Tag: JGI meeting

Video of Carl Zimmer’s talk from the DOE-Joint Genome Institute User meeting

I really love this world of sharing and openness in science.  Here is a video of Carl Zimmer’s Keynote talk from the DOE Joint Genome Institute User meeting.

I note – before his talk I took Carl out to lunch.  Since of course I cannot do anything in a standard way, I bought some sandwiches and some drinks and snacks and took him to the top of Mt. Diablo which is nearby Walnut Creek.  Alas, it took a LONG time to drive up to the top and it was very very windy.  And as I started to get a bit queasy from all the turns I think Carl probably was wondering what I was doing.  But the view from the top was nice (even though the firggin’ visitor center and their nice viewing area was closed).  We did see some snow which was also nice.

And then we headed back down, down, down, down, down.  So- I am telling you this because we got back about 1.5 hours before his talk so he did not have much time to recover from the long and windy road.  And yet, I loved his talk.

For his talk I took “visual” notes using my iPad.  I made these using Notability and then it exports as a PDF which was awkward and then I took that an converted to JPGs since Blogger won’t deal with PDFs.

Hope you enjoy the notes.

——–
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.

——–

Notes (from me and mostly others) from the JGI User Meeting #JGIUM7

OK, so the DOE Joint Genome Institute User Meeting is underway. Day 2 just finished. And I have been there for much of it but alas, not in some of the talks since I can’t seem to get past the hallway/gathering area outside the talks. There are way way too many people there who I have not talked to or seen in a while … So … apologies to those who thought I might be live tweeting the whole meeting … it just hasn’t happened. But I did use the Storify web tool to make a “storification” of posts to twitter from the meeting – most of which were from other people. Here is the story in slideshow format.

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js?template=slideshow[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

I will update the storification tomorrow. If you want to see the full details in a scrolling winder see below

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

——–
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.

——–

Meeting of Interest: DOE JGI "Genomics of Energy and Environment" 3/20-22

A meeting of interest: The Annual DOE JGI User Meeting.  Note – open to anyone – not just those funded by DOE.
Topics include
  • Synthetic biology & biodesign
  • Systems biology/transcriptional networks
  • Application of single cell genomics in microbial ecology and bioprospecting
  • Genomic analysis of biofuel traits in maize and switchgrass
  • Cloud computing as a platform for large scale sequence analysis
  • Ocean viruses: towards population genomics, understanding virus-host interactions, and accessing the uncultured
  • Omics in the Arctic: Genome-enabled contributions to carbon cycle and biogeochemical research in high-latitude ecosystems
  • Ancient DNA
Plus – Carl Zimmer.  Yes, I said Carl Zimmer.  
——–
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.

——–

My twitter wrap up of the Joint Genome Institute User Meeting #JGIUM

Off to another meeting so don’t have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the road …

kucsbl CSBL at Korea Univ.
RT @phylogenomics Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
5 hours ago Favorite Retweet Reply

CackleofRad CackleofRad
@
@Tideliar @jadebio You know who else I think is awesome? Try @phylogenomics and maybe #JGIUM Not medical per se but cool things in the werks
17 hours ago

phylogenomics Jonathan Eisen

Uy vey: got home from #JGIUM & my kids had chlamydia, anthrax, E. coli, malaria, athletes foot, Helicobacter & giardia yfrog.com/gzk75auj
20 hours ago

phylogenomics Jonathan Eisen
Next up at #JGIUM Dan Distel on Shipworm symbionts – note here is a picture of Dan (foreground) from 1992 cruise http://twitpic.com/4cvb3w
22 hours ago

phylogenomics Jonathan Eisen

Apologies all – have to skip end of #JGIUM – follow this hashtag for other’s posts
23 hours ago

phylogenomics Jonathan Eisen
Scholin hacked into unsecured wireless network while on vacation in Death Valley to communicate w/ his sensors in Newport Beach #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Scholin has some of these remote sensors moored off of Newport Beach pier to survey for toxic diatoms #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Holy ecogenomic sensor batman – this remote ESP thing is very cool mbari.org/ESP/esp_2G.htm – can do DNA analysis remotely #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Chris Scholin on remote detection of marine microbes in coastal waters and deep sea #JGIUM
24 Mar

