How to ask for bioinformatics help online

Part two of a two-part series.

In part one I covered where to ask for bioinformatics help. Now it is time to turn to the issue of how you should go about asking for help. Hat tip to reader Venu Thatikonda (@nerd_yie) for pointing me out to this 2011 PLOS Computational Biology article that tackles similar ground to this blog post. Here are my five main suggestions, with the last one being further broken down into 9 different tips:

  1. Be polite. Posting a question to an online forum does not mean that you deserve to be answered. If people do answer, they are usually doing so by giving up their own free time to try to help you. Don't berate people for their answers, or insult them in any way.
  2. Be relevant. Choose the right forum in which to ask your question. Sites like SEQanswers have different forums that discuss particular topics, so don't post your PacBio question in the Ion Torrent forum.
  3. Be aware of the rules. Most online forums will have some rules, guidelines, and/or an FAQ which covers general posting etiquette and other things that you should know. It is a good idea to check this before posting on a site for the first time.
  4. Be clever. Search the forum before asking your question, there is often a good chance that your question has already been asked (and answered) by others.
  5. Be helpful. The biggest thing you can probably do in order to get a useful answer to a question is to provide as many useful details as possible, these include:
    1. Type of operating system and version number, e.g. Mac OS X 10.10.5.
    2. Version number/name of software tool(s) you are using, e.g. NCBI BLAST+ v2.2.26, Perl v5.18.2 etc. A good bioinformatics or Unix tool will have a -v, -V, or --version command-line option that will give you this information.
    3. Any error message that you saw. Report the full error message exactly as it appeared.
    4. Where possible, provide steps that would let someone else reproduce the problem (assuming it is reproducible).
    5. Outline the steps that you have tried, if any, to fix the problem. Don't wait for someone to suggest 'quit and restart your terminal' before you reply 'Already tried that'.
    6. A description of what you were expecting to happen. Some perceived errors are not actually errors at all (the software was doing exactly what was asked of it, though this may not be what the user was expecting).
    7. Any other information that could help someone troubleshoot your problem, e.g. a listing of your Unix terminal before and/or after you ran a command which caused a problem.
    8. A snippet of your data that would allow others to reproduce the problem. You may not be able to upload data to the website in question, but small data snippets could be shared via a Dropbox or Google Drive link, or on sites like Github gist.
    9. Attach a screenshot that illustrates the problem. Many forum sites allow you to add image files to a post.

Any other suggestions?

 

Updates

2015-11-08 09.44: Added link to PLOS Computational Biology article

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).