Tag Archives: gramene


Video Tip of the Week: Plant Reactome at Gramene

gramene_logoReactome is one of our favorite tools to explore pathways. And they cover a wide range of species, which is helpful for many researchers. But there are times when having a topic-specific tool can be even more useful for a research community. Sometimes these types of tools are disease-specific, or in the case of today’s Video Tip of the Week, plant-centric. If you haven’t seen it before, this introduction to Plant Reactome is worth exploring.

In this overview of Plant Reactome, Justin Preece describes the data model to help understand the foundation of Reactome. And then quickly moves into how you can access this tool from the Gramene portal. There’s guidance on the organization of the interface, and how to access pathways you are interested in. Then there’s an explanation of their process of projecting pathways from well-characterized rice data on to other species that might be less well characterized. They have over 200 curated rice pathways and ongoing curation as well. There are dozens of Arabidopsis curated pathways too. There’s a bit about the move to the new Reactome platform, and analysis tools available with that. There’s an example of time course data shown to illustrate a series of data. The talk touches a little bit on the new main Reactome interface that we also highlighted.

Try it out.

Quick links:

Plant Reactome directly: http://plantreactome.gramene.org/

Gramene main site: http://www.gramene.org/

Reactome: http://www.reactome.org/


Tello-Ruiz, M., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D., Kerhornou, A., Walts, B., Fonseca, N., Huerta, L., Keays, M., Tang, Y., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D’Eustachio, P., Stein, L., Petryszak, R., Kersey, P., Jaiswal, P., & Ware, D. (2015). Gramene 2016: comparative plant genomics and pathway resources Nucleic Acids Research DOI: 10.1093/nar/gkv1179

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Milacic, M., Rothfels, K., Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., & D’Eustachio, P. (2015). The Reactome pathway Knowledgebase Nucleic Acids Research DOI: 10.1093/nar/gkv1351

World tour of workshops, recent stop: Morocco, Africa

Trainers & organizers

Last year I had the opportunity to give a workshop in Ifrane Morocco (UCSC Genome and Table browsers, Galaxy) at Al Akhawayn University. This year, Mary and I returned for a longer 3-day workshop at University Hassan II in Mohammadia. OpenHelix was a co-sponsor of the workshop (donating our time, materials and expertise). The workshop covered a plethora of topics from a world tour of resources (tutorial-free) and introductory UCSC  Genome Browser (tutorial-free) and ENCODE (tutorial-free) to genome variation analysis in dbSNP (tutorial-subscription) and analysis using Galaxy (tutorial-subscription). You can see the full schedule of the topics Mohammadia Workshop Schedule here (pdf).

As last year, we were impressed with the students (there were 117 total, about 50/50 gender ratio). English is their 3rd or 4th language in most cases, Moroccan Arabic, French or various African languages being their language of choice. Yet, they were attentive and asked very perceptive and fascinating questions. They were also very enthusiastic

The workshop students

learners. It was a delight to teach them.

We’d like to thank Mohammed Bourdi at NIH, who spent large amounts of time and financial resources to organize this (and last year’s) workshop. We hope to repeat and expand these for next year and perhaps years to come. We will be looking for sponsors.

Several questions were asked at the workshop we’d like to reiterate the answers here and seek some answers from our readers:

*One student was looking for wheat genome resources for designing primers. The wheat genome is as yet incomplete, but there are some resources to get started:
Wheat Genome Sequencing Consortium
Gramene’s wheat resources
Wheat Genetic and Genomic Resource Center @ Kansas State
Perhaps also COGE for conserved sequences
edited to add:
CerealsDB and
James’ post on the wheat draft sequence might give some insight into that huge genome.
*Another student asked about dotplot tools:
Galaxy offers a large collection of EMBOSS tools including dotplot analysis, as does EBI Emboss tool

* Another question concerned finding a ‘dynamic programming’ (optimal solution) multiple sequence alignment tool as opposed to a heuristic one. The issue with this is the complexity of the search space of dynamic programming solution, this slide set might help with the understanding, particularly slides 1-5 and 17-22. It is too computationally intensive. That said, the student might want to check out MSAProps and this list at Wikipedia.

Do our readers have any other guidance on this?

