Tag Archives: img

Bioinformatics in the local news

I’m on a few local mailing lists, including the one for MassHighTech.  I was perusing the news today and saw this tidbit:

URI taps De Groot to head new vaccine research center

….The purpose of the new program, called the Institute for Immunology and Informatics, is to create vaccines to prevent AIDS, malaria, tuberculosis, dengue fever and other diseases. Researchers will use cutting-edge bioinformatics tools to speed up creating treatments and cures for these illnesses, stated URI. This includes using immunomics — informatics, genomics and immunology –- to design better vaccines, diagnostics and therapeutics…..

Immunomics. Another -omic.  Just what I needed.

I think this is neat, actually, though.  I would like to keep an eye on what they are doing.  As an undergrad in microbiology I was talked out of infectious diseases as a career–I was told that funding was dissipating and there wasn’t much interest in that anymore.  But that was probably the most memorable course I took.

Oh, and if you find yourself here because you are looking for some resources for infectious disease genomes, I’ll add a few here.  Feel free to add your other favorites.

VBRC: http://athena.bioc.uvic.ca/

IMG: http://img.jgi.doe.gov/

GSID: http://www.gsid.org/

CMR: http://cmr.jcvi.org/

VectorBase: http://www.vectorbase.org/

EUPathDB: http://eupathdb.org/eupathdb/

BREAKING (really):  Court says vaccine not to blame for autism

IMG extends capabilities

DOE JGI extended and updated the content of IMG and IMG/M recently as this linked press release shows (here is another), so today I’d like to just make a quick post to highlight that OpenHelix has a tutorial on IMG/M that is sponsored by JGI and thus free.

Metagenomics is a huge new field and IMG/M has some excellent tools and data!

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!

Metagenomes in Nature

Nature had a nice feature on metagenomics last week and another on the Human microbiome metagenomics. You’ll need to have a subscription to access those :(, but the gist of the latter news feature is the possibilities of Human microbiome research, pros and cons and the projects out there. There are a lot. In order of amount of funding they are:

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Metagenomics making the big Times (as in NY)

Metagenomics, which is really a new area of study (barely this last decade) in comparison to most biological areas of research, is already making into the mainstream press. The New York Times has an article yesterday entitled “Bacteria thrive in the inner Elbow, No Harm Done” (you’ll need a free registration to read that). The article quotes from metagenomic studies that show that our inner elbows contain a unique microbiome of species even in comparison to our upper arm, though it goes a  more into metagenomic studies than just that. As the article states:

The research is part of the human microbiome project, microbiome meaning the entourage of all microbes that live in people.
The project is an ambitious government-financed endeavor to catalog the typical bacterial colonies that inhabit each niche in the human ecosystem.

That’d be this project. The article does a decent job of explaining why this project is helpful, but doesn’t really explain how this approach of metagenomics is different or how it’s done (in fact, it never says the word “metagenomics“). Oh well, can’t have everything.

For your edification: There is last year’s report “The New Science of Metagenomics” from the National Research Council (you can read free online, or purchase as a book. Also, of course there are at least two extensive databases of metagenomic data, IMG/M (free tutorial) and Camera.

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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Bacterial Browser ala Google Maps

Came across a nice bacterial genome browser today via “Discovering Biology in a Digital World:” the Genome Projector.Genome Projector The is a map of over 100 bacterial genomes including a circular genome map, a genome map, a pathways map and a “DNAWalk” map. Put in a search term (I put “iron” in here, you know, as in ‘mining for,’ tried gold, but alas.. there is no gold in them thar… anyway…) and the hits show up as numbers in the tabs and pins in the maps. The maps are zoomable (just like GoogleMaps) and the pins are clickable with a popup to links out to databases and more information. It’s not quite as useful or in depth as perhaps IMG as a browser or Reactome or Kegg for pathways, but it’s simple and cool way to browse the genomes for more information and links to databases. Below the fold (continue reading link) are two more screenshots of my search in pathways and zoomed with clicked pin. Continue reading

Tip of the Week: Free bioinformatics training materials

We wanted to take this “tip of the week” to introduce you to some of the materials that we have which are freely available for you to download and use in classes, seminars, or just for your own learning. OpenHelix creates training materials that include tutorial movies (animated + audio), slides with script, and exercises to reinforce concepts developed in the tutorials. Some of them are sponsored by the software provider, so we can make them freely available. We can even send you these great Quick Reference Cards that you can give out to students, or tape next to your computer, which will remind you of many of the features of the site. You can access them from our blog, or from our regular homepage. This tip of the week movie introduces you to how to access these materials.

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!