Fourth Floor Studio

November 1, 2006

Bio::Blogs #5 – tools edition

Filed under: bioblogs, bioinformatics — chris @ 3:23 pm

Where does the time go? One minute I’ve just started a post-doc, the next it’s the end of the year: leaves are gone, grants are due, papers are being drafted, and everyone around me seems to be fixated with end-of-year pagan rituals warding off evil (yes, it’s Hallowe’en). Onwards, however, with another edition of Bio::Blogs. For some reason, we’re heavy on tools this month, many of which require checking by new eyes. So consider this a blanket invitation to beta-test.

Pedro discusses emerging views of protein-protein interaction network, rather neatly illustrating why not setting your mind in stone is crucial in new fields, even if you think you understand what’s going on. Networks are a particular bug-bear of mine, as I’ve been to too many talks by biologically naive speakers claiming to understand such systems. I”m glad that someone is providing the voice of sanity.

Deepak tells us of the second BioIT project, arguing for inherent infrastructure flexibility to cope with the soon-to-come deluge of data. He points out that compute power isn’t really limiting any more (thanks to clustering), but efficient data management is, especially if you don’t know what next year’s data will look like. Whilst I agree in principle with virualisation, I can’t really see an implementation that would address the unknown data types problem. Maybe it’s just me?
Egon mentions Bioclipse, an open-source workbench for bio/chemi-informatics (check out their blog, too). As far as I can see, it’s a point-and-click interface to data management functionality. I can see why this is useful to Joe Schmoe, but I suspect that this class of approach is incompatible with high-throughput data processing. I’m still a fan of CLIs and scriptability. They are, however, looking for use cases, and it behooves us as a bioinformatics community to pitch in. After all, if we don’t, who will?

Yakafokon points to Zotero, a bibliography manager Firefox extension. It bills itself as including the best of old and new, combining full citation storage with automatic tagging and dynamic searching. Bibliography management is something Neil and I love complaining about, and I’ve yet to see the perfect solution.

Speaking of Neil, he has nothing but good words to say about EMBOSS, which we almost lost earlier this year due to funding cuts. It’s now back up for the next three years, but the transient nature of academic funding means that, as most other projects, its long term future is uncertain. I like to think that, in the event of a shutdown, the bioinformatics community would pitch in (more) to keep the codebase under development. I point out that the proportion of R01 investigator initiated grants awarded by the US NIH has dropped from ~25% to ~10%; as an indicator of global trends, this predicts dire times for funding. If bioinformatics projects are likelier to be given the chop, there will be hard times ahead.

To end on a high note, I urge you to watch a potentially significant event in the Redfield lab: the mutation of a lab person to computation. Heather’s code is better than her wet experiments, for the first time. Could this be the beginning of the beginning? Rosie herself is having trouble with random number generators. May I suggest the Mersenne Twister?

Enjoy, and don’t forget that we’re looking for a December editor. Future entries to bioblogs at gmail dot com.

update: you should also check out the Bio::Blogs icon challenge.



  1. […] The November edition of Bio::Blogs has been released here. Thanks to Chris for setting it up. […]

    Pingback by Bio::Blogs #5 « Bio::Blogs — November 1, 2006 @ 3:58 pm

  2. Good job. Of course, Heather will soon find that code always works better and provides more satisfaction than wetlab experiments – and so it begins…

    I’ll point out again that with one more host (and if the existing hosts are agreeable to a rotation system), we’d each have to host Bio::Blogs only twice a year – which isn’t much work. Though I suspect that a Jan 1st edition might not happen.

    Comment by nsaunders — November 1, 2006 @ 7:42 pm

  3. […] Bio::Blogs #5 is out over at Chris’s place, with an emphasis this month on software tools. Go and check it (and them) out. […]

    Pingback by Bio::Blogs #5 « What You’re Doing Is Rather Desperate — November 1, 2006 @ 7:44 pm

  4. […] Bio:Blogs #5, the latest edition of the bioinformatics-focussed blog carnival has been posted at the Fourth Floor Studio. […]

    Pingback by Bio::Blogs #5 at business|bytes|genes|molecules — November 2, 2006 @ 6:26 am

  5. Good point about the 1st of January :), maybe it can be postponed to the 15th for example to give everyone time to clear the minds of the new years’ fun.
    The only thing I don’t like about the rotation systems is that it makes it harder for new people to host. It would be good to have a rotation but with some flexibility to include new blogs.
    It would be nice to do it in Nodalpoint too, if Greg is ok with it.

    Comment by Pedro Beltrao — November 2, 2006 @ 7:27 am

  6. I will personally volunteer to vacate one of my spots if someone new decides to host 🙂

    I wonder if we should slap up an email to 5-10 binf bloggers around to solicit editors? [We know who they are…]

    Comment by chris — November 3, 2006 @ 12:55 am

  7. I’m all for new hosts too. But if volunteers are thin on the ground (hard to believe ;)), rotating between 6 wouldn’t be too bad.

    Comment by nsaunders — November 3, 2006 @ 2:14 am

  8. I’m up for hosting the next Bio::Blogs on nodalpoint, unless there are other takers ?

    Comment by Greg Tyrelle — November 4, 2006 @ 4:33 pm

  9. Hi!,

    Comment by name — September 1, 2008 @ 3:15 am

  10. Hello!,

    Comment by name — September 1, 2008 @ 3:15 am

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