AGBT 2012 Day 1 Tweets

AGBT day 1 tweets! (Day 2, Day 3, Day 4)

Great weather, beautiful beaches, palm trees, copious free alcohol ... why would you want to go to AGBT when you can keep track via Twitter? I've hooked up a little script to monitor all the #AGBT tweets so you can get all the goodness of the conference without the sun-burn, alligator bites, inappropriate liaisons etc.

On the scientific agenda today:

1:30-1:35 pm, Opening remarks, Ken Dewar, McGill University and Génome Québec Innovation Centre
1:35-2:05 pm, Next-Generation Sequencing Technologies and Resources, Mark Adams, J. Craig Venter Institute
2:10-2:30 pm High Throughput Process Development in the Broad Institute Genome Sequencing Platform, Danielle Perrin, Broad Institute of MIT and Harvard
2:35-2:55 pm Resequencing: Approaches & Challenges, Thomas Keane, The Wellcome Trust Sanger Institute
3:30-3:50 pm De Novo Assembly: From Single Cells to Metagenomes Matt Blow, Joint Genome Institute
3:55-4:15 pm Transcriptomics Shawn Levy, HudsonAlpha Institute for Biotechnology
4:20-4:40 pm Epigenomics Olivier Elemento, Weill Cornell Medical College
4:45-5:05 pm Sequencing as an Assay Lisa White, Baylor College of Medicine
5:10-5:30 pm Genotyping by Sequencing Eric Johnson, University of Oregon

All times are local Florida. This page will update every couple of minutes (but you'll have to refresh the page).

Most popular tweets
(9) djschlesinger: JGI is using longer PacBio reads to close gaps in Illumina shorter read assemblies. Able to close 75% of gaps in microbial genomes. #AGBT
(8) dgmacarthur: Tweets from #AGBT are now streaming in. Be sure to also follow the hilarious snark-stream over at #notAGBT.
(8) illumina: Geoff Smith, Illumina UK: Longest perfect overlapping read so far on #MiSeq 678 bp! #AGBT
(7) omespeak: Scaling up of next gen sequencing is producing so much data it's sarurating local power grids in rural UK! (Thomas Keane of Sanger) #AGBT
(7) omespeak: Only three talks into #AGBT and already two of them underlining the sequencing data deluge.
(6) zerojinx: Lah de dah. Sequencing data deluge: Get over it. #AGBT
(4) illumina: HiSeq 2500 "Genome in a Day" data viewable in BaseSpace: http://t.co/ijERyA0X #AGBT
(4) illumina: 4 whole human genomes on 1 USB drive, w/family trio & Genome in a Day datasets gift to all at our User Group mtg #AGBT http://t.co/AubRVWjy
(3) neilhall_uk: Stop what you are doing at #AGBT nanopore has been superseded already http://t.co/6WTuzBMC
(3) neilhall_uk: #agbt follow #notAGBT if you want a chance to win a CrapBip ShtSeq. http://t.co/6WTuzBMC
(3) BiotechMarketer: Strong start from @illumina on the social media front http://t.co/M8LpoJgt #AGBT Nice job!
(3) illumina: Danielle Perrin @broadinstitute : 51 HiSeq systems, only 6 staff needed to run them #AGBT
(3) NJL_Broad: Geoff Smith reporting on paired 400 base reads in R&D on MiSeq. #AGBT.
(3) CrapBio: #AGBT Don't go to Yoga at 7:15 in the Agilent suite. join CrapBIO for skinny dipping on the beach at 7am #notAGBT
(3) assemblathon: RT @illumina: HiSeq 2500 "Genome in a Day" data viewable in BaseSpace: http://t.co/wJ8zvZ99 #AGBT
(3) dgmacarthur: ! RT @SEQanswers Confirmed that @Illumina is offering full trade in value for PGMs against MiSeq or HiSeq2500. #agbt
(2) pathogenomenick: I'm being organised this year and am logging the #AGBT tweets for posterity. Day 1 tweets here: http://t.co/DUTXJBqY
(2) iGenomics: Abizar Lakdawalla's blog on #AGBT abstracts. 17% on sample prep, 15% on targeted seq (exomes & amplicons) & 15% on informatics + others.
(2) BiotechMarketer: #notAGBT is neck and neck with #AGBT (and beating the snot out of #AGBT2012)
(2) lykkebak: Mark Adams, #JCVI, mentions #CLCbio as great software in his talk on NGS Technologies and Resources #AGBT2012 #AGBT http://t.co/aNhEUumt
(2) illumina: Danielle Perrin @broadinstitute : Hybrid selection, 15K whole exomes, ~3K whole genomes, and 12K custom pull-downs last year. #AGBT
(2) neilhall_uk: @illumina: @broadinstitute : 51 HiSeq systems, only 6 staff needed to run them #AGBT you can run 100 crapbio systems with 1 monkey.
(2) omespeak: But 13 people for sample prep! RT @illumina Danielle Perrin @broadinstitute : 51 HiSeq systems, only 6 staff needed to run them #AGBT
(2) omespeak: To explore function of unculturable microbes, JGI plans to sequence 300 novel bacterial genomes from single cells #AGBT
(2) LIFECorporation: Beach party at the Ion Bus!!!! http://t.co/lIgLhSTv #AGBT
(2) BGI_Events: Following the interesting tweets coming from #AGBT (and the wild speculation about our investment in SHTseqtechnology from #notAGBT).
(1) iontorrent: Win a free Ion PGM sequencer at AGBT! Collect Ion symbols at each Ion event, w/ four symbols you can register for PGM at Ion Lounge #agbt
(1) girlscientist: Tentative #AGBT tweetup: in hotel bar after Friday evening sessions. Look for me, @deannachurch, and @bffo.
(1) DNAgame: Beautiful day for DNA!!! #agbt http://t.co/9AKCYlwk
(1) StrandLife: Everyone at #AGBT should chat with our friends at Agilent to get the scoop on the exciting new updates in GeneSpring 12 - Integrated Biology

