Tag Archives: Bioinformatics

Advice needed from a future reviewer…

I found myself writing this email to some collaborators, but halfway through realized that it’d be nice to get EVERYBODY’s input. Probably, one of you is going to review my next paper, so how awesome would it be for you … Continue reading

Posted in Misc. | Tagged , , | 1 Comment

installing STAMP on a Mac

Since this was such a huge pain in the ass for so many of us, I figured I’d share what finally worked for me. First this: pip install STAMP then I got an error about matplotlib, so then this: pip … Continue reading

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Do we need naming regulations for computer software?

Well, just saw this new paper: BMC Bioinformatics | Full text | Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data.  Seems potentially interesting.  But one part of it struck me as very awkward. … Continue reading

Posted in Bioinformatics | Tagged , , | 7 Comments

QIIME workshop at UC Davis (May 2-4, 2013)

UC Davis will be hosting a 2.5 day QIIME workshop following the SMBE Satellite Meeting on Eukaryotic -Omics, running Thursday afternoon May 2nd through Saturday May 4th. Meeting participants and local Bay Area researchers are encouraged to attend. Due to … Continue reading

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Gordon and Betty Moore Foundation hiring fellow for Marine Microbiology program #bioinformatics

Interesting Job Opportunity: Program Fellow, Marine Microbiology Initiative – Gordon and Betty Moore Foundation See key details of the ad below: The Bioinformatics Fellow position will be a 1-2 year term.  The Program Fellow will:  Contribute to developing strategy and implementation … Continue reading

Posted in Bioinformatics, Genomics | Tagged , , | Leave a comment

Attention all metagenomicists: put your pinky in the corner of your mouth & say "1 million dollars"

Already posted this to Twitter and Facebook but had to post here too.  This is wild.  DTRA has announced a $1 million prize for metagenomic analysis: DTRA Algorithm Challenge | Landing Page.  From their page The Prize:As nth generation DNA sequencing … Continue reading

Posted in Bioinformatics, metagenomics | Tagged , , , | 1 Comment

Guest post on "CHANCE" ChIP-seq QC and validation software

Guest post by Aaron Diaz from UCSF on a software package called CHANCE which is for ChIP-seq analyses.  Aaron wrote to me telling me about the software and asking if I would consider writing about it on my blog.  Not … Continue reading

Posted in Bioinformatics, ChIP-seq, Genomics, software | Tagged , , , | 1 Comment

Three talks, 1.5 days at #ISMB … phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the “Intelligent Systems for Molecular Biology” (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three … Continue reading

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Summary of responses to question about metrics for density in phylogenetic trees

I posted a question to Twitter and Facebook about metrics for assessing density in a phylogenetic tree. Here is a “Storification” of the responses. Thanks for the help all. Any other suggestions welcome in comments … http://storify.com/phylogenomics/metrics-to-quantify-density-of-taxa-sampling-in-a.js?template=slideshow%5BView the story “Metrics … Continue reading

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Draft post cleanup #11: Tree Hugging

Yet another post in my “draft blog post cleanup” series.  Here is #11 from September. Just a quick one.  In August a nice review paper came out on phylogenetic analysis software: Learning to Become a Tree Hugger | The Scientist.  By … Continue reading

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