Tag Archives: GBrowse

Like shooting catfish genomes in a barrel

You know, when the catfish genome is complete, that will be a cool addition to our “Yet another Genome” posts (which I should make a regular series or some update somewhere).  Till the genome is complete, you can view and analyze catfish genomic data at cBARBEL, reported in this weeks NAR advance access: Catfish Breeder And Researcher Bioinformatics Entry Location. Among other tools and schema, they use GBrowse (we do have a free tutorial ;) to compare the data to the Zebrafish genome.

Mark this database (as with many others) as one whose acronyms were created to fit the name. Barbels are the whiskers on a catfish and cBARBEL stands for “Catfish Breeder and Researcher Bioinformatic Entry Location.” See, I was thinking more along the lines of “Catfish Breeder And Researcher Research Entry Location” or Catfish Barrel, but that is too culturally obscure and specific isn’t it? cBARBEL is good :D.

All kidding aside, it’s a great start to another agriculturally important model organism database.

Next-Generation Analysis Tools

MassGenomics points to a new structured programming framework for analyzing NGS data: A Foundation for Next-Generation Analysis Tools, the GATK (Genome Analysis Toolkit) and points to a few tools that use it.

While I’m at it, let me remind you of a NGS discussion group, GBrowse help to visualize NGS data and Galaxy has a NGS toolbox.

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…

  • A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
  • Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
  • Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
  • VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
  • A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
  • Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
  • On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Choosing a genome browser for your organism…

There are a number of genome browsers out there–we’ve covered that a number of times.  And there are always new ones coming along.  With the onslaught of sequence data we’re about to get from high-throughput sequencing, more and more research groups, communities, and individuals are going to need to choose a genome browser to use to display their data.

One time I stumbled across the survey results for a group that was choosing a new platform to display their community’s data: MaizeGDB.  I wrote about it then because I thought it was interesting, and because I know people are facing this pretty regularly now.  We get asked.  But since that time they have progressed, implemented, and they wrote up their experience.  It’s now been published in Database.

It’s a pretty straighforward paper.  They describe their needs and their assessment of the resources their community had and used.  They surveyed likely users to see what they wanted, and how they felt about the pieces that already existed.  One piece they specifically noted–when asked, many users did not say they used Ensembl, but the Ensembl software was the foundation of one of the items they did say they used.  MaizeGDB writes:

This result shows that users may not be aware of the underlying browser software that the various web sites use.

Ah, yeah.  Here’s another thing this shows: database end users are definitely not thinking about browser software the same way database developers are.  And I do not mean end users are stupid.  They just do not think about this stuff the way software providers think they do.  We keep trying to tell providers this.  It’s not always well received.

So anyway, they move on to assess the candidates for their new implementation.  The focus on Ensembl, GBrowse, Map Viewer, UCSC Genome Browser, and xGDB.  They describe the framework, possibilities, and limitations of each for their purposes.  I think this is a nice look at the various options that lots of people considering the issue should find useful.  They also address that there are other browser that have since, or may still, come along in the future that could be considered, but at the time these were the focus.

They go on to describe their implementation experience.  They seem pleased with it.  And they highlight a one of their favorite pieces, a Locus Lookup tool, that they have added as well.  It sounds like it’s serving their community really nicely.

This is a highly useful paper for the people in the market for genome browsers.  It’s not for everyone, for sure.  Well, at least not yet.  But your day is coming. You’ll need a browser eventually….

You can check out their GBrowse implementation at: http://gbrowse.maizegdb.org/

And if you are interested you can see our free GBrowse training suite here: http://www.openhelix.com/gbrowse

Sen, T., Harper, L., Schaeffer, M., Andorf, C., Seigfried, T., Campbell, D., & Lawrence, C. (2010). Choosing a genome browser for a Model Organism Database: surveying the Maize community Database, 2010 DOI: 10.1093/database/baq007

Andorf, C., Lawrence, C., Harper, L., Schaeffer, M., Campbell, D., & Sen, T. (2010). The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps Bioinformatics, 26 (3), 434-436 DOI: 10.1093/bioinformatics/btp556

EDIT: added links to a couple of older blog posts, should have had them in before….

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.

What would you do with your genome?

So last week I treated myself to my first vacation in a long time.  It was my birthday, and I wanted to disconnect a bit and recharge.  Mostly it worked, although the hundreds of emails I’m facing this morning are a bit daunting.  But just before I left I got an email from a colleague who asked me a really great question:

….I would love to know where you would start when you get back a personal genome sequence….