10 - 11am EST
+12m EpicentreBio: Live blogging from #AGBT by @Illumina scientists: http://t.co/HQ4Akx61
+20m girlscientist: Have just realized there is not yet a plan for #AGBT tweetup. Where and when, people? @deannachurch?
+30m stuka: Yep, all PIs & other such people at #AGBT, time to just slack off and do nothing for the rest of the week
+31m chloe46037: On the way to #AGBT, @girlscientist will have everything ready by the time I get there, right?... :)
+32m deannachurch: @girlscientist maybe after Friday evening sessions? #tweetup #agbt
+32m vitcarey: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: ... for whole human chromosome ... http://t.co/juyO73hS
+35m Verbal_SeduXion: @bongopondit FL? AGBT conf is it?
+35m notSoJunkDNA: @girlscientist Isn't #agbt a giant tweetup in itself? You'd better make a workshop session for attendees who are not yet on Twitter.
+42m GloriaAnderson2: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: Structural variations in human ... http://t.co/asIMfKGw
+48m bongopondit: @Verbal_SeduXion ah ok. If you want even more updates from agbt, will be tweeting stuff from my other a/c. Can send you link if interested..
+51m iontorrent: Win a free Ion PGM sequencer at AGBT! Collect Ion symbols at each Ion event, w/ four symbols you can register for PGM at Ion Lounge #agbt

11 - 12pm EST
+0m fluidigm: BYPASS library preparation? Learn more in Suite 285. #AGBT
+3m girlscientist: Tentative #AGBT tweetup: in hotel bar after Friday evening sessions. Look for me, @deannachurch, and @bffo.
+7m fluidigm: Prepare yourself for #AGBT with one of these, stop by Suite 285 to get one. http://t.co/iYXRh6XQ
+8m pathogenomenick: I'm being organised this year and am logging the #AGBT tweets for posterity. Day 1 tweets here: http://t.co/DUTXJBqY
+14m illumina: Blog post by Abizar Lakdawalla on Anticipating #AGBT: http://t.co/py652hSN
+26m omespeak: Hadn't evermore checked imo yet when got the first swag at #agbt
+27m omespeak: Hadn't even checked imo yet when got the first swags from Illumina at #agbt
+30m NorthernAutumn: @pathogenomenick #AGBT view. Weather sucks - can't you tell :) http://t.co/JZoQf7yL
+30m EdgeBio: Are you at #AGBT? Dont forget to check out @AGXP during the poster session on 2/16 & 2/17! #WhereisAB
+34m BlueSEQ: CrapBio, an exciting nth gen sequencing company from @neilhall_uk! http://t.co/qCeHZJwH (should we add this to http://t.co/nZzAM0nS?) #AGBT
+37m neilhall_uk: Stop what you are doing at #AGBT nanopore has been superseded already http://t.co/6WTuzBMC
+42m RainDanceTech: RDT customers showcase cancer research at #AGBT. More info @ http://t.co/FE3NlLQr. Also, visit Lanai #287 to see new ThunderStorm System.
+46m DNAgame: Beautiful day for DNA!!! #agbt http://t.co/9AKCYlwk
+47m neilhall_uk: #agbt follow #notAGBT if you want a chance to win a CrapBip ShtSeq. http://t.co/6WTuzBMC
+47m BlueSEQ: CrapBio, exciting nth gen seq from @neilhall_uk! http://t.co/43QqIwkd (should we add this to http://t.co/nZzAM0nS ?) #AGBT
+49m Copenhagenomics: It's nice to see #AGBT adopting a new open media policy, similar to our 'sharing is caring' from #CPHx last year. Let the tweeting begin! :)
+55m StrandLife: Everyone at #AGBT should chat with our friends at Agilent to get the scoop on the exciting new updates in GeneSpring 12 - Integrated Biology
+58m girlscientist: Laughing on plane to #agbt at #notAGBT track. Nice.

12 - 1pm EST
+0m fluidigm: INCREASE the number of amplicons per sample by 10X. Learn more in Suite 285. #AGBT
+5m thinkgenome: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: GAITHERSBURG, Md., Feb 15, 2012... http://t.co/ajyvlyXS
+7m pathogenomenick: woop de woop, #AGBT tweets streaming live (ish) to my blog now http://t.co/DUTXJBqY
+8m EdgeBio: The Flight in blog from #AGBT: Marco Island Never Gets Old via @dgaalaas http://t.co/RBMg7ExE
+11m dgaalaas: On a packed bus to #agbt. Feels like a combo of a TED conference and a Dead show. Miracle tix found at #notagbt.
+13m iGenomics: Abizar Lakdawalla's blog on #AGBT abstracts. 17% on sample prep, 15% on targeted seq (exomes & amplicons) & 15% on informatics + others.
+18m CLCbio: Looking forward to this year's #AGBT and meeting with a lot of interesting people!
+19m daweonline: Awesome! @neilhall_uk: #agbt follow #notAGBT if you want a chance to win a CrapBip ShtSeq. http://t.co/ojdO4Nvr
+22m BiotechMarketer: #notAGBT is neck and neck with #AGBT (and beating the snot out of #AGBT2012)
+33m Gavin_Oliver: Under 800 people at #AGBT according to the attendee list. Surely they could have let a few more in?
+38m EdgeBio: We have our first winner of our scratch off cards at #AGBT. James Han has won a $50 Amazon Gift Card! Congrats! #WhereisAB
+38m BioTeam: MiniLIMS for Ion Torrent PGM Sequencer Launched - http://t.co/THSGMk2S #AGBT
+40m dgaalaas: Nothing says #agbt like passing a Waffle House on the way in! http://t.co/V5XG6asZ
+56m geneiam: Wish I was at #AGBT maybe next year. Dr. Peter Meintjes is there to answer all of your #Biomatters #Geneious questions! #genomics

