Difference between revisions of "User Guide"

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(New page: GENERAL DOCUMENTATION CAVEAT: ALWAYS UNDER CONSTRUCTION At this writing, Wormbase is very much a dynamic, ongoing project. A good consequence of this is that new features and options are...)
 
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GENERAL DOCUMENTATION
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# [[UserGuide:General_Description|General Description]]
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## [[UserGuide:Release_Notes|Release Notes]]
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CAVEAT: ALWAYS UNDER CONSTRUCTION
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## [[UserGuide:Display_Tools|Display Tools]]
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# [[UserGuide:Basic_Search_Tools|Basic Search Tools]]
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At this writing, Wormbase is very much a dynamic, ongoing project. A good consequence of this is that new features and options are added and old ones are removed at a noticeable rate. A draw back, however, is that documentation written for a given feature of the WormBase Web interface may be obsolete by the time you are reading this text.
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## [[UserGuide:Simple_Search|Simple Search]]
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## [[UserGuide:Browse_Genome|Browse Genome]]
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Therefore, this documentation is based upon the main WormBase web site at Cold Spring Harbor Laboratories (http://wormbase.org). The Greek mirror (http://worm.imbb.forth.gr/), at this writing, has many of the same features as the main site but lags behind the main site in some respects; that is because the Greek mirror represents the last version of the WormBase web site that was stable enough to be ported by non-WormBase staff.
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## [[UserGuide:Blast_Search|BLAST Search]]
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## [[UserGuide:Batch_Downloads|Batch Downloads]]
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http://www.wormbase.org/wiki/images/Wb_index.jpg
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## [[UserGuide:Marker/Strain_Search|Marker/Strain Search]]
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## [[UserGuide:Genetic_Map|Genetic Map]]
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NEW RELEASE AND RELEASE NOTES
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# [[UserGuide:Advanced_Search_Tools|Search Tools]]
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## [[UserGuide:Advanced_Search|Advanced Search]]
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WormBase is updated every two weeks, with each release assigned a new version number (for example: WS10, ... WS51, ... WS97). Release notes can be accessed directly from the WormBase home page: see the help page for Release notes.
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## [[UserGuide:ePCR|ePCR]]
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## [[UserGuide:Gene_Ontology|Gene Ontology]]
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QUICK SEARCH:
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## [[UserGuide:Cell_Search|Cell Search]]
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## [[UserGuide:Neuron_Search|Neuron Search]]
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Select a class from the pull-down menu to "Search for", and then type key words in the box. If you leave the search box blank, everything from the selected class will appear as the search result. For example: if you select class "Cell", and type nothing in search box, all C. elegans cells will appear in the search result. For anything you are not sure of, try using * as the wild card insertion; it can be placed anywhere in the keyword. Example: if you type "ad*", all data that begin with "ad" will appear in the search result.
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## [[UserGuide:Expression_Search|Expression Search]]
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## [[UserGuide:Expression_profile_Search|Expression Profile Search]] '''DEPRECATED'''
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What can be typed into the "Quick Search" box? The following objects can be entered in the search box, which is case sensitive and space sensitive. You can search for a certain class such as "Any Gene" or "Author", or search for "Anything", which will return related objects from all classes.
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## [[UserGuide:RNAi_Search|RNAi Search]]
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## [[UserGuide:Interval_Search|Interval Search]]
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    * Any Gene Example: lin-3
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## [[UserGuide:Genome_Dumper|Genome Dumper]]
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    * Author Example: Lee RYN
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## [[UserGuide:Autocompletion|Wormbase Suggest]]
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    * Cell Example: ADFL
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# [[UserGuide:Individual_Pages|Individual Pages]]
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    * Genbank Accession Number Example: AL032609
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## [[UserGuide:Gene_Page|Gene Page]]
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## [[UserGuide:Sequence_Page|Sequence Page]]
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See more details on the explanation of Quick Search tool.
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## [[UserGuide:Gene_Ontology_Page|Gene Ontology Page]]
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## [[UserGuide:Microarray_Page|Microarray Page]]
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MENU FOR WORMBASE
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## [[UserGuide:Person_Page|Person Page]]
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# [[UserGuide:Other_Resources_provided_by_WormBase|Other Resources provided by WormBase]]
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The WormBase menu includes five basic options on the top of the WormBase homepage. More advanced search tools can be found under the "More Searches" option.
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## [[UserGuide:How_to_Obtain_Reagents|How To Obtain Reagents]]
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## [[UserGuide:Full_Text_Journals|Full Text Journals]]
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To learn how to use these search tools, please read the User's Guide help pages for Basic Search Tools and Advanced Search Tools.
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## [[UserGuide:Nomenclature#How_to_Register_a_New_Gene_Class_or_Gene_Name|How to Register a New Gene Class or Gene Name]]
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## [[UserGuide:Nomenclature#How_to_Register_a_New_Laboratory_and_Receive_Lab.2C_Strain_and_Allele_designations|How to Register a New Laboratory and Receive Lab, Strain and Allele Designation Codes]]
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Sometimes a submenu will appear when you search for certain items such as genetic map, sequence report or cell lineage. The submenu usually is for different displays of information, for example, "Tree display" versus "Graphic display", etc. For more information, please read the help page for Sub Menu.
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## [[UserGuide:Embryonic_Cell/Time_Correlation_Table_1|Embryonic Cell/Time Correlation Table 1]]
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## [[UserGuide:Embryonic_Stage/Time_Correlation_Table_2|Embryonic Stage/Time Correlation Table 2]]
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## [[UserGuide:Life_Stage_System_in_WormBase|Life Stage System in WormBase]]
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## [[UserGuide:Definitions_for_Life_Stages|Definitions for Life Stages]]
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## [[UserGuide:Wormpep_file_descriptions|Wormpep file description]]

Revision as of 21:50, 23 September 2007

  1. General Description
    1. Release Notes
    2. Display Tools
  2. Basic Search Tools
    1. Simple Search
    2. Browse Genome
    3. BLAST Search
    4. Batch Downloads
    5. Marker/Strain Search
    6. Genetic Map
  3. Search Tools
    1. Advanced Search
    2. ePCR
    3. Gene Ontology
    4. Cell Search
    5. Neuron Search
    6. Expression Search
    7. Expression Profile Search DEPRECATED
    8. RNAi Search
    9. Interval Search
    10. Genome Dumper
    11. Wormbase Suggest
  4. Individual Pages
    1. Gene Page
    2. Sequence Page
    3. Gene Ontology Page
    4. Microarray Page
    5. Person Page
  5. Other Resources provided by WormBase
    1. How To Obtain Reagents
    2. Full Text Journals
    3. How to Register a New Gene Class or Gene Name
    4. How to Register a New Laboratory and Receive Lab, Strain and Allele Designation Codes
    5. Embryonic Cell/Time Correlation Table 1
    6. Embryonic Stage/Time Correlation Table 2
    7. Life Stage System in WormBase
    8. Definitions for Life Stages
    9. Wormpep file description
Retrieved from "https://wiki.wormbase.org/index.php?title=User_Guide&oldid=84"