Tag: meetings

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
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some quick links on #OSS2010 Open Science Summit 2010

Just posting some links from the web relating to the Open Science Summit 2010 meeting which is continuing today … started Thursday.  If you want to follow today, check out twitter with hashtag #OSS2010

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

What is not getting any love at this #metagenomics meeting

Well, Here I am for day 2 in Snowbird at a meeting/workshop discussing the potential for “Terrabase metagenomics”. The main point of the meeting is to discuss whether there would be value in massive massive Metagenomic sequencing in one way or another. I note I have enjoyed this meeting so far greatly – nice and small with some really good people.

Yesterday i gave a talk on microbial evolution and a few others talked about other topics (Rob Knight talked about microbiomes, Jeroen Raes discussed multiple Metagenomic projects, and Rachel Mackelprang discussed permafrost metagenomics). I will write more i hope soon about the science side of this meeting. But that is not what I am here to write about today. I am going to tell you what topics were not getting any love so far at this meetings. And this is not a completely snarky thing here – what people complain about does give some feel for what people are thinking about. In no particular order, here are some examples.

  • The human microbiome project (well, some parts of it)
  • The CAMERA metagenomics DB (significant disappointment in their progress )
  • NCBI (or specifically the short read archive)
  • Bureaucracy (and how it impedes science)
  • Lack of support for informatics
  • Lack of air (we are at 8000+ feet)
  • Large meetings
  • Jet lag
  • IRBs
  • Lack of RAM (many Metagenomic analyses require massive amounts RAM)
  • Bad alcohol (as in drinks)
  • Plants and animals (this is a meeting focusing on microbes)
  • Lack of cooperation among funding agencies
  • Pathogens (most people here are interested in either human commensals or environmental organisms)
  • Difficulty in founding joint projects between US and Europe
  • Projects that don’t collect metadata
  • Software tools that don’t work with each other
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Summary of #iEVOBIO Day 2, #phylogenetics #informatics #opensource #biodiversity #evolution

This is a continuation of notes on iEVOBIO meeting.  Much of this comes from twitter.  Additional comments will be posted over the next few days.  See notes on Day 1 here. Note – thanks to the people who answered my query on twitter about how to remove spurious html code from pages – I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html.  I ended up using Zubrag which was suggested by brendanwlocke.

Day 2. Beginning.

Since I was leaving that PM I could not borrow a hotel bike and bike over again.  So I walked from the hotel, along the river 2 or so miles, after getting coffee.  I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seemed very good.  But I find if I do not get some exercise every day at a meeting I go crazy so it was worth it.  Here are some notes on Day 2.

Day 2. Part 1. Keynote

Alas, I missed much of the keynote.  But what I caught was good.  Here are some notes, mostly from twitter. And also see Rob G’s slides below

RPG iEvoBio 2010 Keynotehttp://static.slidesharecdn.com/swf/ssplayer2.swf?doc=ievobiokeynote3-100630154451-phpapp02&stripped_title=rpg-ievobio-2010-keynote

Rob Guralnick: Biodiversity Discovery and Documentation in the Information and Attention Age

    Day 2. Part 2. Short talks.

    Day 2. Part 3. Lunch

    Went to lunch with a small group to the People’s Sandwich of Portland.  Took the light rail over the river.  Portland has some really nice features – like free light rail in the city.

    Day 2. Part 4. Lightning Talks

    Day 2. Part 5. Birds of a feather


    Then there were breakout sessions which were called “Birds of a feather”  I went to one discussing open access and fair use issues. 

    Day 2. Part 6. Wrap up and other general information

    And then I had to go home.  The meeting wrapped up as I was leaving. Here are some ending tweets:

    Some other general info tweets:

    Post meeting posts and blogs
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    3rd Annual Western Evolutionary Biology Meeting 12/5/09 at Berkeley

    The 3rd Annual Western Evolutionary Biology Meeting will be at UC Berkeley. This is a meeting of the UC Network for Experimental Research on Evolution (NERE), attendees from the UC campuses will be present, other evolutionary biologists, researchers, teachers and writers are encouraged to participate as well.

