Tag Archives: MaizeGDB

Tip of the Week: MaizeGDB Genome Browser & other videos


Occasionally we highly video tips and tutorials from other sites. Today I’d like to point to you MaizeGDB. Last year the folks at MaizeGDB highlighted their video tutorials in Database, As they state in their abstract:

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases.

We obviously agree here at OpenHelix. We have over 100 full tutorials and 200 tips in agreement :D.

Embedded above is their tutorial on using the MaizeGDB Genome Browser (v2). They have seven additional tutorials on their resources such as how to find a genetic map position of a locus and doing a phenotype search. On that page of tutorials they also have links to various other tutorials from others on Maize research and MaizeGDB.

You can learn more about MaizeGDB from our blog. We highlighted MaizeGDB in several posts of the last few years chronically their move to GBrowse,  it’s success and their experience.

Useful Links:
MaizeGDB
MaizeGDB tutorials
GBrowse
OpenHelix GBrowse Tutorial
Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, & Sen TZ (2011). The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video. Database : the journal of biological databases and curation, 2011 PMID: 21565781

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….

How to pick a genome database platform

I was reading a newsletter I get from Biotechniques, and their WebWatch often has some fun items. (You may need to get a free login to see the WebWatch.) This week they referred to the MaizeGDB database in the post Amaizing Base. Although I had been aware of MaizeGDB before, it was a nice reminder to go over and have a look to see what’s new.

When I went over there I was intrigued by the new browser they are about to launch (in mid-October). The link says “coming soon” and I went to check out the information there.

Currently that link goes to a page that describes their move to a more sequence-centric representation of their data. It was a fascinating look at their decision process to move to a new browser platform and what they decided to do. For database geeks like me, seeing their ranking of the importance of various features was very compelling.

And what they decided? GBrowse!

We have a tutorial available on GBrowse. Usually we do tutorials on specific sites, but as we kept seeing GBrowse over and over at different sites we created a tutorial for that. It helps me to understand the underlying basic browser when I visit any site that employs it. Even though the wrappings and the data types will vary at different sites, understanding how it works makes it much easier to use at any new site that uses it. HapMap, MGI, WormBase, FlyBase, TAIR, Watson’s personal genome, and a whole bunch of other sites use the GBrowse software.

Looking forward to checking out the MaizeGDB GBrowse version when it launches!