Gender ratio of speakers at today's Festival of Genomics California conference

The Festival of Genomics Conference California conference starts today. From the speaker lineup I count 132 speakers with a gender ratio of 72.7% men and 27.3% women. This is a good ratio compared to many (most?) genomics conferences — see Jonathan Eisen's many excellent posts on this subject — and it exceeds the background level of women in senior roles in genome institutes around the world (a figure I previously calculated as 23.6%).

However, it was because the ratio of women speakers was below my self-imposed target of 33.3% that I withdrew Front Line Genomic's kind offer of a speaking position and requested that they instead offer my slot to a woman.

I think Front Line Genomics are ahead of many conference organizers in addressing gender bias, and I look forward to seeing the final lineup at their upcoming Festival of Genomics London conference.

This post is to serve as a reminder that we, as a community, still need to do much better at addressing gender bias in our field, and that men can actively help this process by refusing to speak or present at conferences which show extreme bias. Preferably, I would like others to adopt my 33.3% target as a minimum ratio that we should be aiming for (this applies both ways, though there doesn't seem to be much likelihood of men feeling underepresented any time soon).

A timely call to overhaul how scientists publish supplementary material [Link] →

Great new editorial piece in BMC Bioinformatics by Mihai Pop and Steven Salzberg that tackles a subject that people probably don't think about too much:

They highlight some of the problems that arise from the growing trend in some journals to publish very short articles that are accompanied by extremely lengthy supplementary material. They single out a few particularly lop-sided papers — including a 6-page article that has 165 pages of supplementary material — and make some solid observations about why this facet of publishing has become problem. Perhaps most importantly, citations that are buried in supplementary material do not get tracked by citation indices.

They conclude the paper with a proposal:

The ubiquitous use of electronic media in modern scientific publishing provides an opportunity for the better integration of supplementary material with the primary article. Specifically, we propose that supplementary items, irrespective of format, be directly hyper-linked from the text itself. Such references should be to specific sections of the supplementary material rather than the full supplementary text.

Yes, yes, a thousand times yes!

Where to ask for bioinformatics help online

Part one of a two-part series. In part two I tackle the issue of how to ask for help online.

You have many options when seeking bioinformatics help online. Here are ten possible places to ask for help, loosely arranged by their usefulness (as perceived by me):

  1. SEQanswers — the most popular online forum devoted to bioinformatics?
  2. Biostars — another very popular forum.
  3. Mailing lists — many useful bioinformatics tools have their own mailing lists where you can ask questions and get help from the developers or from other users, e.g. SAMtools and Bioconductor. Also note that resources such as Ensembl have their own mailing lists for developers.
  4. Google Discussion Groups — as well as having very general discussion groups, e.g. Bioinformatics, there are also groups like Tuxedo Tool Users…the perfect place to ask your TopHat or Cufflinks question.
  5. Stack Overflow — more suited for questions related to programming languages or Unix/Linux.
  6. Google — I'm including this here because I have solved countless bioinformatics problems just by searching Google with an error message.
  7. Reddit — try asking in r/bioinformatics or r/genome.
  8. Twitter — this may be more useful if you have enough followers who know something about bioinformatics, but it is potentially a good place to ask a question, though not a great forum for long questions (or replies). Try using the hashtag #askabioinformatician (this was @sjcockell's idea).
  9. Voat — Voat is like reddit's younger, hipster nephew. However, the bioinformatics 'subverse' is not very active.
  10. Research Gate — you may know it better as 'that site that sends me email every day', but some people use this site to ask questions about science. Surprisingly, they have 15 different categories relating to bioinformatics.
  11. LinkedIn — Another generator of too many emails, but they do have discussion groups for bioinformatics geeks and NGS.

Other suggestions welcome.

 

Updates

2015-11-02 09.53: Added twitter at the suggestion of Stephen Turner (@nextgenseek).

A rare example of a simple, fun, non-bogus name for a bioinformatics tool

Recently published in the journal Genome Biology, we have:

I like this name a lot because it is:

  • Memorable
  • Pronounceable
  • Simple, but also clever (combining elements of HiC and 5C)
  • Fun (a play on 'high five')
  • Not an acronym (so not a bogus acronym either)
  • Unique (can't find any other tools with this name)
  • Relevant (the short name has a connection to the data that the tool works with).

Maybe I need to start designing some sort of 'Anti-JABBA' award?