    When: Sat. 5 December FREE registration – deadline, 29 October 2009 Submit Abstracts – deadline 16 October 2009 – or present a poster

    Where: On the UCB Campus in VLSB, see website for details NOMINATE: Western Evolutionary Biologist of the Year by 9 Oct. 2009

    See website for details. Open to Researchers, Teachers, Writers.
    REGISTER at http://www.lifesci.ucsb.edu/nere-web/

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Can’t get much worse than this: soaking my shorts before my 1st conference talk. Other bad experiences?

    Well, I was talking with some people recently about someone who had a bad experience giving their first talk at a scientific conference. And so I said – you think that is bad – how about this? And I told them the story below. But before telling the story I am asking here for others to post comments about the worst thing that has happened to you during a talk at a scientific conference/meeting. Please fire away.

    OK – so my talk. It was 1995. The SSE (Society of the Study of Evolution) meeting was in Montreal. And somehow I was going. I am not sure anymore how I ended up registering for the meeting. I do remember other evo-grad students who were or had been at Stanford like David Pollock, Joanna Mountain, maybe David Goldstein, maybe Sally Otto, Sarah Cohen, and a few others were going. And so I registered, got accepted to give a talk on the “Evolution of RecA” and made plane reservations to get to Montreal.
    I arrived the night before my talk, found my dorm room on the McGill campus, and then went wandering around town for the Jazz Festival which was going on that night. After staying out pretty late, I got back to my room and had a bit of a panic attack when I looked at the schedule and found that the session in which I was talking started at 8:30 in the morning the next day and I did not have an alarm clock, nor was there one in my room. (I note, fortunately I was using real slides and could not spend the night modifying my talk in the way I do now with Keynote/PPT). Anyway – I pretty much knew I would sleep late without some work and so I made some notes with my room # and a plea to others to bang on my door if they could by 6:30 or 7 AM and I slipped these under the other doors in the hall. Fortunately in some ways, I barely slept b/c I was so scared of missing my first talk.
    So at 6:30 AM or so I headed out to the conference area. I think I got some coffee and then headed to the room where my talk was to be. Nobody was even there so I wandered around for a bit and came back and the projectionist was there getting the room set up. When I said I was one of the speakers – he said “Are you planning on doing any side by side slides where you need two projectors?” Well, I had not thought of doing this, but now that he mentioned it, it sounded perfect b/c the main point of my talk was that the phylogenetic trees of RecA and rRNA were very similar to each other (see my 1995 J. Mol. Evol. paper on the topic here), supporting earlier suggestions by Lloyd and Sharp that RecA was a potentially useful phylogenetic marker. So I said “sure” and proceeded to load up two slide carousels for my talk. We checked them out and all looked good.
    As the room started to fill up (I recall there were a lot of people interested in the “Molecular Evolution” session I was in) I decided to go grab a seat (in the far back on an aisle – I was a lurker even before blogging from meetings) and try to relax. I think I was the fourth talk and while speaker #3 (Michael Purugganan) was getting started I got nervous about the side by side slides so I went over to ask the projectionist if all was OK and he said it was. Alas, someone had grabbed my seat when I was up. I saw a table in the back back of the room with some misc. fliers on it so I went there to sit down for a few minutes and try to relax. And here was the trouble.
    The table was also being used to hold some pitchers of water for people. And alas, someone had just spilled an entire pitcher of water on the table and I did not notice. I sat in the puddle. And there I was, in my tan shorts, now dripping wet. Minutes before my first talk. Looking like I had gotten a bit too nervous. Underwear showing through. As I desperately looked around to borrow a sweatshirt from someone to tie around my waist, the chair said “And our next speaker is Jonathan Eisen …”. Holy Crap. I was on.
    So I went up there and I had thought to myself to crack a joke about just getting in from a swim. Or something. But as I still do, I entered another zone for my talk and forget everything but the talk. And so – there I was – dripping wet in my see through shorts – turning around and pointing to the screen talking about RecA as though all was fine.
    Only when I was done with the talk did I re-remember that I was basically doing a “wet-shorts” contest for all in the audience. Yay. I can say truthfully that when I start to worry about things going wrong in talks, I remember this one and say “well, it could be worse …”
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    A genomic encyclopedia of bacteria and archaea (video of my talk from the JGI user meeting)