1 - 2pm EST
+0m fluidigm: 480 AMPLICONS per sample for targeted resequencing? Learn more in Suite 285. #AGBT
+14m GenomeBiology: Name badge on the beach or round pool, between or before sessions:uncool. #agbt
+17m djschlesinger: #AGBT on my way to opening remarks
+24m neilhall_uk: CrapBio launch SHTstorm bench top sequencer http://t.co/6WTuzBMC #AGBT #notAGBT
+29m omespeak: Off to the pre-conference workshop. And this is what we scientists are giving up in pursuit of knowledge http://t.co/YgcVzS7Q #AGBT
+31m ShellPear14: Ready for AGBT Ion/QuantStudio simulcast
+32m EdgeBio: Just arrived at #AGBT, looking forward to a great week! #whereisAB
+33m UK_Biomek: Heard #AGBT described as the 'Glastonbury' of scientific meetings. I hope the toilets are nicer!
+41m lykkebak: #JCVI Mark Adams 'Drowning in NGS data'. First talk at #agbt #AGBT2012 http://t.co/LDd1Awh9
+45m djschlesinger: Mark Adams, JGVI - giving us an intro to NGS and WGS. #AGBT
+51m omespeak: "there is now a considerable nomenclature drift in nextgen sequencing...." Mark Adams of JCVI :) #AGBT
+53m djschlesinger: Mark is reviewing Lam paper comparing Illumina and Complete Genomics WGS. says 88% concordance is pretty good. Will we ever see 100%. #AGBT

2 - 3pm EST
+0m dwmohr: #agbt full marketing mode
+3m lykkebak: Mark Adams, #JCVI, mentions #CLCbio as great software in his talk on NGS Technologies and Resources #AGBT2012 #AGBT http://t.co/aNhEUumt
+11m djschlesinger: Danielle Perrin is discussing NGS workflow at Broad. #AGBT
+18m intrepidbio: MT "@djschlesinger: NGS equipment at the @broadinstitute. http://t.co/YivTMUKy" Our system can handle NGS and SNP data. #AGBT
+20m illumina: Danielle Perrin @broadinstitute : Hybrid selection, 15K whole exomes, ~3K whole genomes, and 12K custom pull-downs last year. #AGBT
+21m AppliedBio: And we are live from Marco Island at #AGBT. Keep the questions coming. http://t.co/3hQ3IknR
+21m neilhall_uk: @phylogenomics: Completely brilliant: A new sequencing technology enters the ring: SHTseq(TM) http://t.co/wnsfWc6K #AGBT #notAGBT
+27m SicOnlineCoach: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ... http://t.co/mRso6FVf
+27m illumina: Danielle Perrin @broadinstitute : 51 HiSeq systems, only 6 staff needed to run them #AGBT
+28m NJL_Broad: Great talk by Danielle Perrin of @broadinstitute at #AGBT
+30m fluidigm: MULTIPLEX up to 384 unique samples per sequencing run. Learn more in Suite 285. #AGBT
+31m djschlesinger: Thomas Keane from Sanger discussing approaches and challenges of resequencing #AGBT
+34m caddymob: AGBT
+35m djschlesinger: Keane says storage and computing power are the biggest challenge. Wasn't that the same story last year. Where are the solutions? #AGBT
+36m Symbionticism: #AGBT pic. Nice set up. http://t.co/GmwAKovY
+37m iontorrent: Ion Sequencing Seminar at AGBT Thurs, 5:20 pm, Hilton : Sean Grimmond, Marilyn Li, Tim Triche, Niall Lennon and Jonathan Rothberg #agbt
+37m omespeak: Scaling up of next gen sequencing is producing so much data it's sarurating local power grids in rural UK! (Thomas Keane of Sanger) #AGBT
+37m neilhall_uk: @illumina: @broadinstitute : 51 HiSeq systems, only 6 staff needed to run them #AGBT you can run 100 crapbio systems with 1 monkey.
+40m omespeak: Only three talks into #AGBT and already two of them underlining the sequencing data deluge.
+42m djschlesinger: Keane says 10 bytes of storage per bp, adds up to 200 terabytes by end of year. #AGBT
+43m GenomeBiology: Uk10k project, uses 10bytes data per bp (Thomas Keane) #agbt
+49m nygenome: Just in time for AGBT, our new website is live! Check us out at http://t.co/RvU3J2xy, and let us know what you... http://t.co/bKmZrjor
+50m nygenome: NYGC just arrived in Marco Island for AGBT 2012. If you are here, we'd love to meet you. Check out our online... http://t.co/MtinC6Xt
+51m AppliedBio: @iontorrent Sequencing on the beach... Nice! #IonBus #AGBT
+52m nygenome: Just in time for AGBT, our new website is live! Check us out at http://t.co/RvU3J2xy, and let us know what you think.
+54m omespeak: First mention of fast (one day) high-depth genome data: from Illumina HiSeq 2500 (Thomas Keane outlining future challenges of data) #AGBT
+54m nygenome: Speaking of AGBT, NYGC just arrived in Marco Island. Drop by our suite! Our presentation schedule is online: http://t.co/95pn6py8
+54m steinpal: If you wanna know just how nerdy biotech can be, search #notAGBT. #AGBT
+57m EmilyGreger: TRADE NEWS: Agilent Technologies Extends Target-Enrichment Platform to Desktop ...: (BUSINESS WIRE)--(AGBT)--Agi... http://t.co/xSDZjqIs

