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Page title matches

• 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
• 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
• 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
• 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
• 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
• 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
• Chado::AutoDBI Presentation
  * Database connection: use a base class
  6 KB (795 words) - 23:33, 8 October 2012
• June 2006 GMOD Meeting
  GMOD Generic Model Organism Database
  3 KB (426 words) - 19:30, 23 January 2008
• Chado Update via GFF
  There has frequently been interest in updating a [[Chado]] database using a [[GFF]] file, and I've finally gotten around to trying to implement ...ld be able to trigger updates to an existing feature, where CRUDop is your database Create/Replace/Update/Drop operation.
  3 KB (459 words) - 19:23, 30 December 2008
• Questions on Testing
  * load test file into test database * use API to fetch objects from database
  2 KB (361 words) - 17:16, 5 April 2007
• GMOD Project Page
  * database processing of '''high throughput genomics analyses''' with input, output, i
  2 KB (274 words) - 22:07, 29 October 2010
• MOD
  ...ism databases, so that the MOD in GMOD can apply to any organism or genome database projects.
  1 KB (155 words) - 20:21, 6 March 2013
• Face Caucus SGN: Associating Solanaceae loci with phenotype
  ...k ([[:Category:SGN|SGN]], http://www.sgn.cornell.edu/) is a Clade Oriented Database (COD) containing genomic, genetic and taxonomic information for species in ...permissions vary according to the user-type. The framework for editing the database is now being extended for developing an online ontology annotation tool, an
  2 KB (259 words) - 01:15, 19 August 2009
• January 2007 GMOD meeting agenda
  | tentative Chado database discussion/tutorial session
  2 KB (295 words) - 15:02, 13 February 2007
• NIH 2002 Workshop on Model Organism Databases
  ...n broader meaning in recent years, and now signifies any curated community database that is dedicated to a single species or related clade of species. ...se resources include management structures, standard operating procedures, database models and software. Such reuse of existing resources will result in higher
  26 KB (3,975 words) - 05:03, 28 January 2008
• MOD User Interface Caucus
  ...ne, searching with broader concepts, extracting focused answers, and cross-database facilitation. We hope most presenters can touch on these to give the audien [*]] MOD in the generic sense of an organism/genome-related database,<br /> defining the M as you would: Model, Many, or My organism.
  4 KB (599 words) - 01:32, 29 March 2007
• MOD User Interfaces: outline of topics
  ...questions that presenters should address from their<br /> organism/genome database project's perspective: ...ki><br /> -- simple/general, "search by" genome classes<br /> -- advanced (database fields, combining operators, structured queries, ...)<br /> -- hierarchical
  4 KB (644 words) - 01:37, 29 March 2007
• MOD User Interfaces: Sample of several MOD Top Level functions
  ...<br /> Use Ensembl to...<br /> * Run a BLAST search<br /> * Search Ensembl database<br /> * Data mining [[/> * Display your own data<br /> * Export data<br /> '''[http://www.informatics.jax.org/ MGI Mouse Genome Database]'''<br /> ------------------------------------<br /> Sidebar / Gene Detail<
  7 KB (948 words) - 19:51, 23 January 2008
• Java Testing - by Jon Slenk
  ...l is to produce reusable components which would allow a new Model Organism Database (MOD) to be assembled by mixing components from GMOD [4]. Clearly, to meet
  6 KB (855 words) - 23:50, 25 January 2008
• XORT Presentation
  * An [[Glossary#XML|XML]]-database mapping system for data exchange between DB and XML-driven application * Database & Schema
  5 KB (737 words) - 18:54, 9 October 2012
• Load RefSeq Into Chado
  ...ence data in Genbank RefSeq files into the [[Chado_-_Getting_Started|Chado database]]. ...ado organism table]]. If you are unsure if this entry exists log into your database and execute this [[Glossary#SQL|SQL]] command:
  3 KB (531 words) - 21:09, 15 July 2015
• Interface test
  [[MOD User Interface Caucus|Model Organism Database User Interface Caucus]] ...help guide searches (can be implemented with javascript doing asynchronous database lookups)
  18 KB (2,786 words) - 17:34, 31 January 2008
• InterMine Presentation
  * Can adapt performance optimisation to usage of live database
  7 KB (796 words) - 21:16, 9 October 2012
• Presentations
  ===Chado - Generic module organism database schema=== ===Chado - generic model organism database schema===
  1 KB (143 words) - 05:33, 28 January 2008
• GMODWeb
  [[Turnkey]] takes a relational schema of a given database as input and transforms it into a fully-functional and customizable website ....com/2008/9/6/R102 GMODWeb: a web framework for the generic model organism database],
  2 KB (288 words) - 19:30, 4 April 2011
• SynView
  ...may be possible to use this as a template for creating an adaptor for any database.
  3 KB (374 words) - 18:55, 8 October 2012
• Turnkey
  Turnkey is an application that takes the schema of a given database as input and transforms it into a fully-functional and customizable website
  409 B (63 words) - 19:31, 4 April 2011
• February 2003 GMOD Meeting
  Generic Model Organism Database Construction Set
  886 B (116 words) - 17:43, 26 May 2008
• May 2003 GMOD Meeting
  Generic Model Organism Database Construction Set
  790 B (110 words) - 14:02, 6 April 2007
• September 2003 GMOD Meeting
  Generic Model Organism Database Construction Set ** Completed (includes: data associated with the Pub database, Table name adjustments, Field name adjustments, Data Type Adjustments). Th
  28 KB (4,338 words) - 22:06, 29 October 2010
• April 2004 GMOD Meeting
  Generic Model Organism Database Construction Set 1:50 Shannon Schlueter (Arabidopsis thaliana Plant Genome Database, Iowa State University)<br>
  42 KB (6,309 words) - 20:37, 30 November 2010
• October 2004 GMOD Meeting
  Generic Model Organism Database Construction Set
  3 KB (355 words) - 15:30, 6 April 2007
• May 2005 GMOD Meeting
  Generic Model Organism Database Construction Set
  7 KB (915 words) - 17:07, 14 March 2008
• October 2005 GMOD Meeting
  Generic Model Organism Database Construction Set
  5 KB (752 words) - 22:15, 28 July 2010
• January 2007 GMOD Meeting
  GMOD Generic Model Organism Database | Candida Genome Database
  4 KB (601 words) - 22:33, 10 September 2009
• Overview
  ...s ''given the data I have, what database should I use?", "do I even need a database?'', or ''how hard is this going to be?''. ...o appear and many of the first genome databases used GMOD components. GMOD database and software components have developed and expanded with the massive growth
  34 KB (5,526 words) - 19:56, 7 October 2013
• News/GMOD Community Support Specialist
  The Generic Model Organism Database project ([http://gmod.org GMOD]) is a collection of open source software to ...er science or related field; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one
  2 KB (359 words) - 16:42, 22 August 2012
• Chado CV Module
  ==Similarities to the GO Database schema== The schema is similar to the [http://geneontology.org/GO.database.shtml GO database schema], which was also developed by
  37 KB (5,506 words) - 04:35, 18 February 2015
• Chado General Module
  relational database instance to violate them. ...dbxrefs have further information fully fleshed out in other tables in the database, and others
  10 KB (1,650 words) - 04:36, 18 February 2015
• Chado Sequence Module
  sequence of other features in the database. For example, exon sequences are generally not stored, ...nce coordinates. This design decision is crucial for the use of Chado as a database
  64 KB (9,963 words) - 22:17, 18 December 2013
• Chaos XML
  ...ntically very similar, but they are different in how the XML to relational database mapping is performed. Chado XML is also considerably more verbose than Chao ==Differences between Chaos XML and the Chado Relational Database Schema==
  4 KB (647 words) - 21:08, 22 January 2008
• MOD Face Summary
  <big>Model Organism Database User Interface Caucus</big><br /> database (MOD), and arguably has the most direct impact on the
  24 KB (3,905 words) - 16:54, 11 August 2008
• Introduction to Chado
  * At first, a database for FlyBase: incredibly interesting dataset * A database for '''very''' deep curation
  14 KB (2,071 words) - 22:45, 11 January 2019
• Chado Audit Module
  We consider the implementation of auditing policy as a database administration issue and subject to the local requirements of specific database groups. We therefore
  4 KB (679 words) - 04:31, 18 February 2015
• Chado Companalysis Module
  .... For instance, there may be lots of separate analyses done against a cDNA database. ...directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).
  12 KB (1,592 words) - 10:04, 26 May 2010
• Chado Library Module
  ...lse ''<br /><br />Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its cu
  11 KB (1,556 words) - 04:36, 18 February 2015
• Chado Tables
  A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NC ...base instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the na
  121 KB (17,433 words) - 21:13, 2 November 2012
• Chado XML
  ...se these elements ALWAYS correspond to a table or column in the relational database, where the meaning of this element is (hopefully) documented. ...e documentation. Until that time it is best to also consult the relational database documentation.
  10 KB (1,539 words) - 21:16, 9 October 2012
• CMap API
  This document is intended to help you interface with the CMap database using the CMap API. As CMap is written in Perl, that is the language used t ...our program and the CMap database; "Importing Data" and "Querying the CMap Database". Each type of interaction is performed in its own way.
  28 KB (3,928 words) - 23:06, 15 September 2009
• Chado Mage Module
  ...array experiments. It is based on the [http://www.cbil.upenn.edu/RAD2/ RAD database] but has been substantially modified to contain the necessary foreign keys The researcher would load the data into the database in this order:
  31 KB (4,363 words) - 23:33, 8 October 2012
• Chado
  |type=Database schema, Database tools |about=Chado is a relational database schema that underlies many GMOD installations. It is capable of representin
  2 KB (238 words) - 22:55, 2 December 2013
• GMOD Users
  | http://amborella.org || Amborella Genome Database || Amborella || GBrowse, Tripal || 2014 ....ca/ || The Comprehensive Antibiotic Resistance Database || Bioinformatics database of resistance genes, their products and associated phenotypes. || Chado, GB
  31 KB (3,762 words) - 10:43, 12 August 2014
• Modware
  ...[[Chado]]. It allows object-oriented querying and loading of a [[Chado]] database and returns data structures that a programmer can readily use without knowi
  4 KB (543 words) - 23:01, 15 August 2013
• Chado Tables to Wiki
  ...will be something like this (substitute your own user name, password, and database name):
  2 KB (366 words) - 21:27, 10 December 2010
• Mage FAQ
  ...bles#Table:_acquisition|acquisition.uri]] to point to the file outside the database, in the file system.
  2 KB (251 words) - 21:54, 7 January 2009
• Chado Best Practices
  Chado is a generic [[Glossary#Database Schema|schema]], which means anyone writing software to query or write to c ...ontology.org SO], it gives false counts to the number of real genes in the database). Note that this is the current default for [http://flybase.org FlyBase].
  30 KB (4,629 words) - 08:47, 16 April 2013
• MOD Face Talks
  | Chado database discussion/tutorial session
  2 KB (244 words) - 01:35, 29 March 2007
• FlyBase Chado
  ...which runs our current release. Information about how to connect to this database is detailed in [[Public Chado Databases]].
  830 B (116 words) - 14:18, 5 June 2008
• FlyBase Field Mapping Tables
  ! Source for database identity of ! Source for database merge of
  245 KB (40,451 words) - 15:46, 15 November 2017
• Jim's installation notes
  ...ML files. It is also required by the go-db-perl library for loading the GO Database.<br><br>If you do not intend to use either Obo-XML or go-db-perl, then you STEP 3 WILL DELETE ANY DATA IN A DATABASE WITH THE
  16 KB (2,472 words) - 23:54, 25 January 2008
• Zheng's installation notes
  There suppose to be an easy way and a hard way to install Chado database on Fedora: ...your home directory. this must be a user with privilege to create and drop database. this is purely for the purpose of smooth installation.
  7 KB (1,034 words) - 05:56, 28 January 2008
• Chado::AutoDBI
  ...l in [[Modware]]. Chado::AutoDBI is automatically generated from the Chado database schema which makes it very easy to update when changes are made. This code
  1 KB (183 words) - 21:23, 15 August 2013
• Load GFF Into Chado
  ...annotation data in [[GFF3]] format into a [[Chado_-_Getting_Started|Chado database]]. to load data into the database is to use a [[GFF3]] file and the script
  4 KB (642 words) - 15:43, 20 July 2015
• Zheng's notes on wormbase migration
  Preparing data for inserting into the zha database Unable to find srcfeature IV in the database.
