Tag Archives: MGI

Mouse KOMP, all over the browsers

An email from the MGI mailing list alerted me to some interesting new data on the browsers. The mouse KOMP project is generating knock-out mouse ES cells for every gene in the genome (well, that’s the goal anyway). This means you will be able to buy off-the-shelf mouse knockout cells for lots of regions you might want to study. You can grow ‘em up, and then breed ‘em with other mutants. You can characterize them in your favorite developmental stages and tissues. What a terrific reagent collection. In fact, if I was a post-doc, I would be looking for very interesting genes in this data set to pursue. You could start a whole career characterizing some of these beasts.

The email from MGI says:

The NIH funded Knockout Mouse Project (KOMP) is in full swing and reagents (vectors, ES cells, mice) from this project are becoming available to the research community.

Find out more about the KOMP project, which genes are being targeted, and which genes have reagents available for distribution by visiting the Knockout Mouse Project Data Coordination Center at http://www.knockoutmouse.org.

The UCSC genome browser (http://genome.ucsc.edu) now has a “KOMP Gene” track that shows which mouse genes are being targeted by the KOMP project. The tracks are linked to the KOMP Data Coordination Center site for the most recent information on project status and reagent availability.

KOMP gene information is also available in the Ensembl genome browser for mouse (http://www.ensembl.org/Mus_musculus/index.html) and will soon be available on the MGI Mouse Genome Browser (http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_current/).

Of course I went looking for some examples. I found a couple to show you on the UCSC Genome Browser and I created sessions to share. If you would like to look at tracks that indicate the region of the knockout you can see this one that indicates the gene Xpr1 is knocked out and ready for you–see the bright green bar track in about the center of the page.

Another example is March4. Here blue and yellow tracks indicate a different status at the 2 groups performing the knockouts. Blue is “not started/on hold” and yellow is “in progress” according to the code on the details page (click the blue or yellow track to see that color code info on the description page).

Although it says the data is also in Ensembl I couldn’t find it–I have a query in to the help desk on that. Will let you know what I learn.

Edit: word back from ensembl = “KOMP data is in a track along with other KO alleles (EUCOMM and NorCOMM). In Ensembl it is called “Alleles”, available in the drop-down list in contigview.” But I’m looking in those same regions as I know data exists from the UCSC stuff and I still don’t see anything. You can go to those URLs but you’ll have to open the DAS sources menu and check the “alleles” box. March4 in ensembl. Xpr1 gives me an error message in the track (Error retrieving KO_vectors features (Can’t connect to the host!). Second attempt said No KO alleles in that section.

And it will be on the MGI GBrowse soon, too. I’ll try to find a sample of that when it is available too.

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!

Animal Colony Management Software

The field that comprises “bioinformatics” is really huge. Some people think it is mostly about sequence analysis. But I have been charged with everything from image analysis (for microscopy) to animal colony management software (for mouse breeding) in my career–and everything in between.

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.

Short Course on Systems Genetics at Jax

The Jackson Lab courses are really terrific–I took a couple of them while I was up there for my post-doc. This announcement just came over the mailing list and I thought I would pass it along. I’m thinking a lot about systems biology and the tools for it right now (more details on that later), and so I’m going to need more people generating data so I can play with the tools. And September in Maine is a nice time, btw:

Applications continue to be accepted for the Short Course on Systems Genetics being held September 23-29, 2008 at The Jackson Laboratory in Bar Harbor, Maine.

This one-week course will cover computational and experimental approaches to genetic studies that utilize the whole genome approaches. Lectures and computer workshops are designed to accommodate students with a wide variety of backgrounds. Biologists seeking to gain a deeper understanding of statistical and computational methods as well as quantitative scientists desiring exposure to biological problems are welcome. Topics to be covered include genetic mapping, gene expression microarray analysis and computational modeling of complex systems.

For more information, including the course schedule and application instructions, please visit http://courses.jax.org/2008/systemgenetics08.html

The tourists are mostly gone at this point, and the town is still running. Good time to visit Bah Hahbah. :)

http://courses.jax.org/2008/systemgenetics08.html

Database of Databases

I was wondering when someone was going to use that name for their resource! We know of a bunch of software collections/compilations and we are always looking around for new ones. Today on the MGI mailing list I learned about DBoDB: http://bioit.fleming.gr/mrb/

It is currently under development, and the focus is mouse resources. But the question that led to this answer was something like: I need mouse anatomical resources–where are they? And this database has 12 listed under that topic.

