Tuesday, August 31, 2010

Human microbiome project meeting (HMP2010) Day 1 wrap up w/ mea culpa

Well, Day 1 of the Human Microbiome Project meeting is over. And overall, I think it was quite good. So now for a Day 1 wrap up.

First, a bit about the meeting. The meeting is formally called the "Human Microbiome Research Conference" and more information about it can be found here. It is directly tied to the NIH "Human Microbiome Project", also known as the HMP, which has been in operation for a few years now. The HMP is one of a small number of NIH "Roadmap" initiatives (these are also known as NIH Common Fund Projects). These are cross cutting projects that are funded outside of the normal NIH departments/centers. The HMP started a few years ago and is focused on studies of the communities of microbes that live in and on humans. The HMP has so far funded a wide array of projects including some big scale and some smaller scale. This meeting is I think the first to try to cover the diversity of different projects funded by the HMP at once.

Day 1 covered a bit of introduction and then a diversity of HMP related and some not so related (but good) talks. The talks were perhaps a bit too reviewy for my liking, but I think actually, all of them were interesting. Some lessons I got from today include the following:

  1. The human microbiome is becoming a fascinating area of research with an ever growing set of data to look at
  2. The data for the HMP seems to be openly available, which is good. Reference genomes can be found here. Some rRNA data can be found here. Strains of microbes are available too. Not sure where the metagenome data.
  3. Ease of access and use of data is more important than just access to data; the HMP DACC is doing a decent job with helping access data.
  4. As important as access is metadata about samples. Not sure how much of this is available right now nor how easy the metadata is to make sense out of.
  5. As with most (all?) large scale, top down projects, there are multiple areas where improvements could be made in communication and engagement with the broader community. It seems like the HMP is working hard on this issue.
  6. There are some possible complicated issues around release of microbiome data and medical records from people
  7. There is still a big risk in overselling the potential benefits of microbiome research
  8. Correlations ≠ causation. Sorry I had to put that here. See #5 above.
  9. Analyzing and making sense of metagenomic data is still very very hard
  10. We desperately need more ecology driven studies of the microbiome
  11. To me, the HMP should really try to mimic the human genome project and focus on producing reference data (genomes, metagenomes, and rRNA) for everyone to use. Trying to do complex scientific/clinical studies in this project seems inappropriate. We all need the baseline to do the science.
  12. As with every meeting, the best stuff that happens is in between talks.
  13. Having the meeting room be something like 40 °C is probably not the best idea nor use of resources (hotel issue, not HMP issue).

Those are some of the lessons I am thinking about now, a few hours after the last talk. But if you want to get a "real time" feel for the talks, the best way to do this, if you weren't here, is to look at twitter posts about the meeting. If you do not know, the common practice these days is to use a code within twitter specific for the meeting called a hashtag. For this meeting the hashtag is #HMP2010 and you can find the tweets about the meeting easily by searching twitter for this code. There were other twitter posts about the meeting, but may be somewhat hard to find b/c they did not use this code. Such is life I suppose.

Anyway, if you want to see all the tweets from the first day of the meeting with this hash tag I have appended them at the bottom of this email. This includes anyone who may have reposted (aka retweeted) these tweets to their twitter feed.

As I have tweeted many meetings I guess I am used to various aspects of such activities but many out there clearly are not. Live tweeting a meeting is a rough thing in many ways, at least for me. I want to give people a feel for the meeting, as it happens. I want them to know what I actually think about talks, at least within some reasonable limits. But alas sometimes, hopefully not too often, I get things wrong. And sometimes I post something obnoxious. And sometimes I miss key points. To me, this is analogous to the conversations people have about talks all the time. Overall, I think mostly I do an OK job tweeting meetings. But occasionally I write something that does not sit right with others or myself. And alas, today has one such tweet (well, only one I know of right now).

It happened during Brice Birren's talk. Birren, from the Broad, was discussing a few different things including studies done by the Broad in which they have tried to compare and contrast and use rRNA PCR studies done at different centers associated with the HMP. Much of what he was discussing was technical details of the control experiments they did to assess how variable the results were between centers. I felt at the time that he was placing this work in enough of the context of other rRNA studies of the human microbiome. And I tweeted this feeling.
phylogenomics
Birren presenting clustering of samples based on rRNA analysis - but could do much better referencing prior lit on this #HMP2010
phylogenomics
Birren - given that they trust their PCR, now comparing many human samples - seems like they are way behind the field here #hmp2010
But in the end, after discussions at the bar later, I think I may have missed the point of his talk. I thought at the time that he was discussing solely new findings and new analysis tools that they developed. To me, I did not like that he did not spend much time discussing other analysis tools nor how their work compared to other studies of the human microbome. And that gnawed at me.

But in retrospect, I think perhaps he was focusing more specifically on the comparison across the centers. In that context, the way he laid out his talk and what other work he referenced makes more sense. I think perhaps he could have still placed things in a broader context but my comments in retrospect were a bit over the top and unnecessary. As I said above, I think it is useful to try and post what I am actually thinking at the time. I try to filter this if I know what I am thinking is rude, biased, obnoxious, etc; but I do post critiques if they seem relevant. But my filtering was a bit off here. Alas, now Bruce (if he reads twitter) probably wants to dump a beer on my head and people from Broad think I am a putz (well, some may have thought that before). I guess I may have to change the tuning on my filter a bit ... but I still will try and post what I think at the time. It is a fine balance I do not always do precisely ... off to sleep and in the AM - Day 2 plus time to make some in person apologies ...