    My talk at the JGI meeting on “A genomic encyclopedia of bacteria and archaea” is now up at SciVee.  See below:

    http://www.scivee.tv/flash/embedPlayer.swf

    And the slides are up at Slideshare
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Live Blogging the JGI Users Meeting

    Well, I am at the JGI (Joint Genome Institute) User Meeting – and I am going to try and do some live blogging right here.  I am going to do it differently than I have previously and do things in the comments not in the main page here.  If it works, great.  If not I might switch to FriendFeed.  So check out the comments for new updates ….

    So – see the comments for this posting but also see FriendFeed where Jason Stajich and I posted many comments.  Here are some links:
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Metagenomics 2008 Meeting Notes

    I am going to post notes here for the Metagenomics 2008 meeting.

    #1 – most everyone here seems really happy about the election
    #2 – mooched a ride this morning to the conference site from some of the folks who run “The Seed” and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. 
    #3 – Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote “Physiology is not a bulk or an average property” basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that there are real compartments in communities.  Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007).   Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics
    #4 – a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).  
    #5 – Oded Beja is talking now.  He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin
    #6 – Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean.  It is basically a series of filter systems that works on a platform that is run by a deep sea submersible … this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)
    #7 – a little note — already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes.  Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools …
    #8 – Yuri Gorby — gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around.  This stuff is beyond cool — it is completely fascinating.
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Lake arrowhead notes – UPDATED

    Well I gave my talk

    Seemed to go ok except getting cutoff early because the chair ignored
    that the session started late but that is ok

    George Weinstock is now speaking using my laptop so I am trying to
    post from my phone

    He said one key thing I left out … Big scale microbial sequencing
    projects are now possible thanks to next gen sequencing in particular
    454-Roche tools

    More later
    Sent from my iPhone

    ————————————————-

    More now

    George Weinstock gave a good overview of the “Human Microbiome Project” which is a NIH Roadmap initiative to catalogue the genomic content of the microbes associated with humans. He described some of the big picture of why do the project, of the different fundingin initiatives being done through NIH and he gave some detail on the “jumpstart” project going on at the big genome centers right now. He outlined how the current plan is to select a few hundred people and to survey their mcirobiomes from multiple sites using rRNA PCR and possibly metagenomics. In addition, he described how there is also an effort to sequence 100s if not a 1000 genomes of cultured organisms that have been isolated from human environments. He did say one thing I disagreed with which is that he thinks it is somewhat reasonable to treat the environment that microbes live in in essence as a big bag of genes. In other words, if you sequence from a community, he implied that one can focus just on the genes and their functions and not the organisms that they come from. On this I disagree (and pointed this out after the next talk). But overall George gave anice overview of the project and its goals.

    Eric Wommack gave a good talk about viral metagenomics work he has been doing. He pointed out that a lot of the viral world is “unknown” but that does not mean it is unimportant. And this is consistent with what I and George Weinstock said which is that we need more genome data from viral isolates. Eric presented some very useful results on the challenges of using short read sequence data in metagenomics and he referenced a few papers on this. He also referred to a cool viral genome survey project that I was not aware of by Hatfull which involved undergraduates in sequencing and analyzing the genomes of phage that infect Mycobacterium smegmatis.

    Jim Bristow on Biofuels. He is now giving a summary of some of the JGI work on the genomics of cellulolytic organisms and processes. He is focusing on the termite gut community and had some good one liners about this (e.g., he said many people want to kill termites but not JGI. They are our friends; he also said “it takes a village to sequence a termite gut”).

