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  • Apollo-Chado example database
    ...used to build the database, database dumps at a few steps of building the database, and an [[Apollo]] <tt>chado-adaptor.xml</tt> config file in the {{SF_SVN|s
    587 B (98 words) - 21:08, 15 September 2009
  • Insertional Mutagenesis Database (IMDB)
    ...This project was developed from ATIDB, the Arabidopsis thaliana insertion database. : See [http://atidb.cshl.org/ http://atidb.cshl.org] for a database of Arabidopsis insertional mutants.
    1 KB (150 words) - 07:22, 30 January 2008
  • News/Virtual Issue in Journal Database
    ...e:DatabaseJournal.jpg|link=http://database.oxfordjournals.org/|300px|right|Database: The Journal of Biological Databases and Curation]] ...h one of the editors of the journal [http://database.oxfordjournals.org/ ''Database''], an open access journal whose aim for publications lines up very nicely
    2 KB (282 words) - 23:08, 9 October 2012
  • Category:Database Tools
    This broad category includes high level and low level database topics.
    19 members (5 subcategories, 1 file) - 05:47, 1 March 2008
  • News/Sea Urchin Genome Database
    [[File:SpBaseLogo.png|link=http://spbase.org/|right|Sea Urchin Genome Database]] Today, Tuesday April 4th, the [http://spbase.org Sea Urchin Genome Database] went public. Based on the GMOD tools and applications the site organizes
    787 B (118 words) - 23:09, 9 October 2012
  • News/Long Term Database Funding
    ...tabases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''. ...proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International S
    3 KB (395 words) - 23:09, 9 October 2012
  • GBrowse syn Database
    ...the database that GBrowse_syn uses, and how to get syntenic data into that database. =Loading the alignment database=
    7 KB (897 words) - 21:27, 14 August 2012
  • JBrowseDev/Using a Database With JBrowse
    51 B (6 words) - 14:27, 29 March 2013
  • GBrowse User Database
    [[GBrowse]] has the option to use a database to manage users, so that a user may save their session for use on multiple To use the user database, you will need to install the [http://search.cpan.org/~gbarr/libnet-1.22/Ne
    7 KB (1,094 words) - 22:41, 29 December 2010
  • BrowseDev/Using a Database With JBrowse
    101 B (11 words) - 15:54, 1 April 2013
  • JBrowseDev/Current/Usage/Database
    #REDIRECT [[JBrowseDev/Using a Database With JBrowse]]
    54 B (7 words) - 17:31, 29 July 2011
  • News/BioMart Special Issue in Database
    I am very pleased to announce the publication of the DATABASE special issue dedicated to the [http://www.biomart.org/ BioMart] project ...ast ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and Sou
    949 B (135 words) - 04:25, 19 November 2011
  • Example ChIP database
    40 B (6 words) - 19:41, 17 April 2012
  • News/Xenbase Hiring Database Manager
    '''[http://www.xenbase.org Xenbase] is looking for a new database manager.''' We need an experienced software developer / designer looking fo Xenbase is the model organism database for Xenopus, a frog used extensively in biomedical research for understandi
    4 KB (523 words) - 00:27, 21 August 2012

Page text matches

  • GMOD Middleware
    ...ough GMOD uses the [[Chado]] [[Glossary#Schema|schema]] for its underlying database, each group has developed a separate interface to their databases. This mee ...approaches and components that it supports. This applies to applications, database schemas, as well as to middleware, a software ''layer'' that mediates the e
    40 KB (5,672 words) - 21:27, 15 August 2013
  • PSU Presentation
    * GeneDB is the organism data and annotation database for the Pathogen Sequencing Unit (PSU) at the Sanger Institute, UK * Connection to the database is specified graphically, so the '''iBatis''' configuration file has varia
    4 KB (513 words) - 21:16, 9 October 2012
  • Hibernate Presentation
    ** Wrote Ensembl API Database adaptor for Chado... Not maintainable. * Need API for Database I/O
    12 KB (1,477 words) - 21:16, 9 October 2012
  • IBatis Presentation
    * iBatis does not create your database in memory as objects * Generates ibatis CRUD objects by introspecting database tables
    12 KB (1,304 words) - 21:10, 9 October 2012
  • GBrowse (DasI) Presentation
    =====Create the database===== ** Database connection object
    3 KB (415 words) - 20:05, 8 October 2012
  • Modware Presentation
    * Database transactions supported # Inserts chromosome into database
    13 KB (1,574 words) - 21:24, 15 August 2013
  • Main Page
    ...ratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at [[MOD|many large and small community databases]]. [[File:ChadoLogo.png|250px|thumb|none|link=Chado|Chado: Biological database schema]]
    5 KB (651 words) - 18:22, 30 March 2021
  • GMOD Developer's Guide
    ...tional database, it should be able to interact with a Chado database via a database adaptor.
