The pipeline analysis model

Posted on 3 October 2008 by James Taylor

Titus recently posted some thoughts on the “unix” scripting/pipeline model for analysis. The model is essentially one of discrete components that do one thing and produce and consume standard (or at least easily parsed) data formats. The components are naturally reusable, and are chained together to perform more complex analysis. Higher level facilities such as make) facilitate reproducibility.

This model has a lot of nice features. In particular, it makes reuse easy and thus encourages the development of reusable components. In fact, this is exactly the analysis model that Galaxy makes available to non-computational users. In doing so we tackle several of the “deficiencies” of this model that Titus mentions…

The state of python and bioinformatics

Posted on 27 September 2008 by James Taylor

Chris Lasher and Titus Brown recently posted on bioinformatics in python, briefly igniting the same old discussion on the biology-in-python list. The usual questions and concerns: “why is Perl ‘winning’ in bioinformatics”, “why don’t people like / use / contribute to BioPython”, “let’s make a new BioPython, I’m sure it will work better this time!”…

Genome Informatics 2008

Posted on 15 September 2008 by James Taylor

The joint CSHL / Wellcome Trust meeting on Genome Informatics is one of my favorite meetings, particularly because the presentations generally contain an excellent mix of cool biology and informatics. This year’s meeting was no exception, and my session (Data Management, Mining & Curation), though likely among of the least biological in overall content, turned out very well. All of the talks were excellent, and I was happy to see an (unexpected) theme among many of them: putting more power in the hands of biologists without informatics support…