phylogenomics Jonathan Eisen
In the Q and A period for Dan Distel some music has now come on over the speakers #oscars? #exitmusic #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel discussing proteomics of shipworm symbionts communities – uses method that focuses on proteins in symbionts not host #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Oh no – Distel mentioned the CaZome when discussing carbohydrate active enzymes in shipworm symbionts #badomicsword #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: the gill symbionts are in addition to symbionts living in the gut that are known to degrade cellulose #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: many (~10) types of closely related bacterial symbionts live inside the cells of shipworm in the gill #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Note – here is a link to my #PLoSONE paper with Distel on the genome of a shipworm symbiont plosone.org/article/info:d… #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms are very diverse and can live off all sorts of wood & wood like stuff – major wood consuming organisms in ocean #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Dan Distel Works at the Ocean Genome Legacy foundation #JGIUM #coolgroup oglf.org/DistelCV.htm
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms (which are actually clams) cause billions of dollars of economic damage each year #JGIUM
24 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his acctg dept #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his accounting department #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Dan Distel on shipworm symbionts – note here’s a pic of Dan (foreground) from ’02 http://www.scancafe.com/p-59386415-38fa9f
24 Mar

sharmanedit Anna Sharman
Wow. MT @phylogenomics [Ed] Buckler: any two corn [maize] plants are as different from each other as humans and chimpanzees #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Mary Ann Moran; Note paper I have w/ her is one Nature fails to make free despite promises nature.com/nature/journal… #opengate
24 Mar

phylogenomics Jonathan Eisen
Buckler described Genotyping by sequencing method from his in press #PLoSOne paper #JGIUM maizegenetics.net/images/stories…
24 Mar

phylogenomics Jonathan Eisen
Buckler suggests the genetic diversity in maize allows it to adapt to local environments better than other species #JGIUM #notbuyingit
24 Mar

phylogenomics Jonathan Eisen
Buckler: genomic domestication analysis w/ Ross-Ibarra lab from #ucdavis: little loss in diversity from landraces -> improved lines #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler: Tripsacum genome has different retrotransposons than maize but otherwise may be useful as source of genetic variants #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler also sequencing Tripsacum – sister genus of maize #JGIUM no chromosomal duplications, very similar gene content to maize
24 Mar

phylogenomics Jonathan Eisen
Buckler: doing maize HAPMAP2 to survey genetic diversity in corn #JGIUM
24 Mar

leonidkruglyak Leonid Kruglyak
So are yeast strains RT @phylogenomics: Buckler: any two corn plants as different as human and chimp #JGIUM #myspeciesisbetterthanyours
24 Mar

phylogenomics Jonathan Eisen
Buckler: any two corn plants are as different from each other as humans and chimpanzees #JGIUM #myspeciesisbetterthanyours
24 Mar

leonidkruglyak Leonid Kruglyak
Ed Buckler RT @phylogenomics: Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

sarahcpwilliams sarahcpwilliams
@phylogenomics enjoying yr tweets from #jgium. i’m a big fan of ley and knight. covered their work last year for hhmi: http://bit.ly/g2NEug
24 Mar

phylogenomics Jonathan Eisen
Ley : to study diversity of microbes associated with maize had to get primers that did not amplify chloroplast rDNA #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley: doing a QTL experiment on maize/corn treating microbes as their quantitative trait #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley now expanding human microbiome GWAS twin study to include surveying microbes all over body #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley: GWAS studies of human twins has IDd many loci that appear to affect microbial diversity – including some immune system loci #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley is now doing GWAS studies w/ human twins where the phenotype they are looking at is microbial diversity #JGIUM #verycool
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley discussing survey of microbes in one child over two years #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley now up at the JGI User Meeting discussing maize, human microbiotas #JGIUM … Note – I love her work #brilliant
24 Mar

kevinswilson66 Kevin Scott Wilson
@
@phylogenomics : Many thanks for your notes on #JGIUM . I was captivated by them
23 Mar

Symbiologica Juliana Mastronunzio
Thanks for tweets on the JGI meeting #JGIUM from @phylogenomics and @iGenomics.
23 Mar

sdaxen Seth D. Axen
RT @phylogenomics: Schuster: “I would like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