  9 KB (1,388 words) - 05:57, 28 January 2008
• GBrowse Windows HOWTO
  install a database management system such as MySQL. ===Install the MySQL database (optional)===
  4 KB (707 words) - 15:07, 27 July 2011
• Load BLAST Into Chado
  ...a [[:Category:BLAST|BLAST]] analysis to a [[Chado_-_Getting_Started|Chado database]]. =Have an existing Chado genome database =
  5 KB (781 words) - 23:34, 8 October 2012
• Learn XMLXORT
  I started with class Paper. acedb classes are mixture of c structure and database description. pointers are to other class object. class paper points to clas ==chado database ddl==
  8 KB (1,174 words) - 20:52, 23 January 2008
• Load GenBank into Chado
  In summary, to load ''Saccharomyces'' chromosome X to Chado database 'mychado', from a Unix command-line, do:
  4 KB (729 words) - 21:49, 30 December 2008
• BioPerl
  ...est script, problems with CGI script used for sequence retrieval at public database, and so on. Remember that there are over 800 modules in Bioperl and the tes
  7 KB (1,121 words) - 17:28, 3 October 2012
• Html.tmpl.main
  <title>Index for <!-- TMPL_VAR ESCAPE="HTML" name="database" --></title> <h1><a name="index">Index of database - <!-- TMPL_VAR ESCAPE="HTML" name="database" --></a></h1>
  9 KB (1,365 words) - 21:28, 10 December 2010
• Html.tmpl.module
  <title>Index for <!-- TMPL_VAR ESCAPE="HTML" name="database" --></title> <h1><a name="index">Index of database - <!-- TMPL_VAR ESCAPE="HTML" name="database" --></a></h1>
  9 KB (1,369 words) - 21:29, 10 December 2010
• Sample Chado SQL
  view basic genome data from a Chado database. The simplest way to test contents of a Chado database is with the
  12 KB (1,695 words) - 05:20, 28 January 2008
• GBrowse MacOSX HOWTO
  [[MySQL]] database. You can install these prerequisites using the Fink ...://localhost/gbrowse and click the link for the example yeast chromosome 1 database.
  11 KB (1,849 words) - 22:55, 15 August 2013
• GBrowse Install HOWTO
  ...of annotated features), you can skip installing MySQL and use an in-memory database instead. ...POSTGRESQL.pod|ORACLE_AND_POSTGRESQL.pod}}. To run on top of a [[BioSQL]] database, see {{SF_SVN|Generic-Genome-Browser/trunk/docs/pod/BIOSQL_ADAPTER_HOWTO.po
  35 KB (5,565 words) - 22:39, 8 August 2012
• GBrowse Ubuntu HOWTO
  * If you plan to use a MySQL database, you may need to install mysql ;Install MySQL database (optional, but recommended)
  8 KB (799 words) - 20:37, 8 August 2018
• GBrowse RPM HOWTO
  You can now visit the documentation and try out the example Yeast database by visiting http://localhost/gbrowse
  3 KB (350 words) - 11:32, 28 October 2008
• Databases and GMOD
  .... It also covers how databases are implemented and used in GMOD, and what database management system choices are available. == Database Terminology ==
  9 KB (1,355 words) - 22:31, 25 March 2014
• Chado Tutorial 2010
  ...esign and architecture, and then goes into detail about how to use a Chado database. === Database Terminology ===
  54 KB (8,190 words) - 23:34, 8 October 2012
• Chado Tutorial 2012
  ...esign and architecture, and then goes into detail about how to use a Chado database. ==== Database Terminology ====
  50 KB (7,599 words) - 16:26, 2 September 2018
• Galaxy
  ...y self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be s
  6 KB (748 words) - 19:43, 13 December 2018
• GBrowse Popup Balloons
  <p>In the config file for the database you wish to modify, set ``balloon
  20 KB (2,839 words) - 20:06, 8 October 2012
• GBrowse Annotation File Management Proposal
  ...ew [http://klab.ist.unomaha.edu/CLAB/index.php/Request_Tracker_%28RT%29 RT database], which will drive my workload upon my return.
  2 KB (258 words) - 23:04, 25 January 2008
• June 2007 Progress Report
  ...ing was well attended by approximately 60 people representing more than 25 database projects and organizations. ...re, comprising and updated Chado schema and tools for interacting with the database. The scheduled release is timed to correspond to the August Hackathon at D
  26 KB (4,096 words) - 01:17, 19 August 2009
• GBrowse Gentoo HOWTO
  Create the initial mysql database This will also inform you to set the root password of mysql database. If you have more than one version of mysql installed on your machine, plea
  5 KB (743 words) - 21:00, 23 September 2009
• CMAE
  ...s for the maize sequencing project. Using the [[CMap]] comparative mapping database, CMAE allows sequence assemblies to be
  2 KB (272 words) - 20:47, 15 September 2009
• Integrating CMAE
  CMAE uses CMap configuration files and reads data from the CMap database. These can be on the local machine or on a web server that the program can Since, CMAE uses the CMap database, the data will have to be loaded. The "Importing Data" section discusses wh
  6 KB (1,072 words) - 18:53, 23 January 2008
• Hackathon 2007 info
  ...ing a server that could be picked up and used for a nascent model organism database for use with community annotation. *A good example config that works with the dicty example database.
  11 KB (1,683 words) - 19:54, 9 June 2010
• Standard URL
  ...to simplify the retrieval of common datasets, the Generic Model Organisms Database (GMOD) community has recommended a series of standard URLs, or a common dow
  4 KB (607 words) - 22:44, 15 September 2009
• TableEdit
  ...rate annotations made in [http://mediawiki.org MediaWiki] with a [[Chado]] database for better comprehensive genome data management. MediaWiki is a widely use ...this gene-oriented [[:Category:Community Annotation|community annotation]] database. TableEdit provides a somewhat more friendly way to edit simple tables in
  8 KB (1,315 words) - 18:12, 9 October 2012
• November 2007 GMOD Meeting
  * [[User:Stevef|Steve Fisher]] - [[GBrowse]]: [[SynView]] and the Generic database adaptor Apollo can talk directly to a database or it can use XML files instead. FlyBase, VectorBase, BeeBase, and BovineB
  28 KB (4,093 words) - 05:54, 5 January 2011
• DBD::mysql on the Mac
  ...n shell is difficult, as tests will frequently require a connection to the database via a non-root account (that is, your real account that has permission to r
  1 KB (158 words) - 18:54, 23 January 2008
• Apollo PureJDBCTransactionWriter HOWTO
  ...without having to install any stored procedures or triggers in the target database. ...ly supports '''two''' methods for saving changes made in Apollo to a chado database via JDBC. These two methods are implemented by the following (Java) class
  13 KB (1,912 words) - 21:58, 15 September 2009
• Hackathon wikidb
  Wiki-text file (script 1). This is then loaded into Mediawiki database with gene page templates (script 2). Community folks edit the genes thru T
  4 KB (660 words) - 01:23, 10 December 2009
• Genome grid
  The customers for this project are small to medium genome database projects, and individual bioscience research labs. We expect some familiar ...w.sdsc.edu/srb/index.php/Main_Page Storage Resource Broker]: file-oriented database with metadata, already part of TeraGrid standard services. Has some workfl
  7 KB (1,032 words) - 22:42, 15 September 2009
• NBrowse
  ...sly. Although created for applications in biology, N-Browse uses a generic database schema that can be adapted to network representations in any knowledge doma ...on 2 currently supports MySQL databases and is integrated with the modMine database web service [link [http://intermine.modencode.org/query/ modMine: search,
  6 KB (920 words) - 16:57, 30 September 2010
• GBrowse UCSC Plugin Install HOWTO
  * Temporary disk space for MySQL dump files used to load the database tables. * MySQL server disk space requirements for database tables.
  19 KB (3,009 words) - 19:45, 15 January 2014
• News/Pathway Tools Workshop 2010
  This workshop is oriented around SRI's [[Pathway Tools]] software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Datab ...ent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
  2 KB (223 words) - 23:09, 9 October 2012
• News/GBrowse 2.13 Release
  * Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to
  2 KB (346 words) - 23:10, 9 October 2012
• News/Hiring @ Dolan DNALC
  ...as [[Chado]]), browsers, and annotation tools. Expertise in Java, SQL and database schema, and Unix/Linux are essential. Experience developing web user inter
  1 KB (157 words) - 23:08, 9 October 2012
• News/InterMine/BioMart Job @ FlyBase
  ...data management systems. The developer will be responsible for the web and database aspects of these technologies, which will be hosted at the Indiana Universi
  1 KB (198 words) - 23:29, 3 October 2012
• News/BioMart Openings @ OICR
  ...//www.recruitingsite.com/csbsites/oicr/JobDescription.asp?JobNumber=633985 Database programmer/Technical Analyst]
  1 KB (136 words) - 23:10, 9 October 2012
• News/InterMine Java / DB Developer
  ...he server side InterMine code, in particular taking responsibility for the database access and performance of the system.
  1 KB (188 words) - 23:12, 9 October 2012
• News/InterMine 0.94.1 Release
  * a new full text search over the entire database * sequences stored as CLOBs in the database
  1 KB (167 words) - 23:12, 9 October 2012
• News/Pathway Tools 2010 Deadline!
  ...is workshop is oriented around SRI's [[Pathway Tools]] software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Datab
  766 B (107 words) - 23:09, 9 October 2012
• News/Opening at Cancer Research UK
  ...es/jobs.php?id=2042|180px|right|Bioinformatician and Pancreatic Expression Database]] ...ng] working on the [http://www.pancreasexpression.org/ Pancreas Expression Database]:
  1 KB (201 words) - 23:13, 9 October 2012
• 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
• News/GMOD Spring Training: Apply Now
  * [[Chado]] - biological database schema
  2 KB (268 words) - 23:45, 3 October 2012
• News/Sr DB Programmer @ FlyBase
  The FlyBase genome database project group at Harvard University is [https://sjobs.brassring.com/1033/as
  447 B (62 words) - 23:24, 9 October 2012
• News/Opening @ Cancer Research UK
  ...es/jobs.php?id=2122|180px|right|Bioinformatician and Pancreatic Expression Database]] ...ng] working on the [http://www.pancreasexpression.org/ Pancreas Expression Database]:
  1 KB (208 words) - 23:13, 9 October 2012
• News/GMOD Evo Hackathon Report
  :Worked on establishing a common database backend and {{GlossaryLink|JSON|JSON}}-based API for comparative genomics d ...of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory.
  4 KB (504 words) - 23:11, 9 October 2012
• XORT Dumper HOWTO
  ...le feature table dump that extracts all gene features from the YFGdb Chado database. Then feature location information is added followed by associated CDS fea ==Chado Database Setup==
  9 KB (1,311 words) - 21:16, 9 October 2012
• Public Chado Databases
  =Public [[Chado]] [[Genome]] Database Releases= These projects provide [[Chado]] database dumps that you can copy and learn from.
  1 KB (203 words) - 14:56, 25 June 2019
• Community Annotation System
  ...and copies name, description and synonym data from Chado to the MediaWiki database and then redirects to the newly created page.
  2 KB (263 words) - 18:57, 29 February 2008
• GMOD Online Training 2014/WebApollo Tutorial
  * Relational Database Management System [officially supported: PostgreSQL] * User database helper scripts
  77 KB (11,812 words) - 00:39, 21 May 2014
• FlyBase Comparative Genomics Data
  ...he relevant genomes need to be implemented independently in the same Chado database instance. The Chado standards of genomic sequences and annotation are detai ...genes being object and subject (arbitrarily set and consistent across the database) and the feature_relationship type being 'putative_ortholog_of'. The detail
  5 KB (769 words) - 20:01, 12 April 2008
• PostgreSQL Performance Tips
  == Database initialization == One step that can be taken to optimize your PostgreSQL database is to properly initialize it with [http://www.postgresql.org/docs/8.2/inter
  5 KB (774 words) - 17:57, 5 February 2014
• Materialized views
  database administrator desides that the downsides of the MV scheme is The name of the DB profile to use for database connectivity. These
  5 KB (791 words) - 05:23, 28 January 2008
• Computing Requirements
  ...op can easily be set up to run a server that can run a genome browser or a database. If you are anticipating large amounts of traffic, you will want to invest ...different software to support them. Some require Perl or Java support, a database management system, a web server (such as Apache), or any number of other th
  11 KB (1,778 words) - 05:03, 20 November 2013
• PostgreSQL
  ...See [[Databases and GMOD]] for other choices, and for an introduction to database terms. This page is in an introduction to Postgres for GMOD users. ...ms]]. Postgres's primary role in GMOD is to be the DBMS for the [[Chado]] database schema. Chado was developed with Postgres as its target DBMS and Chado off
  2 KB (356 words) - 00:52, 18 November 2010
• Glossary
  === Database === ...ase Schema|database schema]] in a particular [[#Database Management System|database management system]] to regular files that have a defined format.
