Please read “It’s time to reboot bioinformatics education”

I guess I’ve been around bioinformatics for the best part of 15 years. In that time, I’ve seen almost no improvement in the way biologists handle and use data. If anything I’ve seen a decline, perhaps because the data have become larger and more complex with no improvement in the skills base.

It strikes me when I read questions at Biostars that the problem faced by many students and researchers is deeper than “not knowing what to do.” It’s having no idea how to figure out what they need to know in order to do what they want to do. In essence, this is about how to get people into a problem-solving mindset so as they’re aware, for example that:

  • it’s extremely unlikely that you are the first person to encounter this problem
  • it’s likely that the solution is documented somewhere
  • effective search will lead you to a solution even if you don’t fully understand it at first
  • the tool(s) that you know are not necessarily the right ones for the job (and Excel is never the right tool for the job)
  • implementing the solution may require that you (shudder) learn new skills
  • time spent on those skills now is almost certainly time saved later because…
  • …with a very little self-education in programming, tasks that took hours or days can be automated and take seconds or minutes

It’s good (and bad) to know that these issues are not confined to Australian researchers: here is It’s time to reboot bioinformatics education by Todd Harris. It is excellent and you should go and read it as soon as possible.


…is the new community blog from PLoS ONE. They write:

This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.

You’ll need a account to contribute; it’s a quick, unobtrusive sign-up and why not start a blog there too, if you haven’t already done so.
Bora writes:

and spread the word, outside of just twitter and friendfeed ;-)


Couple of new blogs in my Google Reader that you may want to investigate:

  • Bioinformatics on Rails
    Few posts, updated infrequently – going to follow for a while and see where it goes.
  • Bench Press
    “We’re four science and tech geeks who decided that the world needs yet another science blog.” A good recent post on electronic lab notebooks.

Bio::Blogs #20

Bio::Blogs #20 is up, over at Pedro’s place. Lots of interesting material from the bioinformatics blogosphere this month, so go and have a read.

As I suspected, now that Pedro is a bright young US postdoc (no doubt working 18 hour days), his time commitments have pushed Bio::Blogs down the priority list. If anyone can help out, or suggest alternatives to the current system of monthly compilation by one person, do get in touch with him at his blog. I wonder if we can use some of the aggregated content at places like FriendFeed or the Nodalpoint news aggregator as an easier way to generate monthly summaries of activity?

FeedJournal: silly but fun

Via LifeHacker:

Web application FeedJournal turns your RSS feed(s) of choice into a newspaper-formatted PDF.

A little clunky and buggy when I tried it out, but I eventually generated this PDF from a few of my Google shared items. I’m not keen on the way articles are headed “by neilfws” – I didn’t write any of them!

What use is it? Not much – perhaps a nice way to generate a PDF for the next edition of Bio::Blogs.

Bio::Blogs #17

Glancing through my November archive, I note (1) few if any bioinformatics posts and (2) few posts of any kind. Well, sometimes blogging has to take a back seat. It seems many of us are snowed under in the run-up to the holidays.

Despite this, Paulo has compiled an excellent edition of Bio::Blogs, number 17. Go there for a summary of news from the bioinformatics blogosphere in the past month. Remember, volunteers to host future editions are always welcome.

Bio::Blogs #16

We have a first for Bio::Blogs this month: a holiday-themed edition. Pumpkins are involved.

Pawel has done a great job and put together lots of interesting material from the bioinformatics blogosphere. The categories this month are scientific communication, bioinformatics workspaces and software tips. Go and have a read. Volunteers to host future editions are always welcome; email bioblogs at gmail dot com.