    6 KB (985 words) - 05:18, 28 January 2008
  • Chado - Getting Started
    Chado is a [[Glossary#Database Schema|relational database schema]] that underlies [[GMOD_Users|many GMOD installations]]. It is capab First you will need database software, or Relational Database Management System (RDBMS). The recommended RDBMS for Chado currently is [ht
    3 KB (469 words) - 18:08, 13 February 2014
  • Chado FAQ
    ...called DBIx::DBStag, which does the actual writing of ontology data to the database. When it loads the Gene Ontology (and possibly other ontologies), it destr : Instead, you must run a SQL command to repair the database:
    6 KB (1,058 words) - 17:50, 5 February 2014
  • Apollo-Chado
    Reading and Writing to a Chado database with Apollo vocabulary terms that Apollo expects to be in the database. This
    4 KB (635 words) - 18:06, 28 December 2007
  • CMap
    |type=Genome Visualization & Editing, Comparative Genome Visualization, Database schema * A relational database, e.g. [http://www.mysql.com MySQL (4.0+)], Sybase Adaptive Server Enterpris
    7 KB (996 words) - 23:40, 17 October 2013
  • TIGR-Workflow / Ergatis
    ...database instance. In the past, due to its primary use at TIGR/JCVI, the database support was limited to Sybase, though flat-files could also be generated.
    2 KB (354 words) - 23:49, 25 July 2012
  • Flash GViewer Documentation
    The Rat Genome Database has an SVG-based genome viewer that shows the location of genes and QTLs ag ...tation XML files or create a CGI/JSP script that retrieves the data from a database. Details of the various file formats are given below.
    30 KB (4,819 words) - 21:16, 9 October 2012
  • GBrowse
    |about=GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on ge ...nly for applications where legacy browser support is required and a single database is used.
    11 KB (1,422 words) - 16:47, 10 April 2023
  • File:05-chado overview.pdf
    == Chado: Generic Model Organism Database Schema ==
    (953 KB) - 21:16, 6 February 2008
  • File:ChadoCSHMay03Slides.pdf
    = Chado: Generic Model organism database schema =
    (1.3 MB) - 21:46, 6 February 2008
  • GMOD - Getting Started
    ...-_Getting_Started|Getting Started with Chado]] discusses GMOD's relational database schema. Chado is useful for organizing your data and is also integrated wi
    1 KB (240 words) - 20:32, 15 September 2009
  • Community
    A proposed database module for Chado. * The community module uses a relational database, a Servlets and JSP engine, and the Struts Web application framework.
    2 KB (254 words) - 00:52, 18 November 2010
  • GMODTools
    ...rom several Chado dbs, and add other sources that may not be in your Chado database. * each genome Chado database has different policy and choices with respect to feature, vocabulary and ot
    10 KB (1,496 words) - 23:00, 15 August 2013
  • Summary of Fall 2005 CHSL Meeting
    '''During the meeting it was suggested that we have a common database against which to test software. A first step would be to provide Postgres d Allen Day suggested that he will provide a Postgres dump of the database for human, yeast and mouse.
    2 KB (257 words) - 15:02, 13 February 2007
  • Comparison of XORT and Hibernate for Chado reporting
    ...t up by hand but the JBOSS Eclipse IDE has a nice tool that will read your database schema and generate them for you. This is also the first place we encounter ...s file that describes your schema matches the actual schema that is in the database. Once that is done all you need to do is write a dumpspec to dump the data
    9 KB (1,641 words) - 15:48, 12 September 2011
  • Apollo-Chado example database
    ...used to build the database, database dumps at a few steps of building the database, and an [[Apollo]] <tt>chado-adaptor.xml</tt> config file in the {{SF_SVN|s
    587 B (98 words) - 21:08, 15 September 2009
  • GeneXplorer
    ...al web supplements for papers arising from data in the Stanford Microarray Database. As an example, see:
    2 KB (364 words) - 18:57, 13 July 2012
  • GO Graphic Viewer
    ...ult from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational r
    2 KB (264 words) - 23:44, 3 December 2013
  • Pathway Tools
    ...=Community Annotation, Comparative Genome Visualization , Database schema, Database tools, Gene Expression Visualization, Genome Visualization & Editing, Molec
    5 KB (650 words) - 00:07, 16 October 2013
  • PubSearch
    ...h and annotate genes to keywords from articles. It has a simple, [[MySQL]] database backend and uses a set of [[:Category:Java|Java]] Servlets and JSPs for que
    1 KB (178 words) - 00:52, 18 November 2010
  • Restriction Graphic Viewer
    ...ite analysis tool. It is a component of the Generic Model Organism Systems Database project.