  14 KB (2,081 words) - 02:50, 14 March 2014
• MySQL
  ...lity in both the open source and commercial worlds. An excellent ''first'' database for those who have no prior experience with relational databases. MySQL is a very good database for some things: it is very fast as a read only database, and so is quite good for driving data displays like [[GBrowse]]. My exper
  4 KB (699 words) - 19:28, 4 September 2013
• GBrowse syn
  ...fig=Configuration of GBrowse_syn is much the same as for [[GBrowse]], with database and display options controlled by a configuration file. GBrowse_syn uses a * GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
  6 KB (800 words) - 21:39, 15 October 2013
• Comparative Genomics
  ...GMOD tools are used to create an example comparative genome model organism database.
  3 KB (395 words) - 22:26, 2 November 2009
• C briggsae.syn
  This is the species database for ''C. briggsae''. This is one of the three species currently represente description = C. briggsae Database
  1 KB (167 words) - 17:16, 14 January 2009
• IGS Data Representation
  ...vention, which is db.feature_type.N.M, where 'db' is an abbreviation for a database or project (usually an organism), feature_type corresponds to a value in cv The actual GO:NNNNNNN value is a database reference (dbxref_id returned in last query):
  17 KB (2,330 words) - 23:34, 8 October 2012
• MAKER
  ...s accessible as part of the GFF3 output and can be loaded into a [[Chado]] database, [[JBrowse]], [[GBrowse]], [[WebApollo]] or [[Apollo]]. *MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. <ref name=PMID:22192
  9 KB (1,211 words) - 21:53, 2 February 2014
• GMODTools TestCase
  ...test case for GMOD, loading a GenBank format genome (chromosome) to Chado database, then dumping it out, including GenBank submission format with GenBank outp [[Category:Database Tools]]
  2 KB (338 words) - 17:03, 20 June 2008
• Sybil Chado Comparative Genomics Data
  ...based on bi-directional best BLASTP hit. Top BLASTP hits are stored in the database via 'match' and 'match_part' features independent of the clustering analysi
  2 KB (302 words) - 20:04, 12 April 2008
• GBrowse 1 Configuration HOWTO
  ...WTO|installing GBrowse]] is to get the genomic data you want to see into a database that GBrowse can read. ...that database.<br/><code>mysql -uroot -prootpassword<br/>mysql&gt; create database antgenome;<br/>mysql&gt; GRANT SELECT ON antgenome to 'www-data'@'localhos
  79 KB (12,563 words) - 16:45, 15 August 2011
• GBrowse Configuration/DAS
  description = Das Example Database (dicty) ...f the remote DAS server, and a -dsn pointing to the name of the annotation database.
  2 KB (385 words) - 20:05, 8 October 2012
• GBrowse Configuration/URL schema
  Specify the URL of a remote annotation source to load into the database. You should also supply an "id" argument as well, as described earlier, in
  8 KB (1,385 words) - 15:45, 6 June 2011
• GBrowse Configuration/BioMOBY
  ...ct aims to design and deploy platforms that enable and simplify biological database interoperability. ...ce in the MOBY namespace ontology (which is derived from the Gene Ontology Database Cross-Reference Abbreviations list). Currently, this requires editing of th
  9 KB (1,441 words) - 10:45, 9 July 2010
• GBrowse Configuration/Balloons
  In the config file for the database you wish to modify, set "balloon tips" to a true value:
  7 KB (1,138 words) - 13:06, 29 September 2010
• GBrowse Configuration/Authentication
  ...rictions such as possession of a crypto card. Restriction can apply to the database as a whole, or to particular annotation tracks. You can also make a datasou #Authentication via a built-in user accounts database (GBrowse versions 2.16 and higher).
  21 KB (3,308 words) - 17:08, 4 December 2012
• GBrowse Configuration/Feature frequency histograms
  Assuming that your database is named "dicty", you have a feature named SNP, and you wish to generate a ...bin option) and to count the occurrences of the SNP feature throughout the database. In addition, the -merge option says to merge all types of SNPs into a sing
  5 KB (734 words) - 10:34, 9 July 2010
• GBrowse syn Configuration
  The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files and ...ains information about the alignment (joining) database and the individual database for of the species in the browser. For details of each setting, see below.
  6 KB (815 words) - 19:51, 18 October 2011
• InterMine
  |type=Database tools
  4 KB (623 words) - 16:36, 6 November 2014
• WebApollo2
  ...tion process: edit within a temporary workspace, then publish to a curated database *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation
  3 KB (445 words) - 23:04, 4 January 2016
• GBrowse Adaptors
  ...veloped for use with [[GFF3]]; about 2X slower than Bio::DB::GFF to load a database | A [[Glossary#Database Management System|relational database server]]: [[MySQL]], [[PostgreSQL]], Oracle, or BerkeleyDB
  3 KB (443 words) - 16:22, 7 August 2012
• GBrowse Plugins
  ...reateBlastDB.pm]] : Creates a Blast-formatted database from a Bio::DB::GFF database
  2 KB (320 words) - 17:00, 4 December 2012
• RubberBandSelection
  DATABASE = nr
  7 KB (827 words) - 23:05, 8 October 2012
• 2008 GMOD Summer School
  ...[Glossary#Schema|schema]]: Chado's modules and extensibility, how IDs and database cross references are handled, the central role of [[:Category:Ontologies|on
  11 KB (1,550 words) - 22:11, 16 April 2014
• GBrowse karyotype ideogram.pl
  ...and data for the human genome and also for other species is in the ensembl database. my $database = shift;
  3 KB (421 words) - 20:06, 8 October 2012
• ParameciumDB
  ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a model organism database for the unicellular eukaryote ''Paramecium tetraurelia''. ParameciumDB con ...mecium tetraurelia genome sequence with genetic data], in the January 2007 Database Issue of [http://nar.oxfordjournals.org/ ''Nucleic Acids Research''].
  10 KB (1,362 words) - 08:29, 6 April 2013
• PrimerDesigner.pm
  ...u must ensure that all dependencies (described above) are that the GBrowse database has DNA sequence.
  8 KB (1,187 words) - 11:19, 22 August 2013
• Glyphs and Glyph Options
  ...ll be replaced with the name of the feature as specified in the underlying database. database = scaffolds...
  23 KB (2,202 words) - 22:35, 27 March 2015
• August 2009 GMOD Meeting
  ...set of modules for [http://drupal.org Drupal] to interact with a [[Chado]] database. ...al very different data sources: [[:Category:FlyBase|FlyBase]] (a [[Chado]] database), [http://www.fruitfly.org/ BDGP], [http://www.fly-ted.org/ FlyTED], [http:
  59 KB (8,741 words) - 19:37, 4 September 2013
• BioDIG/tool data
  | full_name = Biological Database of Images and Genomes ...= Community Annotation, Database schema, Database (Chado) web front ends, Database tools, Genome Visualization and Editing, Tool Integration, Image annotation
  2 KB (278 words) - 19:05, 10 September 2013
• CMap Version 2 Design
  * Map and feature types originally existed in the database but were moved into configuration files in past versions. They will be res
  3 KB (455 words) - 20:22, 12 May 2009
• Annotation
  ...pular [http://mediawiki.org/ MediaWiki] extension for updating tabular and database data. Work is currently under way to build a wiki front end to [[Chado]] u
  2 KB (245 words) - 22:08, 29 October 2010
• GMOD Utility Scripts
  ...the query sequence was for a similarity analysis. It prints the extracted database and accession information to standard out, and another script, [[GMOD_Utili ...ata, it is best to have both the query and subject features already in the database. When a fasta file of a collection of sequences are blasted against a refe
  3 KB (485 words) - 17:55, 24 March 2008
• July 2008 GMOD Meeting
  |Rearchitecting [[Apollo]] and the need for a database independent Biological API layer Our experience is that the database is usually the bottleneck with existing GBrowse installations.
  28 KB (4,301 words) - 18:53, 8 October 2012
• Apollo-Chado Integration at BovineBase: Bugs and Suggestions
  In preparation for the Bovine Annotation effort, we set up a [[Chado]] database containing annotation evidence, allow annotators to connect via [[Apollo]] .... This can result in a very long start up if the network is down or if the database in question is unavailable for some reason. Is there a way we could delay t
  5 KB (788 words) - 15:04, 25 March 2008
• Chado Documentation Reorganization
  ...ry:Chado|Chado related documentation]] in this web site. [[Chado]] is the database schema of GMOD and it has quite a bit of documentation in this web site. H | Explains chado from a database practitioners point of view.
  7 KB (1,015 words) - 22:30, 29 December 2010
• GBrowse/Uploading Wiggle Tracks
  #Load the GFF3 file into your gbrowse database using bp_seqfeature_load.pl or bp_load_gff.pl.
  15 KB (2,251 words) - 21:22, 25 April 2013
• Debian Stable Installation Notes
  ...tions below, otherwise some tests fail. I added user 'chado' for the chado database installation. a quick look at the database user phpPgAdmin: the database looks fine.
  8 KB (1,270 words) - 06:14, 25 September 2009
• Common Gene Page
  ...nyms; Map locations; Sequences and Reagents; Gene ontology; Similar Genes; Database cross-refs and external links; Alleles and Transcripts; Proteins, Structur ==Daphnia genome database use case==
  7 KB (1,051 words) - 19:24, 4 September 2013
• News/FlyBase Converts to Chado
  .../FlyBase|finished its reimplementation]] using [[Chado]], the modular GMOD database schema which [http://flybase.org/ FlyBase] originated and continues to deve in collaboration with GMOD and several GMOD-affiliated database
  889 B (114 words) - 20:50, 24 January 2011
• News/GMODTools 1.1 Released
  ...${golden_path}, ${seq_ontology}. This step, on now by default, checks that database contains configured values. If failed, db is inspected for real values.
  826 B (116 words) - 20:52, 24 January 2011
• News/Modware Feedback Wanted
  ...de a familiar and intuitive interface for objects stored inside of a Chado database.
  1,012 B (151 words) - 20:54, 24 January 2011
• News/GMOD at Arthropod Genomics
  * ''Chado: A Database Schema for Integrating Biological Data'' - [[User:Scott|Scott Cain]] and [[
  1 KB (189 words) - 20:57, 24 January 2011
• News/Ant Genomics Bioinformatician
  ...s, as well as sharing the results with molecular myrmecologists via a GMOD database.
  868 B (122 words) - 23:06, 9 October 2012
• News/Ten Recent Web Site Changes
  # '''[[Databases and GMOD]]''' - An overview of database concepts and how databases are used in GMOD.
  2 KB (351 words) - 20:59, 24 January 2011
• News/GMOD 1.0 Released
  * Tools for creating a new database.
  2 KB (272 words) - 21:07, 24 January 2011
• News/Chado Doc Reorganization
  Chado is the database schema of GMOD and it has quite a bit of documentation in this web site. H
  819 B (116 words) - 21:09, 24 January 2011
• 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/CMap 1.01 Released
  No updates to the database or config files are needed.
  1 KB (173 words) - 21:16, 24 January 2011
• News/cas-utils-0.1 Released
  to the database is blocked for outside users, future releases of these
  2 KB (374 words) - 21:20, 24 January 2011
• News/InterMine Workshop
  ...mming in either Java or PERL is essential. Some experience with relational database would also be very useful.
  1 KB (235 words) - 23:08, 9 October 2012
• News/Job Openings at Georgetown
  ...lop new query interfaces; develop scripts for automated data retrieval and database loading; develop computational pipelines for updating homology, functional Duties include system administration, bioinformatics database maintenance, system backup management, problem diagnosis, and creation of s
  1 KB (159 words) - 21:36, 24 January 2011
• News/Opening at Dow AgroSciences
  # Install the open source software components for the [[Chado]] database, data loaders, and genome browser. ...internal databases, such as Variety, markerDB, QTL locate, and microarray database.
  1 KB (172 words) - 23:08, 9 October 2012
• News/2009 GMOD Summer Schools
  * [[Chado]] - a modular and extensible database schema
  2 KB (301 words) - 23:41, 3 October 2012
• News/Pathway Tools Workshop, August
  ...national]. This two-part workshop covers [[Pathway Tools]] and the BioCyc Database Collection. ...hoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database.
  2 KB (297 words) - 23:09, 9 October 2012
• News/GMOD Workshops at SMBE, AGS
  | '''[http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database Tools for Evolutionary Genomics: An introduction to GMOD software for manag ...of the most widely used GMOD software components, including the [[Chado]] database, the [[GBrowse]] genome browser, the [[CMap]] comparative map browser, and
  2 KB (337 words) - 23:47, 3 October 2012
• News/Insect Pest Workshop, 16-17 Nov
  ...tional community that will form a functional network for insect genome and database development
  2 KB (326 words) - 23:43, 3 October 2012
• News/Aug 2009 GMOD Meeting Report
  ...g#Linked Data for GMOD Databases|RDF implementation]] of data from a Chado database.
