CMap
- Mature release
- Development: inactive
- Support: active
Contents
About CMap
A browser-based tool for the visual comparison of various maps (sequence, genetic, etc.) from any number of species. The CMap package also includes tools for curating map data.
Visit the CMap website.
Screenshots
Here are some sample maps from the Gramene Project. See also other Gramene views.
Downloads
- Download CMap: http://sourceforge.net/projects/gmod/files/cmap/
- The source code for CMap can be downloaded from https://gmod.svn.sourceforge.net/svnroot/gmod/cmap.
Using CMap
System Requirements
- Perl 5.6.0 or higher
- A web server with CGI capabilites (e.g., Apache 1.x or 2.x)
- A relational database, e.g. MySQL (4.0+), Sybase Adaptive Server Enterprise, PostgreSQL, SQLite or Oracle (9.x)
- libgd (2.0.28 or higher) and [GD GD.pm (2.16 or higher)]
- Various Perl modules available on CPAN
Documentation
- Gramene CMap User Tutorial,
- Available in both PDF and PowerPoint formats.
- CMap_API (SVN)
- README
- Changes
- INSTALL.pod
- ADMINISTRATION.pod
- CODE_OVERVIEW.pod
- TODO
- attributes-and-xrefs.pod
- CMAP Schema
- CMAP Tutorial at Texas A & M
- CMap Version 2 Design
Also see the CMap FAQ.
Publications, Tutorials, and Presentations
Publications on or mentioning CMap
- CMap 1.01: a comparative mapping application for the Internet. [1]
Tutorials
Presentations
- File:CMapGenomeInformatics2009.pdf, poster from Genome Informatics 2009
- File:CMapGBrowseSMBE2009.pdf from the GMOD Workshop at SMBE 2009
- File:2007 11 05 CMap GMOD.ppt from November 2007 GMOD Meeting
- File:BenFaga GMOD June 2006.ppt from June 2006 GMOD Meeting
- File:Cmap-050516.pdf from May 2005 GMOD Meeting
- File:Gramene-cmap-pag-poster-2005.pdf poster form 2005 Plant and Animal Genomics meeting.
- File:Cmap update sept 03.ppt from September 2003 GMOD Meeting.
- File:CMap Overview.pdf from May 2003 GMOD Meeting.
Contacts and Mailing Lists
Mailing List Link | Description | Archive(s) | |
---|---|---|---|
CMap | gmod-cmap | Discussion of CMap development, installation problems, etc. | Nabble (2010/05+), Sourceforge |
gmod-cmap-commits | Notification of SVN activity for CMap. | Sourceforge |
CMap in the wild
Public installations of CMap: The following is a partial list of groups using CMap.
- Gramene: Comparative mapping resource for grasses (plant)
- NCGR's Legume Information System: A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons
- BeeBase: The Honey Bee genome database
- BASC: Brassica database
- GrainGenes
- MAGI
- Genome Database for Rosaceae
- Cotton Marker Database
- SCRI Plant Bioinformatics Group
- Pristionchus pacificus Physical Map
- Comparitive Location Database
- Soybean Breeders Toolbox
- Composite Wheat Map
- PeanutMap
- CottonDB
- TropGene
- Populus at Oak Ridge
CMap Development
Development team
Lincoln Stein, Doreen Ware, Ben Faga, Ken Youens-Clark
Current status
No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version.
See also
More on CMap
See Category:CMap
CMap Logo
The CMap logo was created by Kathy Bracken, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.
- ↑ PMID:19648141
Raw tool data at CMap/tool data