Tag Archives: rat

Tip of the Week: Model Organism Database tutorials

gbrowseFor the tip of the week today, we’d like to point out a number of new (free to you) tutorials on model organism database resources. These seven tutorials (include flash movie tutorial, slides for downloading, exercises and handouts) were partly funded by a NHGRI grant. We just put out a press release on this, but I thought the Tip of the Week would be a great place to introduce you to these tutorials. We have seven tutorials that are (or will soon be) publicly available (this link takes you to a list and links to all these tutorials). The first four available are on GBrowse, WormBase, RGD (Rat Genome Database) and MGI (Mouse Genome Informatics. GBrowse (the tutorial linked to here), was developed by the Generic Model Organism Database (GMOD) project and is a great tool to develop genome browsers for model and research organisms. Many model organism databases use GMOD resources in full or part, including many of the ones we have tutorials on here. Three more will be coming very soon on ZFIN (Zebrafish), FlyBase (Drosophila) and SGD (yeast). Check them out :).

Tip of the Week: RGD's GViewer

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.

caMOD 2.4 released

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.