The OpenHelix Blog

Sorry for the sparseness of late. We were all  over the place doing UCSC Genome Browser (we do intro + advanced), ENCODE, and Galaxy workshops.  At NIH we also did IMG and VISTA (Man, that security at NIH is fierce….).  Trey is still on the road, in fact, doing the training in Morocco.

Ok, you couldn’t be there…but all of those trainings are available on our web site right now, except for ENCODE. The same material we do in the online materials is what we do in workshops. The only one of those that requires subscription is IMG. And you won’t find ENCODE as a stand-alone tutorial yet–but that’s coming. We now have sent the script to the studio and we’ll be assembling that soon.

I do want to mention one thing that we think is interesting, and we see in almost every training we do. Nearly every time, more than half of the attendees at our trainings are female. Based on what you read about women falling out of the pipeline in science, you’d think there would be no way we’d even get 50%. But generally it is more than half women in these trainings. (We have the data if anyone can think of a way we can use that to get a grant )

Our current theory is that women are more likely to admit they could use the training (something like asking for directions…you know…?).  Or do men prefer documentation? We don’t know. What’s your theory?

Comprehensive tutorials on the publicly available Ensembl and an overview of genome browsers enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA (PRWEB) April 26, 2010 — OpenHelix today announced the availability of a new tutorial on Ensembl, and an updated tutorial suite on the Overview of Genome Browsers.

Ensembl is a genome browser to visualize and analyze human and many other species genomes. Though Ensembl recently updated the browser software, many species genome browsers still use the older versions of the browser. OpenHelix has a tutorial on the latest version, and has now created a new tutorial, Ensembl Legacy, to acquaint researchers with the older versions they might encounter. Overview of Genome Browsers is an updated tutorials which introduces researchers to some of the more popular genome browsers including Ensembl, Map Viewer, UCSC Genome Browser, the Integrated Microbial Genomes (IMG) browser and the GBrowse software. These two tutorials, in conjunction with larger, in-depth OpenHelix tutorials on UCSC Genome and Table Browsers, GBrowse. IMG, IMG/M, Ensembl and MapViewer and others will give you a set of training resources to help be efficient and effective at accessing and analyzing genome data.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

These tutorials will teach users:

Ensembl Legacy

*about the Ensembl software and its developers
*how to access older versions of the browser from the Ensembl archive
*the differences and similarities between versions
*about some example installations of Ensembl at other databases

Overview of Genome Browsers

*where to find these 5 useful tools
*an overview of the organization and display features
*some guidance on how or why to choose a given browser for your research needs
To find out more about these and over 85 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

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…

• ROFL: Marriage vs PhD illustrated comparison. Hat Tip James. [Mary]
• DGV: Database of Genomic Variants newsletter arrives for March.  Nearly 30k CNVs at this time. They are now releasing annotations to the new human assembly (hg19 or GRCh37).  You can see the newsletter here (warning, PDF). [Mary]
  
• Want to catalog leaves from plants around the world? There’s an app for that: Leafview (hattip: ABW) [Trey]
• The beginning of a long battle: Federal Judge Rules Against Patents On Human Genes . [Trey]
• Ever wonder why the Department of Energy has a Joint Genome Institute? Here’s why. [Trey]
• Sean Eddy on HMMR help, reading documentation, and more in his blog post at Cryptogenomicon. [Jennifer]
• ‘nother day, ‘nother genome: Zebra Finch. While you are looking into genomes, Nature has an interesting 10 year retrospective of the completion of the Human genome. [Trey]

Just caught the announcement via GenomeWeb that the GEBA project paper has been published with 53 bacterial genomes (see Nature for a summary article that is available, and the paper itself is here).  They deliver 53 bacteria and 3 archaea.

GEBA is the Genomic Encyclopedia of Bacteria and Archaea.  They developed a strategy to select microbial genomes not because of some important physiology of that microbe, or because it was a disease-causing organism, but more based on looking across the world of species via phylogeny, and selecting some that might have been otherwise neglected.  This is a neat strategy in many ways, because usually we only look under the flashlight for stuff we are kinda looking for already.  This turns that around and looks in the dark as well.   That does make it something of a fishing expedition, and I can understand those criticisms of an approach like that.  But we are sure to learn useful things from stuff we weren’t really looking for too.

Have a look at the paper and consider that strategy.

A great place to look at the organisms online will be IMG, the Integrated Microbial Genomes database.  They have a special subset of IMG/GEBA available here: http://img.jgi.doe.gov/cgi-bin/geba/main.cgi . We’ve got a tutorial on using IMG that covers the main aspects of the IMG foundation as well (requires subscription).

You might also consider “adopting a genome” from the GEBA project as some schools have done!  Trey talked about that one week as a Tip-of-the-Week .

Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656

UPDATE: Jonathan Eisen, one of the authors on this paper, has an excellent post up with more backstory on this work.  Check it out at his blog: http://phylogenomics.blogspot.com/2009/12/story-behind-nature-paper-on-phylogeny.html

UPDATE 2: There’s a great article in the NYT on this work as well: Scientists Start a Genomic Catalog of Earth’s Abundant Microbes

Being summer, a strangely slow connection and some other factors, I am embedding a talk from Doug Ramsey (posted on SciVee) on the GEBA project at JGI (instead of doing a tip myself . The GEBA project recognizes that many, if not most, of the bacterial and archaeal genomes that have been sequenced to date have some relevance to human disease or other human interest. This of course is reasonable, but it also leads to big gaps in our knowledge of bacterial evolution and genomics, knowledge that would help us better understand those genomes that we find relevant and knowledge that in and of itself can be quite interesting and potentially useful. View the talk to learn more about this project to sequence 100 phylogenetically diverse bacterial and Archaeal genomes.
I’m also posting this as an introduction to JGI’s Adopt a Genome project. This project allows student groups to adopt and study a bacteria in the GEBA project and hopefully add to our knowledge and annotations of the genome while learning. The students can then annotate the adopted genome by using IMG-ACT.

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

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!

 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!

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:

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.