Difference between revisions of "User Guide 2010:TOC"

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==Introduction==
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This is the official wiki guide for using WormBase [http://www.wormbase.org WormBase], a biological database of all genomic and genetic data of the model nematode ''Caenorhabditis elegans'' and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.
WormBase is a biological database of all genomic and genetic data of the model nematode Caenorhabditis elegans and related nematodes. This is a guide for using WormBase [http://www.wormbase.org WormBase] the genetic and genomic database of the model organism [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.
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To edit this Wiki, please create an account (click on the 'log in/create account' link at the top of the page). Before contributing, please see the WormBaseWiki usage guidelines.
  
 
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==Getting Started==
 
==Getting Started==
*What is WormBase?
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*Machine/Browser compatibility
 
*What types of nematodes does WB collect data for?
 
*What types of information does WB contain?
 
*How are WormBase data organized?
 
*How does data get into WormBase?
 
*Can I view WormBase data offline?
 
*With what other formats are WB data compatible?
 
*Who are the worm community?
 
*Who are the WB database people?
 
*Who funds WB?
 
 
==Contacting WormBase==
 
==Contacting WormBase==
*Who do I contact if I want to submit data?
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*[[Guidelines for Users on Submitting/Reporting Data to WormBase|Submitting data and reporting errors]]
*Who do I contact if I see an error on the page?
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*Who do I contact if WormBase stops working for me?
 
 
==Viewing and Navigating WB Data==
 
==Viewing and Navigating WB Data==
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===The WB Front page===
 
===The WB Front page===
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===The Genome Browser===
 
===The Genome Browser===
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===Individual Pages===
 
===Individual Pages===
*Gene Page
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*[[WBPage: Gene | Gene Page]]
*Sequence Page
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*[[WBPage: Sequence | Sequence Page]]
*Protein Page
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*[[WBPage: Protein | Protein Page]]
*Allele Page
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*[[WBPage: Variation | Allele Page]]
*Clone/Plasmid Page
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*[[WBPage: Clone | Clone/Plasmid Page]]
*Strain Page
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*[[WBPage: Strain | Strain Page]]
*Molecule Page
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*[[WBPage: Molecule | Molecule Page]]
*[[User Guide:Phenotype|Phenotype Page]]  
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*[[WBPage:Phenotype|Phenotype Page]]  
 
**The NOT annotations
 
**The NOT annotations
*RNAi experiment Page
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*[[WBPage: RNAi | RNAi Experiment Page]]
*Microarray/SPELL
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*[[WBPage: Microarray | SPELL]]
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==Searching WB==
 
==Searching WB==
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*[[Data mining|Data mining]] - ''Learn about the methods for mining WormBase systematically''
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*[[Searching WormBase for Information About C. elegans (Wiley)|Searching WormBase for Information About C. elegans (Wiley)]]
 
===Simple searches===
 
===Simple searches===
 
*Finding  
 
*Finding  
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**gff files
 
**gff files
 
*WormMart
 
*WormMart
==WB Community Tools : tools generated/maintained by wormbase for the community==
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==WB Community Tools==
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These are tools generated and or maintained by WB for the community.
 