    Not sure exactly how to say this, but here goes. There was one talk in the AM I was not overly fond of. This was a talk by Bernard Palsson. Now I confess, I am not overly familiar with much of his work but what I know of it suggests he does some really solid, interesting and important work on metabolic network modeling and analysis. But his talk at this meeting was disappointing. His talk was about his use of genome sequencing to characterize “adaptive evolution” in E. coli. And the results he presented seemed solid enough. The problem I had was that it was a prime example of “overselling genomics”. Why? Here is what they did. They took E. coli mutants. And the then took them through cycles of growth and then dilution. And then they looked at the populations after a certain number of generations and did a variety of analyses. Included in this was some whole genome sequencing that helped identify mutations arising in the cultures. And then they did some characterization of these mutations/mutants including some competition experiments and some pretty interesting gene expression studies of some RNA polymerase mutants. And he made some conclusions based on their results like that E. coli in the lab can find new adaptive peaks and that mutations differ in different replicates, and that different mutations confer different fitness, that they can monitor the appearance of mutations over time, and so on.

    So what is the problem — the problem is that he (1) presented this as though the serial cycling of E. coli was novel when in fact it is not and that (2) he presented the conclusions as though they were novel when they also are not. People have been doing this type of experiment for many decades (in fact, one person, Rich Lenski, has been doing an experiment like this for decades). And they get these exact results. But they have not sequenced genomes as part of their experiment. And thus, at least for this talk, they were not mentioned, and the rediscovery of many truisms in population genetics was presented as novel because it involved genome sequencing.

    Trent Northen created a serious buzz during and after his talk with his presentation of some of the things one can do with Nanostructure Initiated Mass Spectrometry (NIMS). I confess – I want his toys.

    Lynn Silver is now talking about the challenges in the development of new antibiotics. She argues that the focus by some on trying to find new targets for antibiotics has been a bit misguided.

    Julian Parkhill gave a good talk about population genomics of Salmonella. He pointed out a few things people still ignore. For example, if you want to identify polymorphisms in a species to use for population genetics/genomics studies, you really need to do a survey to identify polymoprhisms from diverse members of the population. If you do not, and then you use a biased set of polymorphisms, your population inferences will be wrong. He also said, in response to a quesiton of mine, that at least for this species, they see very little variation in copy number in genes which is different than what people seem to see in humans.

    Tiffany Williams from Baylor gave a talk about using high throughput sequencing in collaborations with developing countries. She outlined some of the challenges as well as the benefits from such collaborations.

    Kim Lewis gave a very interesting talk on microbial biofilms and persister cells, of which I know vanishingly little. He showed some very cool experiments trying to “complement” unculturable organisms and get them to grow.

    Jeffrey F. Miller gave a talk focusing on diversity generating retroelements in bacteria which appear to be a means by which bacteria can target particular regions of the genome for mutagenesis in a comparable way to VDJ mutagenesis in humans. This was perhaps my favorite talk so far at the meeting as it combined microbial genomics, evolvability, mutation processes and other things I tend to focus on.

    Steven Benner gave a talk which I had to skip out on early because I was doing a radio interview. Benner said one thing that annoyed me at the beginning – he made a comment that was complaining about prior talks that referred to “Rosetta Stone” methods of predicting function (I was one of the people who mentioned this) because he thought that we were referring to blast searches. He clearly was not paying any attention as the Rosetta Stone method is a method to predict function for genes by finding connections between non homologous proteins based upon having other proteins that have domains found in both of the original proteins of interest. Oh well, glad I had to leave early because I was itching to jump up and correct him.

    Heather Allen, from Jo Handelsman’s gave a very good talk about doing functional metagenomic screens for antibiotic resistance encoding genes. She has been using DNA from multiple soil sites, including a pristine site in Alaska, and screening the DNA for antibiotic resistance genes in E. coli. These screens identify a wide diversity of genes, including some novel forms. This work helps highlight the need to not just sequence the snot out of the world but to also do some functional assays at the same time. In addition she mentioned that she was able to come to the meeting because Jo Handelsman set up a fund for mothers to pay for babysitters to come to a meeting with them. All I can say is Jo Handelsman was already one of my favorite people in science and this is just another brilliant and wonderful thing that she does.

