CMap

From GMOD

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 1 Requirements 2 Documentation 2.1 Presentations 3 Downloads 4 Demo & Screenshots 4.1 Screenshots 5 Sites Using CMap 6 Code 7 Patches 8 Mailing List 9 Contact

[edit] 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

[edit] Documentation

• CMap_API (CVS)
• /cmap/README
• /cmap/Changes
• /cmap/INSTALL.pod
• /cmap/docs/ADMINISTRATION.pod
• /cmap/docs/CODE_OVERVIEW.pod
• /cmap/TODO
• /cmap/docs/attributes-and-xrefs.pod
• /cmap/docs/cmap-schema-desc.html
• User Tutorial
• CMAP Tutorial at Texas A & M

Also see the CMap FAQ.

[edit] Presentations

• 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.

[edit] Downloads

From SourceForge.

[edit] Demo & Screenshots

See the Gramene Project for a production version.

[edit] Screenshots

Here are some sample maps from the Gramene Project.

[edit] 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

[edit] Code

• CMap CVS

[edit] Patches

• See the SourceForge Patch List.
• 1.0: Patched schema creation file for Postgres: cmap.create.postgresql.

[edit] 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

[edit] Contact

• Ken Youens-Clark
• Ben Faga