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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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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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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Rob Campbell found me by google, and pointed me towards his blog, Science and Software. Funny, well written, and very apropos! Why isn't there more software, commercial or otherwise, for labs?
There has been a lot of local interest (i.e. two or three people have discussed it at various …
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After our long software licensing discussion on the biology-in-python list, I realized that I wanted something different in a license for scientific software.
Specifically, I would like to attach the following clause to either a BSD or L/GPL style license:
Publications relying on derivative works of this software must …read more
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