User contributions
- 22:13, 22 February 2007 (diff | hist) . . (-2) . . Modware Presentation (→Problem 1 - Create and Insert a Gene)
- 20:49, 21 February 2007 (diff | hist) . . (+5) . . GMOD Middleware (→Configuration)
- 22:57, 6 February 2007 (diff | hist) . . (+64) . . GMOD Middleware (→The Middleware Packages)
- 22:52, 6 February 2007 (diff | hist) . . (-31) . . GMOD Middleware (→The Middleware Packages)
- 18:28, 6 February 2007 (diff | hist) . . (+152) . . GMOD Middleware (→Executive Summary)
- 17:51, 6 February 2007 (diff | hist) . . (+84) . . GMOD Middleware (→Configuration)
- 17:48, 6 February 2007 (diff | hist) . . (+83) . . GMOD Middleware (→Background)
- 17:46, 6 February 2007 (diff | hist) . . (-1) . . GMOD Middleware (→Limitations)
- 17:45, 6 February 2007 (diff | hist) . . (+568) . . GMOD Middleware (→Modware)
- 17:40, 6 February 2007 (diff | hist) . . (+233) . . GMOD Middleware (→Special topics)
- 17:36, 6 February 2007 (diff | hist) . . (-5) . . GMOD Middleware (→Technical Overview)
- 17:35, 6 February 2007 (diff | hist) . . (+275) . . GMOD Middleware (→Technical Overview)
- 20:24, 26 January 2007 (diff | hist) . . (+55) . . GMOD Middleware (→Why Modware Was Developed)
- 20:23, 26 January 2007 (diff | hist) . . (+26) . . GMOD Middleware (→Why Modware Was Developed)
- 20:21, 26 January 2007 (diff | hist) . . (+151) . . GMOD Middleware (→Modware Features)
- 19:57, 26 January 2007 (diff | hist) . . (+130) . . GMOD Middleware (→Technical Overview)
- 19:56, 26 January 2007 (diff | hist) . . (+55) . . GMOD Middleware (→Background)
- 19:52, 26 January 2007 (diff | hist) . . (+63) . . GMOD Middleware (→Modware Features)
- 19:51, 26 January 2007 (diff | hist) . . (+2) . . GMOD Middleware (→Modware Features)
- 19:51, 26 January 2007 (diff | hist) . . (+201) . . GMOD Middleware (→Modware Features)
- 19:18, 25 January 2007 (diff | hist) . . (+1) . . GBrowse
- 18:44, 25 January 2007 (diff | hist) . . (+1,873) . . N XORT (New page: <nowiki> Chado-XML ========= Chado-XML is a direct mapping of the Chado relational schema into XML. Currently the only tool for performing this mapping is XML::XORT, which can du...)
- 18:44, 25 January 2007 (diff | hist) . . (+1,337) . . N SynBrowse (New page: ; '''Description'''<br /> : SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help sc...)
- 18:44, 25 January 2007 (diff | hist) . . (+287) . . N Sybil (New page: Sybil is a multi-organism synteny viewer written by developers at TIGR. This page is a placeholder for more content, but I wanted to at least get a few links up: * [http://sybil.source...)
- 18:43, 25 January 2007 (diff | hist) . . (+5,223) . . N GMOD Components (New page: GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by all model organism databases. The applications are linked together by ...)
- 18:43, 25 January 2007 (diff | hist) . . (+1,809) . . N Publications (New page: * Donald G. Gilbert. DroSpeGe: rapid access database for new Drosophila species genomes.<br /> Nucleic Acids Res. 2007 35(Database issue):D480-D485; [http://dx.doi.org/10.1093/nar/gkl997...)
- 18:43, 25 January 2007 (diff | hist) . . (+3,810) . . N Textpresso (New page: ; '''Description'''<br /> : Textpresso is a text mining system for scientific literature whose<br /> capabilities go far beyond that of a simple keyword search engine. The two<br /> key ...)
