CMap

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CMap logo
Status
  • Mature release
  • Development: inactive
  • Support: active
Licence
{{{PAGENAME}}} is open source

GPL

Resources


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.


Screenshots

Here are some sample maps from the Gramene Project. See also other Gramene views.

Downloads

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

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

Tutorial @ Gramene

Presentations

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:

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

CMap3D

More on CMap

See Category:CMap

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.

  1. PMID:19648141
Facts about "CMap"RDF feed
Available on platformweb +
Date published2009 +
Has DOI10.1093/bioinformatics/btp458 +
Has PMCIDPMC2773250 +
Has PMID19648141 +
Has URLhttp://sourceforge.net/projects/gmod/files/cmap/ +, https://gmod.svn.sourceforge.net/svnroot/gmod/cmap +, http://www.gramene.org/db/cmap +, http://www.gramene.org/cmap +, http://www.comparative-legumes.org/ +, http://racerx00.tamu.edu/cgi-bin/cmap/viewer +, http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi +, http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 +, http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info +, http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 +, http://www.cottonmarker.org/ +, http://bioinf.scri.sari.ac.uk/ +, http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM%3Bref_map_aids=109 +, http://medvet.angis.org.au/cmap/ +, http://soybeanbreederstoolbox.org/index.php +, http://map.lab.nig.ac.jp:8080/cmap/ +, http://peanutgenetics.tamu.edu/cmap/ +, http://www.cottondb.org/cmap/ +, http://tropgenedb.cirad.fr + and http://cricket.ornl.gov/cgi-bin/cmap/map_set_info +
Has authorYouens-Clark K +, Faga B +, Yap IV +, Stein L + and Ware D +
Has descriptionComparative mapping resource for grasses (plant) +, A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons +, The Honey Bee genome database +, Brassica database + and 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. +
Has development statusinactive +
Has input formattab-delimited + and GFF +
Has licenceGPL +
Has logoCMapLogo-horiz.png +
Has output formattab-delimited +
Has publication detailsBioinformatics (Oxford, England) 25: 3040-2 +
Has software maturity statusmature +
Has support statusactive +
Has titleGramene +, NCGR's Legume Information System +, BeeBase +, BASC +, 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 + and CMap 1.01: a comparative mapping application for the Internet. +
Has topicCMap +
Is open sourceYes +
Link typedownload +, source code +, demo server +, public server + and wild URL +
Published inBioinformatics (Oxford, England) +
Release date2002 +
Tool functionality or classificationGenome Visualization & Editing +, Comparative Genome Visualization + and Database schema +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.CMap#http://sourceforge.net/projects/gmod/files/cmap/ +, CMap#https://gmod.svn.sourceforge.net/svnroot/gmod/cmap +, CMap#http://www.gramene.org/db/cmap +, CMap#http://www.gramene.org/cmap +, CMap#http://www.comparative-legumes.org/ +, CMap#http://racerx00.tamu.edu/cgi-bin/cmap/viewer +, CMap#http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi +, CMap#http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 +, CMap#http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info +, CMap#http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 +, CMap#http://www.cottonmarker.org/ +, CMap#http://bioinf.scri.sari.ac.uk/ +, CMap#http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 +, CMap#http://medvet.angis.org.au/cmap/ +, CMap#http://soybeanbreederstoolbox.org/index.php +, CMap#http://map.lab.nig.ac.jp:8080/cmap/ +, CMap#http://peanutgenetics.tamu.edu/cmap/ +, CMap#http://www.cottondb.org/cmap/ +, CMap#http://tropgenedb.cirad.fr + and CMap#http://cricket.ornl.gov/cgi-bin/cmap/map_set_info +