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Here are the tweets from Day1: The start with the most recent at the top, so if you want to start from the beginning, scroll to the end. I am going to try and post a prettier version of this ASAP but working on some html pasting issues ...




  • Molecularbond

  • Quickly catching up on the Human Microbiome Meeting news before lecture starts. Thanks to @phylogenomics for good tweet action! #HMP2010 about 7 hours ago via Twitter for iPhone

  • TheGenomeCenter

  • Thanks to @GenomeScience, @phylogenomics, @westr, @genomeresearch and others for the retweets! #HMP2010 about 8 hours ago via TweetDeck

  • TheGenomeCenter

  • Pop: Bambus 2 software http://bit.ly/cxuKzk that can be used with output from most assemblers #HMP2010 about 8 hours ago via TweetDeck

  • TheGenomeCenter

  • Mihai Pop: repeat detection difficult in metagenomics since depth of coverage different in organisms (some abundant, some not) #HMP2010 about 8 hours ago via TweetDeck

  • TheGenomeCenter

  • Mihai Pop: assembler must work well for clonal data (handle repeats, errors, low coverage) and deal w/ polymorphisms #HMP2010 about 8 hours ago via TweetDeck

  • phylogenomics

  • Pop: genome assembly is hard b/c of 1) repeats 2) low coverage 3) sequencing errors - gets even harder for metagenomics #HMP2010 about 8 hours ago via Twitterrific

  • mndoci

  • RT @phylogenomics: Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Tweetie for Mac

  • TheGenomeCenter

  • Mihai Pop: not having coverage may obscure true assembly and sequencing errors make everything more difficult #HMP2010 about 8 hours ago via TweetDeck

  • widdowquinn

  • RT @phylogenomics: Pop showing challenge in assembly by showing assembly of Tale of Two Cities; repeats:"it was the" confuse things #HMP2010 about 8 hours ago via TweetDeck

  • phylogenomics

  • Pop showing challenge in assembly by showing assembly of A Tale of Two Cities; repeats Ike "it was the" can confuse things #HMP2010 about 8 hours ago via Twitterrific

  • TheGenomeCenter

  • Mihai Pop: assembly in general is hard since have repeat regions #HMP2010 about 8 hours ago via TweetDeck

  • phylogenomics

  • Alas Pop didn't end his talk, says one can make (somewhat) useful assemblies from metagenomic data; utility depends on goals #HMP2010 about 8 hours ago via Twitterrific

  • pathogenomenick

  • hah! RT @phylogenomics: Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Seesmic Desktop

  • phylogenomics

  • Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Twitterrific, 3 Retweets

  • TheGenomeCenter

  • Mihai Pop from U Maryland on assembling short reads from metagenomics - will be short since metagenomics assembly is impossible! #HMP2010 about 8 hours ago via TweetDeck

  • fionabrinkman

  • @bffo Yes, I worry bias is forming - archaeal human microbiome is sometimes neglected. Need to ensure whole microbiome is studied #HMP2010 about 8 hours ago via web in reply to bffo

  • 1 Retweet

  • TheGenomeCenter

  • McFall-Ngai: looking at first changes in host gene expression when interact w/ symbiont #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • McFall-Ngai encouraging everyone to study circadian rhythms of host-symbiont interactions #HMP2010 about 8 hours ago via Twitterrific

  • TheGenomeCenter

  • McFall-Ngai: squid-vibrio symbiosis -the two converse through their genes #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • McFall-Ngai's talk is so far an homage to model organisms and how they will be relevant to human microbiome studies #HMP2010 about 8 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • McFall-Ngai: cancer genes arose w/ 1st cellular orgs =caretaker genes; then when cell-cell interaction started =gatekeeper genes #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • McFall-Ngai: most human genes are old; most genes associated with human disease are also old #HMP2010 about 8 hours ago via TweetDeck

  • 4 Retweets

  • phylogenomics

  • McFall-Ngai: humans are not the pinnacle/crown of evolution; me: just YAV (yet another vertebrate) #HMP2010 about 8 hours ago via Twitterrific

  • TheGenomeCenter

  • McFall-Ngai: humans not the pinnacle of evolution, just a recent outcome #HMP2010 about 9 hours ago via TweetDeck

  • phylogenomics

  • Margaret McFall-Ngai : vertebrates are a very old group & likely been associated w/ microbes for hundreds of millions of yes #HMP2010 about 9 hours ago via Twitterrific

  • TheGenomeCenter

  • Margaret McFall-Ngai from U Wisc on host-microbe interaction through animal evolution #HMP2010 about 9 hours ago via TweetDeck

  • TheGenomeCenter

  • Relman: use digital MDA (Multiple Displacement Amplification) on E. coli gDNA fragments - more sensitive than digital PCR #HMP2010 about 9 hours ago via TweetDeck

  • phylogenomics

  • Relman: reagents in molec. biology freq. contaminated w/ DNA; this impacts many amplification studies when DNA levels low; #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Relman: commercial approaches for quantifying small samples of DNA - digital PCR gives advantage by quantifying single molecs #HMP2010 about 9 hours ago via TweetDeck

