Sunday, 17 November 2013

The Great Western Binfo

Classes were cancelled at The Institute this last Friday for the Annual Open Day when we showcase the place and encourage school-children to do science and see that it could be both fun and interesting to do that science with us.  Several people asked me what I was contributing for Friday and my answer "Going to Galway" raised a few laughs. For me the only thing that is more important than a chance of pushing science at young people and young people at science is to attend the annual meeting of my professional association VIBE - the Virtual Institute of Bioinformatics and Evolution.  The 15th Nov 2013 meeting was held in NUIG.  The world of Irish Bioinformatics and Molecular Evolution has grown from a single lab in the mid 1980s to a very broad church today.  The students of that first lab are now full Professors with students of their own who recursively have students of their own who . . .  The topics covered in Galway on Friday were unimaginably wider, deeper and faster flowing than the sorts of data we were analysing back in the day.

The exponential increase in data and the power of the tools to analyse it is illustrated in the observation that my first 1992 paper in molecular evolution analysed 45 complete genes from one fungal species Aspergillus nidulans. I read every paper ever written about each of those genes. Ten years later, just before coming to do his PhD with us, my first student had completed a Master's degree in Ottawa by analysing 40 complete genomes in a similar way.  That was a ~4000 fold increase in the amount of data processed.  At about the same time as our Aspergillus paper, TCD won a contract to help sequence the very first chunk of a eukaryotic genome - Chromosome III from baker's yeast Saccharomyces cerevisiae.  That contract was costed at 1 ecu/€ per DNA base.  This Friday I was told that the cost of sequencing was now $0.10c per megabase: a 10-million-fold decrease in the cost of generating primary data!

After a gallimaufry of excellent talks through the day, and a rich and varied poster session over lunch where graduate students show-cased their latest work, we heard a key-note talk from John Greally now of Albert Einstein College of Medicine in NYC but a graduate of NUIG.  His Title "A feeling for digital organism" deliberately echoed the title of Barbara McClintock's biography. Greally started with an ex-tempore tribute to the organisers of, and contributors to, the day's events, saying that the breadth of interests, skills and experience in the room was a) extraordinary and b) had enormous potential for synergistic lift.  He wasn't flattering us as planet-brained rocket-scientists but as comparatively ordinary people who were holding a space regularly for interactions and hopefully collaborations among widely separated disciplines. Those remarks were immediately followed by a story about two of the stars in his group: a computer-illiterate "good pair of hands" and a somewhat geeky coding-whizz.  These two started by trading the secrets of their tool boxes: the one learning a bit of eppendorf-flipping and blaming-the-buffer and the other the rudiments of code.  This gave them a common syntax and some appreciation for what the other did.  The subsequent discussions were extraordinarily rich and productive.  Greally described the future sans peur et sans reproche biologist as "pipetting with one hand, programming with the other".

He went on to suggest a way to paddle up the biological data-deluge by citing his earlier paper on Astrogenomics.  When astronomers started to collect data digitally rather than by looking at distant objects with eyes or silver-nitrate cameras clapped to telescopes, they quickly found that they could generate galaxies of data in a single night.  Why not, he suggested, learn from the approaches, protocols, wrong-turnings and triumphs of the astronomers and perhaps use some of their tools and ideas on bio-data. He also urged us scientists to visit with Artists to help up our game in presenting data in visually appealing and so more readily understandable ways. After more in the same inspirational vein, I felt that even I could/should shift off my metaphorical sofa and start shoving some big science uphill especially if I was shoulder to shoulder with folks who each brought different tools and ways of seeing to the task.

At the end of that talk we were drained and inspired and looking forward to some liquid refreshment but there was one last item on the agenda - where to hold next year's meeting. After trying to remember who had been the least recent host, someone suggested we foist the task on the group that hadn't made it to this year's meeting.  After some further joshin' and slaggin' the silence began to be uncomfortable and everyone was looking resolutely at their feet, so I said "Dang it, I'll do next year". That suggestion was approved nem. con. and we all went to the bar.

Follow me down to The Institute which as everyone in the County now knows is


  1. Pretty sure the word was not "dang", but otherwise great write up