A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
Monday, November 30, 2015
Admitting to Ignorance on Interpreting Bootstrap Values
Okay, one of the points of this space has always been to crowdsource the project of educating myself, which also means on of the underlying principles is that I sometimes need to admit ignorance in a very public manner. After staring at a lot of phylogenetic trees, I've sufficiently unglued my confidence in my deep understanding of the principals (beyond coming just plain unglued) of confidence / bootstrap values. Despite trying a number of sites and reviews and threads on the Net, I can't quite find a detangling of the particular mental knot I've tied, so I'm throwing out the problem for group help.
Tuesday, November 24, 2015
Well, that was brief!
BGI news today is that they are jettisoning the Revolocity large sequencing system, announced all the way back in June. Along with the product abandonment,
40% of the ex-Complete Genomics group in the Bay Area is being laid off, with remaining staff focusing on the desktop BGISEQ-500 sequencer.
Monday, November 16, 2015
Do Demons Dream of Phylogeny Packages?
Miserable day today - spent my entire day wrestling with bad formats and flaky tools and trying to bull my way past them, leading to many a mad expostulation. The whole day down in the pit, with the pendulum of multiple deadlines swinging just over my head. The MBTA released new schedules that muck with my routines. And the then to top it off, Mick Watson writes a piece titled "The Five Habits of Bad Bioinformaticians" that cuts far too close to home. So I arrived home in a foul mood, my senses unpleasantly heightened to every sound.
Wednesday, November 04, 2015
Comments on "The use and misuse of supplementary material in science publications"
Mihai Pop and Steven Salzberg have an opinion piece in BMC Bioinformatics titled "Use and mis-use of supplementary material in science publications", examining issues arising from the ever growing data supplements accompanying papers, particularly in high-profile journals with strict article length limits. Pop & Salzberg make a number of important points, but there are some topics they didn't cover that I think are also worth treatment.
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