Difference between revisions of "User Guide 2010:TOC"
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==Getting Started== | ==Getting Started== | ||
| + | *[[UserGuide:General_Description|Overview of WormBase]] | ||
| + | *[[UserGuide:WBFrontPage|WormBase Front Page]] ''Portal to WormBase data'' | ||
| + | *[[UserGuide:WBNavigation|Navigating through WormBase]] ''Finding and viewing data pages'' | ||
| + | *[[UserGuide:GBrowse|Using the Genome Browser]] | ||
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==Contacting WormBase== | ==Contacting WormBase== | ||
*[[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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==Searching WB== | ==Searching WB== | ||
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**gff files | **gff files | ||
*WormMart | *WormMart | ||
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==WB Community Tools== | ==WB 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. | ||
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*Transgene markers | *Transgene markers | ||
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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 | ||
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| + | UserGuide:Full Text Journals | ||
| + | UserGuide:Gene Ontology | ||
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| + | UserGuide:Genetic Map | ||
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| + | 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 | ||
==Downloading WB Data== | ==Downloading WB Data== | ||
| − | *[[Downloads| | + | *[[UserGuide:Downloads|Downloading data]] - ''Download commonly requested files and datasets'' |
| − | + | [[UserGuide:Batch_Downloads|Batch downloads]], [[UserGuide:Genome_Dumper|Genome Dumper]] | |
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==General Information== | ==General Information== | ||
Revision as of 16:13, 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.
Contents
Getting Started
- Overview of WormBase
- WormBase Front Page Portal to WormBase data
- Navigating through WormBase Finding and viewing data pages
- Using the Genome Browser
Contacting WormBase
Searching WB
- Data mining - Learn about the methods for mining WormBase systematically
- 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
- 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)
- orthology/homology predictors
Experiment tools
- e-PCR
- Balancers
- Transgene markers
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
Downloading WB Data
- Downloading data - Download commonly requested files and datasets
Batch downloads, Genome Dumper
General Information
- Release Schedule - When to expect the next release of WormBase, and information on past releases
- Citing 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
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
