Difference between revisions of "User Guide 2010:TOC"

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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.
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This is the official wiki guide for using [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.
  
 
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.
 
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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----
 
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==Getting Started==
 
==Getting Started==
 
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*[[UserGuide:General_Description|Overview of WormBase]]
==Contacting WormBase==
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*[[UserGuide:WBFrontPage|WormBase Front Page]] ''Portal to WormBase data''
*[[Guidelines for Users on Submitting/Reporting Data to WormBase|Submitting data and reporting errors]]
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==Navigating WormBase==
 
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*[[UserGuide:WBNavigation|Viewing WormBase Data]] ''What is all this stuff on a page''
==Viewing and Navigating WB Data==
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*[[UserGuide:GBrowse|Using the Genome Browser]] ''Browsing the genome''
 
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==Searching for Data==
===The WB Front page===
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**[[Data mining:Data mining methods|Data Mining Methods]] - ''Learn about the methods for mining WormBase systematically''  
 
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**[[Data mining:Searching WormBase for Information About C. elegans (Wiley)|Searching WormBase for Information About C. elegans (Wiley)]]  
===The Genome Browser===
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**[[Data mining:Ontology browsers|Ontology Browsing]]
 
 
===Individual Pages===
 
*[[WBPage: Gene | Gene Page]]
 
*[[WBPage: Sequence | Sequence Page]]
 
*[[WBPage: Protein | Protein Page]]
 
*[[WBPage: Variation | Allele Page]]
 
*[[WBPage: Clone | Clone/Plasmid Page]]
 
*[[WBPage: Strain | Strain Page]]
 
*[[WBPage: Molecule | Molecule Page]]
 
*[[WBPage:Phenotype|Phenotype Page]]
 
**The NOT annotations
 
*[[WBPage: RNAi | RNAi Experiment Page]]
 
*[[WBPage: Microarray | SPELL]]
 
 
 
==Searching WB==
 
 
 
*[[Data mining|Data mining]] - ''Learn about the methods for mining WormBase systematically''  
 
*[[Searching WormBase for Information About C. elegans (Wiley)|Searching WormBase for Information About C. elegans (Wiley)]]  
 
===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==
 
==Retrieving/Exporting Data==
*Bulk data access
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*[[UserGuide:Downloads|Downloading data]] - ''Download commonly requested files and datasets''
**gff files
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*[[UserGuide:Batch_Downloads|Batch downloads]], [[UserGuide:Genome_Dumper|Genome Dumper]]
 
*WormMart
 
*WormMart
==WB Community Tools==
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==Community Tools==
 
These are tools generated and or maintained by WB for the community.
 
These are tools generated and or maintained by WB for the community.
 
*Sequence analysis
 
*Sequence analysis
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***Synteny Viewer
 
***Synteny Viewer
 
**Cis-Elements (CisOrtho)
 
**Cis-Elements (CisOrtho)
===Experiment tools===
 
 
*e-PCR
 
*e-PCR
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===Reagents made by the community===
 
*Balancers
 
*Balancers
 
*Transgene markers
 
*Transgene markers
  
==Downloading WB Data==
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==Contacting WormBase==
 
 
*[[Downloads|Downloads]] - ''Download commonly requested files and datasets''
 
 
*[[Guidelines for Users on Submitting/Reporting Data to WormBase|Submitting data and reporting errors]]
 
*[[Guidelines for Users on Submitting/Reporting Data to WormBase|Submitting data and reporting errors]]
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*[[WB FAQ]]
  
 
==General Information==  
 
==General Information==  
 
 
*[[Release Schedule|Release Schedule]] - ''When to expect the next release of WormBase, and information on past releases''  
 
*[[Release Schedule|Release Schedule]] - ''When to expect the next release of WormBase, and information on past releases''  
*[[Citing WormBase|Citing WormBase]]  
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*[[Citing and Acknowledging WormBase|Citing and Acknowledging WormBase]]
 
*[[Presentations|Presentations]] | [[Publications|Publications]] - ''public information presented by the developers of WormBase''  
 
*[[Presentations|Presentations]] | [[Publications|Publications]] - ''public information presented by the developers of WormBase''  
 
*[[Local installation of WormBase|Installing WormBase on your own computer]]  
 
*[[Local installation of WormBase|Installing WormBase on your own computer]]  
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== Staying up-to-date  ==
 
== Staying up-to-date  ==
 
 
[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.  
 
[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.  
 
 
* Live Help Desk: [http://friendfeed.com/rooms/wormbase The WormBase Room on FriendFeed]
 
* Live Help Desk: [http://friendfeed.com/rooms/wormbase The WormBase Room on FriendFeed]
 
* Twitter: [http://www.twitter.com/wormbase Status updates], [http://www.twitter.com/wormbase_commit Software commit messages]  
 
* Twitter: [http://www.twitter.com/wormbase Status updates], [http://www.twitter.com/wormbase_commit Software commit messages]  
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*[[WormBase Newsletters|WormBase Newsletters]]  
 
*[[WormBase Newsletters|WormBase Newsletters]]  
 
*[http://www.wormbook.org/announce.html WormBook Announcements] - ''low volume''
 
*[http://www.wormbook.org/announce.html WormBook Announcements] - ''low volume''
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==Glossary==
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==Internal Documentation==
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*[[Developer documentation|Developer documentation]]
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*[[Caltech documentation]]
 +
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----
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UserGuide:Display Tools
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UserGuide:Embryonic Cell/Time Correlation Table 1
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UserGuide:Embryonic Stage/Time Correlation Table 2
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UserGuide:Definitions for Life Stages
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UserGuide:Full Text Journals
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UserGuide:Gene Ontology
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UserGuide:Genetic Map
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UserGuide:How to Obtain Reagents
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UserGuide:Life Stage System in WormBase
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UserGuide:Nomenclature
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UserGuide:Nomenclature nematode
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UserGuide:Release Notes
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UserGuide:Wormpep file descriptions
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UserGuide:ePCR
 +
 +
  
==Glossary==
 
  
==FAQ==
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FAQ<br>
 
*What is WormBase?
 
*What is WormBase?
 
*Machine/Browser compatibility
 
*Machine/Browser compatibility
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*Who do I contact if I see an error on the page?  
 
*Who do I contact if I see an error on the page?  
 
*Who do I contact if WormBase stops working for me?
 
*Who do I contact if WormBase stops working for me?
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*What is an ontology? (What happened to my jargon?)
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*What is GO?
  
 
==Internal Documentation==
 
*[[Developer documentation|Developer documentation]]
 
*[[Caltech documentation]]
 
  
 
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Latest revision as of 09:23, 30 June 2011

This is the official wiki guide for using 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

Navigating WormBase

Searching for Data

Retrieving/Exporting Data

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)
  • e-PCR

Reagents made by the community

  • Balancers
  • Transgene markers

Contacting WormBase

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

Internal Documentation


UserGuide:Display Tools UserGuide:Embryonic Cell/Time Correlation Table 1 UserGuide:Embryonic Stage/Time Correlation Table 2 UserGuide:Definitions for Life Stages

UserGuide:Full Text Journals UserGuide:Gene Ontology

UserGuide:Genetic Map UserGuide:How to Obtain Reagents UserGuide:Life Stage System in WormBase UserGuide:Nomenclature UserGuide:Nomenclature nematode UserGuide:Release Notes UserGuide:Wormpep file descriptions UserGuide:ePCR



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



based on Reactome User's Guide