Thursday, February 24, 2011

Reflecting & Responding on Today's Comments

It's nice to see my piece on the Ion Torrent 318 chip get a lot of comments, as well as being tweeted and some additional comments at SEQAnswers. I love getting comments, especially those that constructively challenge my analysis.

Two commenters threw some cold water on my enthusiasm, pointing out that the 318 is not scheduled to be released until September, and then only to early access customers. I'll confess to not asking careful enough questions on the timing & letting my desires get ahead of me. Ion Torrent will need to deliver these chips on time and working at specifications in order for scientists to believe that there really will be the promised regular upgrades. MiSeq is vaporware at the moment also, but Illumina has a strong track record for rolling out instruments.

One commenter took me to task for suggesting that Ion Torrent will simply roll right over Illumina. I don't mean to suggest this will happen, only that Ion Torrent may offer a very stiff challenge. If the PGM chip upgrades, sample prep improvements and read length improvements come as promised, then the PGM may well march up through Illumina's product line. That's not to say Illumina will remain static; they have clearly demonstrated great skill at pushing their platform to amazing abilities. The MiSeq may offer a new path to greater performance; there has already been speculation over at SEQAnswers on possible paths forward. For example, will the faster cycle times mean an opportunity for longer read lengths (if the reagents are not stable over very long runs)? Will Illumina roll out a multi-flowcell version of the MiSeq, enabling very high-throughput rapid-turnaround sequencing? I'd put more money on the latter than the former. Another thread has surfaced rumors that a HiScan upgrade is imminent which will give it HiSeq-like capabilities; for groups running both arrays and sequencing this could be useful. How much denser can Illumina pack the flowcells? Only time will tell. But, as I pointed out before, longer reads will have limited impact on overall throughput if the two reads are overlapping (though accuracy may be improved).

On the other hand, I do see as excessive cynicism (bordering on editing the truth) that AGBT had only Ion Torrent talking about Ion Torrent; given that two talks (Bolen from NCI and Nusbaum from the Broad; the Bolen talk will apparently be at ABRF as well) described actual experiences. Granted, neither was really independent of the company. It is critical for Ion Torrent's reputation that data start appearing in public spaces, especially data from regular customers.

Ditto for the experimental protocols; one commenter had a question about amplicon sequencing which will be important for Ion Torrent's success. The sooner applications are adapted to the system, the sooner customers will be buying machines and chips. Of course, a great strategy IMHO would be to put some sequencers in the hands of genomics bloggers.

As far as the question of reads per chip increasing faster than the number of sensors per chip, my understanding is that Ion Torrent expects that better sensor loading and utilization. Again, how vaporous is this? That's hard to tell -- and why feedback from actual users is desperately needed.

On the question of amplicon and read length for Ion Torrent, those would seem to be different fish (though I don't have direct experience). Amplicon length will be a matter of the emPCR conditions. I'm unaware of any signal amplification in the 454 chemistry -- I thought the signal cascade was strictly linear. But, again that is outside my expertise and I would enjoy being educated on the subject.

With regard to whether emPCR can be converted from a liability to a non-issue, it's reasonable to be skeptical. But, it isn't obvious why emPCR can't be compressed in time (though I haven't done emPCR, so that's a stretch for me to comment on). In my discussion with them, they pointed to cutting the number of cycles as one time savings. In any case, how hard as anyone tried to really optimize emPCR for speed? Only on the 454 might it have been a serious concern, and the cost of a 454 run is not going to encourage many folks to push for many runs a day. On the other hand, I don't see it as "disingenuous" the comparison I made; I've been at a company that had techs running PCR (again, conventional not emPCR) day in and day out, and any company that runs production Sanger is in a similar boat. Indeed, any big SOLiD or 454 shop must do this as well. What will the nature of the new emPCR kit be? I have some speculations, but that's a whole 'nother post.

One other surprise today from Ion Torrent is the announcement that they have sequenced the genome of Intel co-founder Gordon Moore. One claim from this is that the coverage was more uniform than with other platforms. Obviously, either publication or release of the data is needed to vet this claim. Even if they used 318 chips, this was an expensive demonstration project (I don't know the actual coverage; I don't have a subscription to In Sequence) -- even at 10X coverage it would be $20K (retail) in chips. Apparently this was an exclusive for GenomeWeb's In Sequence, as Ion doesn't even seem to have a press release out. I hope they plan to publish this in a journal soon, or if not make the primary data available for further study.

Wednesday, February 23, 2011

Has Ion Torrent Taken A 318-Sized Lead over MiSeq?

About a week ago, Ion Torrent's President Greg Fergus and Head of Marketing Manesh Jain were kind enough to engage me in a nearly an hour of discussion about the Ion Torrent platform. One agreement prior to our discussion is that I would withhold this piece until their announcement today of the 318 chip for the system (I also volunteered to let them see a draft of this in advance to ensure I had not misrepresented anything).

A key theme on their side is a certain degree of feeling that the wrong questions are being asked in the analysis of PGM versus MiSeq -- and an eagerness to shift the discussion. They wished to emphasize a number of points, and after the discussion I can see the validity of many of these.

Is Being Lucky the Same as Being Smart?

Forbes has an article co-written by Matthew Herper and Robert Langreth titled "The Next Big Move For The Smartest Biotech Investor", profiling Randal Kirk. Kirk is described as one of the few billionaires who can ascribe that status to biotechnology. Kirk made his money through two companies in the psychiatric drug space: New River Pharmaceuticals developed an ADHD drug (lisdexamfetamine) and then was acquired by Shire whereas Clinical Data developed an antidepressant (vilazodone) and was then purchased by Forest. A key part of the article profiles Kirk's investment in a little-known and secretive synthetic biology company called "Intrexon".

The title is probably meant to gall; it certainly raises my hackles. The most obvious quibble is that it isn't clear either of the drug development companies were really biotech. Of course, that would require defining biotech, but it ideally it would refer to companies which highly depend on recombinant DNA and related technologies. Now, such technologies are embedded in virtually all drug development today, but neither of these drugs sounds like they used much. Both drugs are interesting twists on prior approaches (though I'm not enough of a chemist to judge the novelty of vilazodone).

Sunday, February 20, 2011

Will Cheap Gene Synthesis Squelch Cheaper Gene Synthesis?

Among the vast piles of items which I've meant to write about but have slipped are a paper last year on gene synthesis and some subsequent announcements about trying to commercialize the method described in that paper. This is an area in which I have past experience, though I would never claim this gives me indisputable authority or omniscience in the matter.

The paper, primarily by scientists from Febit but also with two scientists from Stanford and George Church in the author list, finally describes an interesting approach to dealing with some serious challenges in gene synthesis which substantially increase the costs. By finally, I mean that the idea has certainly been kicking around for a while and was mentioned when I visited Codon Devices in the fall of 2006 looking for employment.

To fill in some background first, gene synthesis is a powerful way to generate DNA constructs which can enable all sorts of experiments. The challenge is that the cost of gene synthesis, currently starting at around $0.40 per base pair for very easy and short stuff (say, less than 2Kb), tends to restrict what you can use it for. I have a project concept right now that would be a slam dunk for gene synthesis -- but not at $0.40/bp (which I think I couldn't even get for the project). Whack that price by a few factors of two and the project becomes reasonable.

There are many cost components to commercial gene synthesis, and only someone who has carefully looked over the books while wearing a green eyeshade is going to have a proper handle on them. But three of the big expenses are the oligos themselves, the sequencing of constructs to find the correct ones and labor. What the Febit paper does is illustrate a nice way to tackle the first two in a manner that shouldn't require a lot of labor.

The oligo cost is a serious issue. Conventional oligos can be had for around $0.08 or maybe a bit less a base. However, each base in the final construct requires close to 2 bases in the oligo set. Some design strategies might get this down a bit. However, conventional columns generate far more oligo than you actually need. An approach which has been published (but not commercialized as far as I know), is to scale down the synthesis using microfluidics. This method matches better the amount synthesized and the amount you need, though the length and quality of the oligos needs refinements from what was reported in order to be truly useful. Microarrays are a means to synthesize huge numbers of oligos, but their quality also tends to be low and the quantity of each oligo species is much too small without further amplification. Amplification schemes have been worked out, but add to the processing costs of the oligos.

What Febit and company have done is take those microarray-build oligos and screen them using 454 sequencing. The beads containing the amplicons with correct oligos are then plucked out of the 454 flowcell (with 90% success of getting the right bead) and used as starting points.

Now, this has several interesting angles. First, it has been challenging to marry the non-Sanger new sequencing technologies to gene synthesis. The new technologies tend to have short reads, too short to read even a short construct. The new technologies also require library construction and it is difficult to trace a given sequence back to a specific input DNA. In other words, short read technologies are great at reading populations, but not individual wells in a gene synthesis output. Sanger on the other hand, is ill-suited for populations but great for individual clones. One solution to this problem is clever pooling and barcoding strategies, but these necessitate having enough different clones to be worth pooling and barcoding. In other words, second generation sequencing is difficult to adapt to retail gene synthesis, but looks practical for wholesale gene synthesis.

Getting the oligos right has important positive side-effects. While the stitching together of oligos into larger fragments (and larger fragments into still larger ones) can generate errors, and awful lot of the problems stem from bad input oligos. Not only can error rates be troublesome, but some of the erroneous sequences may have advantages over the correct ones in later steps. For example, a deleted fragment may PCR more efficiently than the full length, and slightly toxic gene products may be disfavored in cloning steps over frameshifted versions of the same reading frame. So, by putting the sequencing up front it should be possible to reduce the later sequencing downstream. So even if that sequencing remains Sanger, it should be possible to do a lot less.

Okay, that's the science. Now some worries about the business. Febit announced in January they are looking for investors to fire off a new company to commercialize this approach. This makes good business sense, since Febit itself must be encrusted with all sorts of business barnacles, having lurched from one business to another in trying to commercialize their microfluidic microarray system. Previously failed attempts include gene synthesis as well as microarray expression analysis and hybridization capture (I even ran one experiment with their system, whose results certainly didn't argue for them staying in that business!). The press release stated they were hoping to attain pricing in the 0.08$ per base range, which would make my current experiment concept feasible. That would be great.

Now, they will need to refine their system and perhaps adapt other sequencers. A 454 Jr would probably not be a difficult adaptation, but moving on to Ion Torrent must be tempting. Getting things to work for one paper and one set of genes is unfortunately different than being able to keep things working over an entire spectrum of customer designs.

Which leads me to where I think they will have a great challenge, though one which I think can be finessed with the proper business approach. They will be brining to market a methodology whose benefit is cost at the expense but with the caveat of attaining that cost advantage only with sufficient volume. Initially, they will be unable to reliably predict delivery times (due to kinks showing up). Finally, they are adding some additional processing steps (454 sequencing, bead recovery & oligo recovery from the bead) which may add to the time.

The abyss into which this new company must plunge is a world in which very fast gene synthesis is available from a large number of vendors in the $0.40 price range. So, they must find very large customers who are willing to be a bit patient and keep their pipeline filled. Such customers do exist, but they aren't always easy to find and pry away from their existing suppliers. In theory much cheaper synthesis would unleash new orders for projects (such as mine) which are too costly at current prices, but that is always a risky assumption to bank a company on (c.f. Codon Devices' gene synthesis business).

It's the alternative route that I predict this NewCo is likely to go down. That would be to link up with an established provider in the field. Said provider, through their salespersons and sales software, could offer each customer an option -- I can build your genes for $0.40 if you want them fast or hack that down to $0.10 a base if you can wait. In order to preserve customer satisfaction, that long time would need to include an insurance period to build the genes by the conventional route if the new route fails -- but of course if you are frequently forced to build $0.40/bp genes for which you charged $0.10/bp, that would be financial suicide.

So, in summary, I think this is a clever idea which needs to be pushed forward. But, after a long gestation in the lab, it faces a very rocky future in the production world. I hope they succeed, because it is not hard to imagine projects I would like to do which would be enabled by such a capability.

Thursday, February 17, 2011

Roads That Really Need Taking

There is a provocative Perspective piece in a recent Nature titled "Too many roads not taken". In it, the authors summarize some more extensive work (posted on Arxiv) and others showing that in several major fields of protein research, the biological community seems to be stuck on a few old favorites, with insufficient attention to other key players.

In the Nature piece, the focus is on protein kinases and nuclear hormone receptors, both key druggable classes. In the kinase area, they have a graph (the Arxiv site leads to the actual data) showing that the graph of attention (measured in bibliographic citations) given to kinases prior to 2003 is generally predictive of the attention given them in 2009; only a handful of kinases with little attention in the first time period are hot areas now. Of course, if the rest of the kinome were boring this would be justifiable, but they point to several papers which indicate that many of the unstudied kinases (for example, this series of shRNA experiments)

A very striking conclusion is underlined by their plot of NHR citations by gene, which is expanded upon significantly in the Arxiv preprint. Their contention is that the availability of chemical probes drives analysis in this family, and in their rank-ordered histogram of activity the proteins with chemical ligands are all at the top of the list. Granted, at the breakpoint the bars are nearly equally tiny on either side of the divide, but it does suggest a strong correlation. Easy to build universal approaches such as RNAi are very powerful, but especially for any kind of in vivo study are suboptimal -- not only are they hard to deliver, but utterly wiping out a protein is not a subtle way to probe a system. The Arxiv piece goes into more detail and posits that you really need good compounds, ones with good bioavailability and such. In other words, drug-like compounds.

So, they plead that we need to invest more in getting such compounds into the research community. Some of this could take the form of funding screening efforts in the public sphere, which like sequencing the human genome isn't the sexiest project from a scientific perspective -- just like the foundation is never the sexiest part of a great building. But foundations matter!

An alternative, suggested by the Arxiv paper, is that compounds may exist in the patent literature but are not widely commercially available. So, a public effort might focus on mining the patent literature, synthesizing various claimed compounds and verifying their activity. Of course, some (many?) compounds in the patents might not stand up to scrutiny. Another alternative would be to attempt to devise incentives for industry to release some of the inhibitors they have in house; obviously this would be a challenge as such compounds might prove to be the starting points for valuable drugs -- but of course they never will until someone proves the underlying kinases valueable. Some companies have generated unbelievable databases on kinase inhibitors (for example, this recent study) which have the potential to fill in the missing spots on the kinase tool compound grid.

I can't help thinking of the new translational medicine institute going in at the NIH. Trying to move research findings into the clinic to benefit patients is hard to argue against, but perhaps the NIH needs to also pour some resources into the humble task of finding basic tools.

Tuesday, February 08, 2011

Wrapping up AGBT

AGBT ended on Saturday, but both Saturday & Sunday were crammed with personal stuff. Monday night was some down time, so now tidying up.

