We are acutely aware of the thousands of bioinformatics resources out there, and we are often asked for guidance on finding a particular type of tool for some function or other.  There are some excellent lists out there which attempt to catalog the various tools–the NAR Database Issue and corresponding list, the Resource Collection at the Univ. of Pittsburg, and others.  But recently we saw one developed with a specific focus, which claims to bring together over 200 resources for the mouse.  The Mouse Resource Browser collects and categorizes a number of different types of things–not just databases, as we’ll see.  Find them here: http://bioit.fleming.gr/mrb

The curated collection of sites that may  be of use to mouse researchers has a number of features.  The developers used a questionnaire to elicit some information from the resource providers, and when they don’t have that input they have created some basic information for the records themselves. You can do a basic search for resources with a quick search box. There is an advanced search option.  I found the option of browsing by category (they have 22 categories) the most informative to figure out what kind of resources they had collected.

The data for a given record is organized across a series of tabs:

• General: description, highlights and subject matter of the resource

• Ontologies and Standards: if the resource relies on any of the important vocabularies or standards formats in the field, they are listed here

• Technical: details of implementation, type of database, access methods, if there is a web services component, whether there are downloads or not

• CASIMIR DDF: this is an interesting tab that assesses some of the features of the resources such as currency/updates, quality control process, versioning, technical documentation, user support, and more.

Although the focus is mouse, you’ll see some more broad types of resources in there.  For example, UCSC Genome Browser is listed as there is a mouse database there.  Reactome is listed.  These have a species range and include mouse, but are certainly not focused on mouses.  Other types of resources include commercial suppliers such as Charles River. So it isn’t limited just to things like sequence databases and things of that nature–it’s got more aspects that researchers employing mouse as a model system might find useful.

There are some choices they have made that I’m not sure I would have.  They list the MGI mailing list as a separate feature from MGI.  But as I thought more about it, I could see why.  There is good information there, and if you don’t know of it already a pointer might help.  But as I was thinking of the 200+ resources just for mouse, I thought that sort of affected the total.

If you use mouse as your model system, you will probably find some useful databases and other web sites that are handy for your work.  If you don’t work with mice, there are probably still some useful resources for your work as well.  Check out MRB’s site for more information: http://bioit.fleming.gr/mrb

Reference:
Zouberakis, M., Chandras, C., Swertz, M., Smedley, D., Gruenberger, M., Bard, J., Schughart, K., Rosenthal, N., Hancock, J., Schofield, P., Kollias, G., & Aidinis, V. (2010). Mouse Resource Browser–a database of mouse databases Database, 2010 DOI: 10.1093/database/baq010

Just a quick announcement I got from the Textpresso mailing list today:

Hello!

We have set up a full text search engine for mouse literature. It can be
accessed at

http://www.textpresso.org/mouse

Any feedback is welcome. Please let us know what you think.
The Textpresso Team.

Welcome to Textpresso for Mouse! This is a pilot containing approximately 80,000 full text papers pertaining to the model organism mouse. Textpresso’s strength lies in the sentence-focused search, i.e., multiple keywords and categories are matched in the same sentence to be returned as a search result. Textpresso is enriched by categories (“bags of words”) which can be specified from a cascading menu. For example, if you want to search for sentences that mention the gene shh and a mouse tissue, type shh in the keyword box and choose ‘mouse tissue’ (via ‘mouse specific’ supercategory). The categories are subject to change. Please give us feedback if particular entries don’t make sense.
The software supports phrase searches (enclosed in double quotes) as well as searches for special characters. However, searches for super- or subscript annotations are not implemented yet. We plan to expand the corpus of papers rapidly in the next few months.

We have a tutorial on Textpresso in our catalog, by the way.

[caption id="attachment_2798" align="alignright" width="150" caption="By: Darryl Leja, NHGRI"][/caption]

Ever since I was a post-doc at Jax, I’ve been on the MGI mailing list. Some days it brings back memories.  Some days it brings laughter.  The other day I had a major problem with the spam filter because the discussion was about:  “Breeding from male with low sex drive” which, for obvious reasons, my mail filters thought was naughty.

But most often it is informative about research topics, mutant mice, and about resources that are useful either at MGI or other sites that mouse researchers like to use. Yesterday it was an announcement about a new segment of the MGI database: a Cre-Recombinase Portal.  One of the frequent questions on the list is “does anyone have a floxed mouse with _____ tissue expression….?” or “under control of ______ promoter….?”