*Sequence analysis
 
*Sequence analysis
 
**orthology/homology predictors
 
**orthology/homology predictors
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*Balancers
 
*Balancers
 
*Transgene markers
 
*Transgene markers
==Downloading WB==
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==Citing and Linking to WormBase==
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==Downloading WB Data==
==Keeping in Touch with WB==
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*Database release schedule
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*[[Downloads|Downloads]] - ''Download commonly requested files and datasets''
*Feeds
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*[[Guidelines for Users on Submitting/Reporting Data to WormBase|Submitting data and reporting errors]]
*Twitter
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==General Information==
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*[[Release Schedule|Release Schedule]] - ''When to expect the next release of WormBase, and information on past releases''
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*[[Citing WormBase|Citing WormBase]]
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*[[Presentations|Presentations]] | [[Publications|Publications]] - ''public information presented by the developers of WormBase''
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*[[Local installation of WormBase|Installing WormBase on your own computer]]
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*[[Editorial policy|Editorial policy]] - ''WormBase editorial policy''
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*[[Acceptable use policy|Acceptable use policy]]
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*[[WormBaseWiki:Copyrights|Copyright statement]]
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*[[Acceptable use policy#Privacy statement|Privacy statement]]
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== Staying up-to-date  ==
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[http://www.wormbase.org WormBase] offers a number of ways to stay up-to-date with new features and datasets, to make feature requests, and to ask for assistance with the database.
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* Live Help Desk: [http://friendfeed.com/rooms/wormbase The WormBase Room on FriendFeed]
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* Twitter: [http://www.twitter.com/wormbase Status updates], [http://www.twitter.com/wormbase_commit Software commit messages]
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* Mailing Lists: [[Mailing lists#help|General questions]] | [[Mailing lists#developers|Developers]] -- [[Mailing lists|More...]]
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* RSS Feeds: [http://www.wormbase.org/rss/wormbase-live.xml News and Status] | [http://www.wormbase.org/rss/wormbase-dev.xml Development News] -- [[RSS news feeds|More Info]]
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*[[WormBase Newsletters|WormBase Newsletters]]
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*[http://www.wormbook.org/announce.html WormBook Announcements] - ''low volume''
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==Glossary==
 
==Glossary==
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==FAQ==
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*What is WormBase?
 +
*Machine/Browser compatibility
 +
*What types of nematodes does WB collect data for?
 +
*What types of information does WB contain?
 +
*How are WormBase data organized?
 +
*How does data get into WormBase?
 +
*Can I view WormBase data offline?
 +
*With what other formats are WB data compatible?
 +
*Who are the worm community?
 +
*Who are the WB database people?
 +
*Who funds WB?
 +
*Who do I contact if I want to submit data?
 +
*Who do I contact if I see an error on the page?
 +
*Who do I contact if WormBase stops working for me?
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==Internal Documentation==
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*[[Developer documentation|Developer documentation]]
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*[[Caltech documentation]]
  
 
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Revision as of 15:23, 10 August 2010

This is the official wiki guide for using WormBase WormBase, a biological database of all genomic and genetic data of the model nematode Caenorhabditis elegans and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.

To edit this Wiki, please create an account (click on the 'log in/create account' link at the top of the page). Before contributing, please see the WormBaseWiki usage guidelines.


Getting Started

Contacting WormBase

Viewing and Navigating WB Data

The WB Front page

The Genome Browser

Individual Pages

Searching WB

Simple searches

  • Finding
    • a gene
    • an allele
    • a strain
    • a sequence

Ontology browsers

  • What is an ontology? (What happened to my jargon?)
  • What is GO?

Query languages

  • AQL
  • WQL

Retrieving/Exporting Data

  • Bulk data access
    • gff files
  • WormMart

WB Community Tools

These are tools generated and or maintained by WB for the community.

  • Sequence analysis
    • orthology/homology predictors
      • Blast / Blat
      • Synteny Viewer
    • Cis-Elements (CisOrtho)

Experiment tools

  • e-PCR
  • Balancers
  • Transgene markers

Downloading WB Data

General Information

Staying up-to-date

WormBase offers a number of ways to stay up-to-date with new features and datasets, to make feature requests, and to ask for assistance with the database.

Glossary

FAQ

  • What is WormBase?
  • Machine/Browser compatibility
  • What types of nematodes does WB collect data for?
  • What types of information does WB contain?
  • How are WormBase data organized?
  • How does data get into WormBase?
  • Can I view WormBase data offline?
  • With what other formats are WB data compatible?
  • Who are the worm community?
  • Who are the WB database people?
  • Who funds WB?
  • Who do I contact if I want to submit data?
  • Who do I contact if I see an error on the page?
  • Who do I contact if WormBase stops working for me?


Internal Documentation


based on Reactome User's Guide