WikiPathways

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<analytics uacct="UA-1605246-1" ></analytics>
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<h2 class="frontPagePanel yellowFg">11 April 2019: Scheduled Downtime</h2>
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<font size=2>'''We will be taking the site down for an hour at 24:00UTC on April 11th. We are switching over to new and improved infrastructure! Sorry for any inconveniences.'''</font></div>
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|{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} }}
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<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
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<font size=2>'''We are currently experiencing some technical issues, so some pages are not accessible. We are working hard to fix those issues. Sorry for any inconveniences.'''</font></div>
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<h2 class="frontPagePanel redFg">Share your pathway knowledge in the fight against COVID-19</h2>
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<font size=2>'''''ACCESS'' the rapidly growing [[Portal:COVID-19|collection of COVID-19 pathways]], ''CONTRIBUTE'' your time and domain knowledge about pathway biology as a [[Help:Authors|pathway author]], and ''USE'' these pathways in [[Help:Tools_using_WikiPathways|your research]].'''</font></div>
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<h2 style="margin:0;background-color:#cef2e0;font-size:120%;font-weight:bold;border:0px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">Contents</h2>
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<inputbox>
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|<div class="frontPagePanel greenBg" style="width:95%;margin:1em;width=100%">
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type=search
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<h2 class="frontPagePanel greenFg">Try the New WikiPathways</h2>
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<font size=2>'''Visit https://wikipathways.org to see the new version of WikiPathways.''' This is the "classic" version of WikiPathways will not be maintained for much longer.
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[[:Category:Human|Overview of all human pathways]]
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<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel blueFg">Find Pathways</h2>
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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|-
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|rowspan="2" align="center" style="width:25%;"|
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|align="center" valign="top"|<big>'''Search'''</big><BR>{{#searchPathwaysBox:}}
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|rowspan="2" align="center" style="width:25%;"|
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|rowspan="2" align="center" style="width:25%;"|
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|rowspan="2" align="center" valign="top"|<big>'''Browse'''</big>{{#imgLink:Browse_thumb.png|200|center||special|BrowsePathwaysPage|Browse}}
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'''Browse by species and category'''
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|rowspan="2" align="center" style="width:25%;"|
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|-
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|align="left" valign="top"|'''You can search by:'''
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*Pathway name ''(Apoptosis)''
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*Gene or protein name ''(p53)''
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*Any page content ''(cancer)''
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[[:Category:Mouse|Overview of all mouse pathways]]
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<h2 class="frontPagePanel blueFg">Get Pathways</h2>
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|-
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|rowspan="1" align="center" style="width:25%;"|
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|align="center" valign="top"|<big>'''Download'''</big>{{#imgLink:Download_label.png|215|center|||Download_Pathways|Download}}
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'''Multiple formats and methods'''
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|rowspan="1" align="center" style="width:25%;"|
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|rowspan="1" align="center" style="width:25%;"|
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|rowspan="1" align="center" valign="top"|<big>'''Growth'''</big>{{#imgLink:Wp_growth_label.png|200|center|||WikiPathways:Statistics|Growth}}
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'''New pathways added each month'''
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|rowspan="1" align="center" style="width:25%;"|
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|-
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[[:Category:Rat|Overview of all rat pathways]]
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<h2 class="frontPagePanel blueFg">Edit Pathways</h2>
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|-
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|rowspan="1" align="center" style="width:25%;"|
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|align="center" valign="top"|<big>'''Learn'''</big>{{#imgLink:AcademyPath.png|200|center||external|http://academy.wikipathways.org|WikiPathways Academy}}
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'''Play with the editor tools'''
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|rowspan="1" align="center" style="width:25%;"|
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|rowspan="1" align="center" style="width:25%;"|
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|align="center" valign="top"|<big>'''Request'''</big>{{#imgLink:RequestForm2.png|210|center||external|https://github.com/wikipathways/pathway-curation-tasks/issues|Figure Conversion}}
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'''Queue figures for conversion'''
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[[:Category:Cellular Process|Cellular Process category]]
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<!-- SURVEY -->
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|-
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<h2 class="frontPagePanel yellowFg">We want your feedback! A quick survey to help us focus development: [https://www.surveymonkey.com/r/wikipathways https://www.surveymonkey.com/r/wikipathways]</h2></div>
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[[:Category:Metabolic Process|Metabolic Process category]]
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[[:Category:Physiological Process|Physiological Process category]]
 