  • bffo

  • @fionabrinkman Bruce Birren mentioned archae in that they were missed by the standard primers used for 16S ... not much more :-( #hmp2010 about 9 hours ago via TweetDeck in reply to fionabrinkman

  • TheGenomeCenter

  • Relman: microfluidics reduces enviro contamination, improves detection of rare microbes, increases speed of single cell selection #HMP2010 about 9 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • Relman: single cell #genomics, microfluidics and the human #microbiome #HMP2010 about 9 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • David Relman discussing single cell genomics and other approaches to studying single cells in communities #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • David Relman is w/o a doubt the Philosopher of the Microbiome - always discussing deep questions #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet

  • a2binny

  • Dave Relman opened up by pointing out that the number of people in the room is much larger than it would have been 5 years ago #HMP2010 about 9 hours ago via AOL Lifestream

  • TheGenomeCenter

  • David Relman from Stanford on the human #microbiome 'one cell at a time' #HMP2010 about 9 hours ago via TweetDeck

  • emergentnexus

  • oddly, none of my afternoon microblogging seems to be on twitter yet. catch it at http://friendfeed.com/human-microbiome #HMP2010 about 10 hours ago via web

  • fionabrinkman

  • @phylogenomics If you can, do mention if there's anything said about Archaea in the human microbiome. #HMP2010 about 10 hours ago via Echofon

  • phylogenomics

  • A main worry re: metagenomic studies: like GWAS, lots of genetic variation but w/ few variables, will always find correlations #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet

  • fionabrinkman

  • Thx @phylogenomics for human microbiome meeting tweets (Agenda: http://bit.ly/9FyDlu) #HMP2010 about 10 hours ago via Echofon

  • phylogenomics

  • Denef showing how proteomics can be used in environmental studies - Banfield lab does v. cool stuff in this area #HMP2010 about 10 hours ago via Twitterrific

  • phylogenomics

  • Denef - looking at population shifts over time using metagenomics -getting to correlating pop. changes with specific allelic diffs #HMP2010 about 10 hours ago via Twitterrific

  • phylogenomics

  • Denef discussing metagenomic studies of preterm infant gut -using similar methods as in acid mine drainage studies #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet

  • a2binny

  • Denef presents interesting results showing two distinct strains of Citrobacter "fighting it out" in the newborn gut #HMP2010 about 10 hours ago via AOL Lifestream

  • a2binny

  • Vincent Denef has been roped into studying necrotizing enterocolitis in preterm infants #HMP2010 about 10 hours ago via AOL Lifestream

  • TheGenomeCenter

  • Denef: preterm infant gut colonization shows how functional microbial community emerges #HMP2010 about 10 hours ago via TweetDeck, 2 Retweets

  • phylogenomics

  • Denef now giving homage to the red pill blue pill choice from the Matrix #HMP2010 #Toldyoumetagenomicswascool #geekytoo about 10 hours ago via Twitterrific

  • TheGenomeCenter

  • Denef: The Matrix movie gave red/blue pill option - choose your reality - studying microbial ecology similar - what level to study? #HMP2010 about 10 hours ago via TweetDeck

  • phylogenomics

  • Denef now explaining his talk title - lots of closely related organisms and may have to distinguish at very fine scale #HMP2010 about 10 hours ago via Twitterrific

  • TheGenomeCenter

  • Denef: linking genotypic traits to microbial ecology #HMP2010 about 10 hours ago via TweetDeck

  • phylogenomics

  • Vincent Denef from Jill Banfield's lab discussing "how deep does the rabbit hole really go?" #HMP2010 about 10 hours ago via Twitterrific

  • TheGenomeCenter

  • Next up Vincent Denef from UC Berkeley on studying microbial ecology using community #genomics #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet

  • ASA_CSSA_SSSA

  • RT @TheGenomeCenter: Jo Handelsman from Yale on antibiotic resistance in soil and the human #microbiome #HMP2010 about 10 hours ago via HootSuite

  • TheGenomeCenter

  • Handelsman: kanamycin resistance genes from soil are similar to ea. other (even over a distance) but differ from humans #HMP2010 about 10 hours ago via TweetDeck

  • OmicsKnowmics

  • Not #badomics word 4 me as refers 2 a subset of genomes: MT @phylogenomics: "resistome" = collection of antibiotic resistance genes #HMP2010 about 10 hours ago via TweetDeck

  • TheGenomeCenter

  • Handelsman: found streptomycin resistance gene from human #microbiome that modifies the antibiotic #HMP2010 about 10 hours ago via TweetDeck

  • TheGenomeCenter

  • Handelsman: found kanamycin resistance genes from human #microbiome - all methyltransferases modifying the target of the antibiotic #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet

  • a2binny

  • Handelsman: soil-derived kanamycin resistant determinants are different than clinically significant ones #HMP2010 about 10 hours ago via AOL Lifestream

  • phylogenomics

  • I note, Jo Handelsman coined the word metagenomics many years ago #HMP2010 - this omics word seems OK to me about 10 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Handelsman: use functional metagenomics to find new antibiotics by cloning DNA from uncultured samples from soil and humans #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • Handelsman: hard to culture microbes from soil - ~99% can't be cultured #HMP2010 about 10 hours ago via TweetDeck