Pathh1 Pat Heslop-Harrison
Done that – I found the devil in the detail. RT @phylogenomics: Schuster “like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: “I would like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

iGenomics Dawei Lin
RT @phylogenomics: Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM #fb
23 Mar

phylogenomics Jonathan Eisen
Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster working on thylacine (tasmanian tiger) mitochondrial genomes #JGIUM thylacine.psu.edu
23 Mar

phylogenomics Jonathan Eisen
For more on mammoth genomics see mammoth.psu.edu #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: when you sample extinct organisms you have to remember that different samples may come from different times #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: “You would not believe how much mammoth hair I have washed off myself” #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster – redundancy in genome sequencing with ancient genomes helps build quality genome assemblies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: one reason to focus on mitochondrial genomes is that there are lots of copies of the genome per cell #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster : “dont forget about mitochondrial genomes” still lots of species that do not have mt genome sequences #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: discussing mammoths, moas, thylacines, tasmanian devils and polar bears #JGIUM #museomics #conservation #endangered
23 Mar

phylogenomics Jonathan Eisen
For more on Schusters work on extinct species see cidd.psu.edu/people/scs19 #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Next up Stephan Schuster discussing the Genomics of Extinct and Endangered Species #JGIUM #museomics
23 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

phylogenomics Jonathan Eisen
Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86
23 Mar

phylogenomics Jonathan Eisen

Eddy Rubin at the #JGIUM is soliciting input from crowd on future needs of the community
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

phylogenomics Jonathan Eisen

The perils of giving out #badomics word awards – a prior recipient at #JGIUM just told me he’s still angry at me phylogenomics.blogspot.com/2009/01/worst-…
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM Rob Knight: “There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical” #fb
23 Mar

phylogenomics Jonathan Eisen
All I can say is that when I was rejected by HHMI a few yrs ago I felt better when I heard Rob Knight got it b/c, well, he rocks #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight – in human microbiome studies you actually need VERY few sequences per sample to get overall trends #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight: “There is one universal tree of life” and giving props to my GEBA genomic encyclopedia project #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM Rob Knight: “There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical” #fb
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing how sequencing has gotten so cheap and high throughout that analysis tools are the limiting step in many cases #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight now up at #JGIUM – he publishes more cool papers per month than just about anyone in microbial research
23 Mar

phylogenomics Jonathan Eisen
Silver: took sugar secreting cyanobacterium and got macrophage to take them up and they survive a little bit #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver: injected sugar secreted cyanobacterium into zebrafish zygotes and get functional fish with cyanos all throughout them #jgium
23 Mar

phylogenomics Jonathan Eisen
Silver: engineered a cyanobacterium secrete sugars so thought maybe they could use this to make photosynthetic animals #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver also interested in biohydrogen production #JGIUM but two problems: most hydrogenases are oxygen sensitive and electron competition
23 Mar

phylogenomics Jonathan Eisen
Silver is working on engineering 3hydroxypropionate carbon fixation pathway from Chloroflexus in E. Coli #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver claimed that Cyanobacteria are responsible for 50% of photosynthesis on earth but I think that must be too high #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver working on redesigning photosynthesis via cyanobacteria #JGIUM – says they need to learn a lot of biology still
23 Mar

phylogenomics Jonathan Eisen
Silver: though she tries to get $$ from basic scion agencies , they never fund her #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver: uses “redesign of a system can test our understanding of it’s components” to try to get $$ from basic science agencies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver “Biology is the technology of this century” is the message she wants to gt across #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Jerry Tuskan getting some hard but good questions after his talk at #JGIUM – Q and A much more interesting than talks usually
23 Mar

phylogenomics Jonathan Eisen
Next up at #JGIUM Pam Silver – not only brilliant – but also her lab is the source of a good Lady Gaga spoof youtube.com/watch?v=ZilqYp…
23 Mar

phylogenomics Jonathan Eisen

Tuskan using Genome and RNA sequencing and high throughout phenotyping for massive poplar association study #jgium
23 Mar

phylogenomics Jonathan Eisen

At #JGIUM listening to Jerry Tuscan discuss poplar genomics – the place is packed yfrog.com/h82u1nnj
23 Mar

iGenomics Dawei Lin
@
@phylogenomics Terry Hazen talked about it. It can be easily forgot how many people worked behind the scene. #jgium
22 Mar

phylogenomics Jonathan Eisen

Tell me about it: “@iGenomics: It is hard to include all people working on a project into the author list these days. #jgium”
22 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics: Personal trivia re: SLAC director Perisis Drell at #JGIUM – previous director Artie Bienenstock was a st…
22 Mar

phylogenomics Jonathan Eisen

Personal trivia re: SLAC director Perisis Drell at #JGIUM – previous director Artie Bienenstock was a student of my grandfather Ben Post
22 Mar

EpiExperts Epigenetics Experts
RT @phylogenomics @doe_jgi: SLAC National Accelerator Lab Director Persis Drell kicks off DOE JGI User Mtg 5pm-use #JGIUM to follow
22 Mar Favorite Retweet Reply

——–
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.