And I couldn’t shake this out of my head.  I was sitting on a bridge outside Windsor Castle thinking about it as the sun set on my first day.  (On subsequent days I found that the far superior ciders in the UK were able to push this question out of my head for some periods of time. And also pie.)

I’ve spent some significant time thinking about the onslaught of personal genomics, of course.  It’s all been very theoretical, because I would have refused to even begin the process of obtaining my personal genome sequence until the GINA legislation fully kicked in.  But now that barrier is down.  I’m still not ready to get mine done for a variety of reasons (cost, quality, informative value).  But it’s still worth thinking about what I would do with it if it was handed to me–in specific terms, with concrete actions.  So here’s what I decided I would do.  Your mileage may vary.  And I’d love to hear what others might do with theirs.  Follow the link for the specific actions I’d take.

Continue reading

Create GMOD components? Need a logo?

The GMOD mailing list had an unusual offer the other day.  It seems that the GMOD consortium folks have teamed up with design students to offer to work on a logo for the projects that the science and computer geeks are developing.

This strikes me as a very neat cross-fertilization.  I would love to see more design students get interested in a scientific focus.  It would be great to have more science graphics folks around.  In fact, I was using the freely available images from the NHGRI recently and was offered a survey.  I begged them for more graphics that the un-aesthetics like me could use.

Anyway, if you are a non-profit and create GMOD resources, you can get involved in this project.  The details are found on the mailing list here.  Or you can go directly to the Logo program here: http://gmod.org/wiki/GMOD_Logo_Program

Official GBrowse 2.0 launch announced

Just got this email from the GBrowse mailing list. Lincoln Stein announces the release of GBrowse 2.0. Here’s the link to the full announcement. Here’s a portion of the text; the full email includes a couple of things not included yet:

With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that GBrowse 2.00 is now available for downloading from CPAN, http://search.cpan.org/dist/GBrowse/ and SourceForge, https://sourceforge.net/projects/gmod/files/.

The following are hilights of the many new features that have been added since the 1.70 release:
• A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
• Different database backends can be associated with each track, making backend management much simpler.
• A revamped user interface for a less cluttered and more functional end-user experience.
• A UI theming system with three predefined themes, including a cool “transparent” theme.
• A custom track upload and management system gives users much greater control over custom tracks.
• An optional admin interface allows an authorized user to upload and manage public tracks without editing config files.
• An optional user registration and login system allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
• Support for named subtracks (tracks within tracks) and filtering of those subtracks.
• Support for next generation sequencing data.

For those of you who want a quick feel for the new look/features of 2.0 you should check out the Tip of the Week and you can try it out at WebGBrowse.

And yes, we’ll update our GBrowse freely-available tutorial as 2.0 rolls out at more and more sites.  But lots of sites will maintain the previous versions for some time in our experience, so there is still plenty of value in knowing how the previous versions work.

Tip of the Week: WebGBrowse, now v2.0

From the GBrowse mailing list this week comes word of the new version of WebGBrowse.  I talked about WebGBrowse in the past as a very handy tool for creating a GBrowse visualization of data that you may have.  Using WebGBrowse permits you to upload, view, and interact with the data without the overhead of installing a local copy of GBrowse and having to maintain that.  This short Tip of the Week demonstrates how easy it is to interact with this web-based, customizable, implementation of GBrowse.

The full announcement can be found here, but briefly here were the highlights for me:

- The users will now have a choice of GBrowse display between versions
1.7 and 2.0.
- The display from one version can be migrated to the other by simple
button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.

This would be great for a smaller project team that can’t maintain their own local copy of GBrowse, or as a way to pilot the project before committing to the whole thing.  I also think this could be a very handy teaching tool for instructors who want to get students up to speed on some of the foundations of genome browser display without too much overhead.

GMOD sessions at PAG

Just came across the GMOD mailing list, thought I’d post this as a PSA (public service announcement) for anyone attending the Plant and Animal Genomes Conference:

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego.

There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them.

This includes workshops and posters on GBrowse and GBrowse_syn:


The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse, Sunday, Jan 10, 1:30-3:40pm, California Room, Scott Cain

Comparative Genomics with GBrowse_syn: Visualizing your comparative genomics data with the Generic Synteny Browser, Wednesday, Jan 13, 10:20am-12:30pm, Pacific Salon 3, Sheldon McKay


P858: GBrowse And Next Generation Sequencing Data, Monday, 10-:11:30am, Scott Cain

P861: Comparative Genomics Tools In GMOD, Monday, 3:00-4:30, Dave Clements

See the PAG 2010 page on the GMOD wiki for a full listing and a flier showing highlights:


If you are attending PAG, please consider going to this and the other GMOD-related presentations.


Dave C.