Anthony Fejes has a nice final post on the meeting (along with all his useful notes); it's also interesting to see what a boost in traffic he gets for AGBT (and well deserved!). One very positive Twitter note: one presenter personally thanked him for blogging his talk; I know I get a thrill whenever authors visit this space with comments & it's good to see that sometimes blogging really is opening up a two-way conversation. A more constrained view on the proceedings can be seen in an investment house's research note.

A few last impressions of my own based on Anthony's notes and Twitter. Nanopores seem to be making progress -- but still quite distant from being able to generate any data. PacBio appears to have faced reality and is positioning themselves in areas where their strengths (read length, speed) are strengths and accepting that their per-base quality isn't going to be adequate for many applications. Metagenomics is something I really need to do a personal deep dive into -- it's often sounded cool & I'd love to know more. The whole idea that each region of my skin has a different flora is pretty amazing -- and one wonders what the scale of changes are (indeed, I wonder about how different my scales are than adjacent area -- it's winter and I have several serious dry patches). The Broad is using 500Gb of RAM on their machines doing de novo vertebrate assembly; given that my first and second computers came with 1Kb of RAM, that's pretty mind blowing.

Someone asked for my Twitter table. Alas, I didn't save some intermediate results & Twitter's search mechanism apparently now won't go back beyond Thursday night, but below is what I can spit out -- with the URLs turned into hyperlinks. Maybe before the next meeting I'll engage in some lily-gilding and have this thing build a SQLite database of results. Twitterstatistical summaries for the whole meeting are a bit interesting.

