Difference between revisions of "CMap"

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{{ImageCenter|CMapLogo.png|CMap|180|http://gmod.org/wiki/CMap#Logo}}
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<!-- to edit this page, please use the 'Edit with form' tab -->
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{{Tool data
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|use template=yes
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|name=CMap
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|full name=
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|status=mature
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|dev=inactive
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|support=active
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|type=Genome Visualization & Editing, Comparative Genome Visualization, Database schema
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|platform=web
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|about=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.
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|release date=2002
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|open source=Yes
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|licence=[http://opensource.org/licenses/GPL-3.0 GPL]
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|language=Perl
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|input=tab-delimited, GFF
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|output=tab-delimited
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|audience=Private: handle data in a local system. E.g. an annotation tool where data goes into a local DB, Public: e.g. a web front end
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|logo=CMapLogo-horiz.png
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|screenshot=Here are some sample maps from the [http://www.gramene.org/ Gramene Project].  See also [http://www.gramene.org/cmap/entry.html other Gramene views].
  
__NOTITLE__
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<gallery widths=200px>
 
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File:Cmap_sample1.jpg
{{ComponentBox|{{CMapResourcesBoxItem}}||
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File:Cmap_sample2.jpg
| | |}}
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File:Cmap_sample3.jpg
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.
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</gallery>
 
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|survey link=CMap
== Citation ==
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|mail={{MailingListsFor|CMap}}
 
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|contact email=Ken Youens-Clark <kclark@cshl.edu>
[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp458?ijkey=RH2dYR27nTL4Bw9&keytype=ref CMap 1.01: a comparative mapping application for the Internet.] Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.
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|papers=*CMap 1.01: a comparative mapping application for the Internet. <ref>PMID:19648141</ref>
 
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|presentations=* [[File:CMapGenomeInformatics2009.pdf|Genome Visualization and Comparison using CMap and Circos]], poster from [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics 2009]
1Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, 2Department of Plant Breeding and Genetics, Cornell University, Ithaca and 3USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853, USA
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* [[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]
 
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* [[File:2007 11 05 CMap GMOD.ppt|CMap and CMAE]] from [[November 2007 GMOD Meeting]]
==Requirements==
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* [[File:BenFaga_GMOD_June_2006.ppt|CMap Version 0.16]] from [[June 2006 GMOD Meeting]]
 
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* [[File:Cmap-050516.pdf|CMap Update 2005]] from [[May 2005 GMOD Meeting]]
* Perl 5.6.0 or higher
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* [[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]
 +
|getting started preamble=
 +
|req=* Perl 5.6.0 or higher
 
* A web server with CGI capabilites (e.g., Apache 1.x or 2.x)
 
* 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)
 
* 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] and [http://search.cpan.org/~lds/GD-2.15/ GD.pm 2.15]
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* [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]
 
* Various Perl modules available on [http://www.cpan.org/ CPAN]
 
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|install=
 
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|config=
==Documentation==
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|doc=* [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]] ({{SF_SVN|cmap/trunk/docs/CMAP_API.pod|SVN}})
 
* [[CMap_API]] ({{SF_SVN|cmap/trunk/docs/CMAP_API.pod|SVN}})
Line 38: Line 61:
  
 
Also see the [[CMap FAQ]].
 
Also see the [[CMap FAQ]].
 