- 18:43, 25 January 2007 (diff | hist) . . (+982) . . N Java TreeView (New page: ; '''Description'''<br /> : Java TreeView, a portable Java application that has been tested on Linux, Windows, MacOS9 and MacOSX. Java TreeView is a visualization for various clustering ...)
- 18:43, 25 January 2007 (diff | hist) . . (+659) . . N Caryoscope (New page: ; '''Description'''<br /> : Caryoscope is a reusable Java UI component -- and a set of parsing utilities;<br /> command line tools and an application GUI -- for viewing gene expression d...)
- 18:43, 25 January 2007 (diff | hist) . . (+3,134) . . N PubFetch (New page: : ; '''Description'''<br /><br /> PubFetch is part of the [[web-based literature curation toolset and functions as the interface between the literature curation tools and the online lite...)
- 18:43, 25 January 2007 (diff | hist) . . (+5,594) . . N LuceGene (New page: ; '''Description'''<br /> : This is an open-source document/object search and retrieval system specially tuned for bioinformatics text databases and documents. LuceGene is similar in co...)
- 18:43, 25 January 2007 (diff | hist) . . (+1,686) . . N JavaSEAN (New page: ; '''Description'''<br /> : The javaSEAN tool is a standalone java application which was developed<br /> to facilitate integration and curation of sequence-level data from the<br /> nucl...)
- 18:43, 25 January 2007 (diff | hist) . . (+1,074) . . N Insertional Mutagenesis Database (IMDB) (New page: NOTE: this project is no longer supported ; '''Description'''<br /> : IMDB stores<br /> the sequenced insertion sites for model organisms, provides users with visualization tools to sea...)
- 18:43, 25 January 2007 (diff | hist) . . (+161) . . N Genome Directory System (GDS) (New page: This is a place holder for GDS. The authors of this project have indicated that "This project is on hold until more funding and development time can be found.")
- 18:43, 25 January 2007 (diff | hist) . . (+2,242) . . N Citrina (New page: ; '''Description''' : Citrina (sih-TREE-nuh) is a database management tool that automates the mirroring and processing of databases that are distributed via ftp servers. It is built aro...)
- 18:43, 25 January 2007 (diff | hist) . . (+7,372) . . N Argos (New page: ; '''Description'''<br /> : Argos, a.k.a. Flybase-NG, a.k.a. biodb, is designed to provide automatic<br /> replication, installation and updates of genome and organism databases<br /> a...)
- 18:43, 25 January 2007 (diff | hist) . . (+207) . . N Gene Expression Visualization (New page: Components for visualizing gene expression results; currently focused on microarray based experments. * Caryoscope * GeneXplorer * Insertional Mutagenesis Database (IMDB) ...)
- 18:42, 25 January 2007 (diff | hist) . . (-18) . . Ontology Visualization
- 18:42, 25 January 2007 (diff | hist) . . (+1,555) . . N BioMart (New page: ; '''Description'''<br /> : BioMart is a robust, query-oriented data integration system, based on distributed data warehousing ideas. The system can be applied to a single or multiple da...)
- 18:42, 25 January 2007 (diff | hist) . . (+743) . . N Restriction Graphic Viewer (New page: ; '''Description'''<br /> : The Restriction Graphic Viewer is a simple web_based restriction analysis tool. It is a component of the Generic Model Organism Systems Database project (GMOD...)
- 18:42, 25 January 2007 (diff | hist) . . (+1,223) . . N PubSearch (New page: ; '''Description'''<br /> : PubSearch is a web-based literature curation tool to allow curators to search and annotate genes to keywords from articles. It has a simple, MySQL database ba...)
- 18:42, 25 January 2007 (diff | hist) . . (+1,476) . . N Pathway Tools (New page: ; '''Description'''<br /> : The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). A pathway/g...)
- 18:42, 25 January 2007 (diff | hist) . . (+327) . . N Org.bdgp (New page: ; '''Description'''<br /> : The org.bdgp toolkit is a library of useful Java classes shared by several pieces of gmod software. ; '''Requirements'''<br /> : JDK 1.2 or higher. ; '''Con...)