Tue, 08 Feb 2011 21:30:16 +0000 KamounLab¬タン AGBT Excellent summary: ¬タワ@genomeresearch: What investors heard at - summary & analysis from A Murphy of William Blair
Tue, 08 Feb 2011 18:57:00 +0000 genomicslawyer AGBT What investors heard at - summary & analysis from Amanda Murphy of William Blair:
Tue, 08 Feb 2011 12:07:24 +0000 samuellampa HTSeq,NextGenSeq,AGBT Or maybe is more time-proof (and shorter) than ...
Tue, 08 Feb 2011 12:05:30 +0000 samuellampa sequencing,NextGenSeq,AGBT (Seems clashes with some music production stuff etc ... )
Tue, 08 Feb 2011 12:04:43 +0000 samuellampa NextGenSeq #AGBT Folks, doesn't need a better hash tag? Some brainstorming? ...or what about the one above?
Mon, 07 Feb 2011 23:03:32 +0000 apfejes AGBT @PeroMHC is always at the same place on Marco Island.
Mon, 07 Feb 2011 22:47:05 +0000 PeroMHC AGBT Where is 2012??
Mon, 07 Feb 2011 22:16:49 +0000 finchtalk AGBT #1kgenome and now a chat Cliff Reed and Eric Schadt. From to Seattle. Luke Timmerman will moderate.
Mon, 07 Feb 2011 20:10:54 +0000 apfejes AGBT @drio Was it George Vacek, poster 214 in the book?
Mon, 07 Feb 2011 19:52:04 +0000 drio #AGBT does anyone remember the name of the company that had the poster about using FPGAs with velvet? or the person that presented.
Mon, 07 Feb 2011 18:23:55 +0000 bachinsky agbt @apfejes Thanks you for tweets
Mon, 07 Feb 2011 17:44:09 +0000 drjonboyg AGBT @apfejes thanks for writing up the sessions, your blog is a great resource.
Mon, 07 Feb 2011 17:39:10 +0000 apfejes AGBT Final thoughts and summary of this year's conference.
Mon, 07 Feb 2011 16:53:24 +0000 JVJAI AGBT @apfejes Thank you so much for your tweets & great meeting notes at
Mon, 07 Feb 2011 16:44:34 +0000 apfejes AGBT You're all welcome for the conf notes, @ntuseem, @ChaunceyGrattan, @genomeresearch, etc! I'm glad you're finding them to be useful!
Mon, 07 Feb 2011 16:31:58 +0000 PMedPartners agbt Check out the @twapperkeeper summary: 272 tweeters!
Mon, 07 Feb 2011 16:05:26 +0000 j3moore AGBT? @drjonboyg @djschlesinger: would you mind sharing what you found so impressive about the BioNanomatrix talk at
Mon, 07 Feb 2011 15:46:44 +0000 genomeresearch AGBT Genome Research back in Cold Spring Harbor. Thanks to all tweeps esp @apfejes @deannachurch @djschlesinger @drjonboyg @girlscientist
Mon, 07 Feb 2011 15:44:04 +0000 finchtalk #AGBT - once again, great conf. See photo for my summary.
Mon, 07 Feb 2011 13:02:10 +0000 deannachurch AGBT @drjonboyg thanks! And thanks to all of the tweeps for great feedback.
Mon, 07 Feb 2011 11:13:16 +0000 drjonboyg AGBT On reflection, a big thanks to @deannachurch and the other organizers, it was an excellent and informative meeting.
Mon, 07 Feb 2011 01:25:21 +0000 girlscientist AGBT Have to give recap of for lab mtg tomorrow. Now going to do it with lighted box on head.
Mon, 07 Feb 2011 00:47:11 +0000 girlscientist AGBT Back home -- thanks tweeps, it was a lot of fun. But snow forecast here tomorrow?!? Take me back to the beach....
Sun, 06 Feb 2011 21:21:38 +0000 deannachurch agbt,hoedown new in Roche sales.
Sun, 06 Feb 2011 19:25:09 +0000 ChaunceyGrattan AGBT @apfejes many thanks for the constant information stream. Future conf attendees should take note of how its done.
Sun, 06 Feb 2011 14:19:26 +0000 deannachurch AGBT,detox,sleep Bye-bye see you next year.
Sun, 06 Feb 2011 13:50:12 +0000 apfejes AGBT Apologies to Dr. Mungall, who's name has now been mispelled with one l all over the internet because I can't spell!
Sun, 06 Feb 2011 01:36:25 +0000 djschlesinger AGBT Are fish tacos traditional cowboy food?
Sun, 06 Feb 2011 01:28:56 +0000 omespeak AGBT The final swag: cowboy hats and bandanas at the dinner.
Sun, 06 Feb 2011 00:46:34 +0000 rforsberg AGBT Thanks for a great conference, see you next year at or see you at Copenhagenomics in June !! -
Sat, 05 Feb 2011 23:00:16 +0000 SOLiDSequencing sequencing #AGBT folks: want to stay up-to-date on @SOLiDSequencing news? Join the SOLiD Community:
Sat, 05 Feb 2011 22:54:34 +0000 SOLiDSequencing AGBT?,PGM Missed @LifeCorporation Triathlon Get the recap: Congrats to @iontorrent winner!
Sat, 05 Feb 2011 21:41:54 +0000 phylogenomics AGBT,sarcasm Basking in my brilliance for starting to track meeting during last talk
Sat, 05 Feb 2011 21:38:11 +0000 deannachurch AGBT Discussion on how people want to see improve. Suggestions?
Sat, 05 Feb 2011 21:37:28 +0000 rdeborja #AGBT last talk is now over. Met lots of people in the cancer genomics field.
Sat, 05 Feb 2011 21:37:15 +0000 phylogenomics AGBT,Experiment Alternative Real Time Twitter Feed for
Sat, 05 Feb 2011 21:37:01 +0000 djschlesinger AGBT Amazing meeting. Many thanks to the organizers. Only suggestion: would like to have had more time for posters.
Sat, 05 Feb 2011 21:35:01 +0000 apfejes AGBT After this talk, maybe Ellen Wright Clayton was right - you can go too far with sequencing!
Sat, 05 Feb 2011 21:32:17 +0000 girlscientist AGBT Schadt suggests we should all hook up PacBio machine to efflux from toilets so we can have health report on house occupants.
Sat, 05 Feb 2011 21:31:59 +0000 dsexton_2 agbt that may have been the scariest scenario ever presented
Sat, 05 Feb 2011 21:30:44 +0000 apfejes AGBT Waiting for announcement that Pac bio has collaborated with google to sequence your DNA as google maps & photographs you...
Sat, 05 Feb 2011 21:28:36 +0000 djschlesinger AGBT Pacific Biosciences SMRT + Illumina SBS = some damn cool data
Sat, 05 Feb 2011 21:27:41 +0000 deannachurch AGBT ES: having success combining Illumina and PacBio data.
Sat, 05 Feb 2011 21:26:32 +0000 phylogenomics AGBT Tracking Advances in Genome Biology & Technology meeting w/ Twitter Widget:
Sat, 05 Feb 2011 21:25:14 +0000 deannachurch AGBT ES: Profiling sewage as a proof of principle, because "Everybody poops".
Sat, 05 Feb 2011 21:22:30 +0000 girlscientist AGBT If you see someone in the airport bathroom looking crazy, it's just Eric Schadt sampling toilet flush handles for sequencing.
Sat, 05 Feb 2011 21:21:53 +0000 girlscientist AGBT Schadt: want to develop real-time disease weather map by viral metagenome sequencing of travel centers etc.
Sat, 05 Feb 2011 21:21:21 +0000 deannachurch AGBT ES: "Disease weather map" surveying viral metagenomes to try to predict outbreaks.
Sat, 05 Feb 2011 21:19:43 +0000 djschlesinger AGBT¬タン Has he taken a breath yet? ¬タワ@girlscientist: @apfejes no one, no one can keep up with Eric Schadt. You have done a great job.
Sat, 05 Feb 2011 21:19:16 +0000 deannachurch rapidfire,sorry,AGBT ES: Maybe the 93 contigs was just from Illumina/454- not sure-
Sat, 05 Feb 2011 21:18:02 +0000 deannachurch AGBT ES: Finishing and layering in Pac Bio- complete genome. 8 contigs >1Kb, 6 contigs covering 99% of genome.
Sat, 05 Feb 2011 21:17:40 +0000 girlscientist AGBT @apfejes no one, no one can keep up with Eric Schadt. You have done a great job.
Sat, 05 Feb 2011 21:17:06 +0000 apfejes finallydefeated,AGBT Cool talk from Pac Bio, but I just can't blog fast enough to keep up with the firehose of data presented.
Sat, 05 Feb 2011 21:16:47 +0000 deannachurch AGBT ES: 244X coverage in 454, Illumina and PacBio to do an assembly: still had 93 contigs after hybrid assembly.
Sat, 05 Feb 2011 21:16:26 +0000 girlscientist AGBT Schadt et al. have gone on from NEJM paper to combine Illumina, PacBio regular, and PacBio strobed sequence reads to complete genomes.
Sat, 05 Feb 2011 21:13:55 +0000 deannachurch AGBT ES: sequence in 90 minutes, then on to the comparative genomes; "quick as serotyping or fingerprinting".
Sat, 05 Feb 2011 21:11:36 +0000 djschlesinger AGBT Eric: Cholera strain to sequence data (on PacBio) to published paper in 4 weeks!!
Sat, 05 Feb 2011 21:07:22 +0000 djschlesinger AGBT @apfejes for long term sustainability, I agree. However I think sugar cane would be ideal to fill an immediate need.
Sat, 05 Feb 2011 21:07:00 +0000 djschlesinger AGBT Eric Schadt from PacBio on rapid pathogen ID.
Sat, 05 Feb 2011 21:06:54 +0000 deannachurch AGBT ES: OK- two minutes in and very cool visualization...
Sat, 05 Feb 2011 21:05:14 +0000 deannachurch AGBT Eric Schadt to end the day: sequencing for impacting health.
Sat, 05 Feb 2011 21:05:10 +0000 girlscientist AGBT Last talk of = Eric Schadt and PacBio's cholera work.
Sat, 05 Feb 2011 21:04:29 +0000 girlscientist AGBT Zhong Wang offers ftp address for data, "if you want to stick your hand in cow rumen and see what you get out." Check JGI site.
Sat, 05 Feb 2011 21:03:36 +0000 SEQanswers agbt Ah the fistulated cow, brings back memories of UC Davis!
Sat, 05 Feb 2011 21:03:18 +0000 apfejes AGBT Notes and thoughts on Zhong Wang's talk on cow gut microbiome + cellulases:
Sat, 05 Feb 2011 21:02:21 +0000 djschlesinger AGBT good point, was thinking biological: @mlb_house: @djschlesinginger or, how about improving solar panels and directly harvesting solar?
Sat, 05 Feb 2011 21:01:39 +0000 apfejes AGBT @djschlesinger Sugar cane still produces a lot of cellulosic waste - it's better to use the cellulose than compete for the glucose.
Sat, 05 Feb 2011 21:00:44 +0000 mlb_house AGBT @djschlesinginger or, how about improving solar panels and directly harvesting solar?
Sat, 05 Feb 2011 20:59:52 +0000 MaliciaRogue AGBT . ¬ルᄏ @genomeresearch: JGI cow rumen metagenome assembly by Velvet
Sat, 05 Feb 2011 20:59:21 +0000 deannachurch AGBT Wang: Doing single cell sequencing to try to validate assemblies from metagenomes.
Sat, 05 Feb 2011 20:57:39 +0000 genomeresearch AGBT JGI cow rumen metagenome assembly by Velvet
Sat, 05 Feb 2011 20:52:51 +0000 djschlesinger AGBT Instead of finding or engineering enzymes to turn cellulose to sugar, why not engineer sugar cane to grow in more temperate climates?
Sat, 05 Feb 2011 20:48:46 +0000 djschlesinger AGBT @apfejes I believe switchgrass yields more energy than corn per equal mass.
Sat, 05 Feb 2011 20:46:11 +0000 deannachurch AGBT @apfejes switchgrass is cheaper to grow- and it is not a human food source so you don't create price competition.
Sat, 05 Feb 2011 20:45:20 +0000 SOLiDSequencing PGM,AGBT Congrats to Adam English, Baylor, winner of @iontorrent sequencer. $10K ($1/total points) goes to Komen for the Cure!
Sat, 05 Feb 2011 20:45:09 +0000 apfejes AGBT Odd that switchgrass was used - it's grows fast, but corn cellulose or other grass stalks are plentiful as a wasteproduct...
Sat, 05 Feb 2011 20:41:17 +0000 deannachurch AGBT Wang: JGI has a cow with a "door" so they can efficiently sample rumen.
Sat, 05 Feb 2011 20:41:10 +0000 SOLiDSequencing AGBT,sequencing @apfejes really enjoying your live blogging (where allowed). Thanks for the great conference notes.
Sat, 05 Feb 2011 20:39:46 +0000 cslamo #AGBT folks stop RTing BS or I'll unfollow everyone!
Sat, 05 Feb 2011 20:36:22 +0000 deannachurch AGBT Zhong Wang: using genomics to address our fuel needs.
Sat, 05 Feb 2011 20:34:18 +0000 apfejes AGBT Rather incomplete notes on Mark Akeson's (movie filled) talk on nanopores:
Sat, 05 Feb 2011 20:33:01 +0000 girlscientist AGBT Next talk: Zhong Wang, JGI, metagenomics of cow rumen. Just published in Science.
Sat, 05 Feb 2011 20:32:24 +0000 girlscientist AGBT Akeson: next steps include seq and re-seq indiv DNA templates, and generating read-lengths signif. longer than industry standards.
Sat, 05 Feb 2011 20:29:16 +0000 nanopore AGBT MA: phi29 high processivity and catalysis rate, animation representing data from JACS paper
Sat, 05 Feb 2011 20:24:40 +0000 nanopore AGBT MA: movie - watching Klenow fragment add bases. Trace showing measurement of ionic current
Sat, 05 Feb 2011 20:23:52 +0000 KamounLab AGBT Link to Lorena Beese's movie "processive DNA synthesis in a polymerase crystal" mentioned by Mark Akeson
Sat, 05 Feb 2011 20:18:10 +0000 nanopore AGBT MA: how to control translocation of ssDNA through a nanopore..add a processive enzyme. up first Klenow fragment
Sat, 05 Feb 2011 20:16:09 +0000 girlscientist AGBT Akeson: group of Jens Gundlach doing promising work on changing over from alpha-hemolysin nanopore to MspA.
Sat, 05 Feb 2011 20:13:45 +0000 nanopore AGBT MA: Bayley group's recognition of bases inc modified bases on a strand
Sat, 05 Feb 2011 20:13:04 +0000 nanopore AGBT MA: in wild type hemolysin, many bases contribute to signal - so engineering of reader heads needed for resolution
Sat, 05 Feb 2011 20:11:42 +0000 djschlesinger AGBT Protein nanopores seem to offer more flexibility that solid state. With mutagenesis, you can get them to do almost anything.
Sat, 05 Feb 2011 20:09:23 +0000 girlscientist AGBT Mark Akeson, UCSC: strand sequencing through nanopores. I am going to defer to @nanopore for tweeting details.
Sat, 05 Feb 2011 20:08:27 +0000 rforsberg agbt Allpaths-lg needs 500 Gb memory to assemble a vertebrate genome
Sat, 05 Feb 2011 20:06:49 +0000 nanopore AGBT MA: reagents: 100ml ocean water and the air we breathe
Sat, 05 Feb 2011 20:05:22 +0000 nanopore AGBT Mark Akeson, UCSC: two types of nanopore DNA seq: exonuclease and strand. His talk about strand
Sat, 05 Feb 2011 20:05:11 +0000 apfejes AGBT Notes on David Jaffe's talk on assembly (allpaths-lg) :
Sat, 05 Feb 2011 20:04:22 +0000 deannachurch AGBT Mark Akeson: on Nanopores!
Sat, 05 Feb 2011 20:04:01 +0000 bffo AGBT Ok boys and girls, I'm out of here! It was a fun meeting, and I enjoyed the tweets, and I like where tweeting will be next year!
Sat, 05 Feb 2011 20:02:14 +0000 deannachurch AGBT @djschlesinger de novo gets you insertions, inversions and translocations too- really is the best way to understand variation.
Sat, 05 Feb 2011 19:59:44 +0000 bffo AGBT Did Jaffe just say: if it is in genbank it must be real? :-)
Sat, 05 Feb 2011 19:59:43 +0000 djschlesinger AGBT de novo assembly identifies things (large deletions only?) not found any other way
Sat, 05 Feb 2011 19:58:33 +0000 girlscientist AGBT Take note kids, that's the pickup line for the hoe-down tonight, "don't you want to fully know my genome?"