    David Relman gave a talk about two studies of the human microbiome that his lab has been doing: (1) studies of marine mammals to compare the microbial diversity in their surfaces with the diversity in the water and the diversity on their insides and (2) study the response of the human gut microbial community to antibiotic treatment. I am particularly fond of the antibitotic treatment study because they are treating it as an “ecological disturbance” study and analyzing it much like ecologists would analyze recovery of a forest after fires. I think we definitely need more ecologists to bring their techniques and skills to human microbiome studies and so this was exciting to see.

    Ashlee Earl gave a talk about biofilm formation in Bacillus subtilis. Much like Kim Lamb’s talk earlier, this talk was in an area I know little about and I guess you could say it kind of blew my mind. It seems that in B. subtilis and I guess in many other microbes biofilms are in essence analogous to multicellular organisms. Within a biofilm there are different types of cells that have different roles and the patterns are highly reproducible and organized. It seems to me that the boundary between multicellular and single-celled organisms is getting blurrier and blurrier. Ashlee reported on some cool experiments where she collected strains from around the world and then dod comparative genetics and genomics of their biofilm formation patterns.

    Alas I missed Mary Lidstrom’s talk which based upon prior experiences I am sure was fascinating. She has been working in studying processes inside single bacterial cells and has been developing a suite of techniques and tools to carry out such studies. Maybe someone else from the meeting can post details about her talk.

    Unfortunately, I had a conference call during some of the next talks that I had to do so I do not have details for the blog. Then I returned and served as chair for a session. I did take some notes so here goes.

    Byung-Kwan Cho gave a tour de force talk about reconstructing the transcriptional regulatory network in E. coli. He presented results from a dazzling and dizzying array of genome-scale methods (e.g., ChipChip, tiled arrays, sequencing, etc etc) to characterize transcription regulation. In addition he did some complex and big scale computational work to combine all of the data together to characterize networks. It was quite impressive stuff.

    Ginger Armbrust talked about her favorite critters – diatoms and focused on how they used the genome data to characterize silicon deposition processes. She was convincing as to the importance of diatoms and to the value of having the genome sequences from some species. She did discuss some of the challenges of using the genome data including the challenges in gene prediction for microbial eukaryotes. She also discussed her dream of utilizing some of the new genomic information as part of real time sensors in the oceans.

    Anthanasios Typas discussed work to build tools for carrying out genome-scale analyses of genetic and chemical-genetic interactions. For example they are working on taking two comprehensive gene KO libraries from E. coli and using them to create all possible double mutants and to then screen those mutants for whether they have the same or different phenotypes than the single mutants. This allows them to look for gene-gene interactions. They also are doing this type of analysis with chemical-gene interactions.

    Devaki Bhaya gave a brief talk on what I think is the single most interesting thing in all of microbiology right now – CRISPRs. These are clustered regularly interspaced short palindromic repeats. She is studying them in cyanobacteria from Yellowstone hot springs

    Good quotes from the meeting:

    • So we simply sequenced the genome of the different variants
    • Antibitoics do not kill things, they corrupt them
    • Dormancy is the default mode of most bacterial life
    • Who knows what a yoctomole is?
    • I am going to defend genomics
    • There comes a point in life when you have to bring chemists into the picture
    • Gosh, was that today or yesterday
    • The rectal swabs are here in tan color
    • I’ll try to let the pictures do the talking and I will get out of the way
    • Our model system de jour
    • And there’s Jeffrey Dahmer
    • And this is my cheesy analogy here
    • He could not be here so I am here. His loss. My gain. Hopefully not your loss.
    • We are the environment. We live the phenotype.
    • If I have time I will tell you about a dream
    • Every fifth breath – thank a diatom
    • While we still have poles
    • A paper came out next year
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

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