  2 KB (301 words) - 19:37, 4 September 2013
• News/Bioinformatics Position at SpBase
  The [http://www.spbase.org Sea Urchin Model Organism database (SpBase)] has an opening for a Bioinformatician. From the [http://www2.rec ...ss="indent">The computation group supporting the Sea Urchin Model Organism database, SpBase, is seeking a highly motivated individual to take responsibility fo
  1 KB (203 words) - 23:07, 9 October 2012
• News/Chado in RDF: OpenFlyData
  .../ SPARQL-based] interface to each. Source databases include the [[Chado]] database from [[:Category:FlyBase|FlyBase]], [http://www.fruitfly.org/ BDGP], [http:
  1 KB (217 words) - 23:07, 9 October 2012
• News/GMOD Tutorials! GMOD Training!
  | '''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'''
  4 KB (542 words) - 23:11, 9 October 2012
• News/Opening at SGD
  ...astgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast.
  1 KB (185 words) - 23:09, 9 October 2012
• News/Openings at Syngenta
  ...tems for genome annotation and related information. Experience overseeing database systems is required and experience with Oracle and [[PostgreSQL]] is desira
  2 KB (266 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
• News/GMOD at PAG 2010
  * [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI] (including [[BioMart]]), Sunday
  2 KB (358 words) - 23:08, 9 October 2012
• News/CMap3D
  ...alisation tool for comparative genetic maps that runs on top of a [[CMap]] database. [[CMap]], a [[GMOD Components|GMOD component]], is a common tool for the
  1 KB (199 words) - 23:09, 9 October 2012
• News/Tripal v0.2 Released
  ...rovides a PHP-based [http://drupal.org Drupal] front-end for the [[Chado]] database schema. It his highly customizable and is extendable by anyone with Drupal
  2 KB (249 words) - 23:14, 9 October 2012
• News/GBrowse 2.0
  * Different [[GBrowse 2.0 HOWTO#Database Definitions|database backends]] can be associated with each track, making backend management muc * A custom [[GBrowse 2.0 HOWTO#Configuring the Uploaded Track Database|track upload and management system]] gives users much greater control over
  2 KB (359 words) - 23:25, 9 October 2012
• News/GMOD Summer School - Americas
  * [[Chado]] - a modular and extensible database schema
  2 KB (245 words) - 23:44, 3 October 2012
• News/GMOD Logo Program, Spring 2010
  ...and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced d
  1 KB (161 words) - 23:47, 3 October 2012
• News/Openings @ SGD
  ...astgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast. These positions will be involved in enhancing databases and dat
  1 KB (161 words) - 23:09, 9 October 2012
• News/Sr. DB Programmer @ FlyBase
  ...in Cambridge, Mass. The position consists of roles in two model organism database projects, [http://vectorbase.org VectorBase] and [http://flybase.org FlyBas
  704 B (96 words) - 23:25, 9 October 2012
• News/MaizeGDB: Choosing GBrowse
  ...|link=http://database.oxfordjournals.org/cgi/content/abstract/baq007|right|Database Paper]] ...aizeGDB] team has been published in ''[http://database.oxfordjournals.org/ Database].'' To prepare for the availability of a reference genome, MaizeGDB survey
  2 KB (297 words) - 23:13, 9 October 2012
• News/gmod (Chado) 1.1 Released
  ...hema]], [[Chado]], and a variety of tools for loading and working with the database. The release can be downloaded from the [https://sourceforge.net/projects/
  2 KB (316 words) - 23:00, 24 January 2011
• News/Load Chado into BioMart
  ...d "[[BioMart#How to Load a Chado Database into BioMart|How to load a Chado database into BioMart]]". This step by step document details what how to configure
  911 B (145 words) - 23:27, 3 October 2012
• News/MAKER 2.0, AGS Workshop
  * Easy single-command-line dump of MAKER output to a [[Chado]] database and to [[JBrowse]]...
  1 KB (222 words) - 23:13, 9 October 2012
• JBrowse
  ...uences|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database) ...Guide#Feature Tracks|Feature Tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
  8 KB (1,157 words) - 19:18, 15 April 2016
• Chado Django HOWTO
  ...ngoproject.com/ Django] (Python based) framework for accessing a [[Chado]] database. The Django framework can be used to create web interfaces and command line ...nice choice for data disclosure projects like a website on top of a Chado database. There are other such frameworks like [http://turbogears.org/ Turbogears] (
  16 KB (2,412 words) - 18:11, 9 October 2012
• Bio GMOD GenericGenePage
  ...t all of the methods that are listed under ABSTRACT CLASSES below for your database. These abstract methods are responsible for providing Bio::GMOD::GenericGe .... Bio::GMOD::GenericGenePage::Chado is a simple implementation for a Chado database populated with ''S. cerevisiae'' data obtained from [[:category:SGD|SGD]] a
  6 KB (755 words) - 01:16, 19 August 2009
• GBrowse 2.0 HOWTO
  *'''Multiple database support:''' You can now declare multiple databases for each data source and ...locking in the [[MySQL]] database. It is handy if you already have a MySQL database up and running. The full format of this value is:
  101 KB (15,507 words) - 04:44, 9 January 2014
• Chado SO Views
  [[Category:Database Tools]]
  2 KB (305 words) - 23:34, 8 October 2012
• January 2009 GMOD Meeting
  |Metadata Input and Submission Tool and GIS linked metagenomic database ...df|PDF]], [[#Metadata Input and Submission Tool and GIS linked metagenomic database|Summary]]
  50 KB (7,612 words) - 18:53, 8 October 2012
• PAG 2009
  ! [http://www.intl-pag.org/17/17-ebi.html Database Resources at the EBI Workshop] ...ew Of The Marine Genomics Project, A Web-Based Genomic And Transcriptional Database], Stephen P Ficklin, ''et al.''
  10 KB (1,390 words) - 18:16, 2 October 2012
• Migrating from GBrowse 1.X to 2.X
  ...ed: between [GENERAL] and the track stanzas) declare one or more [''name'':database] stanzas. For example: [volvox_genbank:database]
  6 KB (983 words) - 06:14, 26 August 2010
• Grouping GBrowse Features
  ...NA clone. However many feature databases, including the older Bio::DB::GFF database backends, do not allow for arbitrary hierarchical grouping. To work around ...ay a small portion of it. The '''group_on''' option allows you to create a database in which each quantitative data point is a separate feature, but at run tim
  3 KB (463 words) - 06:09, 25 September 2009
• Running a GBrowse2 render farm
  ...sed database backends, such as the BerkeleyDB and in-memory databases, the database files must be replicated among the hosts, or else mounted on a common files ...assume that your data source has three underlying databases: a "scaffold" database that contains basic chromosome information and the DNA sequence, for use by
  16 KB (2,473 words) - 12:08, 12 October 2011
• 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
• GMOD RPC API
  ...tag called data_version that contains the database release number. If the database does not use release numbers then the date for when the entire data class w from the NCBI's Taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy/) or the genus and/or species name (e
  25 KB (3,166 words) - 23:02, 15 August 2013
• Subtrack HOWTO
  :You also only need one line of GFF in the database for each wiggle_box track/chromosome. ...ored features (> a few thousand/chromosome) as GFF, they will bog down the database and probably pile up in a hopeless jumble in the browser.
  5 KB (815 words) - 21:19, 30 December 2008
• GBrowse 2.0 Prerequisites
  ...quired for basic operation, you will probably want at least one relational database backend. One or both of: #fast lightweight database for managing user accounts
  8 KB (1,147 words) - 21:20, 15 January 2017
• Gmod load cvterms
  *-H hostname for database [required if -p isn't used] *-D database name [required if -p isn't used]
  3 KB (441 words) - 16:54, 20 September 2012
• 2008 GMOD Community Survey
  * What organism(s) or types of organisms is your web site / database about? * Please indicate what types of biological data your database/website is about or that you are interested in now or in the near future, a
  14 KB (1,816 words) - 21:33, 5 October 2009
• TableEdit Loader
  ...fect of making things run much faster because the wiki isn't accessing the database to do writes. # get the box_uid from the database using the page_uid
  10 KB (1,567 words) - 18:12, 9 October 2012
• GFF
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,336 words) - 19:49, 10 September 2012
• GFF3 2011 tutorial
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,387 words) - 22:13, 11 February 2014
• GFF2
  ===Loading the GFF file into the database=== ...QL database on the local host named "dicty", you can load it into an empty database using <tt>bp_bulk_load_gff.pl</tt> like this:
  17 KB (2,719 words) - 13:27, 21 April 2017
• GBrowse img
  <tr> <td>dbid</td> <td>&nbsp;</td> <td>database ID for disambiguating names</td></tr> <tr> <td>source</td> <td>&nbsp;</td> <td>database name</td></tr>
  13 KB (2,066 words) - 22:02, 12 December 2012
• GBrowse Persistent Variables
  ...The currently-logged-in user's ID, corresponding to the main GBrowse user database.
  7 KB (988 words) - 20:06, 8 October 2012
• GBrowse Backends
  This page describes the [[GBrowse]] database back ends. It is incomplete. ...ation_Files | datasource-specific configuration file]] for GBrowse with a [database] stanza like this one:
  10 KB (1,607 words) - 17:16, 23 April 2013
• Gbrowse clean.pl
  ...region. Caching for longer periods increases the time between updating the database and tracks displaying those changes.
  3 KB (513 words) - 14:13, 2 November 2009
• Display CMap Markers in GBrowse
  # database definitions # Database for genome annotations.
  2 KB (319 words) - 20:05, 8 October 2012
• Store an unigene in Chado HOWTO
  = How to store an unigene in a Chado database = Let's store an unigene in the database:
  5 KB (833 words) - 04:42, 22 May 2009
• Tripal
  |type=Database (Chado) web front ends, Database tools, Development Platform (has API) ...ts, and so on--to provide users with an intuitive, flexible interface to a database.
  3 KB (420 words) - 16:33, 29 June 2016
• Load a custom ontology in Chado
  functioning of the database. The commands to load an ontology are: The name of the file should match the database that will go in the db table (although I'm not sure about that). I've named
  3 KB (544 words) - 11:01, 10 June 2009
• Next Generation Sequencing
  ...he ''[http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database tools for evolutionary genomics workshop] at [http://ccg.biology.uiowa.edu/
  3 KB (450 words) - 00:52, 18 November 2010
• Bio::Chado::Schema
  ...:Chado::Schema is a standard set of Perl modules that should work with any database supported by DBIx::Class. So far, it has been used successfully with Chado
  2 KB (281 words) - 18:15, 14 April 2011
• GMOD Evo Hackathon
  ...addressed critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that limited its utility for evolutionary research. Specific :Worked on establishing a common database backend and {{GlossaryLink|JSON|JSON}}-based API for comparative genomics d
  17 KB (2,407 words) - 13:22, 13 November 2015
• BA2009
  ...220%; line-height: 120%">'''[http://www.ausbiotech2009.com.au/bia/workshop Database Tools for Biologists]'''</div> ; Presentation - Database Tools for Biologists ([ftp://ftp.gmod.org/pub/gmod/Meetings/2009/BA/BA2009G
  4 KB (456 words) - 18:52, 8 October 2012
• JBrowse Tutorial 2010
  ...se from the chado session; if you didn't follow along exactly, re-load the database like so: === Data from a database ===
  9 KB (1,327 words) - 22:46, 3 October 2012
• MAKER Tutorial 2013
  ...including supporting evidence) can easily be loaded into a GMOD compatible database for annotation distribution. repeat database, Repeat Masker edition, for RepeatMasker to work.