  • HankCampbell

  • RT @phylogenomics: Richard Sharp discussing how patients seem willing to use GMO probiotics even if they don't like GMO foods #HMP2010 about 10 hours ago via TweetDeck

  • TheGenomeCenter

  • Handelsman: resistant Acinetobacter in Iraq could come from soil #HMP2010 about 10 hours ago via TweetDeck

  • phylogenomics

  • Jo Handelsman refers to the "resistome" - collection of antibiotic resistance genes in a community; #badomics word? - probably #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Handelsman: resistome - collective resistance genes in the environment to understand where resistance comes from #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • Handelsman :“we’re facing one of the worst health crisis in decades” – drug resistance #HMP2010 about 10 hours ago via TweetDeck

  • phylogenomics

  • Jo Handelsman, one of my favorite scientists, now up talking about finding antibiotic resistance genes in the environment #HMP2010 about 10 hours ago via Twitterrific

  • TheGenomeCenter

  • Jo Handelsman from Yale on antibiotic resistance in soil and the human #microbiome #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • Sharp saying that we should not oversell the microbiome project - he should read my blog http://bit.ly/ahXB4n #HMP2010 about 11 hours ago via Twitterrific, 2 Retweets

  • TheGenomeCenter

  • Tweeting from the Human #Microbiome Conference in St. Louis http://bit.ly/b3ZLKD also check out microblog at http://bit.ly/aEtRXl #HMP2010 about 11 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • Sharp: patients may be susceptible to aggressive marketing of probiotics #HMP2010 about 11 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • Richard Sharp discussing how patients seem willing to use GMO probiotics even if they don't like GMO foods #HMP2010 about 11 hours ago via Twitterrific, 1 Retweet

  • a2binny

  • data presented that people would be willing to take GM probiotics, when they wouldn't eat GM food #HMP2010 about 11 hours ago via AOL Lifestream

  • TheGenomeCenter

  • Sharp: Patients don't see GM probiotics in same way as GM foods - may shun GM foods but accept GM probiotics if dr.-approved #HMP2010 about 11 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • Sharp: Patients may be weary of manipulating gut #miccrobiome (i.e. probiotics) as a form of gene therapy #HMP2010 about 11 hours ago via TweetDeck

  • phylogenomics

  • Issues relating to microbiome ethics: genetic discrimination, GMOS, release of probiotics to world, gene therapy #HMP2010 about 11 hours ago via Twitterrific

  • a2binny

  • The ethical, legal and social issues (ELSI) of micro biome research are being discussed #HMP2010 about 11 hours ago via AOL Lifestream

  • TheGenomeCenter

  • Rich Sharp from Cleveland Clinic on why do Ethical, Legal, and Social Issues (ELSI) Research #HMP2010 about 11 hours ago via TweetDeck

  • phylogenomics

  • Oops ... Missed the first part of the talk on ELSI issues associated with the human microbiome project #HMP2010 #importantstuff about 11 hours ago via Twitterrific

  • TheGenomeCenter

  • Ruth Farrell from Cleveland Clinic talks about ethical challenges in the clinical applications of the Human #Microbiome Project #HMP2010 about 11 hours ago via TweetDeck

  • emergentnexus

  • wrapping up morning session #HMP2010 about 12 hours ago via web

  • phylogenomics

  • Alm, in response to my question, says that much of their evolution analyses done on incomplete genomes but he thinks it works fine #HMP2010 about 12 hours ago via Twitterrific

  • phylogenomics

  • A questioner asked about something relating to "higher primates" - come one everyone - stop the evolution bogusness #HMP2010 about 12 hours ago via Twitterrific

  • TheGenomeCenter

  • Eric Alm: bacteria from same habitat tend to share more 'flexible' (changing) genome blocks #HMP2010 about 12 hours ago via TweetDeck

  • mikethemadbiol

  • #HMP2010 Alm: 25 ecotypes of what is basically one species of Vibrio. In four species of seawater! about 12 hours ago via web, 1 Retweet

  • TheGenomeCenter

  • Eric Alm: looking at loci to determine ecological split of bacterial strains from zooplankton #HMP2010 about 12 hours ago via TweetDeck

  • GenomeScience

  • more info re: CloVR & cloud computing w/ DACC - http://www.cloudbook.net/university-maryland-baltimore-research #HMP2010 about 12 hours ago via web

  • TheGenomeCenter

  • Alm: dvlping tool 'Starry Nights' that takes genome sequences and divides into blocks consistent with single phylogenetic tree #HMP2010 about 12 hours ago via TweetDeck

  • phylogenomics

  • Alm: comparing 75 genomes of strains of Vibrio species; note all of these are in essence same OTU/species but lots of differences #HMP2010 about 12 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • Eric Alm describing how microbial samples are collected from ocean water; me: informatics people need to understand these things #HMP2010 about 12 hours ago via Twitterrific

  • TheGenomeCenter

  • Alm: Model system is vibrio bacteria; found could partition resources in ocean #HMP2010 about 12 hours ago via TweetDeck

  • phylogenomics

  • Eric Alm discussing Fred Cohan's ecotype model for species formation in bacteria and archaea #HMP2010 about 12 hours ago via Twitterrific