3 - 4pm EST
+10m maitrehipster: Why cost of sequencing is not a real metric @djschlesinger: Keane says storage-computing biggest challenge. Same story as last year. #AGBT
+14m illumina: Thomas Keane @sangerinstitute :UK10k, 4k WG, 600 exomes, 2K twins. 100 Tbp total, 40 Tbp from BGI. Complete by first half 2012! #AGBT
+29m djschlesinger: Matthew Blow from JGI up next to talk about De Novo assembly, #AGBT
+44m djschlesinger: Matt is now talking about microbial metagenomes using single cell sequencing. Very neat. #AGBT
+45m illumina: Keane @sangerinstitute : #NGS storage challenges, expect 2K Tb sequence in 2012. New file formats needed - CRAM. #AGBT
+48m omespeak: Joint Genome Institute (JGI) plans to sequence 300 novel single cell bacterial genomes to explore function of unculturable microbes. #AGBT
+48m djschlesinger: JGI has sequenced the genomes of 20 "unculturable" microbes. I wish I had this technology in grad school! #AGBT
+49m bongopondit: To explore function of unculturable microbes, JGI plans to sequence 300 novel bacterial genomes from single cells #AGBT
+50m Personal_RX_WI: #agbt 3 hours in. JGI using PacBio to fill gaps in genome assemblies. MCW to do the same.
+50m omespeak: To explore function of unculturable microbes, JGI plans to sequence 300 novel bacterial genomes from single cells #AGBT
+54m Symbionticism: #AGBT Matt Blow from jgi shows that pacbio + Illumina improves assemblies vs just illumina, but did not show pacbio data alone as control.
+55m girlscientist: Thank you to @pathogenomenick for already logging the #AGBT tweets! http://t.co/lFfSXrxJ
+56m djschlesinger: Shawn Levy from Hudson/Alpha inst. for Biotech up next to talk about transcriptomics #AGBT
+56m NorthernAutumn: @NuGENInc also has chocolate covered strawberries for #AGBT In the Sanibel Suite. Come on by.
+57m illumina: Matt Blow @doe_jgi ~1,150 microb, ~78 fungi, ~5 plant, 483 metagenomes & 300 single cell microbes to be seq'd in 2012. #AGBT
+59m NorthernAutumn: @NuGENInc Chocolate covered strawberries for #AGBT. Come by Sanibel Suite to get yours http://t.co/M5VUU1wj

4 - 5pm EST
+0m fluidigm: ANALYZE large sample sets across focused genomic regions. Learn more in Suite 285. #AGBT
+1m omespeak: Finally a speaker who has his own Tweeter feed, Shaw Levy (@genomicslab) from @hudsonalpha. #AGBT
+3m UK_Biomek: If you are at #AGBT then feel free to say hello to our colleagues from BC Genomics. There to answer all your SPRIworks questions!
+4m zerojinx: Lah de dah. Sequencing data deluge: Get over it. #AGBT
+7m CompleteGenomic: Attending #AGBT? Visit us in the Complete Suite (Everglades Room) for customer presentations, demos & interactive tech talks.
+7m iontorrent: informal yoga session tonight @5-6PM on the Palms Lawn in front of the Palms Terrace on the N. side of the Marriott. #AGBT
+11m bioinfosm: #agbt or #notAGBT : it's about sweet or sour grapes :p
+11m Symbionticism: #AGBT Shawn Levy at hudson alpha talks about transcriptomics work with Vanderbilt's Andy Link. Cool.
+14m nabsys: Come see our posters at #AGBT: 36, 265, and 352.
+15m Symbionticism: #AGBT Shawn Levy asks do u really want single cell rna data? Much more variability. Bulk data gives better consistency. Still need reps.
+15m CocoaTresbelle: TRADE NEWS: Agilent Technologies Extends Target-Enrichment Platform to Desktop ...: (BUSINESS WIRE)--(AGBT)--Agi... http://t.co/Iroo19UF
+17m neilhall_uk: @bioinfosm: #agbt or #notAGBT : it's about sweet or sour grapes :p SOUR GRAPES! ours is a better meeting. without the hype!
+19m illumina: For all your #AGBT news, tweets & events, check out Live at AGBT, featuring real scientists & real commentary: http://t.co/py652hSN
+22m djschlesinger: Olivier Elemento from Weill Cornell Medical College discussing Epigenomics #AGBT
+43m GenomeBiology: Olivier Elemento discusses HiC viewer #agbt
+43m dbetel: Excellent epigenomics tour de force from @ElementoLab at #AGBT.
+44m djschlesinger: "Sequencing as an Assay", Lisa White from Baylor up next. #AGBT
+53m djschlesinger: White says that doctors only care about tests that are clinically actionable. #AGBT - how is exome or WGS clinically actionable?
+57m mendelspod: Positional Sequencing: Barrett Bready of @NABsys | http://t.co/AA6jwSZt http://t.co/bULjboGB #AGBT

