How does gender diversity of speakers at CSHL Evolution of Sequencing meeting compare to research institute gender diversity?

Following Jonathan Eisen's recent blog post about the tremendously poor representation of female speakers at the upcoming CSHL Evolution of Sequencing meeting, I was curious about something. Namely, how representative are female scientists in senior roles at prominent genome centers/institutes?

So I found 10 places which all have at least 10 people listed in senior roles (e.g. Faculty or Project leaders), including our own Genome Center. In all but one case, the gender ratio exceeds the pitiful 8.5% of female speakers at the Evolution of Sequencing meeting.

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While it is still depressing that not a single institute has more than 40% of senior roles filled by women, it is a clear sign that there is a great pool of talented female genome scientists out there. Conferences should therefore have no excuses for single-digit percentages for female speakers.

NCBI BLAST+ v2.2.31 released →

NCBI have recently announced the release of v2.2.31 of BLAST+ (hat tip to Torsten Seemann for alerting me to this). Find out more here:

• Release notes
• Download the binaries (FTP link)

This release is of interest to me as it fixes a bug introduced in v2.2.30 that broke our CEGMA software (which relies on TBLASTN):

Reenabled support for word size 5 in tblastn.

This bug was something that I reported on back in February.

Really great presentation on long-read sequencing by Torsten Seemann →

Great overview of where we are at with PacBio, Oxford Nanopore, and other long-read technologies. Thanks to Torsten Seemann @torstenseemann) who put his slides on SlideShare last week:

Long read sequencing - WEHI bioinformatics seminar - tue 16 june 2015 from Torsten Seemann

Command-line bootcamp: learn the basics of Unix

Here is another contribution that I made to a UC Davis Bioinformatics Workshop that I helped teach last week. Adapting from some our much longer Unix & Perl Primer for Biologists, I made a short bootcamp that aims to teach the basics of the Unix/Linux command-line.

Unlike the Primer material that was written from the point of view of someone using a Mac, the new bootcamp course is written from the viewpoint of someone using Ubuntu Linux. Also, no example files are needed. The course is entirely self-contained and should take 1–3 hours to process (depending on your familiarity with Unix).

Download the PDF, view the HTML version, or work with the underlying Markdown file.

• Command-line bootcamp (PDF)
• Command-line bootcamp (HTML)
• Command-line bootcamp (Markdown)

Current version: v1.01 — 2015-06-24