Sat, 05 Feb 2011 19:58:08 +0000 girlscientist AGBT Jaffe, We all should be interested in denovo assembly "to fully know a person's genome."
Sat, 05 Feb 2011 19:57:11 +0000 deannachurch AGBT @djschlesinger It is the technical term!
Sat, 05 Feb 2011 19:56:47 +0000 djschlesinger AGBT Is "crappy" a quantitative term
in bioinformatics?
Sat, 05 Feb 2011 19:52:27 +0000 KamounLab AGBT Genome Biol "Analyzing and minimizing bias in Illumina sequencing libraries"
Sat, 05 Feb 2011 19:51:22 +0000 girlscientist AGBT David Jaffe offering detailed comparisons of genome metrics by multiple assembly algorithms. Somebody's gotta do it.
Sat, 05 Feb 2011 19:50:03 +0000 genomeresearch AGBT SOAPdenovo
Sat, 05 Feb 2011 19:49:38 +0000 djschlesinger AGBT Anyone have a copy of "bioinformatics for dummies" that I can borrow?
Sat, 05 Feb 2011 19:48:11 +0000 deannachurch AGBT @girlscientist yes- that is what I heard...
Sat, 05 Feb 2011 19:46:21 +0000 girlscientist AGBT Did David Jaffe just say currently ~1week for 1Gb of genome?
Sat, 05 Feb 2011 19:46:15 +0000 GenomeRef AGBT DJ: AllPathsLG- still needs significant computational power and memory: can assemble about 1G per week.
Sat, 05 Feb 2011 19:46:07 +0000 new299 AGBT ALLPATHS LG running on 512Gb node for human assemblies, ouch + want!
Sat, 05 Feb 2011 19:44:28 +0000 GenomeRef AGBT DJ: Representing variation- recognizing that one path is not representative of biology.
Sat, 05 Feb 2011 19:41:32 +0000 djschlesinger AGBT Jaffe: method to increase read length is to connect 100bp paired end reads with a 3rd overlapping read from data set
Sat, 05 Feb 2011 19:37:50 +0000 deannachurch AGBT DJ: Need both technology improvements and algorithmic improvements to succeed.
Sat, 05 Feb 2011 19:37:36 +0000 djschlesinger AGBT Jaffe: de novo assembly with short reads requires new computational and new laboratory methods.
Sat, 05 Feb 2011 19:37:23 +0000 new299 AGBT ALLPATHS LG using specific lab protocol.
Sat, 05 Feb 2011 19:37:05 +0000 GenomeRef AGBT First up: David Jaffe talking about a subject we love: Genome assemblies!
Sat, 05 Feb 2011 19:36:27 +0000 girlscientist AGBT David Jaffe, Broad Inst: Goal = each new genome is not a research project. Hmmmm.
Sat, 05 Feb 2011 19:32:54 +0000 djschlesinger AGBT David Jaffe (Broad) discussing high quality draft assembly of vert genomes with NGS data
Sat, 05 Feb 2011 19:32:13 +0000 apfejes AGBT yay... more tweeting allowed for all speakers this session!
Sat, 05 Feb 2011 19:32:09 +0000 deannachurch AGBT Last session: "Genomic Frontiers" and all are tweetable!
Sat, 05 Feb 2011 19:11:12 +0000 apfejes AGBT Argh... "we searchable" should be "web searchable" notes. You'd think I'd have some practice typing by now with all that blogging.
Sat, 05 Feb 2011 19:06:47 +0000 apfejes AGBT hah. I need error correction on my tweets about error rats... or a cage to keep them in. thanks @nilshomer
Sat, 05 Feb 2011 19:04:57 +0000 apfejes AGBT @KamounLab As I said, I really enjoyed hearing it, and the blogging part just means I get we searchable notes. (-:
Sat, 05 Feb 2011 19:04:14 +0000 apfejes AGBT Any time I'm within 2m of a windows computer, the wireless becomes unreliable... coincidence?
Sat, 05 Feb 2011 18:56:04 +0000 KamounLab AGBT @apfejes Thanks for live blogging my talk. Was fun to read your notes!
Sat, 05 Feb 2011 18:53:39 +0000 drjonboyg AGBT Off to the airport. Have safe trips home, twitterers.
Sat, 05 Feb 2011 18:39:46 +0000 omespeak AGBT? @nanopore Are you by any chance showing the system at this
Sat, 05 Feb 2011 18:39:26 +0000 halletecco agbt Thank you planning committee for picking such a phenomenal location!
Sat, 05 Feb 2011 18:20:14 +0000 neilhall_uk agbt @djschlesinger I thought I stepped into the wrong meeting?
Sat, 05 Feb 2011 18:15:07 +0000 nanopore AGBT If you didn't see the electronics platform that underlies Oxford Nanopore's single mol sensing: GridION
Sat, 05 Feb 2011 18:13:38 +0000 djschlesinger AGBT Must have walking into wrong room, talk seems to be about ant colonies??
Sat, 05 Feb 2011 18:11:34 +0000 djschlesinger AGBT Late to 454 workshop, don't know who's speaking.
Sat, 05 Feb 2011 17:59:41 +0000 djschlesinger AGBT Modified bases change the kinetics and the subsequent base call.
Sat, 05 Feb 2011 17:58:44 +0000 djschlesinger AGBT Steve back quickly discussing future directions in detecting modified bases.
Sat, 05 Feb 2011 17:52:25 +0000 djschlesinger AGBT Accuracy was improved to 99% with circular coverage, but read length is severely limited.
Sat, 05 Feb 2011 17:50:58 +0000 djschlesinger AGBT Gen-Probe was able to detect variants with 1% frequency with deep resequencing
Sat, 05 Feb 2011 17:49:16 +0000 djschlesinger AGBT 85% accuracy seems fixed, wonder if they've hit the threshold with single molecule sequencing technology.
Sat, 05 Feb 2011 17:43:42 +0000 djschlesinger AGBT Matt Friedenberg from Gen-Probe up next.
Sat, 05 Feb 2011 17:42:29 +0000 djschlesinger AGBT Requires micrograms of starting material. :(
Sat, 05 Feb 2011 17:42:22 +0000 apfejes AGBT did I get that right? Pac Bio has problems with GC, but was that before or after their new chemistry that fixes GC homopolymers
Sat, 05 Feb 2011 17:42:01 +0000 nanopore AGBT pm session starts 2.30, then 3pm Oxford Nanopore collaborator Mark Akeson on his work at UCSC. Focus: translocation of ssDNA thru pore
Sat, 05 Feb 2011 17:41:43 +0000 djschlesinger AGBT Bias summary: No amplification bias, but limited coverage bias.
Sat, 05 Feb 2011 17:40:31 +0000 djschlesinger AGBT coverage is consistently random across genome, but dips a bit in higher GC genomes
Sat, 05 Feb 2011 17:38:07 +0000 djschlesinger AGBT Accuracy does not decrease with read length, 85% accuracy holds out to 6kb.
Sat, 05 Feb 2011 17:36:57 +0000 djschlesinger AGBT JGI observed no GC bias out to ~85% GC
Sat, 05 Feb 2011 17:36:46 +0000 apfejes AGBT,makessense Interesting changes in Pac Bio's story this year: lower accuracy is acceptable - use platform in combination with others.
Sat, 05 Feb 2011 17:35:55 +0000 djschlesinger AGBT JGI confirms average 1.5kb read length, with longer reads out to 6kb!
Sat, 05 Feb 2011 17:33:03 +0000 djschlesinger AGBT Len Pennacchio (JGI) talking about closing gaps is microbial genome sequences with PacBio platform
Sat, 05 Feb 2011 17:27:31 +0000 djschlesinger AGBT higher error rates are tolerated better when mapping longer reads (>500kb)
Sat, 05 Feb 2011 17:25:26 +0000 djschlesinger AGBT 1Kb read with 10% error maps like a 740bp read
Sat, 05 Feb 2011 17:24:14 +0000 djschlesinger AGBT Couldn't find an alignment algorithm what could support long read lengths with indels, so the designed their own
Sat, 05 Feb 2011 17:21:30 +0000 djschlesinger AGBT Single molecule sequencing platforms dominated by insertion/deletion errors. As expected.
Sat, 05 Feb 2011 17:16:54 +0000 djschlesinger AGBT John Sorenson (PacBio) discussing informatics of their recent Cholera project
Sat, 05 Feb 2011 17:15:03 +0000 djschlesinger AGBT Commercial release expected to have 35-45Mb of mappable data
Sat, 05 Feb 2011 17:13:18 +0000 djschlesinger AGBT Will have an output of 22Mb per run
Sat, 05 Feb 2011 17:12:19 +0000 girlscientist AGBT At PacBio workshop.
Sat, 05 Feb 2011 17:11:49 +0000 djschlesinger AGBT PacBio machine will have average 1.5kb reads on commercial release, with 85% accuracy
Sat, 05 Feb 2011 17:10:02 +0000 djschlesinger AGBT 3rd gen single molecule platforms will have inherently higher error compared to 2nd gen, which looks at an average over many molecules
Sat, 05 Feb 2011 17:06:10 +0000 djschlesinger AGBT Steve Turner up discussing recent advances in PacBio technology.
Sat, 05 Feb 2011 17:02:53 +0000 djschlesinger AGBT Farewell to those Tweeps departing today. Hope you make it back safe and on time. Was a pleasure Tweeting with you.
Sat, 05 Feb 2011 16:57:19 +0000 djschlesinger AGBT Pacific Biosciences workshop about to start, hoping to see some real data!
Sat, 05 Feb 2011 16:54:48 +0000 suganthibala AGBT. Thanks to all tweeters from the forbidden zone :)
Sat, 05 Feb 2011 16:54:00 +0000 omespeak AGBT
Where the conference attendees spend time when not at a session:
Sat, 05 Feb 2011 16:51:58 +0000 omespeak AGBT Where the conference attendees spend time when not at a session:
Sat, 05 Feb 2011 16:50:41 +0000 apfejes AGBT We're slowly coming to the end of the talks, with only a few more to go this aft, but thanks to everyone for the RTs!
Sat, 05 Feb 2011 16:47:26 +0000 apfejes AGBT Notes on AGBT talk: Sophien Kamoun on potato pathogens:
Sat, 05 Feb 2011 16:37:08 +0000 dwmohr AGBT Wondering what/who will repopulate my microbiome once I'm done my antibiotics
Sat, 05 Feb 2011 16:19:24 +0000 omespeak AGBT Interesting variety of talks this morning: from gut micobiome to potato famine pathogens.
Sat, 05 Feb 2011 16:18:14 +0000 new299 AGBT Am I allowed to take pictures of drawings of slides?
Sat, 05 Feb 2011 16:17:14 +0000 apfejes AGBT Notes on James Giovannoni's talk on the Tomato Genome:
Sat, 05 Feb 2011 16:09:02 +0000 drjonboyg AGBT Apparently several people saw my name in one of John Oliver's (NABsys) slides. No idea how, wonder if he'd give me a copy?
Sat, 05 Feb 2011 16:06:20 +0000 drjonboyg AGBT @nanopore well, I was at that talk so I really should have noticed it was Gundlach and not Akeson! Will follow the talk at the airport
Sat, 05 Feb 2011 16:06:06 +0000 bffo AGBT James Giovannoni talking about closing gaps with ngs data, referee to IMAGE software
Sat, 05 Feb 2011 16:03:45 +0000 GenomeRef AGBT JG: working to make a 'gold standard' tomato genome!
Sat, 05 Feb 2011 16:02:13 +0000 nanopore AGBT @dijonboyg @omespeak Jens Gundlach spoke Thursday (as you say MspA pores) and Mark Akeson was moved to Sat.
Sat, 05 Feb 2011 15:59:11 +0000 drjonboyg AGBT @nanopore @omespeak Akeson also spoke on Thursday, didn't he? (MspA pores).
Sat, 05 Feb 2011 15:55:42 +0000 drjonboyg AGBT I think there might be a candidate for LATFH here at (although he maybe saying the same thing about me)
Sat, 05 Feb 2011 15:55:38 +0000 GenomeRef AGBT James Giovannoni talking about sequencing the tomato genome. Started BAC by BAC, now adding NGS
Sat, 05 Feb 2011 15:54:52 +0000 omespeak AGBT After Rob Knight's talk this morning, am wondering what microbes get transferred to my fingers when using a public computer.
Sat, 05 Feb 2011 15:48:31 +0000 apfejes AGBT We've been reminded that photography of slides is not allowed - but does U2 count?
Sat, 05 Feb 2011 15:44:39 +0000 new299 AGBT U2 at
Sat, 05 Feb 2011 15:38:12 +0000 drjonboyg AGBT Although actually it's not even from @nanopore ()
Sat, 05 Feb 2011 15:35:20 +0000 apfejes AGBT For entertainment, some analytics data for my blog during season:
Sat, 05 Feb 2011 15:34:59 +0000 drjonboyg AGBT Rather bummed that the only talk I have any interest in seeing today (@nanopore) is on after I need to head to the airport.
Sat, 05 Feb 2011 15:23:23 +0000 KirstinWrites AGBT @drjonboyg I'm not at the conference ... but I agree with the statement.
Sat, 05 Feb 2011 15:11:49 +0000 omespeak AGBT Baylor U heavily invested solving the viral metageome of Elephant Herpes Virus as a step towards cure.
Sat, 05 Feb 2011 15:11:47 +0000 girlscientist AGBT Both Knight & Petrosino agreed with audience Q that w/their strategies, we'd miss viral/bacterial genomes w/weird, non-seq'able bases.
Sat, 05 Feb 2011 15:11:39 +0000 apfejes AGBT Notes on Joseph Petrosino's talk on Viral metagenomics:
Sat, 05 Feb 2011 15:09:46 +0000 omespeak AGBT Practical application of viral metagenomics: develop therapy for Elephant Herpes virus that kills Asian baby elephants.
Sat, 05 Feb 2011 15:09:25 +0000 drjonboyg AGBT One more good use of twitter at conferences: an excellent way of meeting people.
Sat, 05 Feb 2011 15:08:42 +0000 obahcall AGBT Petrosino: Virus protocol is able to differentiate stool and nasal wash samples. We can tell our nose from our rear.
Sat, 05 Feb 2011 15:05:54 +0000 omespeak AGBT How to tell the difference between your nose & other end? Different virus exist in stool & nasal washes -J Petrosino.
Sat, 05 Feb 2011 15:05:29 +0000 new299 AGBT Nose v arse detection via microbiome sequencing
Sat, 05 Feb 2011 15:05:24 +0000 girlscientist AGBT Sorry tweeps wifi just died so radio silence ensuing.
Sat, 05 Feb 2011 15:04:34 +0000 bffo AGBT JP "pretty cool that the phage can tell you which bacteria re there"
Sat, 05 Feb 2011 15:02:44 +0000 new299 AGBT Random primers for looking at microbiome...
Sat, 05 Feb 2011 15:01:31 +0000 obahcall AGBT Petrosino: What does your poo tell you? Looking at representation of DNA/RNA virsues in stool.
Sat, 05 Feb 2011 14:58:23 +0000 obahcall AGBT Joseph Petrosino: Overview of NIH¬タルs Human microbiome project, showing bacterial communities differ at different body sites.
Sat, 05 Feb 2011 14:57:28 +0000 bffo AGBT HMP data is so fresh, it is "dripping wet" JP
Sat, 05 Feb 2011 14:56:24 +0000 obahcall AGBT Knight: Shows a memorable visualization following the distribution of bacteria across human face.
Sat, 05 Feb 2011 14:56:13 +0000 girlscientist AGBT Joe Petrosino showing figure of vaginal viral microbiomes, with two different collection methods called "swab" & "broom." Eek.
Sat, 05 Feb 2011 14:55:29 +0000 bffo AGBT,HMP @girlscientist what about the biofilm on my iPad?
Sat, 05 Feb 2011 14:52:34 +0000 bffo AGBT Joe Petrosino gave intro to NIH's Human Microbiome project and also viruses ...
Sat, 05 Feb 2011 14:52:33 +0000 girlscientist AGBT [now paranoid about pushing my glasses up on my nose and introducing fingertip bacteria to site.]
Sat, 05 Feb 2011 14:48:05 +0000 girlscientist AGBT J Petrosino: human microbiome project, multiple sides probed in ¬タワworst doctor¬タルs appointment ever¬タン for subjects.
Sat, 05 Feb 2011 14:47:12 +0000 obahcall AGBT Rob Knight: Overview microbiome studies, open microbiome initiative, partnership with Gates for pers medicine in developing nations.
Sat, 05 Feb 2011 14:45:34 +0000 omespeak AGBT Joseph Petrosino: very hard to follow a talk that is probably trending on twitter.