    595 B (80 words) - 22:36, 11 September 2009
  • BioMart
    |type=Community Annotation, Database schema, Database tools, Genome Annotation, Middleware, Tool Integration, Data federation sof |about=BioMart is a freely available, open source, federated database system that provides unified access to disparate, geographically distribute
    2 KB (228 words) - 22:26, 15 October 2013
  • Argos
    ...implemented common database/information service tools needed for organism database systems, which can be automatically distributed and updated to any computer ...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
  • Citrina
    ...o SQL dumps between organism sites and automatically populate the postgres database via Ant's SQL tasks. Ant can also execute external scripts so Citrina can t
    2 KB (397 words) - 22:19, 11 September 2009
  • Insertional Mutagenesis Database (IMDB)
    ...This project was developed from ATIDB, the Arabidopsis thaliana insertion database. : See [http://atidb.cshl.org/ http://atidb.cshl.org] for a database of Arabidopsis insertional mutants.
    1 KB (150 words) - 07:22, 30 January 2008
  • LuceGene
    ...d retrieval with LuceGene is 10x to 20x faster than using a Postgres Chado database. ...orts, or other complex data, can be quite slow. Chado is a good management database, but lacks efficiency for web access to support many customers. Lucene has
    6 KB (792 words) - 15:09, 6 September 2010
  • File:Gmod-argos-sep03.pdf
    [[Category:Database Tools]]
    (5.22 MB) - 06:52, 30 January 2008
  • PubFetch
    ...psis.org/ TAIR]. A standard API and data format will be created to provide database queries and return results, popular existing formats and protocols will be ...be reviewed and adapted to create the main PubFetch module and appropriate database interace modules. Figure 2 below is a schematic diagram of the exising RGD
    3 KB (467 words) - 16:31, 15 October 2008
  • Textpresso
    ...dual sentences, and the implementation of semantic categories, for which a database of articles and individual sentences can be searched. The source of the ful ...publicly (via WWW) accessible database, while the other half is needed for database preparation and maintenance. If necessary, the latter can be reduced.
    5 KB (697 words) - 17:56, 17 October 2013
  • Publications
    ...se join the [http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/ GMOD group] and contribute GMOD and GMOD-related papers to th ...ywidget src="http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/" width="100%" height="400px" n_papers="50" />
    21 KB (3,298 words) - 22:22, 9 February 2015
  • File:1599-1.pdf
    == The Generic Genome Browser: A Building Block for a Model Organism System Database ==
    (881 KB) - 05:53, 5 January 2011
  • File:Gkg222.pdf
    = ATIDB: ''Aribidopsis thaliana'' insertion database = ...resentation of the insertion distribution and a Blast search function. The database is based on open source components and is available under an open source li
    (314 KB) - 20:34, 30 January 2008
  • File:D480.pdf
    = DroSpeGe: rapid access database for new Drosophila species genomes = ...[[User:Dongilbert|Don Gilbert]] in Nucleic Acids Research, 2007, Vol. 35, Database issue.
    (1.5 MB) - 04:41, 30 January 2008
  • File:Gkl777.pdf
    Nucleic Acids Research, 2007, Vol. 35, Database issue D439–D444 is a new model organism database associated with
    (401 KB) - 16:58, 14 March 2008
  • File:1471-2105-6-45.pdf
    == wFleaBase: the Daphnia genome database ==
    (226 KB) - 18:31, 29 January 2008
  • File:Gkl776.pdf
    = BeetleBase: the model organism database for ''Tribolium castaneum'' = Susan J. Brown. D476–D479 Nucleic Acids Research, 2007, Vol. 35, Database issue.
    (235 KB) - 06:30, 30 January 2008
  • GMOD Components
    The diagram below represents a model organism database (MOD) and its typical components. The ''top ten'' types of functionality ar
    3 KB (425 words) - 19:55, 2 December 2013
  • GBrowse FAQ
    * Connect to your database using the mysql command-line client and run the command: ...ure from end to end. When using [[GFF3]] and a Bio::DB::SeqFeature::Store database (see [[GBrowse Adaptors]]), that is all you have to do. For example, using
    11 KB (1,733 words) - 14:48, 18 May 2013
  • CMap FAQ
    ...t them, you have to write a Perl code in the config file that accesses the database through the sql() object. ...ing $self->sql(). The resulting object has methods that interact with the database. For more information about the methods that can be called execute "perldo
    7 KB (1,071 words) - 13:01, 14 October 2010
  • GMOD FAQ
    ...ally any sort of organism or group of organisms can be the focus of a GMOD database (see [[GMOD_Users|the GMOD users list]] for many examples). It's been sugge ...popular components include the genome browser [[GBrowse]], the relational database [[Chado_-_Getting_Started|Chado]], and the comparative map viewer [[CMap]].
    2 KB (238 words) - 18:17, 24 September 2008
  • XORT
    |type=Database tools, Middleware ...ata output and data debug system. Because it originates from the [[Chado]] database, we denote the corresponding XML "Chado XML."
    1 KB (221 words) - 21:22, 16 October 2013
  • Template:GMODComponents
    '''Database schema''' '''Database tools'''
    1 KB (137 words) - 10:26, 22 July 2016
  • Chado Manual
    ;Database ...oftware is an example of a DBMS. The documentation rarely uses the term ''database'' in this sense.
    17 KB (2,655 words) - 13:43, 14 March 2014

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