Tuesday, May 29, 2012

How to Stay Current in Bioinformatics/Genomics

A few folks have asked me how I get my news and stay on top of what's going on in my field, so I thought I'd share my strategy. With so many sources of information begging for your attention, the difficulty is not necessarily finding what's interesting, but filtering out what isn't. What you don't read is just as important as what you do, so when it comes to things like RSS, Twitter, and especially e-mail, it's essential to filter out sources where the content consistently fails to be relevant or capture your interest. I run a bioinformatics core, so I'm more broadly interested in applied methodology and study design rather than any particular phenotype, model system, disease, or method. With that in mind, here's how I stay current with things that are relevant to me. Please leave comments with what you're reading and what you find useful that I omitted here.

RSS

I get the majority of my news from RSS feeds from blogs and journals in my field. I spend about 15 minutes per day going through headlines from the following sources:

Journals. Most journals have separate RSS feeds for their current table of contents as well as their advance online ahead-of-print articles.
Blogs. Some of these blogs are very relevant to what I do on the job. Others are more personal interest.
Forums.

Mailing lists


I prefer to keep work and personal email separate, but I have all my mailing list email sent to my Gmail because Gmail's search is better than any alternative. I have a filter set up to automatically filter and tag mailing list digests under a "Work" label so I can get to them (or filter them from my inbox) easily.

  • Bioconductor (daily digest)
  • Galaxy mailing lists. I subscribe to the -announce, -user, and -dev mailing lists, but I have a Gmail filter set up to automatically skip the inbox and mark read messages from the -user and -dev lists. I don't care to look at these every day, but again, it's handy to be able to use Gmail's search functionality to look through old mailing list responses.

Email Alerts & Subscriptions

Again, email can get out of hand sometimes, so I prefer to only have things that I really don't want to miss sent to my email. The rest I use RSS.
  • SeqAnswers subscriptions. When I ask a question or find a question that's relevant to something I'm working on, I subscribe to that thread for email alerts whenever a new response is posted. 
  • Google Scholar alerts. I have alerts set up to send me emails based on certain topics (e.g. [ rna-seq | transcriptome sequencing | RNA-sequencing ] or [ intitle:"chip-seq" ]), or when certain people publish (e.g. ["ritchie md" & vanderbilt]). I also use this to alert me when certain consortia publish (e.g. ["Population Architecture using Genomics and Epidemiology"]).
  • PubMed Saved Searches using MyNCBI, because Google Scholar doesn't catch everything. I have alerts set up for RNA-seq, ChIP-Seq, bioinformatics methods, etc.
  • GenomeWeb subscriptions. Most of these are once per week, except Daily Scan. I subscribe to Daily Scan, Genome Technology, BioInform, Clinical Sequencing News, In Sequence, and Pharmacogenomics Reporter. BioInform has a "Bioinformatics Papers of Note", and In Sequence has a "Sequencing papers of note" column in every issue. These are good for catching things I might have missed with the Scholar and Pubmed alerts.

Twitter

99.9% of Twitter users have way too much time on their hands, but when used effectively, Twitter can be incredibly powerful for both consuming and contributing to the dialogue in your field. Twitter can be an excellent real-time source of new publications, fresh developments, and current opinion, but it can also quickly become a time sink. I can tolerate an occasional Friday afternoon humorous digression, but as soon as off-topic tweets become regular it's time to unfollow. The same is true with groups/companies - some deliver interesting and broadly applicable content (e.g. 23andMe), while others are purely a failed attempt at marketing while not offering any substantive value to their followers. A good place to start is by (shameless plug) following me or the people I follow (note: this isn't an endorsement of anyone on this list, and there are a few off-topic people I follow for my non-work interests). I can't possibly list everyone, but a few folks who tweet consistently on-topic and interesting content are: Daniel MacArthur, Jason Moore, Dan Vorhaus, 23andMe, OpenHelix, Larry Parnell, Francis Ouellette, Leonid Kruglyak, Sean Davis, Joe Pickrell, The Galaxy Project, J. Chris Pires, Nick Loman, and Andrew Severin. Also, a hashtag in twitter (prefixed by the #), is used to mark keywords or topics in Twitter. I occasionally browse through the #bioinformatics and #Rstats hashtag.

10 comments:

  1. Thank you for this informative post!

    ReplyDelete
  2. Hi Stephen,

    Thanks a lot for the info that guides us through the ocean of information.
    I have 2 questions about old-fashioned microarray analyses:
    1. Does Bioinformatics Core perform predictive modeling on microarray data (i.e. disease versus non, or other phenotype)?
    2. Are you aware of the automated pipeline for microarray pre-proccessing and initial analyses?

    Thanks

    ReplyDelete
  3. 1. Yes
    2. See the affycoretools Bioconductor package.

    ReplyDelete
  4. Sweet mercy. Just the thought of keeping up with your field is overwhelming. And you do this in 15 minutes a day? I think it took me 15 minutes just to read this list!

    Very informative, though. It makes me think I need to dust off my twitter account...

    ReplyDelete
  5. Sounds about right to me, I'm on the same page. We're reading a lot of the same things.

    I also have an aggregate biostar user-of-interest rss feed, to stalk people who I think are smart.

    Occasionally I look at the newest questions tagged "R" on stackoverflow as well, but that's a big hose. Sometimes I'll catch something useful.

    I haven't really found a way to use twitter *usefully*. I think I probably have followed too many people. I try to look at #bioinformatics and #rstats once a week, but it's a little too overwhelming sometimes. Usually I just look to see if there's something that a lot of people seem to be re-tweeting.

    I'm also following a number of bioinformatics people on google plus, and while bioinformatics-traffic isn't super heavy, I feel like I've "gotten to know" a few bioinformatics people on there a little more.

    ReplyDelete
    Replies
    1. Madelaine,

      Interesting - I haven't tapped into G+ yet. I figured it would go the way of Orkut/Wave/Buzz, but apparently it's gained some traction! I'll have to take a look!

      Stephen (vustephen on G+)

      Delete
  6. Fantastic list, Stephen. Thanks for sharing!

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  7. Nice Collection and it's really helpful for keeping updated..thanks for sharing.

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  8. Just to share with everyone here - homolog.us also recently posted a review of bioinformatics blogs. There are a few gems here that I missed in my review above. Go check it out.

    ReplyDelete

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