  80 KB (12,961 words) - 23:47, 29 July 2013
• Artemis-Chado Integration Tutorial
  ...alks you through how to use the Artemis annotation editor with a [[Chado]] database. ...s] and [http://www.sanger.ac.uk/Software/ACT/ ACT] to use with a [[Chado]] database. The first two sections relate to installing [[Postgres]] and Chado, this i
  17 KB (2,626 words) - 23:33, 8 October 2012
• Artemis
  [http://www.ncbi.nlm.nih.gov:80/Genbank/GenbankOverview.html GENBANK] database entries or sequence in [[Glossary#FASTA|FASTA]] or raw format. Extra seque
  1 KB (161 words) - 18:52, 8 October 2012
• MAKER PAG 2010 Workshop
  ...imal and its outputs can be directly loaded into a [[Chado|GMOD compatible database]]. They can also be viewed in the [[GBrowse]] genome viewer, and manually u
  3 KB (468 words) - 18:54, 8 October 2012
• PAG 2010
  ! [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI: Ensembl And Ensembl Genomes - Access To Genome-Scale ...ntl-pag.org/18/abstracts/C01_PAGXVIII_914.html The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation], Takeshi Itoh
  13 KB (1,711 words) - 18:17, 2 October 2012
• News/SGD and ENCODE DCC Jobs
  ...multiple positions open in my group, either with the Saccharomyces Genome Database or the ENCODE Data Coordination Center. The positions include Senior Biocu
  476 B (67 words) - 00:09, 31 March 2013
• Five year plan
  ** SAGE database
  2 KB (262 words) - 20:47, 22 May 2013
• January 2010 GMOD Meeting
  | Bovine Genome Database; BeeBase; NasoniaBase; Hymenoptera Genome Database | BeeBase/Bovine Genome Database/Hymenoptera Genome Database
  26 KB (3,722 words) - 19:17, 4 September 2013
• News/JBrowse 1.8.0 released
  ...For example, if a user is viewing a genome in JBrowse 1.8 at her favorite database website, and she has a 20GB BAM file on her computer for that same genome,
  2 KB (395 words) - 14:44, 1 February 2013
• Databases: Tables, Rows, and Columns
  Introduces some basic relational database terminology. A database table is just that, a table with rows and columns. Different tables contai
  890 B (121 words) - 23:54, 29 September 2009
• Databases: Primary, Foreign and Alternate Keys
  In a database table, certain columns are ''keys''. Keys help identify rows / records and
  1 KB (180 words) - 05:19, 30 September 2009
• 2009 GMOD Community Survey
  ...elements/features, choices to make them permanently or privately part of a database * Native [[Chado]] database connection instead of adapter type chado connection (although the latter ma
  26 KB (3,948 words) - 17:18, 6 October 2009
• GBrowse NGS Tutorial
  ...and then how to add NGS data to it, in the form of a Bio::DB::Sam/SAMtools database. database = annotations
  38 KB (5,742 words) - 18:11, 9 October 2012
• Chado Natural Diversity Module Working Group
  ...with the goal of using for [http://www.rosaceae.org/ GDR], a plant genome database. Sook found that a number of things weren't clear, and her input led to a Ontology/Insecticide Resistance database developer
  6 KB (767 words) - 15:04, 4 February 2012
• GMOD Logo Program
  ...hat, etc.) with the students on a regular basis to first explain what your database/web site/organism is about and what makes it unique, and then to provide fe ...that you can understand their requirements, and what makes their web site/database/organism unique, interesting and useful. This may mean understanding some
  4 KB (668 words) - 01:33, 15 September 2012
• GBrowse syn Scripts
  :Use this script to load the GBrowse_syn alignment database from a multiple sequence alignment file. A variety of formats are supporte |Username for the mysql database
  6 KB (931 words) - 22:39, 21 February 2013
• MWAS Tutorial
  ...and analyse their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline [[MAKER]], and *Output can be easily loaded into a GMOD compatible database for annotation distribution (including evidence associations).
  34 KB (5,308 words) - 22:03, 3 October 2012
• GBrowse syn PAG tutorial
  ==Create a MySQL database== *GBrowse_syn uses a "joining" database to store all of the alignment data
  19 KB (2,507 words) - 18:53, 8 October 2012
• IFALT
  Any data that should get saved to the ''row_metadata'' table in the database should be put here. Avoid tabs and newlines at all costs.
  3 KB (547 words) - 02:27, 15 January 2010
• GBrowse2 REST API
  volvox Volvox Tutorial Database
  6 KB (982 words) - 15:29, 27 August 2012
• 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
• Load ncbi taxonomy
  * <tt>-H hostname</tt> for database [required if <tt>-g</tt> isn't used] * <tt>-D database name</t> [required if <tt>-g</tt> isn't used]
  2 KB (309 words) - 23:29, 29 December 2010
• CMap3D
  ...arative Genomics|comparative]] genetic maps that runs on top of a [[CMap]] database. [[CMap]], a [[GMOD Components|GMOD component]], is a common tool for the
  2 KB (226 words) - 22:53, 23 August 2010
• ABRF2010 Workshop
  ...nt servers, giving GBrowse the ability to work with multiple rendering and database servers to make it faster than it would otherwise be with just one server.
  17 KB (2,763 words) - 18:52, 8 October 2012
• Spring 2010 Logo Program
  | [http://www.pombase.org/ PomBase] - model organism database for ''S. pombe'' | [http://redfly.ccr.buffalo.edu REDfly] - Regulatory Element Database for ''Drosophila''
  8 KB (1,133 words) - 20:56, 24 August 2012
• GMOD Evo Hackathon Proposal
  ...on to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. ...by many large and small, collaborative and single-investigator biological database projects for the dissemination of experimental results and curated knowledg
  12 KB (1,744 words) - 18:53, 8 October 2012
• Audit tracking by mods
  ...f outline of supported use cases. More details available [[#Bovine Genome Database|here]]. || someone@bovinegenome.org ===Bovine Genome Database===
  1 KB (185 words) - 16:43, 5 April 2010
• GMOD Evo Hackathon Proposal Supplemental Information
  GMOD's Chado database schema already includes strong support for storing trees and graphs. This
  9 KB (1,301 words) - 20:44, 7 July 2010
• MolGenIS
  ...s, including [http://www.xgap.org XGAP - eXtensible Genotype And Phenotype database], animaldb, MAGE-TAB db, Pheno-OM and so on. And the fact that each is gene ...ac boxes with Tomcat or Glassfish as web server and MySQL or PostgreSQL as database server. Developers wanting to use the generator to create their own MOLGENI
  2 KB (351 words) - 01:36, 3 October 2012
• ISMB 2010
  ...0/posterlist.php?cat=E E30: Choosing a Genome Browser for a Model Organism Database: Surveying the Maize Community], Taner Sen
  7 KB (1,006 words) - 01:23, 3 October 2012
• Creating and Managing Subtracks with GBrowse2
  in the underlying database. Below each [stanza] heading are a series of tag=value pairs. The database = Peaks
  16 KB (2,414 words) - 19:42, 17 April 2012
• September 2010 GMOD Meeting
  * Can also provide GUI to database tables * Potential to give wiki access to a Chado database
  100 KB (14,725 words) - 17:31, 30 November 2012
• GBrowse DAS HOWTO
  ...at http://localhost/gbrowse2. We will use the ''C. elegans core'' tutorial database as the basis for creating a DAS server. ...s" request is working. This request returns all the feature types that the database knows about. Using a web browser fetch the URL http://localhost/cgi-bin/gb2
  6 KB (947 words) - 20:15, 8 July 2010
• Chado Natural Diversity Module
  ...module. Custom scripts will need to be written to insert your data in the database.
  30 KB (4,604 words) - 16:35, 30 January 2013
• GBrowse 2.0 Install HOWTO
  ...that describes the install configurations you chose, points to an example database to run, and gives pointers to documentation, tutorials and other useful inf
  14 KB (2,116 words) - 20:00, 22 February 2012
• GBrowse 2.0 Install HOWTO/Advanced
  ==Configuring the User Account Database== ...g the required Perl modules; (2) creating and configuring the user account database; and (3) configuring GBrowse to send outgoing email.
  23 KB (3,672 words) - 14:44, 10 July 2013
• GBrowse Run Process
  ...ATABASE }/, where {HTTP_HOST} is the server on which GBrowse resides and { DATABASE } is the name of the current genomic data set being viewed) it runs the fol
  948 B (142 words) - 19:11, 22 July 2010
• GMOD Promotion
  : Generic Model Organism Database (GMOD), http://gmod.org ....g., [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database tools for evolutionary genomics] at [http://ccg.biology.uiowa.edu/smbe/inde
  7 KB (1,003 words) - 18:14, 8 January 2013
• A Green Paper: Informatics for 'Small' Organisms
  ...databases, e.g., FlyBase, Mouse Genome Database, The Saccharomyces Genome Database, WormBase, The Arabidopsis Information Resource. Talk to those with recent ...source rather than proprietary software and tools and (b) making your own database and any tools associated with it open source. The GMOD site will increasing
  10 KB (1,515 words) - 21:18, 8 October 2013
• GMOD Evo Hackathon Open Call
  ...wse_syn]], a comparative genomics viewer; [[Chado]], a generic and modular database schema; [[CMap]], a comparative map viewer; as well as many other component ...on to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research.
  6 KB (906 words) - 18:53, 8 October 2012
• Chado Full Text Search
  Before full text searching can be used, the database must be prepared. Full text searching requires that a view that is present [main:database]
  3 KB (525 words) - 23:33, 8 October 2012
• Chado GBrowse Summary View
  ...g this script, optionally with a <tt>--dbprofile</tt> flag to indicate the database to work on, will create the table if it doesn't exist, as well as a few sto
  2 KB (260 words) - 12:55, 4 May 2011
• Biosoftware bench
  ...do-compatible: It is GMOD compatible and uses the robust, normalized Chado database. As Chado is sequence feature-driven we created sequence-less table set whi ...an upload a multi-FASTA file to be used as the query or even the reference database: there is no need to restrict the user to the administrator's datasets. The
  3 KB (539 words) - 01:55, 16 February 2011
• Gmod-dbsf
  * provides functions to communicate with Chado and Drupal database schemas The [http://insectacentral.org InsectaCentral] database is coded using the GMOD-DBSF engine and the custom genes4all module for vis
  4 KB (562 words) - 22:27, 29 December 2010
• PAG 2011
  | [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_888.html GDR (Genome Database For Rosaceae): Building Resources For Translational Research In ''Rosaceae' .../19/abstracts/W07_PAGXIX_047.html Development Of cBARBEL, A Catfish Genome Database], Jianguo Lu
  11 KB (1,443 words) - 19:19, 4 September 2013
• Est2assembly
  ...raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly
  1 KB (193 words) - 22:51, 23 August 2010
• Drupal
  ...ghtforward for nascent bioinformaticians to learn. It supports a number of database engines, including [[MySQL]], Oracle and the GMOD supported [[PostgreSQL]].
  2 KB (280 words) - 00:52, 18 November 2010
• Genes4all
  ...ttp://insectacentral.org InsectaCentral] database, an insect transcriptome database with 1,578,321 gene models from 12,800,018 ESTs. ...nly administrators can edit it but web-users can retrieve data. The Drupal database offers a bidirectional interface with the users.
  2 KB (375 words) - 22:43, 29 December 2010
• Satellite Meetings - GMOD Europe 2010
  ...lic research institute: Max-Delbrueck-Centrum Berlin (MDC), Researcher and database developer
  4 KB (563 words) - 18:55, 8 October 2012
• Post Reference Genome Tools
  ...where a single species reference helps and where it may not, which a clade database can help with.
  12 KB (1,865 words) - 18:54, 8 October 2012
• InsectaCentral
  ...aim to be species neutral and when released anyone can make a ''Central'' database. ...esearchers working on species without a huge Genome Consortium and rolling database funding to make use of their own and the community's data in a streamlined,
  4 KB (588 words) - 01:37, 3 October 2012
• Community Annotation - September 2010 Satellite
  [http://zfin.org ZFIN], the zebrafish model organism database (MOD), was launched in the mid 1990s with the stated goal of enabling commu Several resources, including [[ParameciumDB]] and the Pea Aphid database, have offered training in genome annotation using [[Apollo]]. Apollo is a
  20 KB (3,079 words) - 18:52, 8 October 2012
• WebApollo
  ...tion process: edit within a temporary workspace, then publish to a curated database *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation
  4 KB (536 words) - 20:37, 6 April 2015
• Chado on Rails
  ...ado on Rails is under active development, and is used in the Bovine Genome Database, BeeBase and NasoniaBase. Chado on Rails is free as in beer/speech. cd cor # edit config/database.yml if necessary
  7 KB (1,041 words) - 22:20, 28 March 2014
• December 2 2010
  ...46wZI6EVdGFYa0V6WXhQaXRDMmhoQm9GRVBVMEE&hl=en&authkey=CJn73pAB UCSC genome database: track counts by type per genome assembly]
  3 KB (421 words) - 17:52, 16 December 2010
• Chado Schema Documentation HOWTO
  ...section describes how to regenerate the Table Templates from a live Chado database as part of creating a new release of Chado. '''If you are not creating a C
  13 KB (1,916 words) - 20:28, 29 January 2013
• GMOD Americas 2011
  '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa
  10 KB (1,435 words) - 00:41, 15 September 2012
• March 2011 GMOD Meeting
  '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa
  18 KB (2,659 words) - 19:19, 4 September 2013
• Satellite Meetings - GMOD Americas 2011
  '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa
  4 KB (576 words) - 18:55, 8 October 2012
• Chado Phenotype Module at FlyBase
  '''These notes reflect the state of the FlyBase Chado database during the first two weeks on November 2010.''' Rank is used for some sort of code that is not stored in the database?
