User Guide 2010:TOC

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.

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Getting Started

• Overview of WormBase
• WormBase Front Page Portal to WormBase data

Navigating WormBase

• Viewing WormBase Data What is all this stuff on a page
• Using the Genome Browser Browsing the genome

Searching for Data

• • Data Mining Methods - Learn about the methods for mining WormBase systematically
  • Searching WormBase for Information About C. elegans (Wiley)
  • Ontology Browsing

Retrieving/Exporting Data

• Downloading data - Download commonly requested files and datasets
• Batch downloads, Genome Dumper
• WormMart

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

• Submitting data and reporting errors
• WB FAQ

General Information

• Release Schedule - When to expect the next release of WormBase, and information on past releases
• Citing and Acknowledging WormBase
• Presentations | Publications - public information presented by the developers of WormBase
• Installing WormBase on your own computer
• Editorial policy - WormBase editorial policy
• Acceptable use policy
• Copyright statement
• Privacy statement

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.

• Live Help Desk: The WormBase Room on FriendFeed
• Twitter: Status updates, Software commit messages
• Mailing Lists: General questions | Developers -- More...
• RSS Feeds: News and Status | Development News -- More Info
• WormBase Newsletters
• WormBook Announcements - low volume

Internal Documentation

• Developer documentation
• Caltech documentation

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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?

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based on Reactome User's Guide