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[[:Category:Molecular Function|Molecular Function category]]
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| valign="top"|
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<div class="frontPagePanel blueBg" style="width:90%;margin:1em;width=100%;">
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<h2 class="frontPagePanel blueFg">Today's Featured Pathway</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:CurrentHighlight | true}}
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<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
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* '''April 2024 Release''': [[Special:RecentPathwayChanges|290 edits]] by [[WikiPathways:Statistics#Contribution_scores|11 contributors]] and [https://www.wikipathways.org/browse/new.html 2 new pathways].
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* '''March 2024 Release''': [[Special:RecentPathwayChanges|542 edits]] by [[WikiPathways:Statistics#Contribution_scores|9 contributors]] and [https://www.wikipathways.org/browse/new.html 10 new pathways].
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* '''February 2024 Release''': [[Special:RecentPathwayChanges|586 edits]] by [[WikiPathways:Statistics#Contribution_scores|12 contributors]] and [https://www.wikipathways.org/browse/new.html 16 new pathways].
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* '''January 2024 Release''': [[Special:RecentPathwayChanges|105 edits]] by [[WikiPathways:Statistics#Contribution_scores|11 contributors]] and [https://www.wikipathways.org/browse/new.html 1 new pathway].
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* '''December 2023 Release''': [[Special:RecentPathwayChanges|120 edits]] by [[WikiPathways:Statistics#Contribution_scores|12 contributors]].
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* '''November 2023 Release''': [[Special:RecentPathwayChanges|120 edits]] by [[WikiPathways:Statistics#Contribution_scores|10 contributors]] and [https://www.wikipathways.org/browse/new.html 3 new pathways].
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* '''October 2023 Release''': [[Special:RecentPathwayChanges|157 edits]] by [[WikiPathways:Statistics#Contribution_scores|13 contributors]] and [https://www.wikipathways.org/browse/new.html 2 new pathways].
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* '''September 2023 Release''': [[Special:RecentPathwayChanges|85 edits]] by [[WikiPathways:Statistics#Contribution_scores|11 contributors]] and [https://www.wikipathways.org/browse/new.html 4 new pathways].
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* '''August 2023 Release''': [[Special:RecentPathwayChanges|207 edits]] by [[WikiPathways:Statistics#Contribution_scores|9 contributors]] and [https://www.wikipathways.org/browse/new.html 22 new pathways].
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&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Updates|more...]]
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<h2 class="frontPagePanel blueFg">Discussions</h2><recentChanges class="blueBg" style="border:none" namespace='90' limit='2'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Discussions|more...]]
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<h2 class="frontPagePanel blueFg">Forum</h2><rss>https://groups.google.com/group/wikipathways-discuss/feed/rss_v2_0_msgs.xml|short|max=2</rss>&nbsp;&nbsp;&nbsp;&nbsp;[http://groups.google.com/group/wikipathways-discuss Google group wikipathways-discuss]
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<h2 style="margin:0;background-color:#cee0f2;font-size:120%;font-weight:bold;border:0px solid #a3b1bf;text-align:left;color:#000;padding:0.2em 0.4em;">A WIKI FOR BIOLOGICAL PATHWAYS</h2>
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<font size=2>In the “tradition” of Wikipedia and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community.</font></div>
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<div style="width:400px;border:1px solid #e0a0a0;background-color:#faf5f5;vertical-align:top;margin:20;color:#000">
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<h2 style="margin:0;background-color:#e0a0a0;font-size:120%;font-weight:bold;border:0px solid #b1a3a3;text-align:center;color:#000;padding:0.2em 0.4em;">''UNDER CONSTRUCTION''</h2>
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'''This site is not ''officially'' open for business.  We are still implementing critical features and making major changes to these pages. If you are interested in what this site is about, please feel free to contact us.  We plan to have the site up and running by the end of April!'''
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Thomas Kelder: ''Thomas.Kelder[AT]BIGCAT.unimaas.nl''
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<br>
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Alex Pico: ''apico[AT]gladstone.ucsf.edu''
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</div>
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=== HOW TO FIND A PATHWAY ===
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:There are many ways to find your pathways of interest. You can search by:
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:* Name of the pathway
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:* Name of a gene on the pathway
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:* Browse by species
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:* Browse by pathway categories
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=== VIEWING PATHWAYS ===
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:<big>'''Image'''</big>
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:Once you are on a Pathway Page you can click on the image of the pathway to view the SVG representation. The pathway image is available for download in SVG and PNG formats.
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:<big>'''Text'''</big>
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:Each Pathway Page has a text description, itemized gene list, references and relevant links.
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:<big>'''Data'''</big>
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:Each pathway is also available for download as a GPML data file (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. This format can be used with [http://wiki.bigcat.unimaas.nl/pathvisio/Main_Page PathVisio]. Pathways are also available as .mapp files for use in [http://www.genmapp.org/ GenMAPP].
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=== EDITING PATHWAYS ===
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:In addition to editing the text fields on a given Pathway Page, this wiki also support the ability to edit the pathway itself!  Click on "EDIT" and a webstart version of PathVisio will open with the current pathway loaded.  You can then add, edit or delete content from the pathway. When you save, updated version of the images, controlled text, and data files are generated and are immediately available.
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== WikiPathways Statistics ==
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There are {{PAGESINNS:100}} pathways. There are {{NUMBEROFUSERS}} registered users.
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----
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[[Help:LiteratureReferences|Help on literature references]]
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Current revision

Try the New WikiPathways

Visit https://wikipathways.org to see the new version of WikiPathways. This is the "classic" version of WikiPathways will not be maintained for much longer.

Find Pathways

Search

 Browse

Browse by species and category

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

Get Pathways

Download

Multiple formats and methods

Growth

New pathways added each month

Edit Pathways

Learn

Play with the editor tools

Request

Queue figures for conversion

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

Today's Featured Pathway

Downregulation of ACE2 by SARS-CoV-2 spike protein (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/4/42/WP4799_2113.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/4/42/WP4799_2113.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), 'Downregulation ...', 'https://classic...', 'Downregulation ...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4799', '300', 'center', 'Downregulation ...', 'pathway', 'Downregulation ...')
  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), 'Saturday 4 May ...', 'Curation:Curren...', '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/OutputPage.php(405): Parser->parse('{| ?<!-- Specia...', Object(Title), Object(ParserOptions), true, true, 129405)
  22. 21 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{| ?<!-- Specia...', Object(Title), true, true)
  23. 22 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{| ?<!-- Specia...', Object(Title), true)
  24. 23 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{| ?<!-- Specia...')
  25. 24 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  26. 25 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  27. 26 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  28. 27 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  29. 28 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  30. 29 {main}

Updates

    more...

Discussions

No recent changes    more...

Forum

        Google group wikipathways-discuss


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