5 - 6pm EST
+1m mendelspod: Sequencing: An Overview with Shawn Baker, @BlueSEQ | http://t.co/AA6jwSZt http://t.co/bULjboGB #AGBT
+1m froggleston: Good afternoon session on experiences with PacBio data. Enjoyed application of GATK for variation discovery. More #agbt action imminent.
+6m KamounLab: @neilhall_uk @bioinfosm Forget about #agbt #notAGBT conference to follow is #LGD2012 Lausanne Genomics Days 2012 http://t.co/zFitLSBu
+6m djschlesinger: White gave an example of a clinical exome test result: 1000+ variants that need review #AGBT - how long does that take?
+9m ElementoLab: #AGBT LW: it takes 6-7 months to get an operational CLIA lab ... having to CLIA compliance officer in house key
+10m djschlesinger: Eric Johnson from the Univ. of Oregon up next to talk about "Genotyping by Sequencing" #AGBT
+11m Personal_RX_WI: #agbt Very interesting talk from Lisa White from Baylor. Sequencing in CLIA environment.
+13m NJL_Broad: So far I've seen PacBio room keys, and Ion torrent coffee cup sleeves #AGBT #productplacement
+13m ElementoLab: #AGBT Eric Johnson: genotyping by sequencing
+15m neilhall_uk: CrapBio early access customers @jgskenny @Christi_Fowler at #AGBT see them to find out about our technology http://t.co/MH080gUt #notAGBT
+16m ElementoLab: #AGBT EJ talking about his RAD protocol
+17m illumina: Interesting talk from Lisa White about #NGS in CLIA lab. A complex circle from patient sample back to patient destiny #AGBT
+19m NorthernAutumn: Eric Johnson UofO GBS=geno by seq DNA quality&quantity, mutiplexity, NGS error rates & under-sampling. All contribute to errors w/GBS #AGBT
+20m TheRealDrT: To everyone who is attending #AGBT, be sure to stop by @nygenome! #nygenome http://t.co/zL9cXfGE
+20m ElementoLab: #AGBT used RAD to identify mutations in C elegans
+20m BioTeam: @nygenome reception at 5:30 in suite 183 #AGBT
+21m ElementoLab: #AGBT EJ: C elegans study was to map genotype to phenotype in large collection of segregants
+22m GloriaAnderson2: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: Structuralvariations in human c... http://t.co/mKq4J3DP
+23m illumina: Eric Johnson, Univ Oregon: Reproducibly sequencing subset of the genome IDs novel changes. Reduced cost, but lower throughput. #AGBT
+23m ElementoLab: #AGBT EJ: in fish RAD could interrogate 8406 markers
+23m ElementoLab: #AGBT EJ: few in gene regions though
+24m ElementoLab: #AGBT EJ: did local assembly of RAD fragments -> contigs
+24m notSoJunkDNA: Very cool High School student summer project! http://t.co/ZmnCeOsN @GenomeBiology: Olivier Elemento discusses HiC viewer #agbt
+24m ElementoLab: #AGBT EJ: 729bp average size of contigs
+25m ElementoLab: #AGBT EJ: fish is a teleost btw
+26m ElementoLab: #AGBT EJ: some contigs identified genes in this non sequenced genome
+27m ElementoLab: #AGBT EJ: stickeback application: find genetic signature of adaptation to lakes
+28m ElementoLab: #AGBT EJ: can interrogate genetic basis of complex phenotypes like predation
+29m ElementoLab: #AGBT EJ: his local assembly approach can work on repeat regions
+29m ElementoLab: #AGBT EJ: RAD combines nicely with RNA-seq for exotic genomes
+30m ElementoLab: #AGBT EJ: work is published, can check it out, open to collaboration (exotic genome anybody?)
+31m ElementoLab: #AGBT final session remarks by Ken Dewar ... last year was small room, this year 100+ people attended tutorial session
+37m maitrehipster: @djschlesinger: White gave an example of a clinical exome test result: 1000+ variants that need review #AGBT - how long does that take?
+39m maitrehipster: More crap from sweatshops... @NJL_Broad: So far I've seen PacBio room keys, and Ion torrent coffee cup sleeves #AGBT #productplacement
+45m ING_SYS: @maitrehipster @djschlesinger -it takes just minutes to ID relevant variants from thousands. Stop by Lanai 179 right now for a demo #AGBT
+46m ING_SYS: @maitrehipster @djschlesinger - we also have beer and wine in Lanai 179 #AGBT
+55m djschlesinger: Jay Flatley making some bold (and valid) comments about Life and their marketing tactics. #AGBT

6 - 7pm EST
+4m illumina: Jay Flatley: Broad Institute now in the Illumina Genome Network, enables FFPE and low input samples. #AGBT
+8m omespeak: Off to see the #IonBus. #AGBT
+9m illumina: Full house at the Illumina User Group Meeting! #AGBT http://t.co/bDMEEy7n
+9m dgmacarthur: Tweets from #AGBT are now streaming in. Be sure to also follow the hilarious snark-stream over at #notAGBT.
+12m vitcarey: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: This novelapplication will allo... http://t.co/S7GHJpKd
+13m mishimahryk: #AGBT#notAGBTw
+16m CrapBio: #AGBT Don't go to Yoga at 7:15 in the Agilent suite. join CrapBIO for skinny dipping on the beach at 7am #notAGBT
+38m schnablep: At #AGBT meeting on Marco Island. Here's the agenda: http://t.co/1K2yOKse
+42m illumina: HiSeq 2500 "Genome in a Day" data viewable in BaseSpace: http://t.co/ijERyA0X #AGBT
+44m bio_insilico: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ... - Business Wi... http://t.co/UzImdKkD #biotech #genomics
+45m Personal_RX_WI: #agbt Penn State using MiSeq to genotype by sequencing polar bears. Very cool.
+46m illumina: Geoff Smith, Illumina UK: Longest perfect overlapping read so far on #MiSeq 678 bp! #AGBT
+54m illumina: 4 whole human genomes on 1 USB drive, w/family trio & Genome in a Day datasets gift to all at our User Group mtg #AGBT http://t.co/AubRVWjy