——–

Upcoming conference: DOE-JGI User Meeting: Energy, Genomes, Environment, Microbes, Trees and more …

Just got this email I thought would be useful to share (with a few edits)

Still time to register for JGI “Genomics of Energy & Environment” 6th Annual User Meeting

The DOE Joint Genome Institute (JGI) hosts the “Genomics of Energy & Environment” 6th Annual User Meeting (March 22-24, 2011):
Here

Explore the agenda of presentations, poster sessions, and valuable hands-on workshops (see below).

The meeting brings together, at the Walnut Creek Marriott, people working on:

  • Synthetic Biology
  • Ecogenomics and Ecoresilience of the Gulf Oil Spill
  • Hardware and Software Trends in Genomics Supercomputing
  • Computational Approaches to Massive Short Read Metagenomic Data Sets
  • Genomics of Biofuel Crops
  • Behavioral Genetics of Pollinating Bees
  • Microbiome Analyses from Humans to Shipworms
  • Metatranscriptomics of Marine Microbial Communities
  • Successful Transposable Elements Secrets
  • Great Prairie Soil Metagenomics

Confirmed speakers include:

  • Peer Bork, (European Molecular Biology Laboratory) EMBL
  • Ed Buckler, Cornell University
  • Dan Distel, Ocean Genome Legacy
  • Persis Drell, SLAC National Accelerator Laboratory/Stanford
  • Terry Hazen, Lawrence Berkeley National Laboratory (LBNL)
  • Scott Hodges, University of California, Santa Barbara
  • Tom Juenger, University of Texas at Austin
  • Rob Knight, University of Colorado
  • Ruth Ley, Cornell University
  • Mary Ann Moran, University of Georgia
  • Magnus Nordborg, Gregor Mendel Institute
  • Gene Robinson, University of Illinois at Urbana-Champaign
  • Christopher Scholin, Monterey Bay Aquarium Research Institute (MBARI)
  • Stephan Schuster, Penn State University
  • Pam Silver, Harvard
  • Jim Tiedje, Michigan State University
  • Mike Thomashow, Michigan State University
  • Jerry Tuskan, Oak Ridge National Laboratory/DOE JGI
  • Katherine Yelick, National Energy Research Scientific Computing Center (NERSC) at LBNL

Workshops will include:

  • Integrated Microbial Genomes (IMG)/Metagenomes data analysis systems http://img.jgi.doe.gov/
  • Mycocosm fungal genomics portal provides data access, visualization, and analysis tools for comparative genomics of fungi http://genome.jgi-psf.org/ programs/fungi/index.jsf
  • Phytozome provides data access and visualization tools for comparative plant genomics http://www.phytozome.net/
  • RNA Technologies & Analysis: a comprehensive suite for transcriptome interrogation, including RNA-Seq for expression profiling, etc.

– Posted using BlogPress from my iPhone

——–
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.

——–

JGI User Mtg Day3 notes (coming up Rita Colwell, ex head of NSF)

Here are links to the Friendfeed Notes for today

http://friendfeed.com/jgi2010/7104a5aa/rita-colwell-university-of-maryland-solving?embed=1

http://friendfeed.com/jgi2010/f73db47f/joseph-noel-salk-institute-substrate?embed=1

http://friendfeed.com/jgi2010/1d5588e4/adrian-tsang-concordia-university-fungal?embed=1

http://friendfeed.com/jgi2010/4b31edd3/tanya-woyke-jgi-genomic-sequencing-of-single?embed=1

——–
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.

——–

And the Joint Genome Institute’s User Meeting Begins (posting notes/feeds here)

Will be posting my notes and feeds (e.g., Friendfeed) here – so stay tuned if you want to hear about the JGI User Meeting

Pictures here:
http://picasaweb.google.com/s/c/bin/slideshow.swf

FriendFeed Notes on Talks here:

http://friendfeed.com/jgi2010/db7a35f5/jay-keasling-jbei-synthetic-biology-for?embed=1

http://friendfeed.com/jgi2010/bf0f4caf/francis-martin-inra-laccaria-and-tuber-genome?embed=1

http://friendfeed.com/jgi2010/5aa5bc12/christina-cuomo-broad-institute-genome?embed=1

http://friendfeed.com/jgi2010/572e9a30/gary-stacey-u-of-missouri-making-good-use?embed=1

http://friendfeed.com/jgi2010/a93e7b55/alexandra-worden-mbari-marine-algal-evolution?embed=1

http://friendfeed.com/jgi2010/8cb1c01d/steven-hallam-ubc-from-fjords-to-open-seas?embed=1

http://friendfeed.com/jgi2010/75aadc9c/dennis-hedgecock-genomics-on-half-shell-so-what?embed=1

——–
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.