  • TheGenomeCenter

  • Eric Alm from MIT on ocean microbes #HMP2010 about 12 hours ago via TweetDeck

  • phylogenomics

  • And now for something completely different but very relevant: ocean microbes and genome evolution from Eric Alm #HMP2010 about 12 hours ago via Twitterrific

  • phylogenomics

  • White: his goal is to teach community to fish not give them food (i.e., to give community tools, rather than run things for them) #HMP2010 about 12 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • White: DACC putting together virtual machines to run all sorts of microbiome/metagenomic analyses - can run locally or on cloud #HMP2010 about 13 hours ago via Twitterrific

  • TheGenomeCenter

  • White: CloVR - Clouid Virtual Resource tool- bunding diff analysis pipelines on virtual machine that you could run on your computer #HMP2010 about 13 hours ago via TweetDeck, 2 Retweets

  • emergentnexus

  • CloVR: Cloud Virtual Resource bundles analysis pipelines into virtual machines #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • emergentnexus

  • DACC has subversion repositories #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • bffo

  • Owen White keeps saying "GenBank" when I think he sometimes means NCBI ... not the same! #microbiome #hmp2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • White: some challenges in downloading data from short read archive from NCBI #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet

  • jacobnix

  • @phylogenomics Key issue: genome and metagenome data is not very useful without metadata about samples, methods, etc #HMP2010 about 13 hours ago via web

  • emergentnexus

  • dbGaP provides patient phenotype information #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • phylogenomics

  • Key issue: genome and metagenome data is not very useful without metadata about samples, methods, etc #HMP2010 about 13 hours ago via Twitterrific, 2 Retweets

  • TheGenomeCenter

  • Owen White: DACC w/ NCBI has set of recommendations for how to describe and present your data most clearly #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • I almost said same thing: RT @mikethemadbiol #HMP2010 *I* care if we sequence another E. coli genome ;) Though metadata ARE critical about 13 hours ago via Twitterrific

  • TheGenomeCenter

  • White: Partner w/ JGI to make Img tool 2 look at metabolic profiling - at http://www.hmpdacc-resources.org/cgi-bin/img_hmp/main.cgi #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet

  • kshameer

  • RT @phylogenomics: Best place to find out about past & ongoing microbial genome projects? http://bit.ly/aOxFhV #HMP2010 #genomics about 13 hours ago via TweetDeck

  • emergentnexus

  • img/hmp website: http://www.hmpdacc-resources.org/cgi-bin/img_hmp/main.cgi #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • phylogenomics

  • Best place to find out about past & ongoing microbial genome projects?: definitely http://www.genomesonline.org/ #HMP2010 about 13 hours ago via Twitterrific

  • GenomeScience

  • O. White from IGS: 1 goal - a nice, easy to use website to coordinate info re: HMP #HMP2010 http://www.hmpdacc.org/ via @phylogenomics about 13 hours ago via web

  • MetaHIT

  • RT @phylogenomics: Key issue: open data is important but ease of access and use of open data also critical #HMP2010 about 13 hours ago via HootSuite

  • mikethemadbiol

  • #HMP2010 *I* care if we sequence another E. coli genome ;) Though metadata ARE critical about 13 hours ago via web

  • phylogenomics

  • Key issue: open data is important but ease of access and use of open data also critical #HMP2010 about 13 hours ago via Twitterrific, 2 Retweets

  • phylogenomics

  • White: major goal is to provide ease of access to certain types of HMP data #HMP2010 about 13 hours ago via Twitterrific

  • TheGenomeCenter

  • White: making a better website to make HMP data available http://bit.ly/cO6Maq #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • White: one of their goals is to have a nice, easy to use website to coordinate information about HMP #HMP2010 see http://www.hmpdacc.org/ about 13 hours ago via Twitterrific, 1 Retweet

  • emergentnexus

  • Website: http://www.hmpdacc.org #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • TheGenomeCenter

  • White: DACC tries to keep data traffic rolling #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Next up Owen White on the HMP Data Analysis and Coordination Center that he runs #HMP2010 http://www.hmpdacc.org/ about 13 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Owen White from U Maryland Data Analysis and Coordination Center (DACC) for HMP #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet

  • emergentnexus

  • Owen White: A Data Analysis Coordination Center for the Human Microbiome Project #HMP2010 http://ff.im/pZ7b9 about 13 hours ago via FriendFeed

  • TheGenomeCenter

  • Mitreva: shout out to @TheGenomeCenter - more info at http://bit.ly/bQVuvk #HMP2010 about 13 hours ago via TweetDeck

  • mikethemadbiol

  • #HMP2010 Either need to go to cloud computing or we're going to need a lot more blades... about 13 hours ago via web

  • phylogenomics

  • Mitreva: current tools for analyzing metagenomic data mostly die (my word, not hers) when analyzing massive new data sets #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet

  • emerlyyy

  • follow @phylogenomics for updates on the Human Microbiome meeting! #HMP2010 about 13 hours ago via web, 2 Retweets

  • TheGenomeCenter

  • Mitreva: looking at how community profile differs based on shotgun seq vs. 16 s data - #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Live from the Human Microbiome Meeting #HMP2010 http://ff.im/-pZ5F6 about 13 hours ago via FriendFeed, 2 Retweets

  • TheGenomeCenter

  • Mitreva: sequence similarity analysis to compare communities without relying on ref genomes; look at seq composition of every comm. #HMP2010 about 13 hours ago via TweetDeck