7 - 8pm EST
+1m neilhall_uk: @jennifergardy there is still time for a keynote keynote at the #notAGBT meeting which is more prestigious than #AGBT
+9m drnaveedaziz: #AGBT
+19m sclancyphd: #Genome #Sequencing on beach @Marco Island, Fla #AGBT. Sea life from #Gulf aboard #Ion Torrent bus from @LifeCorp. http://t.co/5ZMJZMjL
+57m agxp: Join us tomorrow at @AGBT poster 170 at 1:10 pm EST for a cup of coffee, and to learn about the Archon Genomics X PRIZE.
+57m Symbionticism: #AGBT pic. Evening reception is very nice. Agilent sponsored. Can u hear the acoustic guitar players too? http://t.co/FSykf36l

8 - 9pm EST
+17m NorthernAutumn: Warm evening with lights and music #AGBT http://t.co/NiuqWPfn
+24m ofedrigo: AGBT: Not sure if MiSeq kicks ass or if Illumina speakers are better than Ion Torrent speakers...
+27m jgreid: At AGBT visiting the Ion bus http://t.co/ek9EvjLV
+55m BGI_Events: Following the interesting tweets coming from #AGBT (and the wild speculation about our investment in SHTseqtechnology from #notAGBT).

9 - 10pm EST
+43m girlscientist: On the beach looking at the stars with a margarita. Working hard for science. #AGBT

10 - 11pm EST
+10m EdgeBio: Don't forget to check out Views From Edge Blog: #AGBT Marco Island Never Gets Old via @dgaalaas http://t.co/l6gZE3J1
+28m froggleston: Future is sequence data piped directly into a proprietary cloud. Not convinced. Musing this over a peculiarly named 'Cigar City' beer #agbt
+30m SEQanswers: Was hoping for real snark, lets hope not four more days of bad #SHTseq puns. #notAGBT #AGBT #pooisfunny
+35m SEQanswers: Question of the conference: workflow for desktop sequencers. #AGBT
+40m spiremk: @SEQanswers as in simplified or standardized? Pls elaborate #AGBT
+45m SEQanswers: Open this system, please. #drool @illumina: Geoff Smith, Illumina UK: Longest perfect overlapping read so far on #MiSeq 678 bp! #AGBT
+57m drio: if any of my followers is at #AGBT let me know so we can hang out. cheers.

11 - 12pm EST
+25m PacBio: @Tao_zt Yes, we will post some on our website (after AGBT) - those where we get permission
+30m PacBio: At #AGBT ? RSVP for Thurs 2/16 Dinner & Panel discussion led by Eric Schadt on fighting infectious disease in year 2030 http://t.co/hS3WJP40
+32m PacBio: #AGBT RSVP to 2/16 Dinner & Panel Talk with Marc Allard (FDA), Adam Phillippy(Battelle), Matt Waldor (Harvard), Eric Schadt (PACB/Mt. Sinai)
+1m apfejes: I miss #agbt... Hope everyone is having a great time - and thanks to all who are attending for the great tweets!
+1m druvus: Catching up by reading the first day tweets #AGBT

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It’s an immensely useful tool and one we encourage you to use here with Hyde.

Find out more by visiting the project on GitHub.

Ion Torrent Proton Announced: The Chip Is (Not) The Machine

Big announcement today from Life Technologies who have announced the Ion Torrent Proton(tm). This, to all intents and purposes is the PGM-2, the second iteration of their pH-meter-on-a-chip sequencing machine. Indeed it is curious they have dropped the Personal Genome Machine moniker, as this product is the first to explicitly target the $1000 (human) genome market in benchtop format. So what do we know so far?

* Mid-2012 launch for early access customers, Q3 for general release
* $149,000 list price (compared with $50,000 for the PGM)
* Two chips announced
* Ion Proton 1 available at launch - 165m sensors (cf ~12m for the 318 chip and ~1m for the 314 chip)
* Ion Proton 2 in early 2013 - 660m sensors
* Update: 14:28 GMT - According to GenomeWeb, Ion Proton will also require purchase of a $75,000 server

[caption id="" align="alignright" width="300" caption="The iPod dock is gone, as have the milking tubes"][/caption]

Eric Olivares over at Seqanswers.com already did the critical calculations. Assuming a 250bp read length you could expect between 3 and 6 exomes at 100x coverage with the Proton 1 chip, and between 1-1.5x whole human genomes at 30x with the Proton 2.

How will this be acheived? Looking at the picture the chip size is visibly larger, but the increase in area (assuming the picture shows normal sized hands!) is not sufficient to account for the increased number of sensors, implying the wells are closer together and/or smaller than existing Ion chips.

[caption id="attachment_952" align="alignleft" width="300" caption="Proton chips are bigger than the previous generation"][/caption]

So, what to think about this announcement?

Well, the specs are certainly impressive and this is the first concrete evidence demonstrating continued log-scale improvements using the Ion Torrent technology after the 318 chip, something the Life Tech roadmap has deliberately not spelt out until now.

