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  • ...ed notes from the ''Chado Middleware Bake Off'' held at the [[January 2007 GMOD Meeting]]. Although GMOD uses the [[Chado]] [[Glossary#Schema|schema]] for its underlying database,
    40 KB (5,672 words) - 21:27, 15 August 2013
  • * GMOD Demo ** Search Engine and Indexer using Lucene
    12 KB (1,477 words) - 21:16, 9 October 2012
  • <div class="compBoxHdr clear">GMOD is Social</div> ...ht|link=http://twitter.com/gmodproject|It's a bird! It's a plane! It's the GMOD project on Twitter!]]
    5 KB (694 words) - 21:06, 19 November 2019
  • This is the GMOD Developer's Guide. * $GMOD_HOME=<b>/usr/local/gmod/</b> (default -- set before installing)
    6 KB (985 words) - 05:18, 28 January 2008
  • ...abase Schema|relational database schema]] that underlies [[GMOD_Users|many GMOD installations]]. It is capable of representing many of the general classes ...u'll probably get the best support by choosing Unix. (See [[Databases and GMOD]] for more discussion.) Once you've installed your RDBMS you can install C
    3 KB (469 words) - 18:08, 13 February 2014
  • ...genetic, etc.) from any number of species. The CMap package also includes tools for curating map data. ...* [[File:CMapGenomeInformatics2009.pdf|Genome Visualization and Comparison using CMap and Circos]], poster from [http://meetings.cshl.edu/meetings/info09.sh
    7 KB (996 words) - 23:40, 17 October 2013
  • ...ta releases on a regular basis. It produces all the contents needed for a GMOD [[Standard URL]] genome data download folder. Why use this package rather than using other [[:Category:Middleware|middleware layers]] to Chado db - [[Chado XML]
    10 KB (1,496 words) - 23:00, 15 August 2013
  • ...eone new to GMOD development will have a good idea of a recommended set of tools and practices that one should employ to develop reliable software. [[Category:GMOD Developers]]
    819 B (126 words) - 17:14, 5 April 2007
  • ==GMOD Architecture Work Group Discussion (Fall 2005 meeting)== Brain O'Connor agreed on trying out some tools for interfaces testing. Http::Unit, Apache::Test were suggested at the meet
    2 KB (257 words) - 15:02, 13 February 2007
  • ...infrastructure. One emphasis here is on simplified use of grids and genome tools, to make it feasible for new genome projects to take advantage of these rea http://gmod.cvs.sourceforge.net/gmod/genogrid/
    784 B (98 words) - 05:02, 5 September 2007
  • <!-- to alter this page, please edit the raw data, which is stored at http://gmod.org/wiki/Pathway_Tools/tool_data --> |name=Pathway Tools
    5 KB (650 words) - 00:07, 16 October 2013
  • |type=Community Annotation, Database schema, Database tools, Genome Annotation, Middleware, Tool Integration, Data federation software |gmod date=
    2 KB (228 words) - 22:26, 15 October 2013
  • ...llection of pre-tested and implemented common database/information service tools needed for organism database systems, which can be automatically distribute ...ckage management systems such as RPM, pacman and others are well developed tools but don't quite meet the needs of this bio-database distribution.
    12 KB (1,641 words) - 15:41, 16 July 2012
  • ...ced insertion sites for model organisms, provides users with visualization tools to search for insertions in gene of interest and to track progress of multi ...neric Insertional Mutagenesis Database]] presentation from the [[May 2003 GMOD Meeting]].
    1 KB (150 words) - 07:22, 30 January 2008
  • ...reusable Java UI component -- and a set of parsing utilities, command line tools and an application GUI -- for viewing gene expression data in a whole-genom [[Category:GMOD Components]]
    1 KB (154 words) - 17:33, 3 October 2012
  • |type=Literature tools, Text mining ...[[:Image:Jan2010Testpresso.pdf|presented this work]] at the [[January 2010 GMOD Meeting]]. The Textpresso team plans to fold these extensions back into th
    5 KB (697 words) - 17:56, 17 October 2013
  • ...nd applications built using GMOD components. For a list of databases see [[GMOD Users]]. ...s/erss.cgi?rss_guid=1rYqyBTl7b-RGg0Z2VyJ3qxRyk9isw5zsgp2OSmpJNKSu0PoPh new GMOD articles on PubMed].
