Tag Archives: mouse

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.

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: Mouse Genomic Pathology

Ok, so this isn’t the same as our usual tips. But recently I was involved in an animal models project that led me to this resource on genomic pathology. The deeper I got into this animal model project, the more clear it became that a tremendous amount of genomic data is coming that is going to be great–but it will need to be paired with appropriate histology and pathology for a more complete understanding of the genomic biology.

All these model organism projects–knockout mice or rats, mutant mice for cancer studies for example, inbred lines with specific characteristics and genomic regions like the Collaborative Cross, treated animals–need quality pathology assessments. There are phenotyping projects like Europhenome being done on large sets of animals, and they require not only standardized descriptions and ontologies, but also image samples and evaluations.  In an age where we all scan around at all this software looking at genes and genomic regions, we have to have pathology data as well. And that data will also need to be standardized and stored in appropriate database resources for researchers to find and examine. I recently heard Dr. Robert Cardiff talk about his work on Pathobiology of the Mouse and how crucial it is to capture the information in a standardized and searchable ways. He’s one of the drivers of this project, and fully understands the needs in this arena.

More people should be trained in pathology to examine these animals. So during this project I was impressed to find out about an online learning project that could be helpful for people who need to understand the foundations of animal research and be introduced to important aspects of pathology.  This project has won an award for Outstanding Distance Learning (May 25).  So as a public service in genomics I point you to this UC Davis project.

You can have a look at the background and goals for this from the Center for Genomic Pathology site.  From there you can click the navigation for UCD Information Session to get a taste of their course, or click on my image above.  It’s a nice effort.

We have no relationships with UC Davis or this online learning project–we just thought it was a valuable and important component to genomics and wanted to talk about  it.

Mouse Colony Management Software tutorial

One of the most common search terms that brings people to our site is colony management software,  or some variation thereof. We’ve talked about some of the choices in the past: Animal Colony Management Software.

We subsequently see a lot of interest in the free software from The Jackson Lab called JCMS as people click through. So I just wanted to offer as a public service an announcement of a webinar from the Jax folks on Colony Management and Breeding Strategies this week. In the email announcement I saw that it specifically includes a special item:

  • Special bonus: A tutorial on the JAX Colony Management Software (JCMS) by its creator, Chuck Donnely. JCMS is free to download and use

So if this is an area of interest for you, it might be worth checking  out. If you see this at a later time you might want to see if they offer the recordings later as well–I don’t know if they have them, but if you are evaluating this sort of software it might be useful.

Main MGI site: http://www.informatics.jax.org/and access More Resources–>Community Links–>Mouse resources and model organism links to get to Colony Management stuff.

Tip of the Week: Database of mouse databases


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

Textpresso for Mouse now available

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.

Does anybody have a Cre-whatever mouse…?

By: Darryl Leja, NHGRI

By: Darryl Leja, NHGRI

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/

Broad's newly released Genomics Data Viewer IGV

igv1.jpgFrom 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!

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.