Sat, 05 Feb 2011 14:42:55 +0000 omespeak AGBT Very entertaining talk by R Knight on microbiome diversity, especially his digression into the Onion-like NGS techniques too look for.
Sat, 05 Feb 2011 14:42:00 +0000 apfejes AGBT Notes on Rob Knight's talk on the Human Microbiome:
Sat, 05 Feb 2011 14:41:41 +0000 new299 AGBT Microbiome and genetics linked in fat mice
Sat, 05 Feb 2011 14:39:53 +0000 girlscientist AGBT Rob Knight mentions Open Microbiome Initative,
Sat, 05 Feb 2011 14:38:18 +0000 omespeak AGBT Personalized medicine in developing nations based on microbial diversity?
Sat, 05 Feb 2011 14:33:57 +0000 girlscientist AGBT R Knight: lovely visualizations of which bacteria are on which parts of the face, but this reveals subject's habits, shall we say.
Sat, 05 Feb 2011 14:32:20 +0000 omespeak AGBT Just born babies have different microbiomes depending on normal vs c-section birth.
Sat, 05 Feb 2011 14:30:26 +0000 omespeak AGBT Wow! the biogeography of the human face is varied too, but symmetrical.
Sat, 05 Feb 2011 14:27:10 +0000 omespeak AGBT Microbiome habitats are very different in different parts of the body; also changes with time. Rob Knight
Sat, 05 Feb 2011 14:24:57 +0000 SEQanswers agbt Hopefully someone is capturing Rob Knights jokes, they are great and I can't type that fast
Sat, 05 Feb 2011 14:24:46 +0000 girlscientist AGBT Rob Knight certainly a comedian. Treating us to four proposed sequencing technologies to work out for, including unicorns.
Sat, 05 Feb 2011 14:22:51 +0000 omespeak AGBT Rob Knight: why is it called 454? It's the temp at which money burns for sequencing. :)
Sat, 05 Feb 2011 14:20:47 +0000 omespeak AGBT Micriobiomes in extreme environments are interestingly not outliers.
Sat, 05 Feb 2011 14:17:45 +0000 girlscientist AGBT Rob Knight: his keyboard microbiome study published in PNAS but then featured on CSI: Miami ¬タワso you really know it¬タルs true.¬タン
Sat, 05 Feb 2011 14:16:36 +0000 omespeak AGBT Rob Knight: each of us have an unique microbiome on fingertips that is transferred to computer keys.
Sat, 05 Feb 2011 14:13:54 +0000 girlscientist AGBT Rob Knight, UC Boulder: Problem of microbiome sequencing = get big phylogenetic trees which are hard to understand and analyze.
Sat, 05 Feb 2011 14:09:24 +0000 omespeak AGBT Rob Knight: Microbial symbionts are like unique snowflakes ie more varied than human genes.
Sat, 05 Feb 2011 14:07:35 +0000 djschlesinger AGBT Need a break, will pick up after lunch.
Sat, 05 Feb 2011 14:06:28 +0000 djschlesinger AGBT @mbcf, 8 hrs from sample to data, 5min per base, ALL reagents in single cartridge, no cBot or PE module needed, possible 510k approval
Sat, 05 Feb 2011 14:03:05 +0000 apfejes AGBT Yay! All four presenters this morning can be tweeted/blogged.
Sat, 05 Feb 2011 13:53:01 +0000 apfejes AGBT If anyone lost a pair of glasses last night, it's been turned in to reception. (but can you read this tweet?)
Sat, 05 Feb 2011 13:38:46 +0000 mbcf AGBT. Wake Up MiSeq: just a HiSeq Mini Me or something more? Blog on what you think is so clever about this box. "I want one." And ...
Sat, 05 Feb 2011 07:24:00 +0000 SOLiDSequencing PGM,AGBT Adam English of Baylor wins @iontorrent sequencer @ @LifeCorporation Triathlon. Congrats, Adam!
Sat, 05 Feb 2011 06:25:45 +0000 davcraig #AGBT
Sat, 05 Feb 2011 05:09:56 +0000 drjonboyg AGBT @genomicslawyer @lukejostins @mndoci in defense, it's not a default no tweet policy, its up to individual speakers.
Sat, 05 Feb 2011 04:42:14 +0000 drjonboyg AGBT OK, really going to bed now.
Sat, 05 Feb 2011 04:36:57 +0000 LIFECorporation AGBT Adam English of Baylor College of Medicine wins the PGM at the Life Technology Triathlon at Congrats!
Sat, 05 Feb 2011 03:34:49 +0000 girlscientist AGBT Mini tweetup with @deannachurch and @bffo in lobby bar. Stop by!
Sat, 05 Feb 2011 03:18:34 +0000 drjonboyg AGBT Calling it a night. Here's a video of the beach fireworks to keep you occupied.
Sat, 05 Feb 2011 01:53:55 +0000 apfejes AGBT Neat mechanism of disease in the Clinical Sequencing session, but I can't talk about it. DOH! only 56 people get to hear about it.
Sat, 05 Feb 2011 01:52:29 +0000 omespeak AGBT Last talk of the day on Cloud solutions for genomic data storage/transfer. Not doing the answer is 'cloudy since we can't tweet' jokes
Sat, 05 Feb 2011 01:52:26 +0000 dsexton_2 #agbt The Broad is testing their pipelines on Amazon. They will be optimizing Picard for the cloud.
Sat, 05 Feb 2011 01:45:45 +0000 drjonboyg AGBT There seem to be a certain irony in someone presenting on cloud computing but not allowing social media.
Sat, 05 Feb 2011 01:36:46 +0000 apfejes AGBT Notes on Praveen Cherukuri's talk on allele specific expression
Sat, 05 Feb 2011 01:26:02 +0000 dsexton_2 #agbt everyone needs to "value add" for their cores.
Sat, 05 Feb 2011 01:24:55 +0000 SEQanswers AGBT,badbatterylifebutwhocares During this break...I must express that I have a severe case of Macbook Air envy. I'm surrounded by them.
Sat, 05 Feb 2011 01:20:08 +0000 apfejes AGBT Notes from Kateryna Makova's excellent talk on Mitochondria heteroplasmy
Sat, 05 Feb 2011 01:18:41 +0000 dwmohr core,AGBT Why is 'core' not enough? ++
Sat, 05 Feb 2011 01:07:37 +0000 drjonboyg AGBT Is nuclear transfer from one oocyte to another even legal? Seems like the sort of thing bioconservatives freak out over.
Sat, 05 Feb 2011 01:02:46 +0000 deannachurch fail,agbt Session chair
Sat, 05 Feb 2011 00:58:28 +0000 girlscientist AGBT Marc Allard, FDA: no tweetability announced so will just say that the man clearly has difficult problems to solve. Cheers to him.
Sat, 05 Feb 2011 00:54:43 +0000 new299 AGBT Baylor sequencers + 3 ion torrent + Pacbio.
Sat, 05 Feb 2011 00:53:25 +0000 Mikegenome agbt Did I read that right that 6 illuminas = 30 SOLiDs at Baylor? Musny
Sat, 05 Feb 2011 00:47:32 +0000 new299 AGBT More ion torrent error rates, lots of things less than Q17?
Sat, 05 Feb 2011 00:41:31 +0000 SOLiDSequencing PGM!,AGBT In it to win it? Anyone could go home w/ the @iontorrent @LifeCorporation Triathlon NOW (5-9 pm), Suite 1106.
Sat, 05 Feb 2011 00:40:14 +0000 new299 AGBT Ion torrent run reports
Sat, 05 Feb 2011 00:37:21 +0000 apfejes AGBT Notes on Daniel Neafsey's talk on sequencing parasite genomes:
Sat, 05 Feb 2011 00:36:15 +0000 drjonboyg AGBT Horrible AV feedback in the clinical session.
Sat, 05 Feb 2011 00:33:18 +0000 djschlesinger AGBT Joe Boland from NCI is wearing a t-shirt that says "Tweet Me" in huge letters. Speaking on Ion Torrent's PGM.
Sat, 05 Feb 2011 00:32:09 +0000 SEQanswers AGBT Boland: Giant T-shirt "TWEET ME"
Sat, 05 Feb 2011 00:29:23 +0000 girlscientist AGBT Neafsey and Broad colleagues make their own whole genome bait oligos from malaria parasite DNA.
Sat, 05 Feb 2011 00:25:09 +0000 new299 AGBT I vote that all simulated data has this banner from now on
Sat, 05 Feb 2011 00:23:11 +0000 new299 AGBT Errr that looks weird, polyC artefact reads?
Sat, 05 Feb 2011 00:22:20 +0000 girlscientist AGBT Daniel Neafsey, Broad: sequencing of pathogen genomes from human clinical samples, without culturing them.
Sat, 05 Feb 2011 00:21:03 +0000 new299 AGBT Thinks after fiddlings as good as PCR free
Sat, 05 Feb 2011 00:20:29 +0000 apfejes AGBT Nice talk by Matthew Bainbridge, (Clinical seq session), but same (untwitterable) story told by others. Missed the twitter status too
Sat, 05 Feb 2011 00:17:03 +0000 new299 AGBT Effect of Pcr on GC bias
Sat, 05 Feb 2011 00:14:40 +0000 girlscientist AGBT The elevators made me a minute late so I missed what the lovely @deannachurch announced about tweeting policy in her clinical session.
Fri, 04 Feb 2011 23:40:10 +0000 SOLiDSequencing PGM!,AGBT It's a tight race... anyone could go home w/ the @iontorrent @LifeCorporation Triathlon 5-9 pm, Suite 1106.
Fri, 04 Feb 2011 23:15:00 +0000 drjonboyg AGBT Just watched the sun set over the ocean. Haven't been able to do that since I lived in Encinitas.
Fri, 04 Feb 2011 23:10:14 +0000 ChaunceyGrattan HiSeq2000.,agbt @Lyro20 re: David Bently & 1Tbp from How did they increase output? increased cluster density?
Fri, 04 Feb 2011 22:55:46 +0000 djschlesinger AGBT Just got to check out the MiSeq in person. The design was thoroughly thought out. An amazing instrument! Can't wait to get one!
Fri, 04 Feb 2011 22:07:28 +0000 bioinfosm AGBT Broad Institute is seemingly devoting 42 CPUs to processing data from each of its HiSeqs - heard from
Fri, 04 Feb 2011 21:37:57 +0000 Lyro20 AGBT¬タン #Norseqcenter ¬タワDavid Bentley: illumina HiSeq2000 exceeding 1 TERABASE sequence/run (up from 200 Gb launch spec 12 months ago).
Fri, 04 Feb 2011 21:36:10 +0000 SOLiDSequencing SOLiD,AGBT. @LifeCorporation Workflow Automation: AB Library Builder featured at
Fri, 04 Feb 2011 21:28:53 +0000 SOLiDSequencing http://t CE,sequencing,AGBT @LifeCorporation 3500 Genetic Analyzer, gold standard in capillary electrophoresis.
Fri, 04 Feb 2011 21:26:09 +0000 SOLiDSequencing SOLiD,AGBT,sequencing 5500 Series Sequencer featured in @LifeCorporation Suite at
Fri, 04 Feb 2011 21:11:51 +0000 apfejes AGBT Notes from Ion Torrent Talk ... off to the tweetup! See you there
Fri, 04 Feb 2011 21:11:42 +0000 SOLiDSequencing AGBT,sequencing Introducing... the @iontorrent PGM¬トᄁ sequencer, "Personal Genome Machine".
Fri, 04 Feb 2011 21:11:34 +0000 KamounLab AGBT Chad Nusbaum on Ion Torrent: very low GC bias with E. coli, accuracy uniform too, less bias than other technologies
Fri, 04 Feb 2011 21:10:04 +0000 SEQanswers AGBT @drjonboyg @apfejes IonT/Broad talk still going on.
Fri, 04 Feb 2011 21:08:29 +0000 apfejes AGBT. @drjonboyg Talk should be over in a couple minutes, and several of us will be there
Fri, 04 Feb 2011 21:06:50 +0000 drjonboyg AGBT @apfejes I think I'm the only person here.
Fri, 04 Feb 2011 21:06:40 +0000 KamounLab AGBT Chad Nusbaum on Ion Torrent applications: mutation validation, targeted resequencing, QC nextgen libraries, resequencing microbes...
Fri, 04 Feb 2011 21:00:04 +0000 djschlesinger AGBT Chad Nusbaum (Broad) about to show some new Ion Torrent data.
Fri, 04 Feb 2011 20:57:30 +0000 SOLiDSequencing AGBT @LifeCorporation Triathlon REGISTRATION: BE THERE Fri. 5-9pm Suite 1106!
Fri, 04 Feb 2011 20:55:43 +0000 SOLiDSequencing AGBT Scores R tight 4 Triathlon - points R high tonight so U could come back & steal the lead!!! BE THERE: Fri. 5-9pm Suite 1106!
Fri, 04 Feb 2011 20:50:52 +0000 apfejes AGBT Tweetup @4pm in poster room by computers - I'll be 10 minutes late for Ion Torrent Talk, but hope to see everyone there.
Fri, 04 Feb 2011 20:41:03 +0000 bioitworld AGBT Moore's Law, what Law? David Bentley: illumina HiSeq2000 exceeding 1 TERABASE sequence/run (up from 200 Gb launch spec 12 months ago).
Fri, 04 Feb 2011 20:39:04 +0000 drjonboyg AGBT This sure beats being at work. Wait a minute, this *is* work!
Fri, 04 Feb 2011 20:32:03 +0000 apfejes AGBT Notes on Tim Yu's talk on autism:
Fri, 04 Feb 2011 20:25:32 +0000 SOLiDSequencing AGBT @iontorrent Workshop NOW: Fri. 3:30-4:00 pm in ISLAND BALLROOM, Chad Nusbaum of Broad Inst.
Fri, 04 Feb 2011 20:22:57 +0000 delahar 1000g,Illumina?,AGBT By my count 90% of the sequence has been done by Is there a viable challenger?
Fri, 04 Feb 2011 20:22:01 +0000 omespeak AGBT Anyone knows if Oxford Nanopore is presenting anything at their suite?
Fri, 04 Feb 2011 20:14:35 +0000 apfejes AGBT @deannachurch Fantastic - we may all be a bit late, if talks run over.
Fri, 04 Feb 2011 20:12:18 +0000 omespeak AGBT No autism gene but genes; WGS + linkage analysis should help in identifying such heterogeneous diseases. - Tim Yu
Fri, 04 Feb 2011 20:11:43 +0000 djschlesinger AGBT @girlscientist Yes, but does that itself mean? Seems rather ambiguous. How can you do association studies without a clear phenotype?
Fri, 04 Feb 2011 20:11:34 +0000 girlscientist AGBT Are there other fields which use the term "bake-off" as much as genomics?
Fri, 04 Feb 2011 20:10:04 +0000 Awesomics genome,sequencing #AGBT update from @gw_dailyscan:
Fri, 04 Feb 2011 20:09:34 +0000 SEQanswers AGBT TimYu: Two great examples of disorders presenting as autism, revealed as something else by WGS by @CompleteGenomic
Fri, 04 Feb 2011 20:08:08 +0000 girlscientist AGBT @djschlesinger he clarified that they use "the autisms" as there are many different spectra under one umbrella.
Fri, 04 Feb 2011 20:03:02 +0000 finchtalk #AGBT Tim Yu. Nice picture, each complete genomics sequence eliminates an excursion into the weeds of open source tools.
Fri, 04 Feb 2011 19:56:53 +0000 djschlesinger AGBT Tim Yu discussing genetics of Autism Spectral disorders. Maybe I missed it, but was Autism defined?
Fri, 04 Feb 2011 19:48:35 +0000 finchtalk #AGBT illumina talk. The spectrum of sequencing technology. Nice representation of throughput, turn around time, instruments. The future
Fri, 04 Feb 2011 19:47:22 +0000 apfejes AGBT. Bloggable notes on David Bently's talk (Illumina)
Fri, 04 Feb 2011 19:46:11 +0000 Copenhagenomics AGBT Thanks to @rforsberg for the mention of our non-profit genomics conference in at - appreciate it! :-)
Fri, 04 Feb 2011 19:39:12 +0000 KamounLab espresso.,AGBT Thank you @CompleteGenomic for the Was much needed!
Fri, 04 Feb 2011 19:37:55 +0000 girlscientist AGBT @SEQanswers just barely! ;)
Fri, 04 Feb 2011 19:35:36 +0000 SEQanswers AGBT @girlscientist At least it's cheaper than 6 million dollars...
Fri, 04 Feb 2011 19:31:56 +0000 djschlesinger AGBT I want a MiSeq!!
Fri, 04 Feb 2011 19:31:27 +0000 girlscientist AGBT David Bentley of Illumina: we have made sequencing better, stronger, faster. [I paraphrase but you get the gist.]
Fri, 04 Feb 2011 19:27:57 +0000 djschlesinger AGBT David Bentley from Illumina discussing clinical sequencing. Tweeting OK sans patient data
Fri, 04 Feb 2011 19:26:51 +0000 SEQanswers AGBT @djschlesinger 12 channel pippin prep in development....!!
Fri, 04 Feb 2011 19:24:06 +0000 apfejes AGBT. @SEQanswers Ironic that the vendors have the most sane twittering policy... or perhaps not.