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|dev ppl=Lincoln Stein, Doreen Ware, [[User:Faga|Ben Faga]], [mailto:kclark@cshl.edu Ken Youens-Clark]
=== Presentations ===
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|dev status=No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version.
* [[:Image:CMapGenomeInformatics2009.pdf|Genome Visualization and Comparison using CMap and Circos]], poster from [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics 2009]
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|dl tracking=
* [[: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]
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|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].
* [[:Image:2007 11 05 CMap GMOD.ppt|CMap and CMAE]] from [[November 2007 GMOD Meeting]]
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|see also=[[CMap3D]]
* [[:Image:BenFaga_GMOD_June_2006.ppt|CMap Version 0.16]] from [[June 2006 GMOD Meeting]]
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|extra=No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version.
* [[:Image:Cmap-050516.pdf|CMap Update 2005]] from [[May 2005 GMOD Meeting]]
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}}
* [[:Image: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.
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{{SemanticLink
* [[:Image:Cmap_update_sept_03.ppt|CMap Update 2003]] from [[September 2003 GMOD Meeting]].
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|linkurl=http://sourceforge.net/projects/gmod/files/cmap/
* [[:Image:CMap_Overview.pdf|CMap: Visualization of Comparative Maps]] from [[May 2003 GMOD Meeting]].
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|linktype=download
 
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}}
==Downloads==
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{{SemanticLink
 
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|linkurl=https://gmod.svn.sourceforge.net/svnroot/gmod/cmap
[https://sourceforge.net/project/showfiles.php?group_id=27707 From SourceForge.]
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|linktype=source code
 
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}}
 
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{{SemanticLink
==Demo & Screenshots==
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|linkurl=http://www.gramene.org/db/cmap
 
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|linktype=demo server
See the [http://www.gramene.org/cmap Gramene Project] for a production version.
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}}
 
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{{SemanticLink
 
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|linkurl=http://www.gramene.org/cmap
===Screenshots===
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|linktype=public server
 
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}}
Here are some sample maps from the [http://www.gramene.org/ Gramene Project].
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{{SemanticLink
 
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|linkurl=http://www.gramene.org/cmap
 
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|linktitle=Gramene
[[Image:Cmap_sample1.jpg]]
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|linktype=wild URL
 
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|linkdesc=Comparative mapping resource for grasses (plant)
 
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}}
[[Image:Cmap_sample1t.jpg]]
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{{SemanticLink
 
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|linkurl=http://www.comparative-legumes.org/
 
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|linktitle=NCGR's Legume Information System
[[Image:Cmap_sample2.jpg]]
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|linktype=wild URL
 
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|linkdesc=A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons
 
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}}
[[Image:Cmap_sample2t.jpg]]
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{{SemanticLink
 
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|linkurl=http://racerx00.tamu.edu/cgi-bin/cmap/viewer
 
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|linktitle=BeeBase
[[Image:Cmap_sample3.jpg]]
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|linktype=wild URL
 
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|linkdesc=The Honey Bee genome database
 
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}}
[[Image:Cmap_sample3t.jpg]]
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{{SemanticLink
 
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|linkurl=http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi
 
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|linktitle=BASC
==Sites Using CMap==
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|linktype=wild URL
 
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|linkdesc=Brassica database
The following is a partial list of groups using CMap.
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}}
 
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{{SemanticLink
* [http://www.gramene.org/cmap Gramene]: Comparative mapping resource for grasses (plant)
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|linkurl=http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003
* [http://www.comparative-legumes.org/ 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
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|linktitle=GrainGenes
* [http://racerx00.tamu.edu/cgi-bin/cmap/viewer BeeBase]: The Honey Bee genome database
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|linktype=wild URL
* [http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi BASC]: Brassica database
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|linkdesc=
* [http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 GrainGenes]
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}}
* [http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info MAGI]
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{{SemanticLink
* [http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 Genome Database for Rosaceae]
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|linkurl=http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info
* [http://www.cottonmarker.org/ Cotton Marker Database]
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|linktitle=MAGI
* [http://bioinf.scri.sari.ac.uk/ SCRI Plant Bioinformatics Group]
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|linktype=wild URL
* [http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 Pristionchus pacificus Physical Map]
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|linkdesc=
* [http://medvet.angis.org.au/cmap/ Comparitive Location Database]
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}}
* [http://soybeanbreederstoolbox.org/index.php Soybean Breeders Toolbox]
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{{SemanticLink
* [http://map.lab.nig.ac.jp:8080/cmap/ Composite Wheat Map]
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|linkurl=http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17
* [http://peanutgenetics.tamu.edu/cmap/ PeanutMap]
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|linktitle=Genome Database for Rosaceae
* [http://www.cottondb.org/cmap/ CottonDB]
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|linktype=wild URL
* [http://tropgenedb.cirad.fr TropGene]
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|linkdesc=
 
