digital paper
  • Library search tool
  • Calendar

Benefits

Benefits of the in silico experiment repository:

• Reduce the difficulties scientists have when reproducing the results from in silico experiments - experiments are designed and executed almost entirely through a visual interface.
• Enable biologists to carry out simulations without necessarily needing a high level of technical (IT) expertise.

Benefits of the paper notification tool:

• Reduce the amount of effort involved in sifting through biology literature to identify measurements for mathematical cancer models.

Benefits of the collaborative visualisation tool:

• Solve issues scientists have when discussing the results from in silico heart simulation experiments: heart videos can be synchronously played, discussed, and annotated by geographically distributed collaborators.

Benefits of digital paper:

• Facilitate collaboration between mathematical biologists - mathematical ideas, which are normally conceived on paper, can be more easily exchanged between collaborators.
• Provide a secure backup for paper-born material - mainly preliminary mathematical material and paper laboratory notebooks.
• Make paper-born material easier to organise and retrieve.

Benefits of the VRE portal:

• Provide an interface where these different tools can be co-located, and to form a central point of focus for the IB community - a visual gateway to the underlying IB middleware.

Current level of maturity

• VRE portal stable and based on uPortal 2.5. Existing system integrates existing IB grid portlets. Aim to migrate to uPortal 3.0 when this becomes available.
• In silico experiment repository tool currently in development following design elicitation workshops at two biomedical engineering groups in the US.
• Logitech IO2 Digital Writing System is a stable digital paper technology.
• Collaborative visualisation tool Vannotea is being developed by the University of Queensland and is currently being migrated from a research prototype to a production quality solution.
• Paper notification tool, currently in its detailed requirements analysis phase.

Target level of maturity at end of project

The target maturity level for all the bespoke tools is a standard where the tools can be used actively, on a day to day basis by IB research groups to do real science.

Design & technical implementation

Technical implementation

A set of JSR-168 compliant portlets, communicating with the IB middleware through SOAP.

Architecture

Standards compliance

JSR-168

WSRP

SOAP

Shibboleth

Software availability

The solution is not currently available but will be made available as open source as soon as it reaches a sufficient level of maturity.

Documentation

Extensive requirements analysis and design documentation has been prepared but is not yet available publicly. User documentation preparation is in progress.