Tag Archives: JGI

News about the Integrated Microbial Genomes (IMG) resource

I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! They are constantly changing and improving their interface and database.

If you are involved in microbial research and haven’t already checked out this powerful resource, I strongly suggest that you do. We’ve been training on this resource since 2006 and really believe in its value, which seems to increase with each of their releases. Mary & Trey presented an IMG workshop at NIH recently and it was surprising how many of their researchers were not aware of IMG. We hear that pretty often and it is too bad, it has so much to offer the microbial community and others as well.

The second item is that IMG has an annotation tool specifically designed for undergraduate education. Iddo Friedberg  describes this as ‘Way cool’ in a recent tweet. The program/interface is named the “Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT)“, and is somewhat associated with the “Interpret a GEBA Genome for Education” project from JGI. “GEBA” stands for Genomic Encyclopedia of Bacteria and Archaea.  Both efforts are aimed at encouraging undergraduate research in microbial genome annotation, which might lead to the ‘alternative science career’ as a biocurator!

You can read all about the tool in their PLoS Biology article “Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum“, or see a tour of the program/interface here. The tour makes the interface seem a bit clunky to me, but well thought out with lots of solutions to problems/issues often associated with undergraduate classes. The paper really provides a nice overview of the concept, collaborations, and initial outcomes of the 2008-2009 program.

Sign-ups are occurring for the 2011-2012 version of the program. The time frame is as follows:

Timeline to Participate:
1. Apply to be part of the 2011-2012 team by Monday, November 5, 2010 (download the application)
2. After acceptance, attend the workshop at the JGI (January 2011)
3. Implement in 2011-2012 academic year

as can be seen at the bottom of this page.

IMG-ACT Reference:
ResearchBlogging.orgDitty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z., Sanders-Lorenz, E., Axen, S., Kim, E., Johns, M., Scott, K., & Kerfeld, C. (2010). Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum PLoS Biology, 8 (8) DOI: 10.1371/journal.pbio.1000448

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Phytozome

A newly enhanced database and resource is available to researchers called Phytozome. Phytozome is targeted as a hub of genomic data for plants of interest in biofuel research and a joint project of the DOE JGI and UC Berkeley’s Center for Integrative Genomics. As a recent press release states,

The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the transfer of functional information to important biofuel and agricultural crops from model plant systems, as well as allowing users to explore land plant evolution.

This release is v. 4 and includes the genomes of 14 plants from green algae, arabidopsis and corn. The resource uses GBrowse (free tutorial and training materials) as it’s genome browser, BioMart for advanced searching and has BLAST capability. I find Gramene a bit more extensive than Phytozome, but the focus of the two (biofuel plants and agricultural grains for Phytozome and Gramene respectively) are different and Phytozome is becoming quite extensive.

I remember going to a DOE/JGI users conference last year and being quite impressed with the research going on in biofuel, and also more sobered by the obstacles both techological and practical (use of food-producing land, etc) that we face. With rising gas prices and temperatures, can’t ask for too much information!

JGI's Sequencing Plans for 2009

JGI logo Just saw in today’s GenomeWeb Daily News email that the Joint Genome Institute has announced its sequencing plans for 2009. It includes both genomes and metagenomes. You can read the GenomeWeb Daily News article, or the whole JGI announcment of projects which, according to JGI Director Eddy Rubin:

 “The scientific and technological advances enabled by the information that we generate from these selections promise to take us faster and further down the path toward clean, renewable transportation fuels while affording us a more comprehensive understanding of the global carbon cycle”.

 I for one am looking forward to exploring the new information as soon as it is available in IMG and IMG/M!

Miscanthus genome will "fuel" advances

miscanthusI am still digesting (so to speak) the conference I went to the last couple days at JGI. The thrust of the conference was the sequencing and study of genomes (both biomass fuelstock and bacteria/fungus digesters :)) to help create a liquid fuel source for our energy needs. I found it to be a fascinating conference and will definitely write more about it early next week.

For now, I’d like to point you to the work being done on the Miscanthus genome. This is a fascinating plant and possibility for a fuel source. It’s more productive than Switchgrass (and corn and sugar), it has no known diseases or pests (though that will change when/if it becomes a major crop), it is perennial needing much less fertilizer/pesticide input, it grows by rhizomes and sequesters carbon in the ground, it would take much less land to supply liquid fuel needs, it is drought resistant and it can cure cancer. Ok, so the last is not true. Yet, it is a very promising plant. The genome is being sequenced to help scientists and growers determine ways to domesticate it better and to solve the “big” problem… the expense of converting the cellulose to fuel (which is also the topic of metagenomic and genomic research on bacteria at JGI).

jgi user meeting: live blogging

I’m currently at the third annual JGI Users Meeting titled Genomics of Energy and Environment. The first workshop is about IMG and when it finishes I’ll update you on anything new or interesting. A later session is on Biomass Feedstocks (for energy production), so look in this post for updates on that to. I’ll be updating every few hours.Edit (by Mary): for those of us who can’t be there at the workshop, the online tutorial is available: Integrated Microbial Genomes (IMG)
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FYI: The Third Annual JGI User Meeting is coming up

JGI_meet_imageHey, just a quick post to let you know about the upcoming user meeting for the Joint Genome Institute, which is occurring March 26-28th in Walnut Creek, CA. I’ve blogged about the JGI’s phenominal Integrated Microbial Genomes (IMG) resource & that will be discussed as well as LOTS of other interesting stuff. You can check out the meeting announcement & maybe meet some of the OpenHelix gang there!