- 18:42, 25 January 2007 (diff | hist) . . (+1,298) . . N GO Graphic Viewer (New page: ; '''Description'''<br /> : The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provide...)
- 18:42, 25 January 2007 (diff | hist) . . (+1,874) . . N GeneXplorer (New page: ; '''Description'''<br /> : GeneXplorer is a web application that allows clustered microarray<br /> data to be browsed interactively via the web, and can be used either<br /> for resear...)
- 18:41, 25 January 2007 (diff | hist) . . (+685) . . N GenoGrid (New page: '''Genome analysis and annotation via Grid computing''' This subproject builds re-usable tools and workflows for genome analyses and annotation, using shared cyberinfrastructure (Grids ...)
- 18:41, 25 January 2007 (diff | hist) . . (+600) . . N Apollo-Chado example database (New page: There is an example database with GFF3 source files, a log of the commands I ran to build the database, database dumps at a few steps of building the database, and an Apollo chado-adaptor....)
- 18:41, 25 January 2007 (diff | hist) . . (+9,301) . . N Comparison of XORT and Hibernate for Chado reporting (New page: '''Comparison of XORT and [http://www.hibernate.org/ Hibernate ] for Chado reporting''' - written by Josh Goodman, FlyBase - Indiana University '''Introduction'''<br /> At [http://f...)
- 18:41, 25 January 2007 (diff | hist) . . (+1,666) . . N Summary of Fall 2005 CHSL Meeting (New page: '''GMOD Architecture Work Group Discussion (Fall 2005 meeting)''' '''During the meeting it was suggested that we have a common<br /> database against which to test software. A first ste...)
- 18:40, 25 January 2007 (diff | hist) . . (+777) . . N Software Testing Recommendations (New page: This wiki is to provide an interaction space for generating a set of recommendations on software testing for the GMOD group. The documents should contain enough information so that after...)
- 18:40, 25 January 2007 (diff | hist) . . (+2,713) . . N About the GMOD Working Group (New page: ''' About the GMOD Architecture Working Group ''' ''' Goal ''' The Architecture Working Group will make recommendations to the GMOD<br /> consortium on any cross-project policies which...)
- 18:40, 25 January 2007 (diff | hist) . . (+1,891) . . N Community (New page: ; '''Description'''<br /> : The community module provides a directory of people, labs, and organizations<br /> involved in research of a model organism. All of these groups will be able<...)
- 18:40, 25 January 2007 (diff | hist) . . (-202) . . GMOD - Getting Started
- 18:40, 25 January 2007 (diff | hist) . . (-201) . . GBrowse
- 18:40, 25 January 2007 (diff | hist) . . (-207) . . Flash GViewer
- 18:39, 25 January 2007 (diff | hist) . . (-431) . . CMap
- 18:39, 25 January 2007 (diff | hist) . . (-33) . . BLAST Graphic Viewer
- 18:39, 25 January 2007 (diff | hist) . . (-73) . . Bioperl Pipeline
- 18:39, 25 January 2007 (diff | hist) . . (-30) . . Apollo-Chado
- 18:39, 25 January 2007 (diff | hist) . . (-38) . . Apollo
- 18:39, 25 January 2007 (diff | hist) . . (-421) . . Chado - Getting Started
- 18:39, 25 January 2007 (diff | hist) . . (-138) . . GMOD Developer's Guide
- 18:37, 25 January 2007 (diff | hist) . . (-97) . . Genome Visualization
- 18:34, 25 January 2007 (diff | hist) . . (-3) . . Genome Visualization
- 18:32, 25 January 2007 (diff | hist) . . (+1,830) . . N GMODTools (New page: This page is a place holder for when there is a release of GMODTools, when it will be replaced with all sorts of useful information. If you want to try out GMODTools in the mean time, yo...)
- 18:32, 25 January 2007 (diff | hist) . . (+1,883) . . N GMOD - Getting Started (New page: This is a guide to getting started with chado Chado and GMOD. If you want to set up your own model organism database, this is a good place to start; however, if all you want is a par...)