The new portal will help researchers to find the right models.  The first part of the announcement mail (you’d have to go in and find Thursday’s mail; it has more details about how to us Creportal):

MGI has released a Cre Recombinase Data Portal (www.creportal.org) that specifically addresses the need to access cre expression and specificity data. Through this portal, users can access information about all existing cre transgenes and knock-ins. Data include the molecular description of the cre transgene or knock-in, the driver / promoter used, inducibility information, publications, and availability of cre mice through the IMSR. Detailed data, including annotated images showing cre activity / expression for the tissues analyzed are being added as available. Access to phenotypes displayed by cre-deleted mice is provided via integration with MGI’s phenotype data.

Currently, there are over 1,040 recombinase-containing transgenes or knock-in alleles cataloged.

Check it out if you or people you know need these mice.  Might save a lot of time if you can find the right mouse in the database rather than on the mailing lists….

Cre-Recombinase Portal: http://www.creportal.org/

From the Genome-Technology mailing list I found about about this software release from the Broad Institute:

Broad Institute Makes Genomics Data Viewer Public

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – The Broad Institute of MIT and Harvard has created a genomics informatics tool that will allow researchers to visualize genomic information, and has made it publicly available for free, Broad said today….

So of course I went to check it out. Because I love new software! You can check it out yourself here:

Integrative Genomics Viewer: http://www.broad.mit.edu/igv/

There is a quick start introduction and a movie you can watch where someone demonstrates some clicks (no audio, or if there was I didn’t get any). A quick registration gives you access. A little java downloading and you are off to the races. There is a sample data set to get you started.

My first question was: what genomes can I see? Lo and behold–the FAQ says:

Answer: Sequence is read from the genome on a server at the Broad. For sequences to appear, you must be connected to the internet, the server must be available, and the genome that you have selected must be on the server. As of July 2008, the server provides sequence for the following genomes: hg17, hg18, mm8, and mm9.

At first I thought it was a tool to pull in your own genomes and view stuff, but it appears to rely on what’s on their server. But I haven’t dug enough yet, I’m not certain that the final answer. But if you are using one of those genomes, I could see some real utility in pulling in your data as tracks and viewing it alongside the reference sequence.

Looks nice to me. I’ll be checking it out some more and I’ll let you know what I find. Feel free to add your own reviews!

A 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.

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.

I 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.

The Allen Institute for Brain Sceince is a great institution that was founded just under 5 years ago with a 100 million seed money from billionaire Paul Allen (of Microsoft fame). The purpose is,

… dedicated to performing innovative basic research on the brain and distributing its discoveries to researchers around the world. Through its efforts, the Institute aims to advance a new understanding of brain diseases and disorders.

The result of this research is disseminated through some excellent tools at the Allen Brain Atlas. This research and tool focuses on the mouse brain and determining which genes are expressed in different parts of the brain.

Well, it was recently announced that not only are they planning to extend this map to the mouse spinal chord and another atlas of brain development from fetus to adult mouse, they have launched a project to do a similar atlas of the human brain. This project is expected to take four years.

btw, the “brain explorer” tool is just cool. My expertise isn’t mouse or brain science, but I like roaming around the brain as much as the next guy .

We’ll keep you up-to-date on the progress .

Just got an announcement about a new release of the caMOD Cancer Models database. This web-based resource holds information about mouse, rat, and other animal models relating to cancer research. It is also integrated with many other useful data resources.

From their description:

Retrieve information about the making of models, their genetic description, histopathology, derived cell lines, associated images, carcinogenic agents, and therapeutic trials. Links to associated publications and other resources are provided.

If you are a researcher in this field you can also submit this type of information.

The new features in this release are:

• The integration of caMOD with caELMIR
• Object model changes as result of the VCDE review
• Compliance with NCICB Technology Stack Requirements

caELMIR is a data management system for pre-clinical experimental data. It is a LIMS, or more specifically an ELIMS, for Electronic Laboratory Information Management System. This is beyond the scope of our current resource coverage, but some people finding this blog might find it useful.

Well, not all mice–not like the project that studied the history of cats (I can haz domesticashun?). This project examined the ancestry of the laboratory inbred mouse. This poster (small section on the left) is one of those cool nearly-secret things you come across once in a while that just make you go: whew–I’m glad somebody knows this… This work was underway when I was at the Jackson Lab and I often think back to it when I read mouse papers, and you can print up the whole document as a poster (it’s a big PDF). I’m not going to link to the PDF itself, please go to this page at Jax: Genealogy Chart of Inbred Strains and click the downloadable Portable Document Format (PDF) file link for to examine this whole mouse pedigree chart.

From the paper:

We describe the origins and relationships of inbred mouse strains, 90 years after the generation of the first inbred strain.

The paper is actually quite a nice description of the how we got to the mice you probably know and love if you have ever worked with them in the lab. It describes important phenotypic considerations around aging and breeding that could impact your work–even if those topics are not the focus of your work.