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Eclipse meets Systems Biology

Richard Adams

Making With Eclipse · Standard (25 mins)
Wednesday, 16:15, 25 minutes | Cypress

Tags: Business And Industry , UI / RCP
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Using Eclipse RCP technology, we have built an integrated systems biology framework - SBSIVisual. Systems biology attempts to describe the complex behaviour of living processes, by creating quantitative models that can reproduce  experimental results, and predict the effects of drugs and mutations. We believe there are many parallels between software development and systems biology workflows - for example, model creation and validation (cf code creation and compilation) and model execution (cf launching an application), and the Eclipse platform is therefore an ideal base technology. In this talk, I will explain how we have reused the workspace, builders, Eclipse forms and Search API to develop a powerful, user-friendly, extensible application for 21st century biology. Moreover customization of applications for individual users is  also possible, by integrating other Eclipse-based computational biology offerings such as Edinburgh Pathway Editor, Biopepa and Bioclipse.

Richard Adams is Software Development Team Leader at the Centre for Systems Biology, University of Edinburgh, UK.  He first became enamoured with Eclipse development in 2006 whilst developing the Edinburgh Pathway Editor, a graphical editor for creating biological pathways. Recently he has project managed the development of the Systems Biology Software Infrastructure, a multi-component application that attempts to provide parallelised numerical algorithms for systems biology in a user-friendly manner. The client application, SBSIVisual, uses Eclipse  RCP to achieve this goal. He has substantial experience with GEF and Draw2D.

 

He initially trained as a cell biologist /geneticist studying mitosis in the fruit fly Drosophila. before moved up the evolutionary ladder somewhat to do post-doctoral work with Bill Earnshaw  in Edinburgh, using the African clawed toad Xenopus as a model system to search for proteins that interacted with the then little understood protein INCENP.

During this time he became interested in bioinformatics and in 2002 moved to the Western General Hospital working for Kathy Evans and David Porteous, developing bioinformatics applications to help interpret genetic studies into the cause of bipolar disorder. In 2006 he moved to his current position in the Centre for Systems Biology, Edinburgh

Slides