About Me

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I'm project manager of a software development team at www.researchspace.com. I've been developing bioinformatics software for the last 9 years or so, and I'm hoping to share some of the experience and knowledge I've gained with Eclipse RCP, Java web app development and software development in general on these blogs.

Friday, 26 March 2010

EclipseCon2010 thoughts

Well, EclipseCon2010 is now over, and what an excellent meeting it was. It was my first attendance and a great way to find out more about the organisation and future aims of the project, put names to faces and meet people.

I was really impressed with the quality of the tutorials - I attended tutorials on SWTBot, serverside Eclipse, and advanced RCP all of which worked flawlessly and were timed very well. (Finally I have some idea how p2 works!) Since we will be giving a tutorial on SBSI at the upcoming ICSB in October 2010 I got some great ideas, such as providing 'sync points' of downloads of the tutorial at various stages, so that people can catch up, or just start from a point they're interested in. Also the use of EtherPad to keep track of questions and issues arising.

As an Eclipse RCP developer, it was great to see a new SWT-native  scientific charting library presented, called SWT XY Graph. Currently we have come across two choices - BIRT chart designer ( which pulls in a lot of other plugins and can bloat a small application) or JFreeChart via an SWT-AWT bridge ( which works quite well but can be a little unresponsive at times). So this new plugin could be a very welcome alternative. 
Another new project which look interesting is Graphiti, which aims to provide rapid development of GEF based editors. The first release should be in June.

The HPC world is  being included in the Eclipse community now -  the 
Parallel Tools Platform aims to provide static analysis and debugging facilities, and a world class IDE for developers writing applications for HPC

It  was  also good to come across a smattering of life sciences people at EclipseCon, who either attended my talk or congregated around Ola Spjuth's Bioclipse poster. It will be fun to try to collaborate to make  Eclipse plugins for biology more interoperable and expand the potential scope for users.

Thursday, 4 March 2010

RCP apps for Systems Biology at EclipseCon2010

At this year's EclipseCon I'll be giving a talk about the uses of Eclipse technologies for Systems Biology. This is a really exciting discipline in biology involving biologists, mathematicans, computer scientists and engineers trying to build predictive models of biological processes. 
 With its huge assortment of plugins Eclipse provides  the flexible and extensible software services for the wide range of systems biology users. For example, less mathematically inclined biologists can take advantage of the wizards, dialogs and validating editors; while more computationally literate users can use the C++ or Java IDE to develop computational models directly.
 In my talk I'll give an overview of the aims and scope of systems biology, its demands for novel software, and describe how Eclipse technology has been used to develop applications for pathway visualization, process algebra modelling, and  in particular, model optimisation.