WikiPathways

From WikiPathways

Revision as of 03:04, 11 April 2018 by Khanspers (Talk | contribs)
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Welcome to WikiPathways BETA

WikiPathways is a database of biological pathways maintained by and for the scientific community.

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Browse by species and category

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

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Multiple formats and methods

Growth

New pathways added each month

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We want your feedback! A quick survey to help us focus development: https://www.surveymonkey.com/r/wikipathways


Today's Featured Pathway

Biogenic Amine Synthesis (Mus musculus)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/d/d3/WP522_96832.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/d/d3/WP522_96832.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Biogenic Amine ...', 'https://www.wik...', 'Biogenic Amine ...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP522', '300', 'center', 'Biogenic Amine ...', 'pathway', 'Biogenic Amine ...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Tuesday 22 Janu...', 'Curation:Featur...', 'true')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  19. 18 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{| ?<!-- Specia...')
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{| ?<!-- Specia...')
  21. 20 /var/www/wikipathways/includes/Article.php(3406): Parser->parse('{| ?<!-- Specia...', Object(Title), Object(ParserOptions), true, true, 96832)
  22. 21 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('{| ?<!-- Specia...', false)
  23. 22 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  24. 23 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  25. 24 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  26. 25 {main}

Curator of the Week

  Daniela Digles (University of Vienna)
[?]

Updates

  • April 2018 Release: total of 1,538 pathway models in 25 species, edits from 22 contributors and 8 new pathways
  • March 2018 Release: 346 edits by 15 contributors, and 3 new pathways this month
  • February 2018 Release: 247 edits by 10 contributors, and 5 new pathways this month
  • January 2018 Release: 175 edits by 13 contributors, and 10 new pathways this month
  • November 2017 Release: 89 edits by 13 contributors, and 2 new pathways this month
  • October 2017 Release: 261 edits by 11 contributors, and 2 new pathways this month

    more...

Discussions

17 January 2019
Comparing wikipathways from two different analyses (1) by Denise Slenter
11 January 2019
Contacted author for references (1) by Denise Slenter
    more...

Forum

    Google group wikipathways-discuss


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