  • emergentnexus

  • Metarep: http://www.jcvi.org/metarep "an open source tool for high-performance comparative metagenomics" #HMP2010 re: http://ff.im/pYQBa about 13 hours ago via FriendFeed

  • emergentnexus

  • Johannes Goll: The J. Craig Venter Institute's update on the HMP #HMP2010 http://ff.im/pYQBa about 13 hours ago via FriendFeed

  • TheGenomeCenter

  • Mitreva: are looking at metabolic profiling of communities - in oral, nasal, gut, vaginal sites #HMP2010 about 13 hours ago via TweetDeck

  • TheGenomeCenter

  • Mitreva: can separate different body sites based on breadth and depth of coverage of reference genomes #HMP2010 about 13 hours ago via TweetDeck

  • emergentnexus

  • Makedonka Mitreva: Shotgun Metagenomic Sequencing and Analysis at the Washington University Genome Center #HMP2010 http://ff.im/pYWdT about 13 hours ago via FriendFeed

  • emergentnexus

  • greatest challenges computational: takes >2 months to analyze data that took 0.3 months to produce #HMP2010 re: http://ff.im/pYWdT about 13 hours ago via FriendFeed

  • TheGenomeCenter

  • Mitreva: id'd many taxonomies/species in only 6 body sites to indicate common and unique species in a body site #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Ugh: Mitreva referred to "lower eukaryotes" - maybe she says this because the podium is high above the meeting hall? #HMP2010 about 13 hours ago via Twitterrific

  • TheGenomeCenter

  • correction - Mitreva - use publicly available CLOUD computing (not sure what loud computing would be!) #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Mitreva - the big problem in analyzing human microbiome metagenomics data is computational time - #HMP2010 #weneedbettermethods about 13 hours ago via Twitterrific

  • TheGenomeCenter

  • Mitreva: takes over 2 months to analyze data; to accelerate this, use alt algorithms, publicly available loud computing #HMP2010 about 13 hours ago via TweetDeck

  • bffo

  • #hmp2010 #microbiome it is rep, not rap :-) METAREP http://bit.ly/c1VIGz about 13 hours ago via TweetDeck

  • TheGenomeCenter

  • Mitreva: @TheGenomeCenter sampled 54 adults and 16 body sites - nasal, skin, gut etc. - 346 samples = 4 terabases of data #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Makedonka Mitreva from Wash U Genome Center: shotgun metagenomics of 54 people x 5 body sites: oral, skin, gut, vagina, nasal #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Makedonka Mitreva from @TheGenomeCenter on our shotgun metagenomic sequencing activities #HMP2010 about 13 hours ago via TweetDeck

  • bffo

  • Johannesburg Goll from JCVI on METAREP, published as a 2 pager in Bioinformatics #OA #micro biome #hmp2010 http://bit.ly/c1VIGz about 13 hours ago via TweetDeck

  • phylogenomics

  • For software geeks: The MetaREP software is open source & uses CAKEPHP, Solr, MySQL mix to do rapid indexing and searching #HMP2010 about 13 hours ago via Twitterrific, 3 Retweets

  • TheGenomeCenter

  • Goll: Can use METAREP to compare datasets with more intuitive visualization and scaling capabilities #HMP2010 about 13 hours ago via TweetDeck

  • bffo

  • Johannesburg Goll from JCVI on METARAP, published as a 2 pager in Bioinformatics #OA #micro biome #hmp2010 http://bit.ly/c1VIGz about 13 hours ago via TweetDeck

  • phylogenomics

  • Best place to find out about Human Microbiome Project?: probably The HMP DACC #HMP2010 #somecoolthings http://ff.im/-pYTFo about 13 hours ago via FriendFeed 6 Retweets

  • eurogene

  • so how many $ spent on these trials worldwide now? MT @TheGenomeCenter: MMR vaccine and autism-Columbia trial found no correlation #HMP2010 about 13 hours ago via TweetDeck

  • TheGenomeCenter

  • METAREP: to compare two samples e.g. from healthy and diseased individuals; analyze pathways, enzyme presence, search/filter data #HMP2010 about 13 hours ago via TweetDeck

  • phylogenomics

  • Johannes Goll discussing Metarep - JCVI metagenomics analysis tool #HMP2010 - now available / published http://ff.im/-pYRF7 about 13 hours ago via FriendFeed, 2 Retweets

  • GenomeScience

  • Next up: Johannes Goll from JCVI - on METAREP high throughput #metagenomics tool #HMP2010 via @WashU about 14 hours ago via web

  • TheGenomeCenter

  • Goll - METAREP tool is at http://bit.ly/9kvX2r #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet

  • TheGenomeCenter

  • Next up: Johannes Goll from JCVI - on METAREP high throughput metagenomics tool #HMP2010 about 14 hours ago via TweetDeck

  • GenomeScience

  • RT @phylogenomics FYI, agenda for the #HMP2010 human microbiome mtg is here http://bit.ly/9FyDlu http://fb.me/wxpn12gE about 14 hours ago via web

  • TheGenomeCenter

  • Lasken: HMP samples submitted to BEI http://bit.ly/9nw8ue #HMP2010 about 14 hours ago via TweetDeck

