This tip is actually a video done by the RGD group and one of those gems I’ve found at SciVee in our attempts to integrate our tips at SciVee (which will be coming). We occasionally will highlight a short tutorial done by someone else here at our tips (occasionally) and since I’ve found this gem and just got back from vacation in Florida …
Btw, while you are at it, you might want to check out this interesting set of tutorials on biomedical ontologies.

If that is data you are interested in, you might also explore some of the other things I’ve been looking at.  The MGI team Jackson Laboratory has a division that focuses on mouse phenotype data as well.  Called Mouse Phenome Database (MPD), you can access quite a range of data that already exists. They also have protocols for phenotyping that may be useful to folks who are characterizing animal models.

I also came across a project based in the EU that offers data and standardized protocols for phenotyping.  EUMORPHIA offers the Empress SOPs that they are developing, as well as access to the Europhenome database that contains the results.

As much as I still love to look at genomes, I’m ready to move down the path and look at the phenomes too

NHGRI recently pointed out

And it gives me the opportunity to again point out that we do indeed have seven publicly available tutorials and training materials (slides, exercises, etc) on model organism databases including SGD, RGD, MGI, WormBase, FlyBase and ZFIN… and a seventh on GBrowse, a generic genome browser used by some of these and other genome databases.

Check them out (and fill out the new poll to the left .

The tutorial suites, funded in part by a grant from the National Human Genome Research Institute of the National Institutes of Health, include a self run, narrated tutorial introducing the resource and how to use its feature and functions. Each suite also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others.

One of the first tutorials available is on GBrowse, developed by the Generic Model Organism Database (GMOD) project, a popular tool used by researchers to develop genome browsers for model organisms, species of interest, and particular topics. By learning how to use this “generic” genome browser, you can leverage that knowledge to use dozens of resources devoted to a wide range of research areas.

“The OpenHelix GBrowse user tutorial is very well done and will be an excellent resource for the many research communities that use GBrowse to visualize genomic data,” said Dave Clements of the National Evolutionary Synthesis Center who runs the GMOD help desk.

Model organisms, such as yeast, mouse, rat, flies, and many others, have long been used by researchers to expand our understanding of biology and to assess the effectiveness and safety of therapies before going to human trial. Many of the genomes of these organisms have been completely sequenced, giving the scientific community even greater insight into the organisms and their relation to human biology. The genome data is now available and searchable on publicly available online databases and resources.

You can view the Model Organism tutorials at http://www.openhelix.com/model_organisms.shtml. OpenHelix provides over 60 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

This week has been quite busy here at OpenHelix and the U.S. For the tip of this week, as we do occasionally, I’m going to highlight a short tutorial tip done by someone else. This week’s is one done by the developers of RGD and showing the uses of the GViewer. This tutorial is at SciVee, as the description states:

The rat genome comes to life through the use of the Gviewer tool. This video will show you how to use this helpful tool within the RGD website at http://rgd.mcw.edu/. Genes, QTLs, and species syntenies of interest can all be visualized with ease as the Gviewer zooms in and navigates through the rat genome with a few clicks.

Today I wanted to mention that the search for colony management software arises every few months or so on the mailing lists that I’m on. RGD (Rat Genome Database) has collected a list of tools for this purpose, which you can find here:

http://rgd.mcw.edu/wg/strain-maintenance

Most are commercial, MGI’s is freely available. It will really depend on what you need to do (and your budget, of course).

RGD’s list:

Big Bench Software
CircuSoft’s gMouse
Colony Management Software at MGI
Colony Management Software at BRM [Mary: seems a service, not a program...]
LAMS
Locus Technology
Progeny
Topaz Technologies’ Scion
Transgenic Software’s Villager

They have other useful information over there that includes physical aspects of animal breeding, not just electronic needs. Check it out if you find yourself in need of guidance on this topic.

The Rat Genome Database has a disease portal. These portals offer disease-specific data and right now include cardiovascular, neurological and obesity/metabolic syndrome disease portals. There’s a cancer disease portal coming.  If you go to the link, you’ll see they also have a short tutorial they added last month on the portal that has also been uploaded to SciVee (if you haven’t seen it already, SciVee is a community of pubcasts, or video casts of publications. Check it out).

Now, History channel specials and Nature Genetics focuses have set the bar high for next year’s Year of the Ox, the bovine genome was completed last year.

(*Just btw, there have free tutorials on the NCBI Map Viewer as part of a DNA Day celebration and UCSC Genome Browser. We also have others on Ensembl as part of the general subscription and a subscription to an NCBI-specific set including dbSNP, BLAST and OMIM among others. RGD is coming up.)

Hello,

This is just a reminder that “Modern Marvels: Rats” premieres this evening at 8pm ET/PT on the History Channel. Please see the forwarded email below for more details.

Regards,

Your friends at RGD

The details were covered in my blog post about it: Rats hit the small screen. Check it out!

I’m actually sitting in Philadelphia right now (we have a big training tomorrow here), but I was able to log in to my Tivo to schedule it. I’m not sure if I have the History Channel on this TV. I’m interested to see how it turned out.