    21 KB (3,298 words) - 22:22, 9 February 2015
  • |type=Database tools, Middleware ...ry#Schema|schema]] using [[Glossary#XML|XML]] as an interchange format. In GMOD XORT is frequently used to transfer data to and from [[Chado]].
    1 KB (221 words) - 21:22, 16 October 2013
  • ...ic Genome Browser (GBrowse)]] is one of the most widely used visualization tools for sequence display characterized by a rich set of utilities helpful in pr [[Category:GMOD Components]]
    4 KB (540 words) - 18:31, 10 September 2013
  • ...ng able to both read from and write to the database). We have a variety of tools that can be used to load sequence data as [[GFF]] into Chado and there are ...sing the [[Chado_Mage_Module|''mage'' module]]) with sequence data (stored using the [[Chado_Sequence_Module|''sequence'' module]]) from various species (th
    17 KB (2,655 words) - 13:43, 14 March 2014
  • ...iki>[[GMOD_Middleware|GMOD Middleware]]</nowiki></tt> || [[GMOD_Middleware|GMOD Middleware]] ...OD_Middleware|GMOD middleware meeting]]</nowiki></tt> || [[GMOD_Middleware|GMOD middleware meeting]]
    3 KB (399 words) - 20:06, 8 October 2012
  • GMOD Generic Model Organism Database * [[Media:Biocyc-GMOD-2006.ppt|Biocyc-GMOD-2006.ppt]]
    3 KB (426 words) - 19:30, 23 January 2008
  • Many GMOD project file releases are available from [http://sourceforge.net/project/showfiles.php?group_id=27707 Sourceforge GMOD]. Individual package releases include:
    2 KB (236 words) - 08:57, 9 April 2013
  • This page describes a variety of special GMOD project proposals that need developer support. Please contact the proposer ==GMOD needs for 2008 : dgg ==
    2 KB (274 words) - 22:07, 29 October 2010
  • # Overview of UCSC Web Tools for Bioinformatics # GMOD scenarios
    893 B (114 words) - 01:37, 29 March 2007
  • ...ed database schemas, and software, including middleware systems, curators' tools, data analysis pipelines and visualization software. ...research community, circulating questionnaires, holding focus groups, and using other techniques to gain an understanding of what the research community ne
    26 KB (3,975 words) - 05:03, 28 January 2008
  • ...er interface (UI) of a MOD is very important to usability. At the upcoming GMOD meeting (January 18-19 in San Diego at the Town and Country hotel), a day w ...lessons learned' which hopefully will be useful both for developers of any GMOD-specific UIs as well as the implementers at the various participating MODs.
    4 KB (599 words) - 01:32, 29 March 2007
  • ...utside the scope of this document.) Thus, we examine specific subjects and tools which may be used to achieve goals via testing. ===Targets of Testing for GMOD===
    6 KB (855 words) - 23:50, 25 January 2008
  • On the first day of the [[January 2007 GMOD Meeting]], we shared and using one MOD in concert with other MODs.
    18 KB (2,786 words) - 17:34, 31 January 2008
  • The third GMOD working group meeting was held at Lawrence Berkeley National Laboratory on * [[Media:Apollo.GMOD.ppt|Apollo.GMOD.ppt]]
    28 KB (4,338 words) - 22:06, 29 October 2010
  • GMOD Meeting April, 2004 <td>GMOD/Turnkey web demo<br>
    42 KB (6,309 words) - 20:37, 30 November 2010
  • Scott Cain, GMOD coordinator</td> <li>Flybase tools (other than Apollo and chado)
    3 KB (355 words) - 15:30, 6 April 2007
  • * [[Media:Cain-050516.ppt|Cain-050516.ppt]] - GMOD business and setting up [[ParameciumDB]] Scott Cain, GMOD coordinator</td>
    7 KB (915 words) - 17:07, 14 March 2008
  • Scott Cain, GMOD coordinator</td> <td width="85%">GMOD/chado 0.003 and roadmap, including:<br>
    5 KB (752 words) - 22:15, 28 July 2010
  • ...ists most of the mailing lists relevant to GMOD. The default location for GMOD related lists is [http://sourceforge.net/mail/?group_id=27707 SourceForge], We also include pointers to [[#A Few Non GMOD Lists|a few non GMOD lists]] that are of general interest.
