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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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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heh, this applies to many fields, I think...
Luis Ibanez This presentation is a satire of the current obsession with intellectual property, innovation and originality that plagues the field of medical image analysis. The presentation makes the point that most Journals and Conferences focus on Originality and despise Reproducibility and …read more
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My Computer Science department at Michigan State University is looking for an assistant professor! We are casting a fairly wide net (databases, graphics, medical imaging, and bioinformatics) but I'd really like to attract a bioinformatician.
The Computer Science department at MSU is a nice, small department …
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I recently gave an informal talk on Software Carpentry for the Caltech e-Science 101 course. Since even "Intro Software Carpentry" is a whole course of study, I obviously couldn't cover much, but I tried to motivate people to get interested. And, of course, I pushed testing. TESTING, DAMNIT!
Anyway, here …
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So, next May I'm starting as an assistant professor split between the Computer Science and Microbiology and Molecular Genetics departments at Michigan State U., and I'm interested in attracting as many good CS grad applicants as I can from the open source and bioinformatics communities. (I would also like to …
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