model organism database

Implementing a simple web-log based recommender system

July 25, 2008

I’ve now implemented such a system as an extension to Catalyst, the open source Perl web framework. The system isn’t yet ready for general distribution, but I’d like to share my approach. First, I’ve gathered ten years of web access logs from WormBase, a generic model organism database where I work as the project manager. [...]

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Recommender systems for biological databases

July 25, 2008

Recommender systems [Wikipedia] seek to provide users with information related to what they are currently browsing. These are now ubiquitous in e-commerce sites such as Amazon, where each page contains a list of items viewed or purchased by other users. I’ve long felt that a recommender system could revolutionize the browsing and mining of biological [...]

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New genetic map almost complete

March 26, 2006

I’m almost done putting the finishing touches on a new Genetic Map display. Intended as a drop-in replacement for the Acedb GMap, the new Genetic Map leverages the GBrowse infrastructure providing a familiar user interface as that for browsing the genome. I still need to fix a few small things (what in the hell is [...]

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Bio::WormBase.pm released to SourceForge

March 14, 2006

I’ve made a huge number of changes under the hood to make the update process simpler and more stable. A number of things precipitated these changes, including the rapidly expanding size of the database, increasing number of denormalized support databases, the need to run the site in a load balancing situation — and most importantly, [...]

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