Teaching moment

* Another student asked  if we know how to find DC-area internships in biological sciences. Another student (mathematician from Mali) was looking for something in the US in bioinformatics. Any ideas of programs to bring African biology students to the US or Canada?

If our Moroccan students (or anyone else) have any additional questions, please feel free to ask them here!


ANd a side note. Last year I had all of 3 hours to tour Fes. This year I took advantage of my trip. Mary and I spent a few days in Fes and Marrakech. My family joined us in Marrakech and later my family and I toured for 8 days visiting the Atlas mountains, the Sahara and Fes. Needless to say, it was a trip of a lifetime. Morocco is a fascinating and beautiful place. I look forward to visiting again.

Gates and doors of Fes are beautiful

camel excursion to the Sahara





Tip of the Week: Plant comparative genomics using Plaza

ResearchBlogging.orgPlaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots, mosses and algae. There are some obvious tools and data from the homepage, but I suggest you take a look at the documentation and tutorials, you’ll find there is a lot more once you start delving into it. In this tip, I’m going to walk though getting phylogeny of a gene family from a specific clade to illustrate that there is a lot here that you might not see at first.

Plaza: http://bioinformatics.psb.ugent.be/plaza/

For grass comparative genomics you might also want to check out Gramene (tutorial, subscription) and for general comparative genomics, VISTA (tutorial, free) is an excellent resource also.

Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K. (2009). PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants THE PLANT CELL ONLINE, 21 (12), 3718-3731 DOI: 10.1105/tpc.109.071506

Genomics resource training scholarship, sponsored by Gramene and OpenHelix

Just thought our readers might like a heads up. I quote from a recent press release:

Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomic resources to encourage diversity in science.

The Resource for Comparative Grass Genomics, Gramene, sponsors a Gramene tutorial with us, which is thus free to users. Additionally, Gramene is also sponsoring a program, partially funded by NSF,  to open all OpenHelix tutorials to educational institutions serving underrepresented populations. This will give all students, faculty and staff at the institution unlimited access to a wealth of tutorials in our catalog including training on NCBI’s PubMed, Entrez, PlantGDB and over 90 other tutorials on genomic resources. This would be a great opportunity for students and researchers at the applying institution to train on genomics resources!

If you belong to a qualifying institution and would like to apply for this program, please find more information here and send us your application! The deadline for application is June 30th, 2010.

(tweeted here)

Gramene Announces Scholarships for Groups Underrepresented in Science to Learn How to Use Bioinformatics and Genomics Resources

Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomic resources to encourage diversity in science.

Bellevue, WA (PRWEB) April 22, 2010 — The creators of the Gramene Resource for Comparative Grass Genomics and OpenHelixannounce the availability of scholarships to colleges and universities serving underrepresented minorities for full access to over 85 online tutorial suites on bioinformatics and genomics resources. The program is partially funded by the National Science Foundation (NSF).

“An ongoing goal for Gramene, our institutions, and the NSF, has been to provide opportunities for advancement and training to underrepresented groups in science,” said Dr. Doreen Ware, of Cold Spring Harbor Laboratory and Principal Investigator of Gramene, “So we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.”

…we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.

Recipients will have access to the OpenHelix catalog of tutorial suites on a wide range of bioinformatics and genomics resources, including Gramene, PlantGDB, NCBI tools such as Entrez Gene, BLAST and PubMed and many more. A full catalog of tutorial suites is available at http://www.openhelix.com/cgi/tutorials.cgi.

Each tutorial suite includes a 45-60 minute, online, self-run, narrated introductory tutorial on how to use a specific resource. The tutorial suite also includes PowerPoint slides, slide handouts and exercises which can be used as reference material or to build classroom content.

“The study of genomics has affected just about every area of life sciences, so learning how to access and interpret genomic data is critical to research success,” said Scott Lathe, Chief Executive Officer of OpenHelix, “With the convenience and broad accessibility of online training, we hope these scholarships will help in leveling access to this important training and further the potential and ongoing careers of the recipients.”

Institutions can apply for a scholarship for access to the tutorials at http://www.openhelix.com/cgi/scholarships.cgi. The scholarships are available to to minority serving colleges and universities. Underrepresented in science means those racial and ethnic populations that are underrepresented in biology research relative to their numbers in the general population. Individual scholarships are available to U.S undergraduates, graduate students, post-doctoral students, faculty and staff. Application deadline is June 30, 2010 and a limited number of scholarships are available.