  • TheGenomeCenter

  • Lasken: shallow 454 sequencing with barcoding - 50-100 MDA reactions to verify 16S classification of HMP samples #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • Roger Lasken: phylogenetic analysis can help assess MDA samples - note work done by Jonathan Badger who used to work in my lab #HMP2010 about 14 hours ago via Twitterrific

  • TheGenomeCenter

  • @phylogenomics For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu http://fb.me/wxpn12gE about 14 hours ago via Facebook

  • MetaHIT

  • RT @phylogenomics: For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu about 14 hours ago via HootSuite

  • phylogenomics

  • For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu about 14 hours ago via Twitterrific 5 Retweets

  • TheGenomeCenter

  • Lasken on Multiple Displacement Amplification (MDA) used to amplify smaller DNA samples and sequencing from single cells #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet

  • emergentnexus

  • Roger Lasken: The J. Craig Venter Institute's update on the HMP #HMP2010 http://ff.im/pYKwf about 14 hours ago via FriendFeed

  • phylogenomics

  • Roger Lasken from the J Craig Venter Institute now talking about whole genome amplification w/ MDA to get at uncultured organisms' #hmp2010 about 14 hours ago via Twitterrific

  • TheGenomeCenter

  • Roger Lasken from JCVI update on Human #Microbiome Project #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet

  • MetaHIT

  • #HMP2010 feed integrated to our dashboard dedicated to the Human Microbiome http://ow.ly/2xmNL about 14 hours ago via HootSuite, 1 Retweet

  • emergentnexus

  • I am microblogging #HMP2010 on FF; comment tweets showing up w/o hashtag. Follow me to see them! about 14 hours ago via web

  • MetaHIT

  • RT @MikeyJ: Glued to the tweets from Human Microbiome meeting #HMP2010 about 14 hours ago via HootSuite

  • MikeyJ

  • Glued to the tweets from Human Microbiome meeting #HMP2010 about 14 hours ago via Tweetie for Mac

  • mikethemadbiol

  • #HMP2010 Would note about Sutterella that I looked at human data & Sutterella found in ~30% ofadults; might be associated w/stomach illness about 14 hours ago via web

  • mikethemadbiol

  • #hmp2010 Would note about Sutterella that I looked at human data & Sutterella found in ~30% ofadults; might be associated w/stomach illness about 14 hours ago via web

  • TheGenomeCenter

  • Lipkin: Looking in cave in Spain, found novel filovirus - intermediate between Marburg and Ebola #HMP2010 about 14 hours ago via TweetDeck

  • phylogenomics

  • Ok Ian Lipkin has won me over forever . He just quoted Yogi Berra and Neils Bohr in one sentence #HMP2010 about 14 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Lipkin: in last 9 months discovered over 300 viruses due to change in technology #HMP2010 about 14 hours ago via TweetDeck

  • mikethemadbiol

  • #hmp2010 Lipkin-1 series of gut samples from autistic kids & controls suggests elevated levels of Sutterella were associated w/autistic kids about 14 hours ago via web, 1 Retweet

  • phylogenomics

  • Really like how Lipkin caveated his autism work by saying "this is one study in one place" & then asked for others to test if real #HMP2010 about 14 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • Lipkin has looked at microbial diversity in biopsies of people w/ & w/o autism - found microbes associated w/ autism #hmp2010 about 14 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • Lipkin talking about nothing controversial: autism and MMR and microbes #HMP2010 about 15 hours ago via Twitterrific

  • TheGenomeCenter

  • Lipkin: Identified disease of farmed salmon - unable to swim since gills don't work; used high-thruput seq #HMP2010 about 15 hours ago via TweetDeck

  • phylogenomics

  • ian Lipkin referring to Edgar Allen Poe and cryptography in trying to sort through Metagenomic data #HMP2010 #binningishard about 15 hours ago via Twitterrific

  • TheGenomeCenter

  • New Aussie virus isolated from tissues extracted from women - found only 14 out of 100,000 sequences were from virus (vs. host) #HMP2010 about 15 hours ago via TweetDeck, 2 Retweets

  • GenomeScience

  • Now common protocols, benchmarked data accuracy, new tools & control data sets, better at defining variants #HMP2010 via @WashU #microbiome about 15 hours ago via web

  • TheGenomeCenter

  • Ian Lipkin: found a novel rhinovirus - HRV C - implicated in pneumonia, asthma using multiplex sequencing methods #HMP2010 about 15 hours ago via TweetDeck

  • phylogenomics

  • Lipkin showing world wide air traffic to scare us (rightly so) about how fast EIDs can spread #HMP2010 about 15 hours ago via Twitterrific, 3 Retweets

  • phylogenomics

  • Ian Lipkin talking about emerging infectious diseases - says we have only scratched surface of sampling viral diversity #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet

  • phylogenomics

  • Interesting question after Birren's talk re: archiving samples & informed consent - key things to think about in this type of work #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet

  • mikethemadbiol

  • #HMP2010 B. Birren-E. coli K-12 can be assembled into 1 scaffold for hundreds of $s with Illumina seq & new jumps about 15 hours ago via web

  • phylogenomics

  • Ian Lipkin now up discussing microbe hunting in the 21st century #HMP2010 - mentions problems with Koch's postulates at start about 15 hours ago via Twitterrific