    7 KB (928 words) - 17:02, 16 May 2016
  • ''... formerly titled "GMOD for the Biologist". This page provides an overview of the GMOD project. It does not assume any particular background in computing.
    34 KB (5,526 words) - 19:56, 7 October 2013
  • '''[[GMOD Community Support]] Specialist hired''' ...r] in Durham, North Carolina, while serving the international community of GMOD users.
    2 KB (359 words) - 16:42, 22 August 2012
  • GMOD Meeting, January 18, 2007, San Diego, CA, USA satisfaction of its users. On the first day of the January 2007 GMOD
    24 KB (3,905 words) - 16:54, 11 August 2008
  • |type=Database schema, Database tools |about=Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of
    2 KB (238 words) - 22:55, 2 December 2013
  • ...ng [[GBrowse]], [[JBrowse]], [[Chado]], or some other popular component of GMOD. For a list of related publications see [[Publications]]. Check out the [http://gmod.org/worldwide.html map of GMOD users around the world]!
    31 KB (3,762 words) - 10:43, 12 August 2014
  • [[GMOD Middleware|middleware]] or applications) should be aware of the different w ...]] model states that "gene makes mRNA makes polypeptide" - for many people using Chado this may be the only data model that's relevant. This typical protein
    30 KB (4,629 words) - 08:47, 16 April 2013
  • ...ema. Getting Started refers to [http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/INSTALL the INSTALL document] * I installed PostgreSQL using the [http://www.entropy.ch/software/macosx/postgresql/ Installer Package fr
    16 KB (2,472 words) - 23:54, 25 January 2008
  • ...rd and Snow Leopard can be obtained from [https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/libgd-MacOSX/20100406/ sourceforge] ...ownload an installer for libGD for either Leopard or Snow Leopard from the GMOD SourceForge site (it's possible that the Snow Leopard installer will work f
    11 KB (1,849 words) - 22:55, 15 August 2013
  • ...tall GBrowse is with the network installer script, <tt>[https://github.com/GMOD/GBrowse/raw/master/bin/gbrowse_netinstall.pl gbrowse_netinstall.pl]</tt> ...is platforms, you will need to be logged in as root, or to run the command using "sudo" (''sudo perl gbrowse_netinstall.pl'').
    35 KB (5,565 words) - 22:39, 8 August 2012
  • ...="/w/images/e/ef/Nihlogo.gif" alt="National Institutes of Health"></td><td>GMOD is supported by a specific cooperative agreement from the USDA Agricultural [[Category:Wiki Tools]]
    2 KB (201 words) - 18:22, 27 August 2008
  • ...ew to databases. It also covers how databases are implemented and used in GMOD, and what database management system choices are available. ...es more precise terms that should be (but probably aren't) used throughout GMOD.
    9 KB (1,355 words) - 22:31, 25 March 2014
  • | where = 2010 GMOD Summer School - Americas ...] database, Chado being the database {{GlossaryLink|Schema|schema}} of the GMOD project. This session introduces database concepts, provides an overview of
    54 KB (8,190 words) - 23:34, 8 October 2012
  • ...tutorial was presented by [[User:Scott|Scott Cain]] as part of the [[2012 GMOD Summer School]]. Chado is the database schema of the GMOD project. This session introduces database concepts, and then provides an o
    50 KB (7,599 words) - 16:26, 2 September 2018
  • ...he supported distributions (Centos4 is the supported & tested platform for GMOD) and you install biopackages on a clean system (e.g. no source installed so ...platform tested for the GMOD community is CentOS 4 and we highly recommend using Biopackages on this distribution.
    6 KB (783 words) - 20:54, 14 April 2010
  • Progress report submitted by Scott Cain, GMOD Coordinator. ...ess in several areas. There have been meetings, software releases and the GMOD website was revamped to make it more useful and intuitive to users.
    26 KB (4,096 words) - 01:17, 19 August 2009

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