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• Apollo
  ; Apollo tutorials at the [http://www.dynamicgene.org Dynamic Gene] web site. …o executables for several platforms (Windows, Mac Os X, Linux, Solaris and generic Unix) are available from the [http://apollo.berkeleybop.org/current/index.…
  4 KB (492 words) - 22:14, 15 November 2011
• NIH 2002 Workshop on Model Organism Databases
  …operating procedures and data models that would form the basis of a set of generic components for MOD building. …tic constructs and clones; and lastly to provide a common nomenclature for gene symbols, anatomic terms and other elements of the scientific vocabulary. B…
  26 KB (3975 words) - 05:03, 28 January 2008
• Overview
  …/perl/site/emiliania04?page=intro ''Emiliania huxleyi'' Serial Analysis of Gene Expression] database. We even find GMOD databases dedicated to collections… set of Web pages or a Java application. The choice of applications is
  34 KB (5476 words) - 21:00, 14 November 2011
• Introduction to Chado
  * A database that is generic enough to use for any organism …currently the best source of documentation for Chado. Here are more useful pages in the Wiki:
  14 KB (2050 words) - 21:02, 12 October 2010
• NBrowse
  …ultaneously. Although created for applications in biology, N-Browse uses a generic database schema that can be adapted to network representations in any know… …e. Links to the N-Browse GUI at WormBase are available on the Gene Summary pages. TAIR's N-Browse search page can be accessed via the Tools menu on the TA…
  6 KB (920 words) - 16:57, 30 September 2010
• Glossary
  …llowing styles to defined in a single place and then referred to from many pages. === Gene Finder Format ===
  13 KB (1972 words) - 12:42, 11 April 2012
• Site Guidelines
  This means that if a user types "[[Generic Genome Browser]]" in the "Go/Search" box and you have a redirect defined f… … the "create this page" link. In our example, you would enter/search for "Generic Genome Browser".
  12 KB (1859 words) - 21:21, 14 December 2011
• GBrowse 1 Configuration HOWTO
  …is document provides information on configuring version 1 of the [[GBrowse|Generic Genome Browser (GBrowse)]], part of the [[Main Page|GMOD Project]]. For ve… ….gb file. I would copy & paste specific sections (i.e. section for CDS or gene, etc. - any type can be altered) and then change the type to some key word…
  79 KB (12563 words) - 16:45, 15 August 2011
• August 2009 GMOD Meeting
  …neric, lightweight pipeline framework which was initially built to produce gene predictions. DIYA is becoming part of GMOD. ** Good enough for real time user interaction, e.g., <1s for single gene search, 1-4s for multigene search (unions)
  59 KB (8727 words) - 18:37, 16 March 2010
• Common Gene Page
  =Common Gene Page Rationale= Model organism/genome databases (MODs) produce gene pages of similar
  7 KB (1051 words) - 22:52, 15 September 2009
• Bio GMOD GenericGenePage
  …sary#Perl|Perl]] class that provides a render_xml method to crete [[Common Gene Page]] [[Glossary#XML|XML]], but does not fetch the data. In order to eff… … be seen by clicking on the "Download GMOD XML" link on any of there locus pages; for example, this one:
  6 KB (755 words) - 01:16, 19 August 2009
• GBrowse 2.0 HOWTO
  …ttp://http://packages.debian.org/source/sid/gbrowse GBrowse Debian package pages.] <p style="font-size:small">Generic Genome Browser version 1.99. For questions about the data
  99 KB (15141 words) - 23:41, 17 April 2012
• January 2009 GMOD Meeting
  |[[Bio GMOD GenericGenePage|Generic Gene Page XML]] …cGenePage.ppt|PPT]], [[:Image:Jan2009GenreicGenePage.pdf|PDF]], [[#Generic Gene Page XML|Summary]], [[#Data Sharing|Discussion]]
  51 KB (7607 words) - 17:57, 28 July 2010
• Running a GBrowse2 render farm
  …s one or more computers, you can spread out the work of generating GBrowse pages, thereby achieving improved performance. A slave can be attached to a part… % cd Generic-Genome-Browser
  16 KB (2473 words) - 12:08, 12 October 2011
• GMOD RPC API
  … present, this API only covers querying and retrieving information for the gene data class. == Language Implementation Pages ==
  25 KB (3154 words) - 15:56, 23 October 2011
• GFF
  …file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 column, tab-delimited files… …mmonly CDS coding segments and UTRs. This example shows how to represent a gene named "EDEN" which has three alternatively-spliced mRNA transcripts:
  16 KB (2329 words) - 16:40, 14 July 2011
• Galaxy Tutorial
  The dataset we uploaded is a generic tabular data file (dumped out of the UCSC browser, not in any particular f… === 4. Get Gene Annotations from UCSC ===
  33 KB (4952 words) - 20:23, 9 June 2010
• Chado Tutorial
  …eloped completely different modules for community, literature, anatomy and gene expression. If there is a PATO compatible Chado Phenotype solution we'd p… * gene predictions
  54 KB (8317 words) - 13:56, 14 October 2010
• GBrowse syn PAG tutorial
  =The Generic Synteny Browser= …w to install, configure and use GBrowse_syn. To get started, browse these pages:
  19 KB (2508 words) - 23:13, 23 November 2010
• GBrowse Configuration/Glyphs
  | [[bp:Module:Bio::Graphics::Glyph::generic|generic]] | a gene model
  6 KB (919 words) - 13:57, 9 July 2010

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