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:
- My FriendFeed
- Jason Stajich on one talk
- Jason on another talk
- Jason on another talk
- Jason friend feed
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Jonathan Eisen's Lab 
Eddy Rubin just gave a very brief introduction to the meeting and encouraged everyone to come on the tours of JGI over the next few days.
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Jeff Dangl is now talking about Comparative genomics of P. syringae. I note Dangl has a pretty cool new paper on sequencing and assembling microbial genomes – De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL.Genome Res. 2009 Feb;19(2):294-305. Epub 2008 Nov 17.
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Dangl is now talking about the work in that paper — he says the cost of doing a bacterial genome with a 454/Illumina hybrid method is only about $1000 per genome and it will go down
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Dangl says the scaffoloidng that comes from 454 longer reads is VERY important
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Dangl now says that for many purposes you have to have high coverage assembled sequence … I could not agree more
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Dangl is now talking about studying what host genes are involved in influencing the assembly of plant associated microbial communities.
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They are doing soil metagenomics of Arabidopsis roots. Then they want to do some QTL mapping studies regarding the interactions of host genes with the microbes
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It is by the way packed to the gills here …
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James Cate is now going to talk about reverse engineering cellulosomes in CLostridia. He says his goal here is to basically make cellulosomes into some sort of swiss army knife equivalent — to be able to mix and match different subunits to produce different activities He is now discussing how they are using proteomics in combination with the genomic data to try and ID various cellulosome components
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There is a possibly commercial talk now – Bryan O’Neill from Sapphire Energy talking about Algal Engineering … hope he avoids too much promotion
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Oh well – too late for that – seems way way too self promotional in the first few minutes. Not sure why he is here
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Sorry -correction it is Mike Mendez talking
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He is saying the most important chemical reaction on the planet is plants converting CO2 into sugar. I disagree. Yeast converting sugar into alcohol is much more important –He is now saying some convincing things about algae being important … He says genetic engineering will have to be used on the algae since he does not have 7000 years to sort it out –
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He says he has to grow in monoculture because all farming works that way — this baffles me and makes him sound pretty lame
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he is proposing some genome sequencing to help him get his production strain online — not sure why he would not sequence them himself –
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if JGI sequences them, how does he manage the patentability aspects too?
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I think it is completely ridiculous to think a public entity like JGI would sequence these genomes for free for his company
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Cameron Curre is now talking about leaf cutting ants
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he is showing side by side trees of the ants and the fungus that they farm and since the trees are very similar it suggests that this is an ancient symbiosis – go phylogeny
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I have had my computer compromised — sneaky prankster(s) posted something from my laptop while we were on break (I left it out) … I cannot imagine why people would pull a prank on me … pranks are very very bad things
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