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}}
==Code==
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{{SemanticLink
 
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|linkurl=http://www.cottonmarker.org/
* {{SF_SVN|cmap|CMap SVN}}
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|linktitle=Cotton Marker Database
 
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|linktype=wild URL
==Patches==
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|linkdesc=
 
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}}
* See the [http://sourceforge.net/tracker/?group_id=27707&atid=391293 SourceForge Patch List].
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{{SemanticLink
* 1.0: Patched schema creation file for Postgres: <tt>{{SF_SVN|/cmap/trunk/sql/cmap.create.postgresql cmap.create.postgresql]</tt>.
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|linkurl=http://bioinf.scri.sari.ac.uk/
 
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|linktitle=SCRI Plant Bioinformatics Group
== [[Mailing Lists]] ==
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|linktype=wild URL
 
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|linkdesc=
{{MailingListsFor|CMap}}
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}}
 
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{{SemanticLink
==Contact==
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|linkurl=http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109
 
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|linktitle=Pristionchus pacificus Physical Map
* [mailto:kyclark.cshl@gmail.com Ken Youens-Clark]
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|linktype=wild URL
* [[User:Faga|Ben Faga]]
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|linkdesc=
 
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}}
 
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{{SemanticLink
== Logo ==
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|linkurl=http://medvet.angis.org.au/cmap/
 
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|linktitle=Comparitive Location Database
The [[:Image:CMapLogo.png|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].
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|linktype=wild URL
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|linkdesc=
 +
}}
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{{SemanticLink
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|linkurl=http://soybeanbreederstoolbox.org/index.php
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|linktitle=Soybean Breeders Toolbox
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|linktype=wild URL
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|linkdesc=
 +
}}
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{{SemanticLink
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|linkurl=http://map.lab.nig.ac.jp:8080/cmap/
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|linktitle=Composite Wheat Map
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|linktype=wild URL
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|linkdesc=
 +
}}
 +
{{SemanticLink
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|linkurl=http://peanutgenetics.tamu.edu/cmap/
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|linktitle=PeanutMap
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|linktype=wild URL
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|linkdesc=
 +
}}
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{{SemanticLink
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|linkurl=http://www.cottondb.org/cmap/
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|linktitle=CottonDB
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|linktype=wild URL
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|linkdesc=
 +
}}
 +
{{SemanticLink
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|linkurl=http://tropgenedb.cirad.fr
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|linktitle=TropGene
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|linktype=wild URL
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|linkdesc=
 +
}}
 +
{{SemanticLink
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|linkurl=http://cricket.ornl.gov/cgi-bin/cmap/map_set_info
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|linktitle=Populus at Oak Ridge
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|linktype=wild URL
 +
|linkdesc=
 +
}}
  
 
[[Category:CMap]]
 
[[Category:CMap]]

Latest revision as of 23:40, 17 October 2013


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 +
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 descriptionA 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. +, Comparative 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 + and Brassica database +
Has development statusinactive +
Has input formattab-delimited + and GFF +
Has licenceGPL +
Has logoCMapLogo-horiz.png +
Has output formattab-delimited +
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 + and Populus at Oak Ridge +
Has topicCMap +
Is open sourceYes +
Link typedownload +, source code +, demo server +, public server + and wild URL +
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 +, CMap#http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info +, CMap +, CMap#http://www.cottonmarker.org/ +, CMap#http://bioinf.scri.sari.ac.uk/ +, CMap +, 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 +