There are other categories and lists available as well. Check it out and see if you find anything new and useful for your research.

Choose: Resources from the left navigation area, then View. Sort by “anatomy and histology” and there you go.

Bad hair day: now with photos!!

A recent funny exchange on the MGI mailing list has had impact. There are now photos of the Bad Hair Day mouse available from the Jax mutant resource collection!

Bhrd. That’s gotta be a cold phenotype in Maine….
choowawa.jpg

Ok, go see the unadulterated photos. Click on the photo links over at their page. While you’re at it, you might check out the other new mutants lately. If I was Bhrd mouse, I would try to make friends with Wooly to keep warm.

Extinct Genomes in PLOS One

ResearchBlogging.orgtasmanian tigerA paper published today in PLoS One reports on research that shows the feasibility of taking a gene or genomic region from an extinct species and inserting it into the genome of an extant species and resurrect the extinct species DNA function in the transgenic mice. The extinct species was the Tasmanian tiger or Thylacine (that links to the wikipedia page, anyone want to become the curator for the EOL page which is pretty minimal at this point?) and the ‘surrogate’ species was Mus musculus.

And, as the abstract says,

While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

It is an fascinating piece of research.

Continue reading

New Online Tutorials on FlyBase, WormBase and Mouse Genome Informatics (MGI) Resources

Comprehensive tutorials on the model organism bioinformatics databases FlyBase, WormBase and MGI enable researchers to quickly and effectively use these invaluable resources.

OpenHelix today announced the availability of new tutorial suites on several model organism resources including FlyBase, WormBase and an update on the Mouse Genome Informatics (MGI) database. Model organisms are integral to our understanding of basic biology and modern biomedical research. Drosophila, C. elegans and mice are three highly researched model organisms. FlyBase and WormBase are the primary resources for molecular and genetic information on the Drosophilidae and on Caenorhabditis elegans and related species, respectively. MGI is a series of tools and databases that integrate genetics, genomics and biology for the laboratory mouse.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users to:

  • perform Quick Searches and navigate gene summary pages
  • browse genetic features within the context of the entire chromosome
  • construct complex queries across various sets of data stored within FlyBase, WormBase or MGI
  • perform nucleotide or amino acid sequence homology searches
  • output data in various formats, or access large data reports
  • investigate many related resources associated with MGI

To find out more about these and other tutorial suites visit OpenHelix.

Bad hair day, and a deviant search in the basement

badhair_mouse.jpgI have talked about how much I like the Mouse Genome mailing list before. It has high quality discussion, good job postings, handy meeting announcements, software discussions, and more. But today I LOLed at one of the best comments I have ever seen there (by Leigh Brian, of Duke):

I can’t believe you would list a mouse called “bad hair day” and NOT show a picture on the web site!

This was in response to a recent announcement about new mouse mutants that are available in a prior email:

Dear Readers,
Five new mouse models have been added to the MMR web site (http://mousemutant.jax.org/index.html). By clicking on the mutation symbol under the New Gene Mutations heading you will find descriptions for:

  • longjohn 3 Jackson (lgj-3J) a skeleton/limbs mutation on Chromosome 15.
  • Bad hair day (Bhrd) a new skin and hair mutation on Chromosome X.
  • Dreher 10 Jackson (dr-10J) a circling/hearing loss/ head toss mutation on Chromosome 1.
  • Dreher 11 Jackson (dr-11J) a circling/hearing loss/ head toss mutation on Chromosome 1.
  • small swaying lethal a new neurological mutation on Chromosome 6.

Notification of future new mutations and remutations added to the MMR website will be made via the mgi-list.

When I was at Jax as a post-doc one of the funniest announcements I ever heard in the workplace would come across the loudspeakers once a week: There will be a deviant search in the basement at 2 o’clock. There will be a deviant search in the basement at 2 o’clock. Swear to [deity]. At this point all the post-docs (except me) would run down to look at the odd mice that the caretakers observed that week. You could make your whole career with a compelling deviant mouse!! Grants, papers, tenure…those were some deviants. But I was in bioinformatics. All my deviants were code bugs.

Can you imagine–a career made from Bad hair day? That would be something. Almost makes me want to go back to the bench. Or back to MGI.