Thursday, January 27, 2011

AGBT Around the Corner

In less than a week, the AGBT meeting (perhaps better known as Marco Island) begins. Alas, due to my usual dithering around going to meetings I'm not registered -- and I've been told it sold out the day registration opened. Barring some passes showing up on StubHub, I'll be stuck monitoring Twitter again.

AGBT can be a locale for making big announcements -- last year the meeting finished with Jonathon Rothberg unveiling (well, sort of) the Ion Torrent PGM and the year before PacBio was the star. But, I'm not expecting a lot of big announcements from the major players. The recent J.P. Morgan conference was the scene of Illumina's big MiSeq announcement and Ion Torrent's launch of their second generation chip. It's hard to see either of those groups making further announcements. Nor does either have a big talk to launch things, though I'm sure many vendors will be making announcements even without a podium spot. There is one talk featuring Ion Torrent from one of their early access sites, and I'm sure that will be popular for trying to get some ideas as to what really working with the instrument is like.

As far as the other established players, Roche/454 desperately needs to generate some excitement with some advancement; the long-heralded 1Kb reads might do. PacBio has two talks, one on the cholera work and one on detecting modified bases. Perhaps some more details on performance will leak out, but neither sounds promising. Complete Genomics has a workshop but no apparent talk.

The biggest opportunity for metaphorical fireworks (to go with the ones on the beach one night -- I love fireworks; absolutely must register next year!) would be if one of the nanopore or other blue sky technologies actually demonstrated real data. I'd say any read 10 bases or longer would be something, and demonstrating a set of reads in the 20+ basepair range would mean they are really on to something. There's a handful of talks scheduled for such technologies (Oxford Nanopore's founder, Nabsys, UC Santa Cruz on nanopores, BioNanomatrix; apologies if I missed someone). No talk from GnuBio; would be nice to see whether they are at all on their aggressive timeline.

I will be watching Twitter, so if you are there and can tweet it will be appreciated. I did try to follow ASHG in November on Twitter and got a bit frustrated with the standard web interface. So, today I whipped up a quick Perl harness to search for tweets and process them into a table. Most of the heavy lifting, of course, was done by a CPAN library & so I can actually put the code below in case anyone else finds it useful. Once the meeting starts, I might hack some more on it. My dream app would know the conference schedule and assign each tweet to a talk, but that's way beyond what I see myself getting together. Perhaps I'll actually go so far as to generate a SQLite database from the tweets of interest, but most likely it will just feed Excel.

Currently what it does is pull things like hashtags and URLs out of the text & put them in separate columns. The first column is the timestamp and the second is the author. Also, it skips over explicit re-tweets. One issue I may try to deal with is posts which are really re-tweets but not tagged correctly; if those are a nuisance I may try to work on some auto text-clustering. And perhaps I won't resist at least a little crude assignment of tweets to talks (looking for keywords; tracking a given user).

use Net::Twitter::Lite;

my $nt = Net::Twitter::Lite->new(
username => $ENV{'TWITTER_USERNAME'},
password => $ENV{'TWITTER_PASSWORD'}

my $r=$nt->search($ARGV[0]);
my $nt = Net::Twitter::Lite->new(
username => $ENV{'TWITTER_USERNAME'},
password => $ENV{'TWITTER_PASSWORD'}

my $r=$nt->search("Ion Torrent");

foreach my $status(@{$r->{'results'}})
my $origText=$status->{'text'};
next if ($origText=~/^RT/);
my $text=$origText;
my $url="";
if ($text=~m/(http:[^ ]+)/)
$text=~s/ ?$url//;
my @hashes="";
while ($text=~m/ \#([^ ]+)/g)
$text=~s/\ #([^ ]+)//g; $text=~s/ +$//;
print join("\t",$status->{'created_at'},


bioinfosm said...

great work!!

I could not register either .. this will be awesome

Anonymous said...

Oxford Nanopore has some cool details of their machine on their website!