WikiPathways

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Welcome to WikiPathways BETA

WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. More about WikiPathways...

Finding Pathways

Search

 Browse

Browse by species and category

You can search by:
  • Pathway name (Apoptosis)
  • Gene or protein name (p53)
  • Any page content (cancer)

Contributing New Pathways

Create

Create a new pathway page

Suggest

Add a pathway to the wish list

Sample Pathway Pages

Sandbox

Play with the editor tools

Check out the following pages:

For more information see the Help pages


Today's Featured Pathway

DNA Replication (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/0/0a/WP466_46021.svg:
Status:255
Message:[ 0.026] Info: Preferences file /var/www/.PathVisio/.PathVisio doesn't exist, using defaults Error: Unable to read inputfile: /var/www/wikipathways/images/e/ec/WP466_46021.gpml GPML Converter Usage: java Converter <input filename> [<output filename>]

Converts between GPML format and several other formats: - GPML (.gpml/.xml) <-> GenMAPP (.mapp) - GPML (.gpml/.xml) -> SVG (.svg) - GPML (.gpml/.xml) -> PNG (.png) - GPML (.gpml/.xml) -> TIFF (.tiff) - GPML (.gpml/.xml) -> PDF (.pdf) The conversion direction is determined from the extension of the input file. Return codes: 0: OK -1: Parameter or file error -2: Conversion error



Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways/images/e/ec/WP466_46021.gpml" "/var/www/wikipathways/images/0/0a/WP466_46021.svg" 2>&1
' in /var/www/wikipathways/wpi/Pathway.php:1117 Stack trace:

  1. 0 /var/www/wikipathways/wpi/Pathway.php(1092): Pathway::convert('/var/www/wikipa...', '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/Pathway.php(1023): Pathway->saveConvertedCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(100): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(50): makeThumbLinkObj(Object(Pathway), 'DNA Replication', 'http://wikipath...', 'DNA Replication', 'center', 'pwthumb', '300')
  5. 4 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP466', '300', 'center', 'DNA Replication', 'pathway', 'DNA Replication')
  6. 5 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  7. 6 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  8. 7 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  13. 12 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay.php(59): Parser->recursiveTagParse('{{Template:Toda...')
  14. 13 [internal function]: getPathwayOfTheDay(Object(Parser), 'Wednesday 22 Ma...', 'Curation:Featur...', 'true')
  15. 14 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  16. 15 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  17. 16 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('__NOEDITSECTION...')
  19. 18 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('__NOEDITSECTION...')
  20. 19 /var/www/wikipathways/includes/Article.php(3406): Parser->parse('__NOEDITSECTION...', Object(Title), Object(ParserOptions), true, true, 46021)
  21. 20 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('__NOEDITSECTION...', false)
  22. 21 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  23. 22 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  24. 23 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  25. 24 {main}

Latest discussions

10 May 2013
Rename pathway? (2) by Alexander Pico
Rename pathway? (1) by Egon Willighagen
27 April 2013
Qualifying for Analysis Set (1) by Alexander Pico
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Forum

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New!

Community Interest

Portals within WikiPathways for communities with focused pathway interests:

Want to start your own Portal? Contact us!

Statistics

  • There are 1765 pathways
  • Number of pathways (and unique genes) per species:
Anopheles gambiae: 25 (438)
Arabidopsis thaliana: 17 (870)
Bos taurus: 116 (3196)
Bacillus subtilis: 3 (14)
Caenorhabditis elegans: 57 (963)
Canis familiaris: 114 (3117)
Danio rerio: 102 (2542)
Drosophila melanogaster: 37 (605)
Escherichia coli: 5 (9)
Equus caballus: 12 (214)
Gallus gallus: 100 (2388)
Gibberella zeae: 2 (14)
Homo sapiens: 433 (5882)
Mus musculus: 186 (5726)
Mycobacterium tuberculosis: 109 (992)
Oryza sativa: 14 (673)
Pan troglodytes: 118 (3099)
Rattus norvegicus: 165 (4371)
Saccharomyces cerevisiae: 129 (993)
Sus scrofa: 10 (106)
Zea mays: 11 (184)
  • There are 7,722 registered users
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