Difference between revisions of "CMap"
From GMOD
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* [http://www.gramene.org/tutorials/cmap.html Gramene CMap User Tutorial], | * [http://www.gramene.org/tutorials/cmap.html Gramene CMap User Tutorial], | ||
*: Available in both [http://www.gramene.org/tutorials/cmap_tutorial.pdf PDF] and [http://www.gramene.org/tutorials/cmap_tutorial.ppt PowerPoint] formats. | *: Available in both [http://www.gramene.org/tutorials/cmap_tutorial.pdf PDF] and [http://www.gramene.org/tutorials/cmap_tutorial.ppt PowerPoint] formats. | ||
| − | * [[CMap_API]] ( | + | * [[CMap_API]] ({{SF_SVN|cmap/trunk/docs/CMAP_API.pod|SVN}}) |
| − | * {{ | + | * {{SF_SVN|cmap/trunk/README|README}} |
| − | * | + | * {{SF_SVN|cmap/trunk/Changes|Changes}} |
| − | * | + | * {{SF_SVN|cmap/trunk/INSTALL.pod|INSTALL.pod}} |
| − | * | + | * {{SF_SVN|cmap/trunk/docs/ADMINISTRATION.pod|ADMINISTRATION.pod}} |
| − | * | + | * {{SF_SVN|cmap/trunk/docs/CODE_OVERVIEW.pod|CODE_OVERVIEW.pod}} |
| − | * | + | * {{SF_SVN|cmap/trunk/TODO|TODO}} |
| − | * | + | * {{SF_SVN|cmap/trunk/docs/attributes-and-xrefs.pod|attributes-and-xrefs.pod}} |
| − | * | + | * {{SF_SVN|cmap/trunk/docs/cmap-schema-desc.html|CMAP Schema}} |
* [http://racerx00.tamu.edu/cmap/tutorial/index.html CMAP Tutorial at Texas A & M] | * [http://racerx00.tamu.edu/cmap/tutorial/index.html CMAP Tutorial at Texas A & M] | ||
* [[CMap Version 2 Design]] | * [[CMap Version 2 Design]] | ||
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=== Presentations === | === Presentations === | ||
| − | * [[:Image:CMapGBrowseSMBE2009.pdf|The CMap Comparative Map Browser and Displaying Population distributions with GBrowse and PhyloGeoViz]] from the [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 GMOD Workshop at SMBE 2009] | + | * [[:Image:CMapGBrowseSMBE2009.pdf|The CMap Comparative Map Browser and Displaying Population distributions with GBrowse and PhyloGeoViz]] from the [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 GMOD Workshop at SMBE 2009] |
* [[:Image:2007 11 05 CMap GMOD.ppt|CMap and CMAE]] from [[November 2007 GMOD Meeting]] | * [[:Image:2007 11 05 CMap GMOD.ppt|CMap and CMAE]] from [[November 2007 GMOD Meeting]] | ||
* [[:Image:BenFaga_GMOD_June_2006.ppt|CMap Version 0.16]] from [[June 2006 GMOD Meeting]] | * [[:Image:BenFaga_GMOD_June_2006.ppt|CMap Version 0.16]] from [[June 2006 GMOD Meeting]] | ||
Revision as of 21:33, 15 September 2009
CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data.
Contents
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 and GD.pm 2.15
- 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.
Presentations
- The CMap Comparative Map Browser and Displaying Population distributions with GBrowse and PhyloGeoViz from the GMOD Workshop at SMBE 2009
- CMap and CMAE from November 2007 GMOD Meeting
- CMap Version 0.16 from June 2006 GMOD Meeting
- CMap Update 2005 from May 2005 GMOD Meeting
- Gramene Comparative Genome Views: How Can Gramene Leverage Rice For The Other Grasses? poster form 2005 Plant and Animal Genomics meeting.
- CMap Update 2003 from September 2003 GMOD Meeting.
- CMap: Visualization of Comparative Maps from May 2003 GMOD Meeting.
Downloads
Demo & Screenshots
See the Gramene Project for a production version.
Screenshots
Here are some sample maps from the Gramene Project.
Sites Using 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
Code
Patches
- See the SourceForge Patch List.
- 1.0: Patched schema creation file for Postgres: cmap.create.postgresql.
Mailing List
- gmod-cmap@lists.sourceforge.net: Discussion of development, installation problems, etc.
- gmod-cmap-commits@lists.sourceforge.net: Notification of CVS activity
- Subscribe to gmod-cmap
- gmod-cmap archives