- 18:32, 25 January 2007 (diff | hist) . . (+4,565) . . N GBrowse (New page: The Generic Genome Browser (which is also occationally and incorrectly referred to as 'gbrowser') is a combination of database and interactive web page for manipulating and displaying an...)
- 18:32, 25 January 2007 (diff | hist) . . (+6,382) . . N Flash GViewer (New page: {| width="100%" | ; '''[[[Image:gviewer_rat_human.jpg|Rat-Human Comparative Map]]]Description'''<br /> : Flash GViewer is a '''customizable Flash movie''' that can be easily<br /> insert...)
- 18:32, 25 January 2007 (diff | hist) . . (+235) . . N TIGR-Workflow / Ergatis (New page: Ergatis is a Chado-compatible workflow manager for bioinformatics analysis pipelines developed by The Institute for Genome Research for use in whole-genome annotation. More information i...)
- 18:32, 25 January 2007 (diff | hist) . . (+3,750) . . N CMap (New page: ; '''Description'''<br /> : 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. ; '''Demo'...)
- 18:31, 25 January 2007 (diff | hist) . . (+1,079) . . N BLAST Graphic Viewer (New page: ; '''Description'''<br /> : The BLAST Graphic Viewer provides a graphical visualization of the<br /> regions contained within HSPs relative to the query sequence. This<br /> distribution...)
- 18:31, 25 January 2007 (diff | hist) . . (+2,092) . . N Bioperl Pipeline (New page: == Description == The [http://www.genome.org/cgi/content/full/13/8/1904 Bioperl pipeline framework ]is a flexible workflow system that complements the Bioperl package by providing job ...)
- 18:31, 25 January 2007 (diff | hist) . . (+4,344) . . N Apollo-Chado (New page: This page is pulled directly from the README.Apollo documentation in the Chado code repository and is converted to text and dynamically loaded in this page. The README was most recently ch...)
- 18:31, 25 January 2007 (diff | hist) . . (+1,035) . . N Apollo (New page: ; '''Apollo Genome Editor'''<br /> : The Apollo genome editor is a Java-based application for annotating genomic sequences. There are currently two branches of Apollo, one primarily used...)
- 18:31, 25 January 2007 (diff | hist) . . (+3,237) . . N Chado - Getting Started (New page: Chado, properly pronounced. [[files/chado.mp3 [[Image:speaker_0.gif]]]] This is a stub document for describing the Chado schema at a high level. Until this is fleshed out a little more...)
- 18:31, 25 January 2007 (diff | hist) . . (+350) . . N GMOD Developer's Guide (New page: This is the GMOD developer's guide * 1_favored_platforms 1. Favored Platforms * 2_server_side_directory_structure 2. Server Side Directory Structure * [[3_interoperation 3. In...)
- 18:30, 25 January 2007 (diff | hist) . . (+500) . . N Genome Visualization (New page: These components allow you to edit and view genome annotations. The two most popular components are GBrowse, a web-based genome viewer, and Apollo, a Java (desktop) application that allo...)
- 18:30, 25 January 2007 (diff | hist) . . (+266) . . N Ontology Visualization (New page: This is a stub. Other sites that might be of interest: * [http://song.sourceforge.net/ Sequence Ontology] * [http://www.geneontology.org/ Gene Ontology] * [http://obo.sourceforge.net/ ...)
- 18:20, 25 January 2007 (diff | hist) . . (+644) . . Main Page (Undo revision 86 by Special:Contributions/165.124.152.78 (User talk:165.124.152.78))
- 18:15, 25 January 2007 (diff | hist) . . (-645) . . Main Page (Removing all content from page)
- 18:13, 25 January 2007 (diff | hist) . . (-86) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (-854) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (+999) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (-58) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (+159) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (-305) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (+415) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (-1,618) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (+1,207) . . Main Page
- 18:13, 25 January 2007 (diff | hist) . . (+342) . . Main Page