However, I have to admit to being a bit disappointed that this is an entirely new machine coming in at three times the cost of the original machine. It turns out unlike what we have been told countless times at presentations, the chip is not actually the machine. Whilst no surprise to anyone that has looked at the technology carefully, this may be a disappointment to those who just received or ordered their Ion Torrent PGM and have bought into the marketing wholesale. Are  customers now looking at taking delivery of a machine that has hit its performance ceiling as early as mid-2012? We don't know how this announcement affects the PGM1 roadmap, it would be nice to get reassurance on this point. Update 14:31 GMT - GenomeWeb report an Ion Torrent marketing director as saying "The electronics on the PGM were built to handle chips of 1 million to 10 million sensors", which seems like confirmation that the 318 chip hits their density ceiling. However read lengths can still increase to generate additional throughput.

This announcement also has resonance for Ion Torrent's constant comparison to the computer and semiconductor industry. Was it really a wise move to announce a PGM-killer so early into this machines life? I am thinking specifically of the Osborne effect. This is the act of announcing an improved model early, in this case Osborne with their early portable computers, "to reassure current customers that there is improvement or lower cost coming, to increase the interest of the media and investors in the company's future prospects, and to intimidate or confuse competitors".  The announcement can actually have the an unintended effect that customers see something better on the horizon and defer their buying decision.

If I was about to buy a PGM, would I now hold off for the Proton? Life Tech will be keen to target the PGM at cheaper "small genome" applications and the Proton at human genome scale, and this will be fine for many users, perhaps those wanting to replace amplicon sequencing done on capillary sequencers with high-throughput instruments. Me personally, I'd always want to buy the most fully-featured instrument available, akin to choosing a new laptop (which you know will be out of date before it is switched on for the first time). In bacteriology we are moving from 16S amplicon studies and whole-genome studies of single isolates to sequencing of entire communities as metagenomes. Such studies benefit from as much throughput as possible.

It will be fascinating to see how this announcement plays out during the year, particularly so close to AGBT where there is reasonable expectation some new "killer" sequencing platforms will be announced.

Have you just bought a PGM? What do you think? Leave a comment below. Also please head over to Seqanswers.com to read more discussion.

Happy New Year!

2011 Review of a Remarkable Year

2011 has been a remarkable year for me, during which I have travelled widely, met lots of interesting people, recruited substantial grant funding and had a paper published in the journal with the highest impact factor of them all! So, at the risk of producing one of those cheesy round-Robin letters that get stuffed in with Christmas cards, here is a personal round-up of all the exciting things that have happened to me in the last 12 months!

In January, there was a visit to Birmingham by Secretary of State for Health Andrew Lansley, Surgeon General Vice Admiral Philip Raffaelli and Chief Medical Officer Professor Dame Sally Davies to announce the launch of a new multi-million-pound NIHR Surgical Reconstruction and Microbiology Research Centre focused on trauma patients. I had had to write the microbiology component of the bid for the centre in 48 hours a few weeks before and I was amazed at the speed with which the announcement was made. On the plus side, this is going to provide us with an unrivalled opportunity to explore the potential of high-throughput sequencing in the microbiology of trauma patients over the next five years. On the minus side, securing the funding for the centre, even though the outcome was announced back in January, has proven the most bureaucratic and procedural process I have ever encountered. It was not until December that we actually started spending of the money! But mustn't look a gift horse in the mouth--the centre will be funding a MiSeq from March next year, which will provide a welcome boost to our sequencing capacity.

More info on this initiative here:

• http://www.uhb.nhs.uk/news/qehb-to-host-national-trauma-centre.htm
• http://www.bbc.co.uk/news/uk-12229116

In February, I hosted a visit to England of Eugenie Scott, director of the US National Center for Science Education. Genie gave a Darwin Day talk at the University of Birmingham. I also arranged for us to visit Down House with our well-informed and congenial host Darwin descendent Randal Keynes (father of the movie star Skandar Keynes).

Watch our trip on YouTube:

Later that month, I visited Lausanne, a charming town on Lake Geneva in Switzerland, to celebrate the award of an Ion Torrent PGM. I was one of two winners (out of ~150 entries) in the Ion Torrent PGM Grants Program in Europe. Check out the blog post from the time and this interview, which they filmed in the hotel in Lausanne

In March I attended a conference in Cape Town held by the African Society for Bioinformatics and Computational Biology. This was my first trip to this remarkable country. Highlights of the trip included a visit to the University of Cape Town, to the Cape of Good Hope, to Table Mountain and to Robben Island and watching a San bushman create fire! And I even dusted down an old rather idiosyncratic interest of mine and met some African Esperantists.

Later that month the Ion Torrent PGM arrived. Nick Loman delighted in photographing it covered in slinky plastic: Hot Ion Torrent Action!

April was a quiet month. The one signficant event was that our Vice-Chancellor decided that the University of Birmingham needed its very own Institute of Microbiology and Infection.

May, on the other hand, was very busy! My then 15-year-old daughter Emma did work experience with me at the University. She gave a short lecture on the differences between bacteria and viruses during which she appeared ever inch the professional academic. One of her friends pointed out how cool it was for her to have worked at a university before studying at one! In May, I also heard that my book The Rough Guide to Evolution had been chosen for the new Great Read at Birmingham initiative, which meant that in September 2011 it was given out to 6000 undergraduates at the University.

In the second half of the month I attended the American Society for Microbiology meeting in New Orleans. I organised a session on high-throughput sequencing and gave a talk of my own. It was great to see the home of Tremé and meet lots of interesting people (Jennifer Gardy, who was co-organiser of the session, Mike the Mad Biologist, Jonathan Eisen). En route I also made my first visit to NYC, which was fascinating.