Fri, 04 Feb 2011 19:22:44 +0000 girlscientist AGBT MT @apfejes: Tweetup (to discuss policy): 4pm, Poster Room in the corner with the computers by the door. Hope to see you there!
Fri, 04 Feb 2011 19:22:39 +0000 djschlesinger AGBT¬タン Just wish it could run more than 4 samples, 12 would be nice: ¬タワ@SEQanswers: Pippin prep 10kb automated gel isolation in 1.5h. Want.
Fri, 04 Feb 2011 19:20:43 +0000 SEQanswers AGBT Pippin prep 10kb automated gel isolation in 1.5h. Want.
Fri, 04 Feb 2011 19:17:34 +0000 djschlesinger AGBT¬タン Touchᅢᄅ: ¬タワ@SEQanswers: Everyone gushing onafternoon tweeting policy: It's a commercial session! ;)
Fri, 04 Feb 2011 19:16:17 +0000 SEQanswers AGBT Everyone gushing onafternoon tweeting policy: It's a commercial session! ;)
Fri, 04 Feb 2011 19:15:50 +0000 apfejes AGBT Tweetup: 4pm, Poster Room in the corner with the computers by the door. Hope to see you there!
Fri, 04 Feb 2011 19:15:16 +0000 trutane genome,sequencing #AGBT update from @gw_dailyscan:
Fri, 04 Feb 2011 19:14:37 +0000 apfejes doingitright,AGBT Impressed with granularity in tweeting policy in afternoon sessions: don't tweet patient data when discussed.
Fri, 04 Feb 2011 19:14:12 +0000 girlscientist AGBT @apfejes tweetups seem to work best when you name a very specific place. First night's was bust bc reception was too big.
Fri, 04 Feb 2011 19:13:22 +0000 djschlesinger AGBT Chris Boles from Sage showing off the Pippin Prep for automated size selection for NGS library prep
Fri, 04 Feb 2011 19:11:04 +0000 omespeak AGBT Slightly improved tweeting policy for this session: free to blog/tweet except for where patient/clinical info is discussed.
Fri, 04 Feb 2011 19:05:56 +0000 SOLiDSequencing AGBT @neilhall_uk You just might - you're currently in the lead: - good luck!
Fri, 04 Feb 2011 19:02:51 +0000 neilhall_uk agbt Stephan Schuster showing very nice ion torrent data....I hope I win one tonight
Fri, 04 Feb 2011 19:02:35 +0000 apfejes AGBT Partial notes on Eric Boerwinkle's talk
Fri, 04 Feb 2011 19:00:12 +0000 apfejes AGBT Anyone intersted in tweetup @4pm, after talks? Would be nice to present unified feedback to conference organizers.
Fri, 04 Feb 2011 18:54:59 +0000 finchtalk #AGBT Steven Schuster. Helico bacter, is a genome from hell. Doing pilots on ion torrent.
Fri, 04 Feb 2011 18:53:56 +0000 SOLiDSequencing AGBT @iontorrent Workshop Fri. 3:30-4:00 pm ISLAND BALLROOM, Chad Nusbaum of Broad Inst.
Fri, 04 Feb 2011 18:49:43 +0000 SEQanswers AGBT,caffeinated @lukejostins with 12.5 hours of talks per day...they are essential
Fri, 04 Feb 2011 18:44:29 +0000 SageScience1 Sage Science Workshop 2:00pm Island Ballroom. Whats new with the Pippin Prep? Come check it out!#AGBT
Fri, 04 Feb 2011 18:42:24 +0000 lukejostins #AGBT must be pretty hectic for both @NEBiolabs and @CompleteGenomic to both decide "pick-me-ups" are the big sell
Fri, 04 Feb 2011 18:39:23 +0000 obahcall AGBT C Bustamante: Differences in ancestry switching between individuals, likely related to diffs in demographic history of MEX and ASW.
Fri, 04 Feb 2011 18:33:58 +0000 SOLiDSequencing AGBT #FF @LifeCorporation @SOLiDSequencing @iontorrent @Grand_Challenge
Fri, 04 Feb 2011 18:33:41 +0000 obahcall AGBT Carlos Bustamante: Importance studying transethnic populations, discusses sequencing of genome of 2 individs, AA and MEX ancestry
Fri, 04 Feb 2011 18:28:46 +0000 SOLiDSequencing PGM,AGBT You can still enter @LifeCorporation Triathlon & play to win @iontorrent sequencer:
Fri, 04 Feb 2011 18:25:17 +0000 SOLiDSequencing AGBT For @LifeCorporation events, visit from your mobile device.
Fri, 04 Feb 2011 18:22:00 +0000 SEQanswers AGBT Bustamente is a great enthusiastic speaker. Think Jack Black does worldwide admixture pop gen
Fri, 04 Feb 2011 18:20:16 +0000 Mikegenome agbt Na18507 na19240 na12878 used in Bustamante analysis of novel variants
Fri, 04 Feb 2011 18:08:12 +0000 sdcrosby AGBT On behalf of those of us still in the cold, thank you so much to all you tweeters!!
Fri, 04 Feb 2011 18:06:20 +0000 finchtalk #agbt life tech lunch. Interesting how short the life cycles are for sequencing instruments.
Fri, 04 Feb 2011 17:46:42 +0000 kmjones96 #AGBT
Fri, 04 Feb 2011 17:43:38 +0000 ChaunceyGrattan agbt How are samples labeled for BioNanomatrix NanoAnalyzer analysis?
Fri, 04 Feb 2011 17:40:05 +0000 SOLiDSequencing PGM #AGBT @LifeCorporation Triathlon Scores - LEADER in contest to win @iontorrent sequencer is...
Fri, 04 Feb 2011 17:37:58 +0000 SOLiDSequencing AGBT @LifeCorporation Lunch/Workshop Now 12-2 pm PALM ROOM: Sequencing Gets Personal. 5 Amazing Speakers - don't miss it!
Fri, 04 Feb 2011 17:00:40 +0000 KamounLab AGBT Primer Extension Capture (PEC) used to enrich 40K-fold heavily degraded Neanderthal mtDNA
Fri, 04 Feb 2011 16:57:38 +0000 girlscientist AGBT Much of Richard Green talk on Neandertals so far has been published. Still interesting but less tweetable.
Fri, 04 Feb 2011 16:56:58 +0000 drjonboyg AGBT This makes a good companion piece to the current talk on extinct hominid genomes:
Fri, 04 Feb 2011 16:55:01 +0000 finchtalk #AGBT RG. majority of sequences from neaderthal bone (~83%) match nothing in the DBs, others microbes, but get enough to seq the genome
Fri, 04 Feb 2011 16:53:31 +0000 owen_w agbt @deannachurch Thanks I'm sure a copacetic policy can get put together.
Fri, 04 Feb 2011 16:52:46 +0000 obahcall AGBT E Boerwinkle: Progressing from GWAS to medical resequencing to experimental systems to clinical epidemiology, with egs from ERIC.
Fri, 04 Feb 2011 16:47:45 +0000 SEQanswers AGBT Gout effect SNP rs2231142 (in urate transporter ABCG2) is in 23andMe. Just checked cool
Fri, 04 Feb 2011 16:47:12 +0000 finchtalk #AGBT Richard Green, evolution from extinct hominids. What can we learn from the dead?
Fri, 04 Feb 2011 16:45:23 +0000 djschlesinger AGBT Richard Green (UCSC) up next. No stated Tweeting policy, however from UC, so probably open to Tweeting.
Fri, 04 Feb 2011 16:43:09 +0000 genomicslawyer AGBT, At @GenomeQuest announces clinical diagnostic/analysis platform for whole-genomes/exomes:
Fri, 04 Feb 2011 16:42:41 +0000 KamounLab AGBT "Waiting for the (#Genomic) Revolution" in Science this week /via @EricTopol @GenomeScience
Fri, 04 Feb 2011 16:42:19 +0000 deannachurch AGBT @owen_w Message heard and I will bring this up with the other members of the committee.
Fri, 04 Feb 2011 16:40:07 +0000 girlscientist AGBT E Boerwinkle: "gout is the Rodney Dangerfield of diseases."
Fri, 04 Feb 2011 16:36:11 +0000 apfejes AGBT Counterpoint, but not really differnt MT @owen_w: commentary on blogging policy.
Fri, 04 Feb 2011 16:31:14 +0000 larry_parnell AGBT Thanks to all Bloggers/Tweeps! Please keep discussing great work of those who allow & ignoring those who wish 2 stay w/in 4 walls
Fri, 04 Feb 2011 16:26:52 +0000 owen_w #agbt My commentary on the blogging policy.
Fri, 04 Feb 2011 16:17:37 +0000 seqcentral #agbt folks: any chance of you all having an "informal formal" discussion on tweeting/blogging policy for *future* conferences?
Fri, 04 Feb 2011 16:17:15 +0000 SEQanswers AGBT Love the GWAS summarizing figure @ , but colors in legend make Tufte shiver
Fri, 04 Feb 2011 16:13:43 +0000 drjonboyg AGBT @Comprendia @mndoci it's at the speakers' discretion.
Fri, 04 Feb 2011 16:11:56 +0000 Comprendia agbt What's the latest on social media policy? @mndoci
Fri, 04 Feb 2011 16:11:06 +0000 NEBiolabs #AGBT attendees: Need a pick-me-up? Check inside your NEBNext cup for a free coupon to pick up an iced coffee or other beverage!
Fri, 04 Feb 2011 16:10:53 +0000 djschlesinger AGBT Eric Boerwinkle (UTexas) phoning in his talk and says we can "tweet him to death"
Fri, 04 Feb 2011 15:44:20 +0000 completegenomic agbt If you need a morning pick-me up, espresso is flowing at Complete Genomics suite - Everglades Room
Fri, 04 Feb 2011 15:41:56 +0000 drjonboyg AGBT @apfejes I'm happy to talk about it if you want to find me.
Fri, 04 Feb 2011 15:39:46 +0000 owen_w agbt @apfejes: "List of speakers who don't allow public discussion"
Fri, 04 Feb 2011 15:39:29 +0000 owen_w agbt @apfejes jermdemo quote: "haha great stuff - Fejes' list of untweetable talks"
Fri, 04 Feb 2011 15:35:47 +0000 illuminainfo HiSeq,AGBT Illumina's Expert Session on
Fri, 04 Feb 2011 15:33:06 +0000 completegenomic #AGBT Genome-scale searches for novel autism genes. Dr. Tim Yu, Harvard Medical School, to present today, 2:40-3, Island Ballroom.
Fri, 04 Feb 2011 15:32:52 +0000 drjonboyg AGBT @apfejes that's illegal now thanks to GINA:
Fri, 04 Feb 2011 15:31:18 +0000 apfejes AGBT. @owen_w The point wasn't to embarass the speakers - most probably don't even know what it means. Those are the holes in my notes.
Fri, 04 Feb 2011 15:26:47 +0000 owen_w agbt embarrassing speakers who dont want 2b blogged is asinine - the _organizers_ failed to prep the speakers before the meeting.
Fri, 04 Feb 2011 15:26:34 +0000 omespeak AGBT Great discussion on twitter about new-born sequencing/genomics in response to last talk. Esp follow @drjonboyg & @djschlesinger
Fri, 04 Feb 2011 15:25:55 +0000 drjonboyg AGBT @apfejes good post, but in the US, newborn screening is universal and paid for by the states, not the patients.
Fri, 04 Feb 2011 15:25:44 +0000 SEQanswers AGBT @drjonboyg Sure, more phys/patient education is a requirement. Just don't like the throw-up-hands-and-hide-info strategy.
Fri, 04 Feb 2011 15:25:29 +0000 UK_Biomek fridayreads,AGBT. and my is the stream of info coming from All sounds very interesting, wish I was there.
Fri, 04 Feb 2011 15:24:44 +0000 raindancetech #AGBT Visit w/ RainDance in Lanai to learn more about our microdroplet-based platform & the new DeepSeq FFPE app.
Fri, 04 Feb 2011 15:22:16 +0000 drjonboyg AGBT @SEQanswers there needs to be a huge improvement in physician understanding of genomics before that happens.
Fri, 04 Feb 2011 15:21:42 +0000 jermdemo AGBT haha great stuff - Fejes' list of untweetable talks: (via @apfejes)
Fri, 04 Feb 2011 15:20:12 +0000 SEQanswers AGBT Not worried about incidentalome. Much like you get conf intervals/ranges on your blood tests...WGS will be presented similarly
Fri, 04 Feb 2011 15:19:58 +0000 drjonboyg AGBT Final note on NBS and genomics: not only is it a fascinating topic, it generates awesome posters
Fri, 04 Feb 2011 15:19:17 +0000 digitalbio AGBT @mndoci According to @finchtalk there were extenuating circumstances at from weather-related travel challenges
Fri, 04 Feb 2011 15:17:40 +0000 Lyro20 AGBT¬タン #Norseqcenter ¬タワ@djschlesinger: Won't the "Incidentalome" prohibit WGS of newborns, or anyone, in a clinical setting?
Fri, 04 Feb 2011 15:14:34 +0000 deannachurch AGBT Martin Hibbard from GIS: No tweeting. I guess we'll just keep discussing that last talk- which was great!
Fri, 04 Feb 2011 15:14:21 +0000 drjonboyg AGBT @djschlesinger the US has 4+ million births a year, more than half under medicaid. Stratified access and disparity is a problem
Fri, 04 Feb 2011 15:13:31 +0000 apfejes AGBT List of speakers who don't allow public discussion @ keeps growing:
Fri, 04 Feb 2011 15:13:13 +0000 omespeak AGBT Liked how Ellen W Clayton referred to Infinite Jest and GATTACA in her talk.
Fri, 04 Feb 2011 15:12:53 +0000 drjonboyg AGBT @djschlesinger right, but there's a difference between individuals and public health, and newborn screening is public health.
Fri, 04 Feb 2011 15:12:42 +0000 SEQanswers AGBT Unfortunate that ChadN had to stop the discussion re: information sharing. Was just getting interesting.
Fri, 04 Feb 2011 15:11:54 +0000 omespeak AGBT Ellen Wright Clayton's talk was informative, entertaining and thought provoking. Also thanks to her for allowing tweeting/blogging.
Fri, 04 Feb 2011 15:11:48 +0000 obahcall AGBT Clayton: Evidence and policy based use is the key to surfing the tsunami of whole genome sequencing.
Fri, 04 Feb 2011 15:11:40 +0000 drjonboyg AGBT We raise some of these issues in this paper: (You can tell this is a policy area I work on and care about)
Fri, 04 Feb 2011 15:10:11 +0000 omespeak AGBT +then should we share the information with patients. However, we may not have a choice, considering patients may demand it.
Fri, 04 Feb 2011 15:09:06 +0000 omespeak AGBT Summary: there will be huge amount of genomic information soon, but do we know what that information means? And if we don't know that+
Fri, 04 Feb 2011 15:08:38 +0000 rhodesmd #AGBT Ellen Clayton gave a talk on ethics of medicine when we have sequence argued against giving out all info brave talk to this audience
Fri, 04 Feb 2011 15:08:36 +0000 obahcall Ellen Wright Clayton: Surfing tsunami of whole genome sequencing, need for developing a policy consensus for access and use of results.#AGBT
Fri, 04 Feb 2011 15:08:14 +0000 djschlesinger AGBT If you can't prevent parents requesting (& getting) antibiotics for their kid's viral ear infection, how will you hold back WGS data?
Fri, 04 Feb 2011 15:07:40 +0000 drjonboyg AGBT Without saying too much, I'm confident that we'll see a lot of research into all of these questions and issues quite soon.
Fri, 04 Feb 2011 15:06:33 +0000 apfejes AGBT: Notes from Ellen Wright Clayton on dangers of human genomic information.
Fri, 04 Feb 2011 15:05:51 +0000 SEQanswers AGBT This is a fantastic talk re:"Incidentalome". Undercurrent of overwhelmed paternalistic pessimism.
Fri, 04 Feb 2011 15:05:13 +0000 omespeak AGBT We have to be rigorous about science and policy to make best use of the upcoming data deluge. Otherwise we will drown: Ellen W Clayton
Fri, 04 Feb 2011 15:04:33 +0000 drjonboyg AGBT In my experience, many in the NBS world are currently really dismissive of WGS unfortunately. we need time to change attitudes
Fri, 04 Feb 2011 15:04:24 +0000 dwmohr AGBT Meant several good arguments FOR limiting patient access to WGS
Fri, 04 Feb 2011 15:03:49 +0000 dsexton_2 #agbt how much protection will governments give?