  13 KB (1,711 words) - 23:33, 8 October 2012
• GMOD in the Sequencing Center
  * [[User:Chemmeri|Chris Hemmerich]] - Biological Database Unit Leader, and Project Lead for [[ISGA]] at the [http://www.cgb.indiana.e
  3 KB (423 words) - 18:53, 8 October 2012
• Web-apollo-meeting-2010-12-16
  ...46wZI6EVdGFYa0V6WXhQaXRDMmhoQm9GRVBVMEE&hl=en&authkey=CJn73pAB UCSC genome database: track counts by type per genome assembly]
  1 KB (221 words) - 23:02, 16 December 2010
• GBrowse User Uploads
  [[GBrowse]] allows users to supplement the database with their own data as Custom Tracks in a variety of file formats including ...itional tools in a basic mode, or use a more advanced mode that requires a database but allows more flexible sharing. It has been tested using [http://www.sqli
  12 KB (2,045 words) - 22:35, 29 December 2010
• GBrowse Program Structure
  ...ted by clicking a button. In addition to the backend, there is an optional database to hold named users & sessions, uploaded files, and sharing information. ...t events require data from the database, or need to perform actions on the database. For the most part, they will send AJAX requests to the current script with
  10 KB (1,464 words) - 18:13, 24 December 2010
• GMODviews
  ...ubMed, ''etc.'' User-selected data can then be stored in the local Drupal database, to thus create a custom-knowledge-base for further data integration and an
  1 KB (194 words) - 05:38, 5 January 2011
• Arthropod Genomics 2011
  ...nerating annotations, visualizing the genome, saving into a web-accessible database, and analyzing, refining and integrating the data will be presented. The wo | ''ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods''
  3 KB (379 words) - 18:52, 8 October 2012
• Gbrowse/authentication plugins/PamAuthenticate
  ...rn, provides connections to the traditional '''/etc/group''' file, the NIS database, or LDAP databases, depending on how it is configured. For example, to fetc
  4 KB (730 words) - 14:18, 4 May 2011
• News/BioMart 0.6 Released
  [[BioMart]] is a query oriented database management system for biological data.
  351 B (49 words) - 20:47, 24 January 2011
• GSoC
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration, and algorithms. Students are also encouraged to propose their
  5 KB (719 words) - 16:07, 12 February 2024
• GSOC Project Ideas 2015
  ...cts include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. ...tion:'' Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualizatio
  16 KB (2,455 words) - 09:10, 23 February 2015
• GSOC Groups
  ...amene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. Links: [http://www.gmod.org Website], [http://blog.gmod.org GMOD Blog] ...atform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programmin
  4 KB (561 words) - 18:02, 19 February 2016
• News/GMOD Helpdesk Position Open
  The Generic Model Organism Database project (GMOD, http://gmod.org) is a collection of open source software too ...database management systems; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one
  3 KB (378 words) - 00:01, 5 March 2011
• October 2011 GMOD Meeting
  ...er Center in New York. Gary developed the Biomolecular Interaction Network Database (BIND) during his Ph.D. in the lab of Christopher Hogue in the Department o | The Mycoplasma Genome Database: marrying microscopy and genomics
  13 KB (1,892 words) - 18:54, 8 October 2012
• GSoC/IDEA 10
  Personally I'd like one database of 'risk factors' including genetic > 3)Does the database have to be seeded initially with information or
  8 KB (1,297 words) - 21:55, 27 February 2014
• GSoC/IDEA 9
  Well... a big organization putting a version on a certain database that you can begin to research. Firstly, the Chado database system
  12 KB (1,905 words) - 20:08, 5 April 2011
• Bugs
  ...a better impression than a project with no bug database, or a nearly empty database.''
  2 KB (246 words) - 14:03, 27 March 2011
• SettingUpReactome
  ...oot access to the computer onto which you are planning to install Reactome database and website. The instructions are split into two sections, non-Reactome and ...database being used. Reactome Perl API uses DBI to interact with Reactome database.
  24 KB (3,874 words) - 14:55, 28 March 2011
• SupplementaryInformation
  ==Database schema== To understand Reactome's database schema, look at: [http://www.reactome.org/static_wordpress/data-model/ Data
  1 KB (198 words) - 10:50, 12 April 2011
• Chado Natural Diversity Module/natdiv schema changes call
  ...t in a designated well defined table. This is also better for querying the database. With cvalue_id you need to ask does my prop has a cvalue? what is the mean
  11 KB (1,777 words) - 15:05, 4 February 2012
• A Brief Guide to Databases
  A database provides infrastructure for storing, managing, and retrieving information. Databases store information in '''tables'''. A database usually has multiple tables containing data on different types of things.
  4 KB (606 words) - 21:18, 7 September 2012
• WebApollo/tool data
  ...tion process: edit within a temporary workspace, then publish to a curated database *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation
  5 KB (636 words) - 20:34, 15 October 2013
• Apollo Tutorial 2011
  We'll see an option for which data we want to load. We'll choose '''Chado database''' as our data source. Since we still don't have annotations on our data, Make sure that <code>Chado database</code> is selected at the data source (should already be).
  34 KB (5,242 words) - 00:21, 14 February 2013
• Chado Natural Diversity Module/natdiv call notes
  ...af size in an adult plat' - supporting post-composed terms in a normalized database is important in normalized database design we realize we have a many-many relationship, adding a linking table
  4 KB (690 words) - 01:02, 1 June 2011
• Tripal Tutorial (pre version 0.3b)
  * Audit - for database audits |Genome Database for Vaccinium
  80 KB (12,830 words) - 20:41, 2 October 2012
• Arthropod Genomics 2011/Genome Project 101 Workshop
  |Database server ...d after PostgreSQL is configured, so it is installed now. First, create a database called "test":
  15 KB (2,338 words) - 18:52, 8 October 2012
• News/Tripal v0.3b Released
  * Support for Feature/Stock Properties, Synonyms, Database References and Relationships
  1 KB (198 words) - 23:14, 9 October 2012
• GBrowse syn Tutorial new
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  21 KB (2,890 words) - 22:24, 3 October 2012
• GBrowse syn AGS Tutorial
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  23 KB (3,325 words) - 20:52, 3 October 2012
• Tripal Tutorial (v0.3.1b)
  * Audit - for database audits |Genome Database for Vaccinium
  92 KB (14,708 words) - 23:27, 5 September 2012
• WebApollo Tutorial 2012
  * Relational Database Management System [officially supported: PostgreSQL] * User database helper scripts
  43 KB (6,301 words) - 20:52, 27 August 2013
• GFF3
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,350 words) - 20:25, 12 July 2016
• JBrowse Configuration Guide
  ...ce" will depend on how you are using JBrowse. For a model organism genome database, each reference sequence would typically represent a chromosome or a [http: ...ces from a gff file or a database. In order to read fasta sequences from a database, a config file must be used.
  185 KB (26,536 words) - 02:48, 30 September 2020
• Tripal Tutorial v1.1
  * Audit - for database audits |Genome Database for Vaccinium
  131 KB (21,091 words) - 21:53, 2 January 2014
• Tripal Tutorial (v0.3.1b VM)
  * Database: tripal_demo ...virtual machine comes pre-installed with the Apache webserver, PostgreSQL database server, Drupal, Tripal and Chado. It is not necessary to perform these tas
  2 KB (375 words) - 23:28, 5 September 2012
• April 2012 GMOD Meeting
  including dbVar, a database of genomic structural variation, the NCBI Map Viewer, the Clone database, and the NCBI Remap service.
  10 KB (1,319 words) - 18:52, 8 October 2012
• Tripal Developer's Handbook
  ...PI provides an interface for module developers to interact with the Chado database as well as the other Tripal core functions such as jobs management, materia ...anism content type) from the [http://www.citrusgenomedb.org/ Citrus Genome Database].
  70 KB (10,442 words) - 16:45, 14 October 2013
• News/dictyBase is Hiring
  chado database as well as integration of various gmod tools (gbrowse, intermine, apollo, b
  558 B (77 words) - 23:09, 9 October 2012
• Cloud
  ...ped with a suite of preconfigured GMOD components, including a '''Chado''' database, '''GBrowse2''', '''JBrowse''', '''Tripal''', and '''Apollo or WebApollo'''
  3 KB (505 words) - 18:10, 16 December 2013
• News/CARD
  ==New Database Announcement== ...http://arpcard.mcmaster.ca/ arpcard.mcmaster.ca]). CARD is a bioinformatic database of antibiotic resistance genes, their products and associated phenotypes th
  723 B (101 words) - 15:27, 15 September 2011
• Updating Chado
  which determines the version of the current Chado database and is also '''NOTE:''' Since this is a new tool, I strongly suggest you back up your database before trying to upgrade via this method! You have been warned! :-)
  1 KB (248 words) - 23:48, 22 July 2013
• Tripal Tutorial (v1.0)
  * Audit - for database audits |Genome Database for Vaccinium
  99 KB (16,007 words) - 17:43, 12 July 2013
• News/Intern @ Aniseed: work on Chado
  ...ww.aniseed.cnrs.fr/ Develop modules for a '''Chado'''-based Model Organism Database dedicated to the developmental biology in tunicates].'' ...iological data and their interactions with data already represented in the database, modification/extension to the schema, use/adaptation of ontologies, and th
  3 KB (423 words) - 23:12, 9 October 2012
• 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
• GBrowse Volvox SAM Tutorial
  Start with a [[Media:Volvox.sam.gz|SAM file]] and save in the GBrowse database directory for the volvox tutorial. Also make sure that the volvox fasta fi ==Add a database stanza to the volvox config==
  5 KB (853 words) - 00:19, 23 October 2012
• News/ZFIN Project Manager Wanted
  ...ts and biologists to design, develop and maintain a dynamic bioinformatics database infrastructure that includes [[GBrowse]] and [[InterMine]] deployments. Th * Familiarity with relational database systems and Java programming environment.
  2 KB (300 words) - 23:48, 9 July 2012
• Tripal Tutorial 2010
  * [[PostgreSQL]] database management system * phpPgAdmin (for easy database administration)
  58 KB (8,529 words) - 18:12, 9 October 2012
• Mimosa
  ...lly deploy into a standalone SQLite database, or an already-existing Chado database.
  1 KB (190 words) - 20:20, 14 November 2011
• JBrowse Tutorial 2013
  ...se from the chado session; if you didn't follow along exactly, re-load the database like so: Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  14 KB (1,948 words) - 20:48, 27 August 2013
• News/Textpresso Software Developer
  * Knowledge about database management systems and similar software such as PostgreSQL or MySQL.
  1 KB (146 words) - 23:09, 9 October 2012
• GSoC 2011
  ...mation resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. Wor ...atform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programmin
  20 KB (2,895 words) - 23:51, 25 July 2012
• 2013 GMOD Summer School
  ..., [[JBrowse]], [[MAKER]], [[Tripal]], [[WebApollo]], and the [[Chado|Chado database schema]]. The sessions are taught by developers of the tools, so they can g
  5 KB (638 words) - 21:52, 22 January 2014
• News/ZFIN Software Dev Manager
  ...biologists] to design, develop, and maintain the biological model organism database for zebrafish. ZFIN supports [[GBrowse]] and [[InterMine]] deployments.
  1 KB (191 words) - 23:32, 9 July 2012
• News/Friedberg Lab Hiring
  ...ic database web site; implement data management tools including relational database management applications for efficient storage and retrieval of genomic data
  2 KB (273 words) - 23:26, 20 July 2012
• News/Xenbase Hiring Two Developers
  ...ill work on interfaces that allow our 1,000 daily users to interrogate our database on ''Xenopus'' genomics, cell and developmental biology. [http://www.xenbase.org Xenbase], the ''Xenopus'' model organism database is looking for an experienced <strike>skiier/rider</strike> senior software
  2 KB (343 words) - 23:22, 9 October 2012
• Using the vista plot Glyph
  [chip:database] database = chip
  320 KB (22,410 words) - 19:48, 17 April 2012
• News/Software Developer - Phytozome
  ...web user interface design concepts and implementation, data modeling, and database schema design, as well as extensive familiarity with standard genomic seque * Create and maintain database-backed web applications for the display and querying of genomic data.
