I spent some time over the last week adding fairly simple motif searching to Cartwheel, my bioinformatics site for biologists doing cis-regulatory analysis of genomic sequence. The new features include the ability to define and search with IUPAC and position-weight matrix (PWM) motifs, as well as visualization of motif search …
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I'm having trouble with some tests of a PostgreSQL-based system. Briefly, I have a set of functional tests that
- create a new database
- populate it with a data model
- run a Web server (in-process)
- test the integrated Web server - database functionality
The tests are now slow enough that I'm averse …
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Noah and Grig have been CCing me on a conversation about JoelOnChecklists and Grig's post. Noah's writing a book chapter on this stuff, and asked for some tips.
Here are mine.
First, I have a bunch of individual twill scripts in a directory that are run every hour. These scripts …
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Tracy recently asked me if there were any good guidelines about how to write configuration files -- not coding-level guidelines, but guidelines on structure and content.
I was unable to come up with anything: my Google-fu failed me, and my DevonThink database was silent (although it did have some nice testing …
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Via http://www.nodalpoint.org/2008/01/18/one_thousand_databases_high_and_rising, on the Nucleic Acids Res "database" issue:
As we pass the one thousand databases mark (1kDB) I wonder, what proportion of the data in these databases will never be used?
This is an unsettling thought for those (wonderful) people who spend …
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I just finished a chapter for a book, Methods in Avian Embryology, being edited by my boss, Marianne Bronner-Fraser. This chapter is intended for developmental biologists who are interested in locating regulatory modules and analyzing them for binding sites. It ended up being my outlet for a compilation of problems …
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As many people have doubtless read, PyCon '08 has announced the tutorial sessions. This year, Grig and I are doing a workshop-tutorial on testing rather than a teaching-tutorial; what this means is that our tutorial will focus on actually applying testing tools effectively to your source code.
We're billing this …
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