Tag Archive for 'biomart'

IWPLS 2009: The Sanger Mouse Resources Portal - a Testbed for Collaborative Data Integration

Published on 5 months, 3 weeks ago in other. 0 Comments Tags: , , , , , , .

Last week I enjoyed some time up in Edinburgh for the International Workshop on Portals for Life Sciences (IWPLS ‘09), hosted at the e-Science Institute. It was a good workshop - there were good presentations, lively debates, and good social planning for the evenings!

I have to admit that quite a lot of the content of the workshop was completely irrelevant to me and went straight over my head at times, but I did enjoy it, and it’s good to hear what other people are doing.

I was there for two reasons, first was an interest in the content of the workshop, and second was that I was one of the people presenting a lightning talk! The content of my talk was pretty different to most of the other presentations - they were mostly about grid computing and development of portal interfaces for said grids - whereas mine was about the architecture I developed for the new Sanger Mouse Resources Portal.

It seemed to go down pretty well, it got a couple of laughs, no one fell asleep and quite a few asked questions at the end, so I was quite happy at that. Here’s the slides from the talk, just in case anyone would like to take a look. Copies of all the presentations from the workshop can be found here.

My First Gem: Biomart

Published on 6 months, 2 weeks ago in ruby. 0 Comments Tags: , , .

A lot of my work these days involves building and querying biomart datasets. Interacting with the webservices (for queries) is pretty simple, you just have to post a piece of xml at the right url, but I found myself reusing a lot of boilerplate code in each and every new script.

So, to make my life a little easier (and hopefully some others) I packaged all of the code up in a module with classes to handle all of the monkey work for me and decided to release it as a gem. :)

The source code is available from github, and the documentation is on rdoc.info.

For more details, check out the release anouncement.

It’s my first ruby module so any advice or pointers on how to make things better would be most appreciated. :)