Tag Archives: img

Rare photo of me in the wild….

Of downtown Boston, at Tufts Medical Center, singing the praises of IMG and the Integrated Microbial Genomes resources.

I love workshops that only require a trip on the Orange Line.

Today we were doing the World Tour of Genomics Resources. Tomorrow it is UCSC Genome Browser (intro + advanced), and Thursday ENCODE. So if you want to workshop vicariously you can check out all of our tutorials on those. The slides, handouts, and exercises are all over there for you to download if you’d like.

As much as I love the online training and webinars and all, you really do get important information about the needs of folks in the room that you just don’t really get from the intertubz, and I do like to do the material live.

Video Tip of the Week: Microbiome Resources From JGI


Just over a month ago an issue of Nature had two articles from the Human Microbiome Project Consortium – you may have seen them, or noticed the Friday SNPets items we had on them. I promised myself that I’d read the articles (which I did), and that I’d visit my old friends the IMG (Integrated Microbial Genomes) & IMG/M (IMG with Microbiome Samples) to see what is new at these powerful microbial genome resources. In today’s tip I decided to take you along on my visit with me, because I found that IMG now has a resource dedicated to the analysis of genomes related to the Human Microbiome Project called the Integrated Microbial Genomes-Human Microbiome Project, or IMG/HMP. We visit both IMG/M (briefly) and the IMG/HMP in today’s tip.

When I referred to IMG as an old friend, I really do feel that way – our tutorial on IMG* was one of my first projects for OpenHelix. I was new, and IMG was new, having been released in March of 2005, only a few months before I created our tutorial (on their June 2005 release, if I am remembering correctly). They have grown into such an extensive, powerful resource. To give you an idea of how fast they have grown & developed, our current IMG tutorial is version 12 and I’ll be working on version 13 as soon as I finish updating our SGD tutorial. When we first created our IMG/M tutorial*, metagenomes were a relatively new concept and the resource included a total of 24 microbiome samples – now it has over 1000!

But enough with the nostalgia, let’s get to the resources! :) IMG/M integrates metagenome data with isolate microbial genome sequences from the integrated microbial genome (IMG) system to enable the analysis of phylogenetic composition and functional or metabolic potential of the aggregate genomes (metagenomes) in microbial communities (microbiomes). Genomes generated as part of the Human Microbiome Project (HMP) are included into IMG/M from RefSeq via IMG. IMG/M resources allow users analyze metagenomes, genomes, genes and functions by making lists of items and then manipulating them in “analysis carts”. Metagenomes can also be analyzed using the tools provided from their ‘Metagenome Details’ page. These options are explained in much more detail than I can cover here in the IMG/M reference that I site below. I also link to the most recent IMG publication, since an understanding of it is essential to understand any IMG/M-based resource.

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick Links:
Integrated Microbial Genomes (IMG): http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

Integrated Microbial Genomes with Microbiomes (IMG/M): http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Integrated Microbial Genomes-Human Microbiome Project (IMG/HMP): http://www.hmpdacc-resources.org/imgm_hmp/

OpenHelix Introductory Tutorial on IMG: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=54

OpenHelix Introductory Tutorial on IMG/M: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=24

References:
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012).
IMG/M: the integrated metagenome data management and comparative analysis system Nucl. Acids Res. , 40 DOI: 10.1093/nar/gkr975

Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012). IMG: the integrated microbial genomes database and comparative analysis system Nucl. Acids Res., 40 DOI: 10.1093/nar/gkr1044

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: Comparing Microbial Databases


A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I’ve been exploring & thinking since then & am going to give a very brief comparison of those two resources in today’s tip & I’ll expand the comparison to other resources here in the text of this post.

Continue reading

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

Ok, really, I’m going to blog again…

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?

New and Updated Online Tutorials for Ensembl Legacy and Overview of Genome Browsers

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.

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…

Another day, another genome…or 56…

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

Tip of the Week: Genomic Encyclopedia of Bacteria & Archaea (GEBA)


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.