Tag Archives: Mouse Genome Informatics

What’s the Answer? (Online mouse resources)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Need online resources for mouse research? Andrew Su at Biostar asked for a list of such resources and started it with a couple dozen:

I’d like to create a collection of the most useful online resources for mouse researchers. Here’s my list so far…

A comment thread continues with some great addition including many from Mary such as the Mouse resource browser: http://bioit.fleming.gr/mrb/, Jax: http://informatics.jax.org/and others which Andrew added to the list.

Video Tip of the Week: A Mouse for All Reasons

At first the title of this paper made laugh, as I am a major fan of Paul Scofield’s performance in A Man for All Seasons.  And then I remembered what happened to Thomas More.  Well, the analogy drops away for me there…. A Mouse for All Reasons by the International Mouse Knockout Consortium presented the framework and foundations of the project to knock out every single protein-coding gene in mice, generate the corresponding ES (embryonic stem) cells, and make them available for development of subsequent transgenic mice.  Some of these mice will go on to give their life for science in a noble manner, I guess–so maybe the analogy picks back up :)

The project has made tremendous progress since that paper was published, and there are a lot of knockouts you should know about if you are interested in using mouse as a model organism.

For this tip of the week we’ll explore the new portal for the International Mouse Knockout Consortium (IMKC), which used to be at the URL for the KOMP, or Knock Out Mouse Project. It appears that the groups referenced in the Mouse for All Reasons paper have now harmonized on to the knockoutmouse.org site, and use a single portal for access to the information and reagents.  There are a variety of ways to search: browsing genes, specific text searching, and even a BioMart interface for the portal.  This short movie takes a look at those pieces to introduce you to the site.

The announcement for this came over the MGI mailing list as this:

The IKMC web portal

The International Knockout Mouse Consortium (IKMC) has launched its official web site at www.knockoutmouse.org, formerly the URL for the Knockout Mouse Project (KOMP). This extended site, supported by the NIH and EU, now serves as the common web portal for access to information on knockout vectors, ES cells and mice available from the international high-throughput knockout projects: KOMP, EUCOMM, NorCOMM and TIGM. Stay tuned for future enhancements as the content continues to evolve. We welcome your comments and feedback. (Please email to contact@knockoutmouse.org).

This site is maintained by the I-DCC and the KOMP-DCC

(http://www.knockoutmouse.org/about) . Supported by the European Union (Project number: 223592) and the National Institutes of Health (Grant number: NIH HG004074).

The International Mouse Knockout Consortium (2007). A Mouse for All Reasons Cell, 128 (1), 9-13 DOI: 10.1016/j.cell.2006.12.018

Free Tutorials on Model Organism Genomic Databases Released by OpenHelix

OpenHelix today announced the free availability of tutorial suites on model organism databases and resources used extensively in research. The first tutorial suites available are GBrowse, Rat Genome Database (RGD), Mouse Genome Informatics (MGI), and WormBase. To be added in the coming weeks are Zebrafish Information Network (ZFIN), FlyBase and Saccharomyces (Yeast) Genome Database (SGD).

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.

Weight gain and weight loss – a complicated story

I’m sure a lot of you, like me, have signed up to receive free GenomeWeb Daily News Bulletins. In yesterday’s email, I saw an article featuring research about the number of genes effecting weight in mice. I found the article interesting not only because it reminds me of certain reoccurring New Year’s resolutions that I have, but also because it is another example of how information in public databases, in this case MGI, is being used in important research.  Continue reading