  6 KB (822 words) - 19:16, 16 May 2012
• GMOD Cloud Tutorial
  |Files for the PostgreSQL database
  8 KB (1,350 words) - 01:26, 13 September 2012
• 2012 GMOD Summer School
  ...several widely used GMOD components in the context of a organism or clade database. The course is taught by members of the projects' development teams. Appl
  4 KB (584 words) - 18:09, 8 January 2014
• News/GMOD Summer School 2012: Apply Now
  * [[Chado]] - biological database schema
  1 KB (212 words) - 02:17, 15 June 2012
• WebApollo v2013-05-16 Installation
  ...e using Tomcat 7 as our servlet container and PostgreSQL as our relational database management system. We'll use sample data from the Pythium ultimum genome, * Relational Database Management System [officially supported: PostgreSQL]
  55 KB (8,533 words) - 19:02, 24 August 2013
• News/Pathway Tools 17.0 Released
  ...site, downloadable data files, and downloadable [[Pathway Tools]] software/database bundle. Version 17.0 of BioCyc contains 2,920 Pathway/Genome Databases.
  3 KB (483 words) - 13:37, 15 April 2013
• GMOD at Biocuration 2013
  *Andrew Oberlin, Miami University. Biological Database of Images and Genomes: tools for community annotations linking image and ge
  563 B (68 words) - 15:52, 15 April 2013
• CMap/tool data
  * A relational database, e.g. [http://www.mysql.com MySQL (4.0+)], Sybase Adaptive Server Enterpris ...ttp://racerx00.tamu.edu/cgi-bin/cmap/viewer BeeBase]: The Honey Bee genome database
  6 KB (814 words) - 18:31, 10 September 2013
• SOBA 2011 Tutorial
  files. The data can optionally first be loaded into a database.
  15 KB (1,843 words) - 23:03, 20 August 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
• Pathway Tools/tool data
  ...Community Annotation, Comparative Genome Visualization , Database schema, Database tools, Gene Expression Visualization, Genome Visualization & Editing, Molec
  5 KB (661 words) - 18:32, 10 September 2013
• GFF Tutorial 2012
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,352 words) - 21:54, 11 September 2012
• GBrowse 1.x
  ...n in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.
  1 KB (212 words) - 15:01, 24 August 2012
• GBrowse2 VMs
  ===Expanding Database Storage on the GBrowse EC2 VM=== ...name, such as ''hg19''. The second is the description to attach to the new database. This description will appear in the GBrowse datasources menu. When this sc
  18 KB (2,956 words) - 20:37, 13 February 2013
• Galaxy Tutorial 2010
  ...to the database schema. On first load it runs all migrations to ensure the database is in a known state, which may take a little time. Once the database is initialized, the normal startup process proceeds, loading tool configura
  32 KB (4,846 words) - 21:16, 9 October 2012
• GBrowse Tutorial 2012
  And we'll load it into an existing Chado database like this: ...rof chado #use the database profile called chado (which is the name of the database)
  8 KB (1,132 words) - 20:52, 27 August 2013
• MAKER Tutorial 2010
  *Output can be easily loaded into a GMOD compatible database for annotation distribution (including evidence associations). ...tify transposable element and viral proteins from the RepeatRunner protein database. Because protein sequence diverges at a slower rate than nucleotide sequen
  62 KB (9,933 words) - 22:41, 14 February 2013
• Galaxy Tutorial 2012 Extras
  ...lt of moving to Postgres. On startup, Galaxy will again have created a new database from scratch.
  16 KB (2,444 words) - 21:16, 9 October 2012
• Galaxy Tutorial 2012
  === Use a more robust database === ...d for tool development. However, for any multi-user scenario a more robust database will be needed for Galaxy to be reliable. We '''highly''' recommend [[Postg
  18 KB (2,654 words) - 22:18, 11 September 2012
• MAKER Tutorial 2012
  ...including supporting evidence) can easily be loaded into a GMOD compatible database for annotation distribution. repeat database, Repeat Masker edition, for RepeatMasker to work.
  80 KB (12,923 words) - 20:52, 27 August 2013
• Canto
  ...paper or in bulk. The JSON data from Canto can be loaded into a relational database using the Chado schema (as at PomBase) or alternative schemas.
  3 KB (358 words) - 23:11, 18 April 2014
• GBrowse syn Tutorial 2012
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  19 KB (2,685 words) - 17:23, 22 July 2013
• SOBA Tutorial 2012
  files. The data can optionally first be loaded into a database.
  15 KB (1,830 words) - 20:52, 27 August 2013
• Load Balancing GBrowse2 with AWS Spot Instances
  ...c_aws_script.pl script should be run on the master each time you add a new database to an existing data source, or if you add a whole new data source. What it ...created mysql or postgres databases, you must also give the paths to their database file directories, as shown in the example.
  21 KB (3,083 words) - 20:20, 10 January 2013
• WebApollo Installation
  ...e using Tomcat 7 as our servlet container and PostgreSQL as our relational database management system. We'll use sample data from the Pythium ultimum genome, * Relational Database Management System [officially supported: PostgreSQL]
  88 KB (13,531 words) - 19:06, 20 March 2017
• News/GSC 15 Meeting
  ...for standards developers, genome and metagenome researchers and biological database developers to discuss their research, initiate collaborations, join GSC wor
  1 KB (218 words) - 19:55, 14 November 2012
• News/GMOD is tweeting
  ...ch if you want us to retweet your GMOD-related publication, check out your database, answer a question, or share your news.
  712 B (116 words) - 21:25, 16 November 2012
• News/BioCyc 16.5 Released
  ...major new version that includes updates to the [[Pathway Tools]] software/database bundle, as well as significant data updates and website changes.
  3 KB (407 words) - 18:45, 19 November 2012
• Apollo/tool data
  ...ack to the underlying database. Apollo can run off [[GFF3]] or a [[Chado]] database, and it can also integrate with remote services, such as BLAST and Primer B
  4 KB (640 words) - 18:44, 10 September 2013
• JBrowse/tool data
  ...uences|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database) ...Guide#Feature Tracks|Feature Tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
  8 KB (1,143 words) - 08:09, 28 January 2014
• GBrowse/tool data
  | 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.
  8 KB (1,065 words) - 18:35, 10 September 2013
• Tripal/tool data
  ...ts, and so on--to provide users with an intuitive, flexible interface to a database. * Allows rapid development of an online genomic database.
  5 KB (734 words) - 18:39, 10 September 2013
• MAKER/tool data
  ...s accessible as part of the GFF3 output and can be loaded into a [[Chado]] database, [[GBrowse]], or [[Apollo]]. * MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. <ref name=PMID:22192
  7 KB (963 words) - 18:29, 10 September 2013
• GBrowse syn/tool data
  ...g = Configuration of GBrowse_syn is much the same as for [[GBrowse]], with database and display options controlled by a configuration file. GBrowse_syn uses a * GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
  5 KB (748 words) - 18:33, 10 September 2013
• Galaxy/tool data
  ...y self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be s
  6 KB (839 words) - 00:12, 3 October 2013
• LDAPAuthenticate.pm
  LDAP database. Users can log in using their Unix login names and
  3 KB (415 words) - 17:05, 4 December 2012
• XORT/tool data
  | type = Database tools, Middleware ...ata output and data debug system. Because it originates from the [[Chado]] database, we denote the corresponding XML "Chado XML."
  4 KB (518 words) - 18:48, 10 September 2013
• News/Chado 1.23 released
  which should update the schema (after backing up your database, of
  1 KB (208 words) - 23:13, 14 December 2012
• GO Graphic Viewer/tool data
  ...he {{CPAN|GO::TermFinder}} Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational r
  2 KB (293 words) - 18:38, 10 September 2013
• PAG 2013
  ...essiondetails.cfm?ScheduledSessionID=18A8C6C2 CottonGen: An Integrated Web-Database for Cotton Genomics, Genetics and Breeding Research] || Posters ...sessions/sessiondetails.cfm?ScheduledSessionID=18ABCFC0 Hymenoptera Genome Database: Resources for Annotating and Comparing Hymenopteran Insect Genomes] || Pos
  12 KB (1,491 words) - 16:10, 15 April 2013
• Apollo Tutorial 2010
  We'll see an option for which data we want to load. We'll choose '''Chado database''' as our data source. Since we still don't have annotations on our data, Make sure that <code>Chado database</code> is selected at the data source (should already be).
  34 KB (5,278 words) - 22:36, 12 February 2013
• GBrowse syn Tutorial 2010
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  18 KB (2,519 words) - 11:43, 9 January 2013
• Galaxy Tutorial 2013
  === Use a more robust database === ...d for tool development. However, for any multi-user scenario a more robust database will be needed for Galaxy to be reliable. We '''highly''' recommend [[Postg
  23 KB (3,328 words) - 23:33, 10 June 2014
• Jan 2014 GMOD Meeting
  "A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes" | '''Keynote:''' A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes
  5 KB (666 words) - 07:49, 8 May 2014
• News/Tripal v1.0 Released
  ...0 development version you should update your version of Tripal and perform database updates (e.g. 'drush updatedb').
  1 KB (170 words) - 00:41, 9 March 2013
• JBrowseDev/Using Configuration Files With JBrowse
  #REDIRECT [[BrowseDev/Using a Database With JBrowse]]
  53 B (7 words) - 14:23, 29 March 2013
• Chado Tutorial 2011
  ...esign and architecture, and then goes into detail about how to use a Chado database. === Database Terminology ===
  53 KB (8,083 words) - 20:52, 27 August 2013
• GBrowse Tutorial 2011
  *Get rid of <tt>database = main</tt> [annotation:database]
  7 KB (932 words) - 22:50, 13 February 2013
• GBrowse syn Tutorial 2011
  ==Setting up the Alignment Database== ...e sequence alignments between the two rice species. It will be in a MySQL database.
  20 KB (2,712 words) - 22:39, 13 February 2013
• Galaxy Tutorial 2011
  ...to the database schema. On first load it runs all migrations to ensure the database is in a known state, which may take a little time. Once the database is initialized, the normal startup process proceeds, loading tool configura
  38 KB (5,631 words) - 23:56, 13 February 2013
• VMware 2011 Spring Training
  | MySQL database; used as a backend to [[GBrowse]]. Root password is same as for the system | Postgres database management system. Used by [[Chado]]
  12 KB (1,876 words) - 00:08, 14 February 2013
• GFF3 Tutorial 2011
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,345 words) - 00:23, 14 February 2013
• InterMine Tutorial 2011
  ...uses of integrated genomics data fast and flexible. It provides a back end database solution, a front end web-application, and a fully capable webservice API t ...d to integrate data from different datasets (even your own data!) into one database.
  43 KB (6,258 words) - 17:56, 14 February 2013
• JBrowse Tutorial 2011
  ...se from the chado session; if you didn't follow along exactly, re-load the database like so: === Data from a database ===
  9 KB (1,328 words) - 17:58, 14 February 2013
• MAKER Tutorial 2011
  *Output can be easily loaded into a GMOD compatible database for annotation distribution (including evidence associations). ...tify transposable element and viral proteins from the RepeatRunner protein database. Because protein sequence diverges at a slower rate than nucleotide sequen
  69 KB (11,026 words) - 20:52, 27 August 2013
• SOBA Tutorial 2011
  files. The data can optionally first be loaded into a database.
  15 KB (1,835 words) - 03:36, 24 June 2014
• Tripal Tutorial 2011
  * Audit - for database audits |Genome Database for Vaccinium
  80 KB (12,788 words) - 22:37, 14 February 2013
• Chado Tutorial 2013
  ...esign and architecture, and then goes into detail about how to use a Chado database. ==== Database Terminology ====
  50 KB (7,599 words) - 12:36, 20 May 2014
• GMOD Online Training 2014/Chado Tutorial
  ...esign and architecture, and then goes into detail about how to use a Chado database. ==== Database Terminology ====
  50 KB (7,595 words) - 12:53, 20 May 2014
• WebApollo Tutorial 2013
  ==Database Setup== * Create a database for managing the WebApollo users
  12 KB (1,839 words) - 00:11, 20 February 2014
• GBrowse syn Tutorial 2013
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  20 KB (2,714 words) - 10:44, 22 May 2014
• News/Support Your Friendly Local GMOD
  The Generic Model Organism Database project is applying for a [http://grants.nih.gov/grants/guide/pa-files/PAR-
  1 KB (231 words) - 17:46, 20 August 2013
• News/Tripal 1.1 Publication
  ...al] or at the [http://database.oxfordjournals.org/content/2013/bat075.long Database journal]. ...nt software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to sup
  2 KB (333 words) - 18:46, 1 November 2013
• News/GMOD Paper Cuts, Nov 8th, 2013
  ...set up [http://morse-ccmar.ualg.pt/edge Rdecusdb, the Ruditapes decussatus database], built with [[Tripal]] ;The database of genomic variants<nowiki>:</nowiki> a curated collection of structural va
  2 KB (227 words) - 00:28, 9 November 2013
• WebApollo v2013-09-04 Installation
  ...e using Tomcat 7 as our servlet container and PostgreSQL as our relational database management system. We'll use sample data from the Pythium ultimum genome, * Relational Database Management System [officially supported: PostgreSQL]
  64 KB (9,974 words) - 18:35, 14 November 2013
• News/GMOD Paper Cuts, Nov 15th, 2013
  '''The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structu <blockquote>The Aspergillus Genome Database ([http://www.aspgd.org AspGD]) is a freely available web-based resource tha
  3 KB (476 words) - 17:29, 15 November 2013
• News/GMOD Paper Cuts, Nov 22nd, 2013
  '''The Genome Database for Rosaceae (GDR): year 10 update''' <ref name="DOI:10.1093/nar/gkt1012" / <blockquote>The [http://www.rosaceae.org Genome Database for Rosaceae (GDR)], the long-standing central repository and data mining r
  4 KB (522 words) - 00:10, 23 November 2013
• News/New WebApollo Release (2013/11/22)
  *database/history merger tool (command line)
  3 KB (411 words) - 19:24, 26 November 2013
• News/Canto, a GMOD tool for functional annotation
  The JSON data from Canto can be loaded into a relational database using the Chado schema (as at PomBase) or alternative schemas.
