Career

I work in the field of computational biology, or bioinformatics, the use of computational and mathematical approaches to solve biological problems. Throughout my career I have worked on a diverse collection of problems using a variety of tools.

• In my current position of Associate Director, Bioinformatics at Five Prime Therapeutics I am responsible for the design and development of bioinformatics software, focusing on the following areas:
  • software to track, visualize and analyze data generated in the screening process.
  • development of rich client interfaces to various bioinformatics algorithms.
  • integration and visualization of external data sources into the Five Prime infrastructure.
• As a group leader at BD Biosciences Clontech I managed the bioinformatics software development team. The team was responsible for the design and implementation of web based, customer support software for various products, in particular Clontech's gene and protein chip products. In addition, I designed and developed software tools used in-house for product development.
• At the Neurosciences Institute I developed large scale simulations of the brain with the goal of understanding the mechanisms of brain function and development, specifically perception, in terms of the underlying physiology and anatomy.
• My PhD thesis work in the Department of Physiological Sciences at the University of Newcastle Upon Tyne focused on the mathematical analysis of artificial neural networks and the application of that analysis to the elucidation of non-linear aspects of cellular dynamics.

Further details can be found on the resume page

Java

The vast majority of my current work is implemented using the Java programming language, utilizing a number of excellent open source programs, libraries and frameworks. My personal contributions to open source projects include:

• BioBrowser, a Swing based browser of the Cancer Bioinformatics Infrastructure Objects (caBIO) Model provided by the National Cancer Institutes via web services. New version, Feburary 2008
• Project providing integration between Spring Rich Client Project and JIDE Swing components.
• Plugin for the Hudson continuous integration engine providing integration with the Polarion web client for Subversion.

Further details can be found on the Java page

You can contact Jonny Wray at jonny at jonnywray dot com

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