Difference between revisions of "CMap"
From GMOD
m (Switching to semantic version.) |
|||
(12 intermediate revisions by 4 users not shown) | |||
Line 1: | Line 1: | ||
− | {{ | + | <!-- to edit this page, please use the 'Edit with form' tab --> |
+ | {{Tool data | ||
+ | |use template=yes | ||
+ | |name=CMap | ||
+ | |full name= | ||
+ | |status=mature | ||
+ | |dev=inactive | ||
+ | |support=active | ||
+ | |type=Genome Visualization & Editing, Comparative Genome Visualization, Database schema | ||
+ | |platform=web | ||
+ | |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. | ||
+ | |release date=2002 | ||
+ | |open source=Yes | ||
+ | |licence=[http://opensource.org/licenses/GPL-3.0 GPL] | ||
+ | |language=Perl | ||
+ | |input=tab-delimited, GFF | ||
+ | |output=tab-delimited | ||
+ | |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 | ||
+ | |logo=CMapLogo-horiz.png | ||
+ | |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]. | ||
− | + | <gallery widths=200px> | |
− | + | File:Cmap_sample1.jpg | |
− | + | File:Cmap_sample2.jpg | |
− | | | + | File:Cmap_sample3.jpg |
− | CMap | + | </gallery> |
− | + | |survey link=CMap | |
− | = | + | |mail={{MailingListsFor|CMap}} |
− | + | |contact email=Ken Youens-Clark <kclark@cshl.edu> | |
− | [http:// | + | |papers=*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]] | |
− | * Perl 5.6.0 or higher | + | * [[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://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] | ||
− | + | |install= | |
− | + | |config= | |
− | = | + | |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]]. | ||
− | + | |dev ppl=Lincoln Stein, Doreen Ware, [[User:Faga|Ben Faga]], [mailto:kclark@cshl.edu Ken Youens-Clark] | |
− | = | + | |dev status=No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version. |
− | + | |dl 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=[[CMap3D]] | |
− | + | |extra=No development in several years. Future development at Gramene.org hopes to replace CMap with a lighter, Javascript version. | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://sourceforge.net/projects/gmod/files/cmap/ | |
− | + | |linktype=download | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=https://gmod.svn.sourceforge.net/svnroot/gmod/cmap | |
− | + | |linktype=source code | |
− | + | }} | |
− | + | {{SemanticLink | |
− | = | + | |linkurl=http://www.gramene.org/db/cmap |
− | + | |linktype=demo server | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.gramene.org/cmap | |
− | = | + | |linktype=public server |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.gramene.org/cmap | |
− | + | |linktitle=Gramene | |
− | + | |linktype=wild URL | |
− | + | |linkdesc=Comparative mapping resource for grasses (plant) | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.comparative-legumes.org/ | |
− | + | |linktitle=NCGR's Legume Information System | |
− | + | |linktype=wild URL | |
− | + | |linkdesc=A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://racerx00.tamu.edu/cgi-bin/cmap/viewer | |
− | + | |linktitle=BeeBase | |
− | + | |linktype=wild URL | |
− | + | |linkdesc=The Honey Bee genome database | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi | |
− | + | |linktitle=BASC | |
− | = | + | |linktype=wild URL |
− | + | |linkdesc=Brassica database | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 | |
− | + | |linktitle=GrainGenes | |
− | + | |linktype=wild URL | |
− | + | |linkdesc= | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info | |
− | + | |linktitle=MAGI | |
− | + | |linktype=wild URL | |
− | + | |linkdesc= | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 | |
− | + | |linktitle=Genome Database for Rosaceae | |
− | + | |linktype=wild URL | |
− | + | |linkdesc= | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.cottonmarker.org/ | |
− | + | |linktitle=Cotton Marker Database | |
− | + | |linktype=wild URL | |
− | = | + | |linkdesc= |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://bioinf.scri.sari.ac.uk/ | |
− | + | |linktitle=SCRI Plant Bioinformatics Group | |
− | = | + | |linktype=wild URL |
− | + | |linkdesc= | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 | |
− | + | |linktitle=Pristionchus pacificus Physical Map | |
− | + | |linktype=wild URL | |
− | + | |linkdesc= | |
− | + | }} | |
− | + | {{SemanticLink | |
− | + | |linkurl=http://medvet.angis.org.au/cmap/ | |
− | + | |linktitle=Comparitive Location Database | |
− | + | |linktype=wild URL | |
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://soybeanbreederstoolbox.org/index.php | ||
+ | |linktitle=Soybean Breeders Toolbox | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://map.lab.nig.ac.jp:8080/cmap/ | ||
+ | |linktitle=Composite Wheat Map | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://peanutgenetics.tamu.edu/cmap/ | ||
+ | |linktitle=PeanutMap | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://www.cottondb.org/cmap/ | ||
+ | |linktitle=CottonDB | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://tropgenedb.cirad.fr | ||
+ | |linktitle=TropGene | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://cricket.ornl.gov/cgi-bin/cmap/map_set_info | ||
+ | |linktitle=Populus at Oak Ridge | ||
+ | |linktype=wild URL | ||
+ | |linkdesc= | ||
+ | }} | ||
[[Category:CMap]] | [[Category:CMap]] |
Latest revision as of 23:40, 17 October 2013
Status
- Mature release
- Development: inactive
- Support: active
Licence
Resources
Contents
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
- 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.
Publications, Tutorials, and Presentations
Publications on or mentioning CMap
- CMap 1.01: a comparative mapping application for the Internet. [1]
Tutorials
Presentations
- File:CMapGenomeInformatics2009.pdf, poster from Genome Informatics 2009
- File:CMapGBrowseSMBE2009.pdf from the GMOD Workshop at SMBE 2009
- File:2007 11 05 CMap GMOD.ppt from November 2007 GMOD Meeting
- File:BenFaga GMOD June 2006.ppt from June 2006 GMOD Meeting
- File:Cmap-050516.pdf from May 2005 GMOD Meeting
- File:Gramene-cmap-pag-poster-2005.pdf poster form 2005 Plant and Animal Genomics meeting.
- File:Cmap update sept 03.ppt from September 2003 GMOD Meeting.
- File:CMap Overview.pdf from May 2003 GMOD Meeting.
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:- MAGI
-
Gramene
- Comparative mapping resource for grasses (plant)
- Populus at Oak Ridge
- Soybean Breeders Toolbox
- Genome Database for Rosaceae
-
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
- Composite Wheat Map
- Cotton Marker Database
-
BeeBase
- The Honey Bee genome database
- PeanutMap
- SCRI Plant Bioinformatics Group
-
BASC
- Brassica database
- CottonDB
- Pristionchus pacificus Physical Map
- GrainGenes
- TropGene
- Comparitive Location Database
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
More on CMap
See Category:CMap
CMap Logo
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.
- ↑ PMID:19648141
Facts about "CMap"RDF feed