  1 KB (223 words) - 18:39, 2 December 2013
• News/GMOD Paper Cuts, Dec 6th, 2013
  ...r bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating inf '''The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse''' <ref
  4 KB (568 words) - 15:54, 9 December 2013
• GMOD in a Box/Resizing a VirtualBox Disk
  ...f it is running. Open the settings for the machine and attach the resized database file to the GMOD in a Box instance using the directions in the [[GMOD in a
  3 KB (525 words) - 03:31, 12 December 2013
• GMOD in a Box/WebApollo
  ...atabase and permissions, run the JBrowse setup scripts, and setup the BLAT database all from just a GFF3 file. Let's try it with our sample data. Adding annotation tracks to database
  16 KB (2,600 words) - 20:09, 17 December 2013
• GMOD Malaysia 2014
  ...ning in, the bioinformatics software offered by the Generic Model Organism Database project. Over three days, participants will learn about GMOD's free, open-s *[[Tripal]] website generator and database interface
  3 KB (450 words) - 20:59, 26 March 2014
• News/Announcing GMOD Malaysia 2014
  *[[Chado]] database schema *[[Tripal]] website/database interface
  740 B (100 words) - 22:37, 26 January 2014
• GSOC Project Ideas 2016
  ...cts include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. ...sualizations. Tripal is used or in development by over 25 different genome database websites, and is developed by an international group. A Tripal module curre
  28 KB (4,153 words) - 14:34, 8 March 2016
• Jun 2016 GMOD Meeting
  '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa
  6 KB (789 words) - 03:23, 23 August 2016
• JBrowse FAQ
  This is because BLAST does not tell you which database your hits come from. ...e if you are linking to genomic coordinates of JBrowse. If you BLAST a CDS database, you may need to load CDS sequences into JBrowse, or translate the CDS coor
  65 KB (10,432 words) - 15:23, 16 September 2020
• JBrowse Tutorial Programming for Biology 2014
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  13 KB (1,909 words) - 19:41, 23 October 2014
• Using the topoview Glyph
  <li><b>database:</b> The same database as you used for the chromosomes</li>... ...t to the same kind of kind of feature as the chromosomes in your scaffolds database
  61 KB (1,369 words) - 22:29, 6 April 2018
• JBrowse Tutorial Programming for Biology 2015
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  18 KB (2,519 words) - 23:33, 19 October 2015
• GMOD Online Training 2014//SOBA Tutorial
  files. The data can optionally first be loaded into a database. ...features in a GFF3 file. GAL loads features into a light-weight relational database and thus selecting sets of features based on complex data queries (get all
  19 KB (2,557 words) - 14:38, 19 May 2014
• News/Precompiled Ontologies in Chado
  ...Texas A&M University] are making [https://cpt.tamu.edu/~docs/chado/ Chado database dumps of precompiled ontologies publicly available] to save other Chado use * dump database as SQL
  1 KB (186 words) - 20:47, 20 February 2014
• PAG 2014
  ...1AACC7 Bioinformatic Solutions in Forest Genomics: Accessing the Treegenes Database] || Poster session ...show.com/5_0/myshow/event_view.cfm?ScheduledSessionID=1AAFCA Bovine Genome Database: Resources for Re-Annotating the Bos taurus Genome] || Poster session
  10 KB (1,357 words) - 23:55, 14 January 2015
• GSoC 2013
  ...amene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. Links: [http://www.gmod.org Website], [http://blog.gmod.org GMOD Blog] ...Microarray Database], and [http://pantherdb.org PANTHER] protein families database. PortEco is responsible for maintaining the [http://geneontology.org Gene
  17 KB (2,555 words) - 19:59, 12 February 2014
• News/Postdoc Position in Computational and Plant Evolutionary Biology
  ...ly focusing on the large legume family, and development of a corresponding database and on-line tools for accessing and exploring gene families and associated
  1 KB (166 words) - 19:30, 24 January 2014
• Precompiled Chado Databases
  [https://cpt.tamu.edu/chado-prebuilt-schema/ Chado database dumps of precompiled ontologies are publicly available] to save Chado users * dump database as SQL
  1 KB (189 words) - 09:51, 11 September 2017
• News/GMOD Paper Cuts, Feb 10th, 2014
  ...the initial assembly. The [http://hymenopteragenome.org Hymenoptera Genome Database] uses numerous GMOD resources, including [[MAKER]] for automated genome ann '''Production of a reference transcriptome and transcriptomic database ([http://cnidarians.bu.edu/EdwardBase/cgi-bin/index.cgi EdwardsiellaBase])
  10 KB (1,433 words) - 22:15, 10 February 2014
• GMOD Malaysia 2014/JBrowse Tutorial
  ...se from the chado session; if you didn't follow along exactly, re-load the database like so: Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  14 KB (1,931 words) - 00:01, 20 February 2014
• GMOD Malaysia 2014/MAKER Tutorial
  ...including supporting evidence) can easily be loaded into a GMOD compatible database for annotation distribution. repeat database, Repeat Masker edition, for RepeatMasker to work.
  85 KB (13,463 words) - 00:56, 27 February 2014
• GMOD Malaysia 2014/WebApollo Tutorial
  ==Database Setup== * Create a database for managing the WebApollo users
  12 KB (1,863 words) - 00:15, 20 February 2014
• GMOD Malaysia 2014/Tripal Tutorial
  * Audit - for database audits |Genome Database for Vaccinium
  131 KB (21,099 words) - 00:18, 20 February 2014
• GMOD Malaysia 2014/Chado Tutorial
  ...esign and architecture, and then goes into detail about how to use a Chado database. ==== Database Terminology ====
  51 KB (7,657 words) - 00:19, 20 February 2014
• GMOD Online Training 2014
  [[File:ChadoLogo.png|150px|right|link=Chado|Chado: Biological database schema]] ...ning in, the bioinformatics software offered by the Generic Model Organism Database project. Over five days, participants will learn about GMOD's free, open-so
  3 KB (445 words) - 16:12, 29 April 2014
• News/Applications Open for GMOD Online Training
  ...laxy]], [[MAKER]], [[Tripal]], [[WebApollo]], [[Canto]], and the [[Chado]] database.
  563 B (82 words) - 20:18, 1 April 2014
• WebApollo v2013-11-22 Installation
  ...e using Tomcat 7 as our servlet container and PostgreSQL as our relational database management system. We'll use sample data from the Pythium ultimum genome, * Relational Database Management System [officially supported: PostgreSQL]
  86 KB (13,281 words) - 00:37, 19 November 2014
• GMOD Online Training 2014/GFF3 Tutorial
  * ontology association and database cross references ...won't display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. This lets users find the gene by sear
  16 KB (2,318 words) - 04:56, 19 May 2014
• GMOD Online Training 2014/MAKER Tutorial
  ...including supporting evidence) can easily be loaded into a GMOD compatible database for annotation distribution. repeat database, Repeat Masker edition, for RepeatMasker to work.
  80 KB (12,952 words) - 03:53, 19 May 2014
• JBrowse Tutorial PAG 2016
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  19 KB (2,697 words) - 06:25, 13 January 2016
• GMOD Online Training 2014/JBrowse Tutorial
  ...se from the chado session; if you didn't follow along exactly, re-load the database like so: Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  13 KB (1,905 words) - 14:21, 21 May 2014
• GMOD Online Training 2014/GBrowse syn Tutorial
  ===Setting up the Alignment Database=== ...alignments between the two rice species. It will be in a [[MySQL|MySQL]] database.
  20 KB (2,751 words) - 19:05, 22 May 2014
• News/BBOP Job Openings
  *Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
  10 KB (1,399 words) - 19:51, 16 February 2021
• News/Now Hiring JBrowse Lead Developer
  *Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
  4 KB (619 words) - 19:51, 16 February 2021
• PAG 2015
  ...ripal]] || Stephen Ficklin and Dorrie Main || California Room || [[#Tripal Database Network and Initiatives Workshop|See below]] == Tripal Database Network and Initiatives Workshop ==
  19 KB (2,492 words) - 18:29, 31 March 2015
• JBrowse Tutorial PAG 2015
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  19 KB (2,615 words) - 16:21, 11 January 2015
• JBrowse Tutorial Programming for Biology 2016
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  20 KB (2,903 words) - 19:59, 16 October 2016
• News/Computational Biologist GrainGenes
  * Ensures smooth, reliable, and secure operation of biological database computational infrastructure ...guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers.
  1 KB (149 words) - 20:52, 16 February 2021
• JBrowse Tutorial PAG 2017
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  20 KB (2,867 words) - 19:38, 15 January 2017
• GSOC Project Ideas 2017
  ...ts include a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. ***Some database experience (ability to query using SQL)
  18 KB (2,646 words) - 05:18, 16 March 2017
• JBrowse Tutorial PAG 2018
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  21 KB (2,962 words) - 05:00, 14 January 2018
• GSOC Project Ideas 2018
  ...ts include a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. *'''Project Idea 1: Incorporating different database searching algorithms into SequenceServer (SequenceServer/Wurmlab)'''
  12 KB (1,846 words) - 18:55, 29 January 2018
• Reproducing gbrowse img functinality with JBrowse
  ...o a web page, like what one might want for a gene page at a model organism database.
  10 KB (1,310 words) - 20:14, 10 April 2018
• Migrating from GBrowse to JBrowse
  ...ier to create a JBrowse instance from the original GFF that from a GBrowse database like Bio::DB::GFF or Bio::DB::SeqFeature::Store.
  2 KB (286 words) - 18:24, 9 July 2018
• GSOC Project Ideas 2019
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. ...tion:'' Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualizatio
  7 KB (1,064 words) - 15:52, 19 February 2019
• JBrowse Tutorial PAG 2019
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  22 KB (3,098 words) - 21:05, 13 January 2019
• JBrowse Tutorial PAG 2020
  Next, we'll use <tt>biodb-to-json.pl</tt> to get feature data out of the database and turn it into [[Glossary#JSON|JSON]] data that the web browser can use.
  22 KB (3,210 words) - 20:11, 12 January 2020
• GSOC Project Ideas 2020
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. ...tion:'' Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualizatio
  20 KB (3,057 words) - 02:14, 19 March 2020
• GSoD
  ...iption: Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualizatio ...er Guide provides an introduction to Reactome, the user interfaces and the database content. Exercises are also provided to help user practice what they have l
  4 KB (632 words) - 02:38, 7 May 2020
• GSOC Project Ideas 2021
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. **''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to
  18 KB (2,539 words) - 18:58, 1 April 2021
• JBrowse 2 Tutorial PAG 2022
  ...t adding some SNP data for peach from [https://www.rosaceae.org the Genome Database for Rosaceae (GDR)]. The peach genome JBrowse that we want to look at is th
  24 KB (4,099 words) - 19:23, 29 January 2022
• GSOC Project Ideas 2022
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. ...tion:'' Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualizatio
  11 KB (1,658 words) - 18:33, 25 March 2022
• GSOC Project Ideas 2023
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms. ...s developer will both design interfaces for displaying data from the Neo4j database and provide interfaces for modifying the information.
  9 KB (1,387 words) - 18:23, 16 March 2023
• GSOC Project Ideas 2024
  ...ts can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms.
  4 KB (580 words) - 16:41, 12 February 2024