Tag Archives: GMOD

GMOD Hackathon, evo tools, Nov 2010

Got an announcement over the weekend for this adventure in coding–sounds useful:

Tools for Evolutionary Biology Hackathon
November 8-12, 2010
NESCent, Durham, North Carolina, USA

We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply.  Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, …), or documentation wizard, then your skills are needed!

How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.  Applications are due August 25.

More at the link, and I got the email from the Biocurator mailing list.

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

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.

Tip of the week: Sol Genomics Network

sol_genomics_networkAside from a short stint at the ASHG meeting, where it is all about the human genome with a smidge of attention to the microbes that hang around with us, I’m back and I’m focusing on plant resources again.  Recently I began to explore the Sol Genomics Network site, and that will be the focus of this tip of the week.

Sol Genomics Network focuses on “Solanaceae as model system for diversity” as they describe themselves.  And they aim to link genotypes to phenotypes for a collection of plant species.  Currently species information found at this site include: tomato, potato, eggplant, pepper, petunia, tobacco, and coffee.  Not all of them have browsers available here, but there are some maps for several, and there are links to other sources that may provide more information about the projects, clone collections, and additional details. They are also developing a breeder’s toolbox and they’d like to have some feedback on the needs of the community on that.

We will take a look at their tomato browser today, which is implemented in GBrowse, the Generic Genome Browser from the GMOD project tool kit that supports so many species and data types–and if you want some help using GBrowse you should see our freely available tutorial on that.

The site also include a number of outreach activities for students at varying levels–including a lab exercise for the high school level, a word find puzzle for youngsters with these species (we like puzzles here), and the fun and interactive animated series with a sequencing puzzle where you generate a small assembly with some sample BAC fragments (ok, they are really small BACs, but you get the point).   I know a lot of, ah, mature scientists who could stand to work with the concept of the assembly to grok that a bit better, actually….

Go directly to the BAC assembly sequencing puzzle here if you don’t have time for the whole tip of the week:  http://bti.cornell.edu/multimedia/puzzleComplete.html

Sol Genomics Network site directly: http://solgenomics.net/

More Solanaceae resources: http://solanaceae.plantbiology.msu.edu/

DragonDB? Who knew….

snapdragonNow, I like to immerse myself in databases–including some pretty obscure species.  But even I had no idea there was a dragon database.

Snapdragon!  http://www.antirrhinum.net/

I’m working on an update for our Gramene tutorial right now, so I’m all over plant resources and following some links today I found the dragon.  There are some other ones I need to check out as well–from the Gramene link to VPIN, the Virtual Plant Information Network.

The Legume Information System was new to me as well.  I’m a big fan of legumes, as they constitute a huge portion of my protein sources.  There was also a link to SoyBase, which also has a soybean breeder’s toolbox.  I see their genetic map is in CMap, which is in that list of GMOD tools I mentioned the other day, and is also used by Gramene.   These tools are popping up all over the place–and if you learn to use them in one place you can usually transfer those skills to other species of interest as they come along.

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.

Ok, say you get a genome. What next?

There may be a lot of opportunity to get one’s genome of interest sequenced in the near future.  And I don’t only mean your own personal genome–I mean your species of interest.  There should be academic centers and service providers who offer genome sequencing at increasingly reasonable pricing soon.

So let’s say you get your favorite sample done: what next?  We have talked about how cool it is to be able to use the GBrowse or WebGBrowse tools to display your data.  But that is missing a step, actually.  To get appropriate data to display you need to annotate your genome.  You need to curate your genome.  The GMOD suite offers some tools to do this–Apollo can be a part of your strategy. JCVI has an annotation service for prokaryotic genomes that uses Manatee. They frequently offer a prokaryotic annotation course around that process as well.

But the other day I heard about another option that I thought I would mention: the BLAST2GO team is announcing a course on Automated Functional Annotation and Genome Mining.  Here is their announcement via the GOFriends mailing listpersonally I would choose the one in Valencia :)


•Are you working in sequencing projects?
(EST projects, Next Generation Sequencing, Microarray desing, etc… )
•Do no have thousands of novel sequences that need functional annotation?
•Do you need a user-friendly tool to functionally analyze your data?
The Blast2GO Team is very pleased to announce:


In this course you will learn tools and tips for functional
annotation, visualization and analysis of novel sequence data making use of Blast2GO.

The course will be offered to 35 participants at 2 locations:
•Valencia, Spain: 28 to 30, September 2009
•Florida, USA: 14 to 16, October, 2009
For more information and registration until the 1 of September please visit:

But Florida in October wouldn’t be a bad option either!

For more information about just the BLAST2GO part, check out this site: http://blast2go.org/

Tip of the Week: DNAPlotter

dnaplotter_movieWe spend  most of our time talking about long linear genomic sequences, organized over multiple chromosomes, which are traditionally well handled by genome browsers like Ensembl, UCSC Genome Browser, GBrowse, etc.  But if you want to represent a circular genome you may prefer other graphics and views.  DNAPlotter is a tool that will enable a circular graphical representation of the data, with annotation tracks that you can customize and manage.  It can also do linear views, but for this example I’ll be illustrating a circular view.

It accepts a variety of input file format types (EMBL, GenBank, GFF3), and since it can access the files with the Artemis library tools the GMOD architecture can be used to provide the underlying database for that.  The paper explains that the Chado relational database can be used to maintain the data if you like (but that is not required).

So if you are seeking circular displays, you might want to try DNAPlotter.  You can launch a nice example from their homepage to start examining the features. This 3 minute movie examines that example and illustrates the track manager menu.

Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009 25(1):119-120; doi:10.1093/bioinformatics/btn578

Access DNAPlotter here: http://www.sanger.ac.uk/Software/Artemis/circular/

Tip of the Week: Model Organism Database tutorials

gbrowseFor the tip of the week today, we’d like to point out a number of new (free to you) tutorials on model organism database resources. These seven tutorials (include flash movie tutorial, slides for downloading, exercises and handouts) were partly funded by a NHGRI grant. We just put out a press release on this, but I thought the Tip of the Week would be a great place to introduce you to these tutorials. We have seven tutorials that are (or will soon be) publicly available (this link takes you to a list and links to all these tutorials). The first four available are on GBrowse, WormBase, RGD (Rat Genome Database) and MGI (Mouse Genome Informatics. GBrowse (the tutorial linked to here), was developed by the Generic Model Organism Database (GMOD) project and is a great tool to develop genome browsers for model and research organisms. Many model organism databases use GMOD resources in full or part, including many of the ones we have tutorials on here. Three more will be coming very soon on ZFIN (Zebrafish), FlyBase (Drosophila) and SGD (yeast). Check them out :).