——–

Lessons Learned at the JGI Users Meeting

Well, the Joint Genome Institute (JGI) Users Meeting is Over. For some rapid fire notes on the meeting see the FriendFeed room here. where Jason Stajich, Tom Sharpton and I (and occasionally a few others) took notes on the whole thing as it was happening.

So – what were the lessons learned? What were the main points? So – if you want to know what we were writing about – and don’t want to read the notes (they are quite fun actually) how about a word cloud? Well, here is one, which I made by taking the notes, editing out some of the names and other non notes text, and then pasting them into TagCrowd.Com and I got this to the left here:

Not actually a bad representation of many of the topics.  
But you know, this does not per se capture the big points, just the common points.  So I guess if you want the key points, you have to think a bit. First, you have to realize this is a JGI focused meeting (which of course is the whole point of the meeting – it is the JGI User Meeting after all) and most of the people work with JGI in some way so it is a bit hard to see the forrest of genomics for the JGI trees.    And here are my top lessons I got out of the meeting after trying to not get too biased by the JGI focus (note – I have an Adjunct Appt. at JGI and do lots of things through there so I am sure I cannot remove the JGI focus completely)
  1. NextGen sequencing continues to open up new windows into biology.
  2. Ecological and population genomics are truly the next big thing.
  3. Related to the above point, one of the next revolutions is going to be in high throughput phenotyping — after all, we cannot solve the genotype-phenotype problem when we only know the genotype.
  4. Model / reference organisms are still in, but every single organism on the planet is now in play.
  5. NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and to use it well.
  6. Related to the above point, the NextNextGen (e.g., Pacific Biosciences) seems to be barreling along and almost ready for prime time.  WTF are we going to do in terms of informatics then?
  7. Following up on the above point- we desperately need a MASSIVE effort in the development of tools for “normal” biologists to make better use of massive sequence databases.
  8. I am happy to report that just about everyone seems to be trying to use an evolutionary perspective as part of their work – especially in the selection of organisms for sequencing
  9. I am sorry to report that many of the evolutionary “perspectives” are a bit off kilter.
  10. Sequencing is definitely not over – it is just getting started.
  11. People pushing the technology (e.g., George Church, Craig Venter) into new arenas definitely inspire the crowds.
  12. If you study a plant or an animal and are not studying the microbes that live with them, you are missing something.
  13. If you study ANY organism and are ignoring epigenetics you are behind the curve
  14. Open Access journals like PLoS Biology and PLoS One and Open Science got some huge props at this meeting, for example, with Venter showing many PLoS related images, many others showing stuff from OA journals, George Church talking about Open Source sequencers and Open personal genomics, and many referring to Open genomics databases.  Still some areas in need of improvement (e.g., not enough publishing in open access journals still) but the move in the direction of openness is great.
  15. Genome Centers definitely each have their own flavors with JGI positioning itself well in the niches of Ecology, Evolution, and Energy.
  16. Genome Centers are definitely going to have to reinvent themselves as the sequencing capacity for individual labs goes up and up with Illumina/Roche/ABI Solid continuing to spread.  Bigger, better, faster, more is one way they can stay ahead of the curve.
  17. Education and training did not get as much play during the talks as I would have hoped.  I mentioned it a bit but I do not recall too many other mentions.  Too bad as the real potential for the democritization of sequencing comes from people getting trained in how to generate and handle the data and how to at least think about it even if they do not use it directly.
  18. Organismal biology is still desperately important in all of this work – if you know a lot about the organism as a whole then you already are a systems biologist.
  19. Genomic characterization of entire multi-organism systems is on the rise and this is not just microbiota stuff but also things like host-pathogen interactions and symbioses and so on.
  20. Reading DNA is being used in every which way imaginable.  Next up – writing DNA.  
——–
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.

——–

JGI Day2

Jason Stajich set up a friendfeed room for today. See below where I am using the FriendFeed embed function …

http://friendfeed.com/rooms/jgi-user-meeting/realtime?embed=1

——–
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.

——–