Tag Archives: JBrowse

Friday SNPpets

Welcome to our Friday feature link collection: 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…

Edit: check out what one of the top searches over the last week has been:

Their genomes, unzipped

So. the bloggers at Genomes UnZipped (we blogged about before), have entered a new stage. They’ve decided to expose themselves. In the spirit of open source taken personally, they are unzipping their own genomes and posting their genomic information online for everyone to see. You can begin to view that data on their genome browser (using JBrowse- tip of the week for Jbrowse here).

Why are they doing it?

As we discussed the notion of a group of experts analysing their own genomes, one thing rapidly became clear: for maximum public benefit the analyses had to be open and reproducible, and that meant making the underlying data public. In other words, for this to work, members of the group had to be ready to spill their genetic secrets to the world.

Genomes Unzipped has turned into a great resource for understanding personal genomics. This move should be interesting

Forgive the image, I just couldn’t help myself :-), but I’m not the only doing it. Check out Razib’s link below :D. Oh, and an aside… genomes unzipped lead to an … open helix :D.

(more: Razib Khan’s take here - and hat tip)

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

References:
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….

Cutest genome yet

pandaIn the ongoing series of Another Day, Another Genome….we add the giant panda!  By far the cutest genome yet.  Well, ok, I actually haven’t seen the genome yet as the site was down last night when I tried.  But I’m sure it’s adorable. Her name is Jingjing, and she is a 3 year old panda and was also the 2008 Olympic mascot, according to the supplement info.  She’s a supermodel of pandas, I guess.

Hat tip to James and the Giant Panda Corn

The paper is here:  The sequence and de novo assembly of the giant panda genome

The database and sequence is here: http://panda.genomics.org.cn The browser looks nice, but I’ve found some odd implementations.  The ? tools yields the messsage “this tool is empty”. Got the same message from the Config button.  Documentation a bit sparse. Sigh.  More later as I look harder at it.

Update: The browser implementation threw me at first, reminded me of JBrowse but not exactly. As they describe:

We illustrated the panda genome data in a MapView, which is powered by Google Web Toolkit . A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads.

Nice.

GMOD summer school–homework!

Well, ok, you aren’t required to do the homework–it’s just available for you if you want to work on setting up GMOD tools around your projects (or at home, if you want…).

We mentioned that the GMOD summer school was going on, and now that it’s all successfully wrapped up many of the materials are available as tutorials on the GMOD site: http://gmod.org/wiki/Training_and_Outreach

These are mostly installation and configuration tutorials for the software components.  Although the end user tutorial we created for GBrowse is in the list as well–the emphasis is definitely on developers.

The tools included in this tutorial collection are all pieces of the GMOD suite.

  • Apollo, a genome annotation editor.
  • BioMart, a data mining system that lets you build complex queries from the underlying databases.
  • Chado,relational database underlying the GMOD tools.
  • CMap, comparative genomics tool for viewing maps
  • GBrowse, a genome browser used at for many species.
  • MAKER, genome annotation pipeline.
  • Tripal, a front-end to Chado databases.

As more and more people get next-generation sequencing data for their species of interest these tools and support for them will be increasingly crucial.

Tip of the week: JBrowse, a game changer?

jbrowse_tipIn most of software and database development the changes that are coming along all the time seem to be tweaks and polishes on the existing strategies. Every so often, though, there’s a big shift in the strategy or mechanism. This week the JBrowse paper I read made me realize that is now firmly underway. Today’s tip of the week will introduce JBrowse, and here I’ll describe some of the reasons this is a game changer.

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