Fri, 04 Feb 2011 15:02:49 +0000 dwmohr AGBT If tweet policy is any indication, limiting access to WGS will be a hard sell. Several good arguments against it, however
Fri, 04 Feb 2011 15:02:49 +0000 omespeak AGBT Scientific analysis of impact of genetic variation needs to proceed at fast pace for good policy - Ellen W Clayton.
Fri, 04 Feb 2011 15:01:14 +0000 drjonboyg AGBT @djschlesinger great question. I hope so, but tbh don't feel comfortable predicting. So many things have to align (tech, ELSI, budget)
Fri, 04 Feb 2011 15:00:15 +0000 djschlesinger AGBT Ellen: Physicians can't transform SNP data into clinically actionable results.
Fri, 04 Feb 2011 14:59:47 +0000 omespeak AGBT Clayton: Perhaps most controversial - since genetic information *will be* available, patient's desire for info could play minor role.
Fri, 04 Feb 2011 14:59:28 +0000 SEQanswers AGBT "What the patient WANTS will play a minor role" (in genetic information sharing)
Fri, 04 Feb 2011 14:59:03 +0000 drjonboyg AGBT One more thing: there's a difference between individuals sequencing their newborns, and population-level public health NBSeq
Fri, 04 Feb 2011 14:58:03 +0000 djschlesinger AGBT 10+ yrs away? @drjonboyg....I want to see newborn WGS happen population-wide, but there's a LOT that needs to happen first.
Fri, 04 Feb 2011 14:55:37 +0000 omespeak AGBT Clayton: Disclosure of all (genomic) information threatens to sweep away the health-care system
Fri, 04 Feb 2011 14:55:34 +0000 drjonboyg AGBT Don't get me wrong, I want to see newborn WGS happen population-wide, but there's a LOT that needs to happen first.
Fri, 04 Feb 2011 14:54:31 +0000 omespeak AGBT Clayton: Bad science is a problem. Even if we know everything about genome, we cannot predict all disease like they mention in GATTACA
Fri, 04 Feb 2011 14:54:24 +0000 drjonboyg AGBT @djschlesinger certainly something that needs to be worked out. Also, how do you get meaningful informed consent for WGS in 15 min?
Fri, 04 Feb 2011 14:53:24 +0000 djschlesinger AGBT Absolutely! @drjonboyg: Also, clinical WGS needs to get error rates down by three or more orders of magnitude for NBS
Fri, 04 Feb 2011 14:52:15 +0000 omespeak AGBT Clayton: As we look at genomic testing, vast majority of findings will have pleiotropic affects.
Fri, 04 Feb 2011 14:51:49 +0000 drjonboyg AGBT Also, clinical WGS needs to get error rates down by three or more orders of magnitude for NBS
Fri, 04 Feb 2011 14:49:55 +0000 omespeak AGBT Ellen Wright Clayton: debate on incidental findings - how much information do you give back?
Fri, 04 Feb 2011 14:49:40 +0000 drjonboyg AGBT As an example, Illinois balked at deploying a new method of NBS because it would have cost $5 million to conduct the pilot.
Fri, 04 Feb 2011 14:48:36 +0000 djschlesinger AGBT Won't the "Incidentalome" prohibit WGS of newborns, or anyone, in a clinical setting?
Fri, 04 Feb 2011 14:47:55 +0000 drjonboyg AGBT Not sure I agree that we're going to have routine newborn WGS until the costs come down to $200 or less, the States can't afford it.
Fri, 04 Feb 2011 14:46:14 +0000 SEQanswers AGBT Ellen Clayton: In a few years, newborns will be sequenced when they can't get away.
Fri, 04 Feb 2011 14:44:45 +0000 omespeak AGBT Ellen Wright trying to make a case that complete disclosure WGS data could lead to disaster.
Fri, 04 Feb 2011 14:44:37 +0000 dsexton_2 #agbt Ellen is an expert in the bioethics around sequencing
Fri, 04 Feb 2011 14:44:04 +0000 djschlesinger Ellen Wright Clayton (Vanderbilt) wants to "stir things up". Tweet away......#AGBT
Fri, 04 Feb 2011 14:35:33 +0000 KapaBiosystems AGBT Come visit our poster to see latest improvement to NGS sample prep workflow.
Fri, 04 Feb 2011 14:35:10 +0000 KapaBiosystems AGBT Library quantification kit compatible for Ion Torrent instrument. Library quant. kits available for all current NGS platforms.
Fri, 04 Feb 2011 14:25:30 +0000 neilhall_uk agbt this is all published work..why cant we tweet.?
Fri, 04 Feb 2011 14:24:29 +0000 MaliciaRogue AGBT . ¬ルᄏ @genomeresearch: 60 Complete, High-Coverage Human Genomes -- for Study by the Global Research Community...
Fri, 04 Feb 2011 14:10:45 +0000 wyattsgirl AGBT Following the Tweets... wish more folks could give more info to those waitlisted... ha! dang forbidders of the tweet!
Fri, 04 Feb 2011 14:09:06 +0000 deannachurch AGBT Jim Lupski up first thing this AM. No tweets b/c he is talking about patient data.
Fri, 04 Feb 2011 14:07:12 +0000 djschlesinger AGBT Dr. Lupski up first, Tweeting prohibited due to the inclusion of patient data.
Fri, 04 Feb 2011 13:46:59 +0000 BioAcousticGal slow,agbt Sounds like we missed a good one! @neilhall_uk start this morning due to the lifetech party last night...ouch!
Fri, 04 Feb 2011 13:26:29 +0000 neilhall_uk agbt #slow start this morning due to the lifetech party last night...ouch!
Fri, 04 Feb 2011 12:51:39 +0000 completegenomic #AGBT Customer case studies to be presented in Everglades Room today: 10:35-10:50, 1:30-1:45, 5-5:15. Still need an iPad? - drawing @ 6!
Fri, 04 Feb 2011 12:24:04 +0000 raindancetech AGBT Join us @ our workshop today @ 2pm to learn about Ultra-Deep Sequencing & Methylation Analysis of FFPE Tumor Samples w/ Microdroplets
Fri, 04 Feb 2011 12:19:19 +0000 illuminainfo AGBT Illumina will be at the Bronze Sponsors workshop today at 2:00 p.m. Island Ballroom
Fri, 04 Feb 2011 12:18:32 +0000 mndoci AGBT Strata videos go live a day after talks, has a default no blogging policy. Something in the world of science is just not right
Fri, 04 Feb 2011 11:42:14 +0000 pjacock AGBT Galaxy 2011 Community Conference, May 25-26, Lunteren, The Netherlands
Fri, 04 Feb 2011 06:49:48 +0000 bffo AGBT, Great PB user group evening, as well as good LT soiree sorry I missed the tweetup, maybe tomorrow evening?
Fri, 04 Feb 2011 06:02:20 +0000 SOLiDSequencing AGBT Stay Fresh & Focused During Yoga w/ @iontorrent every morning Capri 2 & 3, 7:00 - 8:00 AM
Fri, 04 Feb 2011 05:43:03 +0000 SOLiDSequencing AGBT Fri. @LifeCorporation Lunch/Workshop 12-2 pm PALM ROOM: Sequencing Gets Personal. 5 amazing speakers - don't miss it!
Fri, 04 Feb 2011 05:37:54 +0000 SOLiDSequencing AGBT,PGM @LifeCorporation Triathlon Scores just in! Does Baylor keep lead in competition for @iontorrent sequencer...???
Fri, 04 Feb 2011 04:44:25 +0000 abhishekpratap AGBT 60 Complete, High-Coverage Human Genomes -- for Study by the Global Research Community -- By Complete Genomics :
Fri, 04 Feb 2011 04:42:49 +0000 girlscientist AGBT, If you lose AT&T service on your iPhone here at go to settings then restore network settings. Thanks Shawn Levy for tip!
Fri, 04 Feb 2011 04:04:54 +0000 omespeak AGBT Any other tweeps at the All Night Long party?
Fri, 04 Feb 2011 02:59:08 +0000 infoecho tweetleak,AGBT It seems that we need a for
Fri, 04 Feb 2011 02:24:51 +0000 apfejes AGBT A big thank you and round of aplause for the speakers who allowed twittering/blogging today!
Fri, 04 Feb 2011 02:22:19 +0000 KamounLab AGBT Watch bionanomatrix movie "400 kb DNA entering nanochannel"
Fri, 04 Feb 2011 02:10:34 +0000 apfejes AGBT Notes on Maria Mendez-Lago, BC Cancer:
Fri, 04 Feb 2011 02:09:56 +0000 rafalwoycicki PAG,AGBT I have just forgotten Who can help me? What animal genome announced at was done with optical mapping by @OpGen & @BGI_events ? ?
Fri, 04 Feb 2011 02:03:59 +0000 djschlesinger AGBT Was BioNanomatrix the star this year?
Fri, 04 Feb 2011 02:03:14 +0000 KamounLab AGBT Link to Brian Haas Trinity package for RNA-Seq de novo assembly [coming soon]
Fri, 04 Feb 2011 01:48:13 +0000 drjonboyg AGBT This session has been the highlight of so far. Probably because I'm a total geek.
Fri, 04 Feb 2011 01:47:34 +0000 drjonboyg AGBT Anyone else think these nanochannels look like the matrix?
Fri, 04 Feb 2011 01:45:23 +0000 girlscientist AGBT Kerstin Lindblad-Toh asked me to pass on link to new Science for Life Lab being formed in Uppsala:
Fri, 04 Feb 2011 01:43:50 +0000 djschlesinger AGBT Han Cao from BioNanomatrix showed a cool movie of 400kb DNA fragment traveling through a nanochannel.
Fri, 04 Feb 2011 01:39:34 +0000 SOLiDSequencing AGBT.,PGM @LifeCorporation Triathlon tonight Who gets closer to winning an @iontorrent sequencer?
Fri, 04 Feb 2011 01:33:47 +0000 apfejes AGBT No blogging on Michelle Sam's talk.
Fri, 04 Feb 2011 01:30:51 +0000 apfejes AGBT Notes on Lara Bull-Otterson's talk on finding viruses in unmapped reads for cancer.
Fri, 04 Feb 2011 01:28:59 +0000 deannachurch AGBT JO: solid state nanopore, hyb a probe and measure probe loc. //concept
Fri, 04 Feb 2011 01:28:17 +0000 girlscientist AGBT The Apple haters are winning: AT&T no service specifically for our iPhones/iPads. Can anyone explain it?
Fri, 04 Feb 2011 01:26:49 +0000 djschlesinger AGBT Solid state versus protein nanopores. which do you chose?
Fri, 04 Feb 2011 01:26:00 +0000 djschlesinger AGBT @SEQanswers likely true, but probably not enough. Point is kind of moot because the threat of bioterrorism is over stated.
Fri, 04 Feb 2011 01:24:21 +0000 SOLiDSequencing AGBT Somehow escaped it thus far? Zheng Lab, Lady Gaga Parody / Science Grad School "Bad Project"
Fri, 04 Feb 2011 01:23:31 +0000 deannachurch agbt JO: Not a bioinformatics problem, not enough info content in current reads to get the right answer at all length scales.
Fri, 04 Feb 2011 01:22:32 +0000 SEQanswers AGBT @djschlesinger I agree, but you heard her mention her database...which is prob stuffed with all examples of relevant biothreat bugs
Fri, 04 Feb 2011 01:20:42 +0000 djschlesinger AGBT @SEQanswers microbial genomes are littered w/ mobile element. task is impossible, unless you link it to a modification already publish
Fri, 04 Feb 2011 01:18:58 +0000 deannachurch agbt John Oliver from NABsys on chr lenght contigs. Tweet friendly
Fri, 04 Feb 2011 01:18:05 +0000 omespeak AGBT Ironically it was a speaker from US army who was ok with tweeting/blogging.
Fri, 04 Feb 2011 01:14:12 +0000 SEQanswers AGBT,thearmyisscary @djschlesinger Probably looking for some combination of mobile elements, pieces of vectors, or novel junctions.
Fri, 04 Feb 2011 01:13:35 +0000 omespeak AGBT Lauren McNew from US military's Chemical Bio Centre - 'if you can put a sequencing machine to a camel we will buy it'
Fri, 04 Feb 2011 01:13:22 +0000 deannachurch AGBT LM: looking for a field seq unit, preferably in camo.
Fri, 04 Feb 2011 01:12:44 +0000 apfejes AGBT Notes from Obi Grifith's talk on molecular predictors for drug response:
Fri, 04 Feb 2011 01:12:12 +0000 djschlesinger AGBT How do you tell if a microbial genome has been "engineered"?
Fri, 04 Feb 2011 01:05:35 +0000 djschlesinger AGBT Lauren McNew from ECBC can sequence a microbial genome in 36 hours!
Fri, 04 Feb 2011 01:05:18 +0000 girlscientist AGBT Obi Griffith on cancer genomics: RNAseq analysis for breast cancer subtypes.
Fri, 04 Feb 2011 01:03:16 +0000 rforsberg agbt McNew talk; finally a lab that can handle both genomics and explosives
Fri, 04 Feb 2011 01:02:25 +0000 deannachurch AGBT LM: exercises to plan for identifying pathogens in case of a biothreat, using 454.
Fri, 04 Feb 2011 01:00:27 +0000 deannachurch AGBT Laura McNew tech session. Threat analysis- cool sounding!
Fri, 04 Feb 2011 00:58:00 +0000 drjonboyg AGBT A particularly cool talk on a novel nanopore for sequencing that I can't tell you about.
Fri, 04 Feb 2011 00:38:32 +0000 djschlesinger AGBT @omespeak not so much product placement, but it's patronizing pop-culture tone. While cool, it wasn't suitable for the audience.
Fri, 04 Feb 2011 00:38:15 +0000 omespeak AGBT At the Technology session: talk about nanopores. No tweeting allowed :(
Fri, 04 Feb 2011 00:37:56 +0000 suganthibala AGBT MT @girlscientist Freudian slip? Salzberg means to say he'll give us cursory description of Bowtie, instead says "curse." You decide.
Fri, 04 Feb 2011 00:37:03 +0000 rforsberg AGBT As of this year, Europe will also have a genomics conference inspired by AGBT. It is called Copenhagenomics -
Fri, 04 Feb 2011 00:36:22 +0000 omespeak AGBT Will talk about the movie and PacBio in details later. Some people seem pissed about the product placement.
Fri, 04 Feb 2011 00:35:47 +0000 SEQanswers AGBT Genomic Technology Session = Full. Tweets = Empty by request of speaker.
Fri, 04 Feb 2011 00:35:22 +0000 neilhall_uk agbt Well done to James hayfield for getting in a question on how to end world hunger at the pacbio dinner
Fri, 04 Feb 2011 00:34:38 +0000 omespeak agbt Couldn't Tweet from the Pac Bio dinner & movie. But movie was an interesting documentary about 'new biology' (mostly systems).
Fri, 04 Feb 2011 00:30:18 +0000 apfejes AGBT One more speaker who can't be blogged: Olivier Harismendy.
Fri, 04 Feb 2011 00:29:46 +0000 JoPet39 Not that dinner and a movie wasn't captivating, but coffee should flow freely when evening sessions are scheduled.#AGBT
Fri, 04 Feb 2011 00:29:34 +0000 SOLiDSequencing SOLiD,sequencing,AGBT Stop by Suites 1104-1106 for @LifeCorporation Triathlon and to see + @iontorrent instruments.
Fri, 04 Feb 2011 00:24:50 +0000 nanopore AGBT Jens Gundlach up now on nanopore research in the Island Ballroom
Fri, 04 Feb 2011 00:15:37 +0000 rdeborja AGBT, At the cancer genomics talks at my F-Cancer t-shirt was a huge hit. @letsfcancer, @msfuckcancer
Fri, 04 Feb 2011 00:02:06 +0000 drjonboyg AGBT Explain to me how my blackberry can have an AT&T signal (edge) when neither my iPhone or iPad have one?
Thu, 03 Feb 2011 23:43:55 +0000 SOLiDSequencing AGBT @LifeCorporation Triathlon: Stage 1 REPEAT: 7-11pm Suite 1104, Stage 2: 7-11pm Suite 1105.
Thu, 03 Feb 2011 23:40:53 +0000 SOLiDSequencing #AGBT @LifeCorporation Triathlon, chance to win an @iontorrent PGM sequencer:
Thu, 03 Feb 2011 23:38:29 +0000 rforsberg agbt Would love to see the Monsanto single-corn-chip machine run though. Looked like something out of Brazil, the movie
Thu, 03 Feb 2011 23:36:36 +0000 drjonboyg AGBT Left the PacBio thing before the questions, had a feeling it might have gotten snarky.