  • emergentnexus

  • Ian Lipkin: Microbe Hunting in the 21st Century #HMP2010 http://ff.im/pYdKG about 15 hours ago via FriendFeed

  • mikethemadbiol

  • At #HMP2010 mttg. No fireworks yet, but liked Apollo metaphor by WashU science dean-I've used it myself; good 2 see I'm not only crazy about 15 hours ago via web

  • TheGenomeCenter

  • Ian Lipkin from Columbia U on microbe hunting #HMP2010 about 15 hours ago via TweetDeck, 1 Retweet

  • phylogenomics

  • Thanks to @GenomeScience for giving me the hashtag #HMP2010 for the Human Microbiome meeting I am at ... about 15 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Now have common protocols, have benchmarked data accuracy, created new tools and control data sets, are better at defining variants #HMP2010 about 15 hours ago via TweetDeck

  • phylogenomics

  • Birren presenting clustering of samples based on rRNA analysis - but could do much better referencing prior lit on this #HMP2010 about 15 hours ago via web

  • phylogenomics

  • Birren - given that they trust their PCR, now comparing many human samples - seems like they are way behind the field here #hmp2010 about 15 hours ago via web

  • pgspicer

  • At #HMP2010 in St. Louis about 15 hours ago via Twitter for iPhone

  • phylogenomics

  • Bruce Birren testing diversity estimators from rRNA PCR - for simulation got many more OTUs back than they put in #HMP2010 #sequencingerror about 15 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • Hashtag for Human Microbiome Conference in St. Louis is #HMP2010 - follow the conference going on right now! about 15 hours ago via TweetDeck, 2 Retweets

  • phylogenomics

  • Birren used a mock community to test rRNA PCR methods - wonder if he has read our mock metagenomics paper http://bit.ly/cPaIKF #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet

  • TheGenomeCenter

  • 21 bacteria with finished references used as positive control to test 16S 454 sequencing accuracy and determine data variability #HMP2010 about 15 hours ago via TweetDeck, 1 Retweet

  • OmicsKnowmics

  • I have starting to accept that microbes ARE cool (HOT!) RT @phylogenomics: The human microbiome meeting #HMP2010 is packed - microbes rule about 15 hours ago via TweetDeck

  • EdwardWinstead
    • Follow #HMP2010 for tweets from the Human Microbiome Conference in St Louis about 15 hours ago via TweetDeck, 2 Retweets
  • phylogenomics
    • Bruce Birren says that they developed a 454 rRNA sequencing pipeline that has been tested & is accurate across centers; #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet
  • phylogenomics
    • The human microbiome meeting #HMP2010 is quite packed - microbes rule http://twitpic.com/2jynzt about 15 hours ago via Echofon
  • TheGenomeCenter
    • Bruce Birren from Broad on 16S sequencing in human metagenomics #HMP2010 about 15 hours ago via TweetDeck
  • emergentnexus
    • Bruce Birren: High throughput 16S sequencing in human metagenomics #HMP2010 http://ff.im/pXX52 about 15 hours ago via FriendFeed
  • GenomeScience
    • sample sites for human #microbiome project: oral cavity, skin, nasal, gi tract, vaginal, blood & serum #HMP2010 via @TheGenomeCenter about 16 hours ago via web
  • TheGenomeCenter
    • sample sites for human #microbiome project: oral cavity, skin (behind ear, elbow), nasal, gi tract, vaginal, blood and serum #HMP2010 about 16 hours ago via TweetDeck
  • emergentnexus
    • apparently the hashtag is #HMP2010 re: http://ff.im/pXTTj about 16 hours ago via FriendFeed
  • TheGenomeCenter
    • @TheGenomeCenter is tweeting from the Human Microbiome Conference in St. Louis #HMP2010 about 16 hours ago via TweetDeck
  • TheGenomeCenter
    • @GenomeScience - great suggestion! Human Microbiome Conference in St. Louis hashtag = #HMP2010 about 16 hours ago via TweetDeck, 2 Retweets
  • GenomeScience
    • @TheGenomeCenter - how about a hashtag for HMP mtg? #HMP2010 - does that work for you? about 16 hours ago via web
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Labels: , ,

4 comments:

  1. yowino9/01/2010 5:02 AM

    Thank you very much Jonathan for summarizing your impressions on the 1st day of the HMP conference.

    I think it s tough to live-tweet a conference and give, while doing it, your impressions on what you hear.
    On the other hand, I want to stress that you may be one of the few to offer it to your followers. In that respect, I think tweeting and giving your personal views at the same time is showing respect to the talk that's being given.
    In the end being in critical analyst's shoes is an invitation to further discussions!

    Cheers,

    Yohanan Winogradsky
    MetaHIT team

    ReplyDelete
  2. vanilafrog9/01/2010 1:14 PM

    HEllo,
    thanks for your posting on HMP conference. Do you know if there is a way i can get the video for the talks?

    ReplyDelete
  3. Anonymous9/01/2010 9:44 PM

    Very interesting and useful post, thanks a lot.

    I am looking forward to the post of day 2 and the answer of video for the talks.

    Lenah Hatem

    ReplyDelete
  4. Jonathan Eisen9/01/2010 11:06 PM

    I know of no video recordings being made but may try to record mine tomorrow

    ReplyDelete

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