Towards the end of the month I spent a week-long family holiday in France, just as the German STEC outbreak was kicking off. That week, DNA from an STEC isolate was sent from Hamburg to BGI-Shenzhen, where it was sequenced on their trial model of the Ion Torrent PGM.

In early June I returned to the UK to face two remarkable surprises. The first was an invitation to appear on BBC Radio 4's high-brow discussion programme "In Our Time" with the well-known presenter Melvyn Bragg. On the night of 8th June, the BBC put me up at a posh hotel next to Broadcasting House. I didn't sleep well and at 5am got up and practiced my spiel. The show went out live from 9.00am. But with just four of us huddled around a table in the studio, it was hard to believe that a million or more were listening. As it turned out, Bragg deviated from the list of questions I had been given, but there were no hitches (Links: The programme; my notes ). A friend later comment on my posh Radio 4 voice. I often listen to the "In Our Time" when it is broadcast a second time on Thursday evenings, while waiting to pick up my son from scouts. That proved a surreal experience that evening, as I listened to myself and then excitedly explained to the scoutmaster that it really was me on the radio!

The second surprise started with Nick Loman filling me in on the crowdsourcing efforts that he had jump-started with his assembly of the BGI's Ion Torrent data. I was initially dismissive of all this activity on social media, in the absence of any plans for a peer-reviewed publication. Nonetheless, I agreed to contact the BGI and the German team who had sent the DNA to BGI. To start with, such efforts got us nowhere, but then quite suddenly at midday on Tuesday 28th June I received a phone call from Martin Aepfelbacher, head of the unit in Hamburg, inviting us to join their efforts in analysing the data and writing a paper for the New England Journal of Medicine. This great opportunity came with a catch: we had to have a newly drafted paper and a fresh defensible analysis ready within just over 48 hours! Two days of furious paper writing on my part and bioinformatics analyses on Nick Loman's part culminated in a paper that concentrated on the journey to the genome sequence through what we called Open Source Genomics as much as on the sequence itself.

As we moved into July, it was a fraught time as we waited for the editor's verdict, but when she said that she had started editing our draft, I began to believe we really were going to get the paper published! A couple of weeks later, I had to let down my colleagues by bunking off a local microbiology showcase event to put the finishing touches to the final draft. The paper was duly accepted and we heard that we were going to appear back-to-back with a paper headed up by Dave Rasko on the use of Pac Bio sequecning on the outbreak strain and its relatives.

In August, our NEJM paper was published and Nick and I made a flying visit to Hamburg to share some champagne with our German collaborators, Martin Aepfelbacher, Helger Rohde and Moritz Henschke, who proved excellent hosts.

In September Dave Rasko visited Birmingham and we celebrated our joint success with a meal and yet more bubbly!

I spoke at the Prokagenomics 2011 meeting in Göttingen, which gave me a chance to enjoy some Oktoberfest drinks with Andreas Leimbach, who was a co-author on the very first paper to appear on the STEC genome sequence, and to see this wonderful university town.

I made a slidecast of my talk and vowed to try to engage in open scholarship for the coming academic year, putting all my teaching and research talks into the public domain (check out my YouTube channel).

The last week in September saw the launch of the Great Read at Birmingham initiative, which prompted visits to Birmingham of some amazing guys: Ken Miller, John Hawks, Captain Ben Kirkup and Chris Stringer (see my other blog, The Rough Guide to Evolution for more details).

During October, I participated in and live tweeted from the Applying Advanced Molecular Techniques to Healthcare Infection meeting at Hinxton Hall near Cambridge and also visited Oxford twice in one week, once to lecture doctoral students on Darwin, evolution and microbiology (http://www.scienceandatheism.com/2011/10/13/the-dirty-truth-about-darwin/#.Tv7UDmCJz0s) and once to give a seminar at the Dunn School of Pathology. In the middle of the month, I played grumpy bad cop in 29 one-hour interviews for Birmingham Fellows scheme, which brought me face to face with a wonderful variety of academics and the pursuits. I was stuck with the question "why aren't you publishing in Nature yet"; but quite fairly asked the same miserable question of everyone!

The highlight of November was a performance of the Rap Guide to Evolution for Birmingham students by Baba Brinkman, who flew over from Manhattan specially. Before the show, we filmed a variety of people from the University lip-synching to Baba's I'm a African track against a green screen: two Indians, two Greeks, an Afghan, a number of Europeans, plus some people with African ancestry more recent than 70Kya! I am looking forward to seeing how it all ends up looking in the video made to accompany the track on Baba's UK Rap guide site.

In December, I got to meet several more exciting people. Gabriel Waksman gave a superb seminar on the structural biology of fimbrial biogenesis. Kevin Peterson gave a great Huxley Lecture that deftly wove together the Cambrian Explosion and the proliferation of microRNAs in metazoan genomes (take a look at his recent Science paper). Scott Edmunds visited and gave us the BGI's perspective on the remarkable series of events that summer that culminated in our joint NJEM paper--he is one of a handful of westerners who works at BGI-Shenzhen. We celebrated our success yet again, this time with a curry and a very large nan bread.

The year was capped off nicely with a success in gaining BBSRC funding as co-investigator on E. coli nucleoid structure with Steve Busby, plus the launch of an online presence for our new Institute of Microbiology and Infection at Birmingham as iMicroBham. And we got another key paper on the German STEC genomes into the review process (fingers crossed!). And I started work on my next book, The Last Days of Smallpox. Oh and something else wonderful happened in December, but I won't be able to tell you about it for a few more weeks.

So, here's to a remaarkable 2011 and, let's hope, to an equally or even more remarkable 2012!