Thu, 03 Feb 2011 23:36:06 +0000 rforsberg agbt It seems pretty old fashioned to use "new" biology to select solely for yield in food crops
Thu, 03 Feb 2011 23:28:42 +0000 drjonboyg AGBT Famine only happens when food shortage combines with a government preventing people from moving.
Thu, 03 Feb 2011 23:28:21 +0000 Mikegenome agbt So for a free meal we watched a 30 min PacBio commercial
Thu, 03 Feb 2011 23:27:11 +0000 illuminainfo MiSeq,illuminalounge.,AGBT Meet and greet the instrument at the Fri (2/4): 6-7pm, Sat (2/5): 1-5pm
Thu, 03 Feb 2011 23:24:49 +0000 drjonboyg AGBT Ok, that one I take issue with. Famines are political in nature, they're not going to be solved by GM crops.
Thu, 03 Feb 2011 23:24:11 +0000 djschlesinger AGBT A movie about corn eugenics? @drjonboyg: Actually, this would be a great movie to have shown my science policy class @UK_Patterson.
Thu, 03 Feb 2011 23:21:39 +0000 drjonboyg AGBT Actually, this would be a great movie to have shown my science policy class @UK_Patterson.
Thu, 03 Feb 2011 23:17:33 +0000 drjonboyg AGBT I'll have you all know I'm being incredibly restrained right now. I do like the CGI animations in this movie though.
Thu, 03 Feb 2011 23:15:57 +0000 SOLiDSequencing AGBT. @ChaunceyGrattan You're welcome! We love it, too. Lots of great info at
Thu, 03 Feb 2011 23:11:20 +0000 djschlesinger AGBT True story: @dwmohr: The new biology sounds alot like the old biology. It's the computers that can't keep up
Thu, 03 Feb 2011 23:09:21 +0000 SOLiDSequencing AGBT Accelerate Innovative Solutions: Mike Lelivelt at the @LifeCorporation @Grand_Challenge Workshop
Thu, 03 Feb 2011 23:09:11 +0000 dwmohr AGBT The new biology sounds alot like the old biology. It's the computers that can't keep up
Thu, 03 Feb 2011 23:05:09 +0000 ChaunceyGrattan AGBT this tag is kinda amazing... big shout out to the tweeps keeping me in the loop!
Thu, 03 Feb 2011 22:57:24 +0000 drjonboyg AGBT @dgmacarthur except most of the 'no tweeds allowed' speakers are academics, and most of the data is published or in the process.
Thu, 03 Feb 2011 22:55:30 +0000 dgmacarthur AGBT @drjonboyg Although, to be fair, has a far higher density of commercially sensitive material in presentations.
Thu, 03 Feb 2011 22:54:38 +0000 dgmacarthur AGBT @drjonboyg Sorry to see that attitude of speakers to twitter is so different from, say, BoG (where ~90% of speakers allowed tweets).
Thu, 03 Feb 2011 22:47:29 +0000 drjonboyg AGBT Not having Internet access has saved me from making a lot of sarcastic tweeds. Probably a good thing.
Thu, 03 Feb 2011 22:42:21 +0000 SOLiDSequencing AGBT,PGM High jumper competes in @LifeCorporation Triathlon for chance to win an @iontorrent sequencer.
Thu, 03 Feb 2011 22:35:47 +0000 SOLiDSequencing NGS,AGBT @apfejes Targeted Reseq = 50%+ runs, then RNASeq, ChIPSeq, say JNoonan-Yale, RSteen-Harvard, JMullikin-NIH.
Thu, 03 Feb 2011 22:33:26 +0000 SOLiDSequencing AGBT Player competes in @LifeCorporation Triathlon for chance to win an @iontorrent sequencer.
Thu, 03 Feb 2011 22:29:32 +0000 SOLiDSequencing AGBT. Maneesh Jain opens the @LifeCorporation @Grand_Challenge workshop
Thu, 03 Feb 2011 22:22:08 +0000 djschlesinger AGBT Any Tweeps at the PacBio dinner?
Thu, 03 Feb 2011 22:05:32 +0000 owen_w AGBT @
Thu, 03 Feb 2011 22:03:47 +0000 girlscientist AGBT Awwww look at the kittehs.
Thu, 03 Feb 2011 22:02:38 +0000 KamounLab AGBT @girlscientist @deannachurch @apfejes Cute animal picture show continues. But wait we're not supposed to tweet about it...
Thu, 03 Feb 2011 21:59:00 +0000 NEBiolabs AGBT Check out the posters from New England Biolabs at From sample prep to bacteria making electricity:posters 7,63,92,155,184,199&206
Thu, 03 Feb 2011 21:51:15 +0000 apfejes internet,youredoingitwrong,AGBT This may be the first time in my life I'm being barred from twittering about cute kitten pictures...
Thu, 03 Feb 2011 21:50:56 +0000 deannachurch AGBT This session totally wins for cute animal pictures.
Thu, 03 Feb 2011 21:47:42 +0000 SOLiDSequencing PGM #AGBT Triathlon Scores: It's not too late to take the lead and win an @iontorrent sequencer!
Thu, 03 Feb 2011 21:46:00 +0000 apfejes feb3,AGBT. @paniniVani I proposed we start using the hashtag. :-P
Thu, 03 Feb 2011 21:45:37 +0000 drio AGBT bowtie maps 3% > reads than bwa. What tool has the higher number of correct alignments? What alignments deliver t best SNP calls
Thu, 03 Feb 2011 21:44:57 +0000 apfejes AGBT Has Chip-Seq dissapeared from the map this year? No ChIP-Seq posters, and everyone just glosses over the epigenetics.
Thu, 03 Feb 2011 21:42:28 +0000 dwmohr #AGBT tweeting/blogging drives interest. Isn't that what we're after?
Thu, 03 Feb 2011 21:40:59 +0000 paniniVani AGBT @apfejes When did become Egypt? (via @ronald_duncan)
Thu, 03 Feb 2011 21:40:36 +0000 rafalwoycicki AGBT @omespeak sample prep is crucial
Thu, 03 Feb 2011 21:38:45 +0000 paniniVani AGBT Salzberg: adding onto TopHat- to look for fusion genes. "coming soon" (via @deannachurch)
Thu, 03 Feb 2011 21:37:12 +0000 owen_w agbt my view: when tweeting is outlawed, only outlaws will tweet.
Thu, 03 Feb 2011 21:37:11 +0000 girlscientist AGBT Tried to get my HudsonAlpha colleague Greg Barsh, to allow tweeting etc., but no success.
Thu, 03 Feb 2011 21:36:17 +0000 deannachurch AGBT Greg Barsh up next- no tweeting.
Thu, 03 Feb 2011 21:33:23 +0000 apfejes AGBT Oops, wrong link - Notes on Steven Salzber's (VERY OPEN) talk:
Thu, 03 Feb 2011 21:31:34 +0000 deannachurch AGBT Salzberg: Getting Bowtie2 requirements during Q&A :)
Thu, 03 Feb 2011 21:30:48 +0000 djschlesinger AGBT Salzberg makes me rethink my career I should have been a bioinformatician.
Thu, 03 Feb 2011 21:27:35 +0000 omespeak AGBT Unlike, last year, no major announcements at , other than @CompleteGenomic's release of 60 human genomes.
Thu, 03 Feb 2011 21:23:09 +0000 SEQanswers AGBT Next package in the Tuxedo suite: Handcuffs. Harrrrrr.
Thu, 03 Feb 2011 21:21:20 +0000 deannachurch AGBT Salzberg: adding onto TopHat- to look for fusion genes. "coming soon"
Thu, 03 Feb 2011 21:21:12 +0000 girlscientist AGBT Salzberg: coming soon to a computer near you is TopHat-Fusion! Special-purpose routines for finding gene fusions in seq data.
Thu, 03 Feb 2011 21:21:04 +0000 neilhall_uk agbt Tophat fusion coming soon for finding fusion genes
Thu, 03 Feb 2011 21:17:37 +0000 rdeborja AGBT Bowtie2 definitely sounds interesting. Finally full support for indels.
Thu, 03 Feb 2011 21:16:54 +0000 neilhall_uk agbt Bowtie2 coming in spring
Thu, 03 Feb 2011 21:16:50 +0000 OoohMySeat AGBT. tweet censoring My view: It takes time for some to get comfortable with the power of twitter. Respect them, they will come around.
Thu, 03 Feb 2011 21:16:11 +0000 djschlesinger AGBT Bowtie 2 available this spring.
Thu, 03 Feb 2011 21:15:37 +0000 deannachurch AGBT- @rafalwoycicki not anti-tweet rules. Speaker opt-in policy. No rules broken.
Thu, 03 Feb 2011 21:15:26 +0000 djschlesinger AGBT Salzberg: Bowtie and BWA don't always map the same reads. ~7% difference.
Thu, 03 Feb 2011 21:15:05 +0000 ronald_duncan AGBT @apfejes When did become Egypt?
Thu, 03 Feb 2011 21:14:48 +0000 neilhall_uk agbt For the non-cs crowd (like me) that was a great explanation of bs transform. Thanks Steven
Thu, 03 Feb 2011 21:14:23 +0000 deannachurch AGBT @girlscientist aligns more reads- I haven't seen a measure of accuracy yet.
Thu, 03 Feb 2011 21:14:16 +0000 rafalwoycicki AGBT Thank to everyone who break the anti-tweet rules at
Thu, 03 Feb 2011 21:13:28 +0000 girlscientist AGBT Salzberg: Bowtie program still faster than SOAP2 and BWA programs for alignments, and is more accurate.
Thu, 03 Feb 2011 21:08:29 +0000 girlscientist AGBT Freudian slip? Salzberg means to say he'll give us cursory description of Bowtie, but instead says "curse." You decide.
Thu, 03 Feb 2011 21:07:03 +0000 omespeak agbt Most impressed by Life Tech's Starlight Quantum dot 'nanosequencing machines'. But have heard the talk by Beecham earlier.
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs> AGBT Sequilabs: CompleteGenomic: New genomes will be available through our website < and t...
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs AGBT, Sequilabs: CompleteGenomic: Need a caffeine pick-me up at Expresso in Everglade: CompleteGenomic: Need a ...
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs AGBT Sequilabs: CompleteGenomic: Interested in our commercial sequencing services? Visit our hospitality suite ...
Thu, 03 Feb 2011 21:04:52 +0000 omespeak AGBT NABSys showed *some* data on nanopore sequencing by hybridization. Still no real sequencing information.
Thu, 03 Feb 2011 21:04:27 +0000 rdeborja AGBT Sitting at Steven Salzberg's High Performance Alignment and Analysis of Next Generation Sequences talk on Bowtie
Thu, 03 Feb 2011 21:04:14 +0000 deannachurch AGBT Salzberg: software discussed in talk.
Thu, 03 Feb 2011 21:03:22 +0000 girlscientist AGBT Salzberg covering three of his assembly programs: Bowtie, Tophat, and Cufflinks. (what's next? Spats? Insert your own joke here.)
Thu, 03 Feb 2011 21:02:18 +0000 girlscientist AGBT Next speaker, Salzberg, says "I'd be delighted if you tweet and blog whatever you'd like about my talk,"
Thu, 03 Feb 2011 21:02:12 +0000 deannachurch AGBT Steve Salzberg: High-Performance Alignment and analysis of NGS. tweetable...
Thu, 03 Feb 2011 21:01:53 +0000 omespeak AGBT Lots of posters at focused on improved sample prep for various platforms. Very few on new sequencing techniques.
Thu, 03 Feb 2011 21:00:12 +0000 girlscientist AGBT Ssecond attempt at tweetup tonight at lobby bar, 9:30pm after night session.
Thu, 03 Feb 2011 20:58:45 +0000 omespeak AGBT General feeling from talking with various people at - sharing of and moving NGS data between various sites will be a huge issue.
Thu, 03 Feb 2011 20:54:54 +0000 apfejes AGBT Some thoughts on talks that are forbidding tweeting/blogging.
Thu, 03 Feb 2011 20:47:48 +0000 a__muse AGBT Looks like is asking people not to tweet. So I guess blogging is also out @omespeak ?
Thu, 03 Feb 2011 20:35:29 +0000 bioscribe AGBT Dinner and a movie tonight @ featuring "The New Biology" documentary by PacBio. Palms Ballroom 5:00 pm.
Thu, 03 Feb 2011 20:22:25 +0000 KamounLab AGBT New genomics Institute at Sweden's Uppsala University modeled on the Broad. Recruiting now.
Thu, 03 Feb 2011 20:20:27 +0000 girlscientist AGBT Kerstin ends with saying new institute modeled on Broad is starting in Uppsala and they are looking for bright young scientists.
Thu, 03 Feb 2011 20:19:34 +0000 apfejes wishuwerehere,AGBT I'm sure this part is Tweetable: inbreeding dogs is bad, cancer is complex in dogs too. The rest is secret. (-:
Thu, 03 Feb 2011 20:17:12 +0000 neilhall_uk agbt It's submitted for publication but we can't tweet it!
Thu, 03 Feb 2011 20:16:11 +0000 rafalwoycicki AGBT,PAG I should be there now at the same was with
Thu, 03 Feb 2011 20:10:25 +0000 raindancetech #AGBT @ 7:30pm Thurs. - UCSD's Oliver Harismendy on analyzing chromosomal 'hot spots' in tumors w/ RainDance's DeepSeq FFPE Solution
Thu, 03 Feb 2011 20:09:00 +0000 SEQanswers AGBT I have canine compulsive disorder to tweet the details about this talk.
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs> AGBT CompleteGenomic: New genomes will be available through our website < and the Bionimbu...
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs AGBT, CompleteGenomic: Need a caffeine pick-me up at Expresso in Everglade: CompleteGenomic: Need a caffeine pi...
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs AGBT CompleteGenomic: Interested in our commercial sequencing services? Visit our hospitality suite in the Ever...
Thu, 03 Feb 2011 20:01:24 +0000 apfejes AGBT Not happy about it, but this is my list of talks for which I'm not allowed to publish my notes:
Thu, 03 Feb 2011 19:59:29 +0000 apfejes topsecret,canine,genome,AGBT Yet another no-tweet... this time on dog genomics.
Thu, 03 Feb 2011 19:59:12 +0000 neilhall_uk agbt. Been looking at the illumina miseq at Very very nice piece of kit. But I almost object to them making sequencing too easy.
Thu, 03 Feb 2011 19:54:57 +0000 SOLiDSequencing cancer.,AGBT New term: chromothripsis: a single catastrophic event leading to chromosomes getting interlinked in
Thu, 03 Feb 2011 19:50:30 +0000 Mikegenome agbt @drjonboyg my iPhone lost signal too. Had it in earlier sessions. Wifi working
Thu, 03 Feb 2011 19:48:42 +0000 Mikegenome agbt Blocked from tweeting what turns out midway through the Wein. talk to be published data... Perhaps the second half is unpublished.
Thu, 03 Feb 2011 19:45:33 +0000 drjonboyg AGBT, Furthering connectivity problems at now I can't get an AT&T signal on my iPad or iPhone. eek.
Thu, 03 Feb 2011 19:44:08 +0000 razZ0r AGBT Follow the hashtag for new stuff on genomes, biotech, genome sequencing, etc. (If the speaker allows tweeting, stupid policy, LOL.)
Thu, 03 Feb 2011 19:43:56 +0000 girlscientist AGBT Weinshilboum cites a recent paper, Nov 2010, in J Clin Oncol so I'd say one should look there if one wants an idea of his talk.
Thu, 03 Feb 2011 19:40:09 +0000 girlscientist AGBT Next talk, Kerstin Lindblad-Toh, not going to be tweetable either.
Thu, 03 Feb 2011 19:34:32 +0000 SEQanswers agbt First talk after poster session: Richard Weinshilboum = no tweets.
Thu, 03 Feb 2011 19:33:11 +0000 apfejes AGBT Gah... no blogging for Richard Weinshiboum. Not sure he knows what twittering is, tho... (joke about issues with the mouse...)
Thu, 03 Feb 2011 19:33:11 +0000 girlscientist AGBT First talk at afternoon session is Richard Weinshilboum, but he's requested no tweeting.
Thu, 03 Feb 2011 19:29:50 +0000 LIFECorporation AGBT, Getting ready for tonight's reception at hope to see you here.
Thu, 03 Feb 2011 19:29:39 +0000 cliffmcc #AGBT is asking people to not tweet during conference talks. Guess they can't take notes either?
Thu, 03 Feb 2011 19:26:18 +0000 LIFECorporation AGBT Tonight's event, will we see you there? @solidsequencing @iontorrent