About Gramene
Extensive research over the past two decades has shown significant conservation of gene order within large segments of linkage groups in agriculturally important grasses such as rice, maize, sorghum, barley, oats, wheat, and rye. Grass genomes are substantially colinear at both large and short scales, opening the possibility of using syntenic relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.

As an information resource, Gramene’s purpose is to provide added value to data sets available within the public sector to facilitate researchers’ ability to understand plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species.

Current work is being supported by the NSF Plant Genome Research Resource grant award #0703908.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix 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. More efficient use of the most relevant resources means quicker and more effective research.

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.

Biodiversity databases

nature_reserveI know sometimes I joke about “another day, another genome” as it seems like we can check off another genome daily.  And as the next-gen technology spreads further that’s going to be even more common.  It’s gotten me thinking a lot about which species ought to be done.  And how will sequencing research teams choose?

The folks at the Agricultural Biodiversity Weblog have me intrigued on a bunch of resources that are not the ones that most bioinformatics folks in my sphere have focused on.  I mean, I know why we focus so much effort on model organisms and the big food species like at Gramene and PlantGDB, and I support that.  But when you start thinking about the other organisms that we rely on so much–in the big agriculture way and the small agriculture way–I think we need to bring those animals and plants into the herd :)  And we can soon.

Their recent post Linking up livestock databases was the one that prompted this post.  But they write a lot of things I like (especially about plant genetic resources) and really have me wondering and reading, and thinking about how to raise awareness on the other valuable species.

The livestock post pointed to several nice resources that I was unaware of before.  In an article by Eildert Groeneveld in the Globaldiv Newsletter the focus in animals, and he offers several nice links. Check out the diverse sheep at the Heritage Sheep Breeds web site.  Check out the species in the Central Documentation for Animal Biological Diversity in Germany here.  Or the breed data collection at Oklahoma State–have you ever seen goats like those Alti Mountain goats?  Wowsa.    How about the Domestic Animal Diversity Information System or DAD-IS?  There are other great links as well in the newsletter–check ‘em out.  Another thrust of the article is linking up individual data with breed data via the EFABIS project as well to enhance the knowledge, and you can learn more about that in the newsletter.

Anyway, there are some really fascinating variations here.  Understanding them would be a great project for folks with a next-gen sequencer waiting for input.   Have a look.  And celebrate rare breeds.  We are going to need them in times of climate change.


A newly enhanced database and resource is available to researchers called Phytozome. Phytozome is targeted as a hub of genomic data for plants of interest in biofuel research and a joint project of the DOE JGI and UC Berkeley’s Center for Integrative Genomics. As a recent press release states,

The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the transfer of functional information to important biofuel and agricultural crops from model plant systems, as well as allowing users to explore land plant evolution.

This release is v. 4 and includes the genomes of 14 plants from green algae, arabidopsis and corn. The resource uses GBrowse (free tutorial and training materials) as it’s genome browser, BioMart for advanced searching and has BLAST capability. I find Gramene a bit more extensive than Phytozome, but the focus of the two (biofuel plants and agricultural grains for Phytozome and Gramene respectively) are different and Phytozome is becoming quite extensive.

I remember going to a DOE/JGI users conference last year and being quite impressed with the research going on in biofuel, and also more sobered by the obstacles both techological and practical (use of food-producing land, etc) that we face. With rising gas prices and temperatures, can’t ask for too much information!

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!

You want fries with that?

potato1.jpgWe used to joke in grad school about appropriate phrases to practice for the upcoming job interviews. I imagine they are still doing that….And my well-known love for any potato product earned me a potato cookbook as a graduation present from Trey. (I still have it and actually use it a lot–the herb potato fritters recipe is my favorite. Author is Bodo Schieren)

But I had to smile when I saw the announcements for the potato genome project all over the place. This is an organism that changed my family’s history (we are ancestrally Irish). I can’t wait to look around the potato genome and see what’s in there. And I would love to personally develop training on the potato genome database when it arrives!


I hope like Gramene they’ll have a section in their database for recipes :)

fritters.JPG As per APD request.