Edit Tool data: CMap

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The Basics

Name:
Full name	if name is an abbreviation, acronym, etc.
Status:
Current development:
Support status:
Tool classification or features:	Genome Visualization & Editing, Comparative Genome Visualization, Database schema
Platform:	If the tool linux unix os x windows web vm cloud
Brief description:	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.
Open source:
Software licence:
Type of input data	e.g. genomic sequence; taxonomic group; protein identifier; anatomy ontology, etc.
Input formats:	tab-delimited, GFF
Output formats:	tab-delimited
Programming language(s)
Intended usage
First public release
Use standard tool display template?	yes

Files

Logo (file name)	enter the name of the file on the GMOD wiki, e.g. CoolAppLogo.png CMapLogo-horiz.png
Screenshot(s)

Contact details

Contact email
Mailing list(s)

Links

The majority of links related to the tool should be added using the interface at the bottom of the page.

Download text	If there is not a simple download URL for downloading the tool, please enter download instructions here. Download URLs can be entered in the 'Links' section below.
Download source code text	If there is not a simple download URL for downloading the source code for the tool, please enter download instructions here. URLs can be entered in the 'Links' section below.

Materials

Publications	*CMap 1.01: a comparative mapping application for the Internet. <ref>PMID:19648141</ref>
Presentations	* [[File:CMapGenomeInformatics2009.pdf\|Genome Visualization and Comparison using CMap and Circos]], poster from [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics 2009] * [[File: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] * [[File:2007 11 05 CMap GMOD.ppt\|CMap and CMAE]] from [[November 2007 GMOD Meeting]] * [[File:BenFaga_GMOD_June_2006.ppt\|CMap Version 0.16]] from [[June 2006 GMOD Meeting]] * [[File:Cmap-050516.pdf\|CMap Update 2005]] from [[May 2005 GMOD Meeting]] * [[File:Gramene-cmap-pag-poster-2005.pdf\| Gramene Comparative Genome Views: How Can Gramene Leverage Rice For The Other Grasses?]] poster form 2005 Plant and Animal Genomics meeting. * [[File:Cmap_update_sept_03.ppt\|CMap Update 2003]] from [[September 2003 GMOD Meeting]]. * [[File:CMap_Overview.pdf\|CMap: Visualization of Comparative Maps]] from [[May 2003 GMOD Meeting]].
Tutorials	;[http://www.gramene.org/tutorials/cmap.html Tutorial @ Gramene]

Extra Textual Goodies

Any introductory text for users
Software prerequisites	* 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. [http://www.mysql.com MySQL (4.0+)], Sybase Adaptive Server Enterprise, [[PostgreSQL]], SQLite or Oracle (9.x) * [http://www.boutell.com/gd/ libgd (2.0.28 or higher)] and [{{CPAN\|GD}} GD.pm (2.16 or higher)] * Various Perl modules available on [http://www.cpan.org/ CPAN]
Installation
Configuration
Documentation	* [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. [[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] * [[CMap Version 2 Design]] Also see the [[CMap FAQ]].
Development team	Lincoln Stein, Doreen Ware, [[User:Faga\|Ben Faga]], [mailto:kclark@cshl.edu Ken Youens-Clark]
Development status
Download/usage tracking
Logo info	The CMap logo was created by Kathy Bracken, a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linn-benton.edu Linn-Benton Community College].
See also	Any extra information, links, etc. [[CMap3D]]
Extra items for component box	No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version.

Free text:

[[Category:CMap]] [[Category:Comparative Genomics]] [[Category:GMOD Components]] [[Category:Gramene]]

Links

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