WikiPathways

From WikiPathways

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<big>'''MediaWiki has been successfully installed.'''</big>
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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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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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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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== Getting started ==
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<h1 class="frontPagePanel redFg">To celebrate our 10th anniversary, a [https://gladstone.org/WP18Summit WikiPathways Summit] will be held from <b>8-10 Oct.</b> in San Francisco.</h1></div>
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* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
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* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
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* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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|<div class="frontPagePanel greenBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel greenFg">Welcome to WikiPathways</h2>
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<font size=2>'''WikiPathways is a database of biological pathways maintained by and for the scientific community.'''
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''Read about our 12-year journey so far and [[WikiPathways:ExitBeta_Announcement|official exit from beta]].''</font></div>
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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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|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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<h2 class="frontPagePanel blueFg">Get 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="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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<h2 class="frontPagePanel blueFg">Edit 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="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>'''Convert'''</big>{{#imgLink:RequestForm2.png|210|center||external|https://goo.gl/forms/PqBXnKXAjI1hnQMQ2|Figure Conversion}}
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'''Queue figures for conversion'''
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<!-- SURVEY -->
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{|style="width:100%;margin-top:3em;" border="0" cellspacing="2" cellpadding="1" align="center"
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|-
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|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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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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| 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:FeaturedPathway | true}}
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<h2 class="frontPagePanel blueFg">Curator of the Week</h2>{{#imgLink:DeniseSlenter.png‎|70|center|||http://www.wikipathways.org/index.php/User:DeSl|Denise Slenter}} [http://www.wikipathways.org/index.php/User:DeSl Denise Slenter (Maastricht University)]
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<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
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* '''January 2020 Release''': [[Special:RecentPathwayChanges|96 edits]] by [[WikiPathways:Statistics#Contribution_scores|17 contributors]] and [[WikiPathways:NewPathwayReleases#January_2020|9 new pathways]].
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* '''December 2019 Release''': [[Special:RecentPathwayChanges|312 edits]] by [[WikiPathways:Statistics#Contribution_scores|19 contributors]] and [[WikiPathways:NewPathwayReleases#December_2019|3 new pathways]].
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* '''November 2019 Release''': [[Special:RecentPathwayChanges|172 edits]] by [[WikiPathways:Statistics#Contribution_scores|19 contributors]] and [[WikiPathways:NewPathwayReleases#November_2019|15 new pathways]].
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* '''October 2019 Release''': 728 edits by 16 contributors and 5 new pathways
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* '''September 2019 Release''': 905 edits by 15 contributors and 5 new pathways
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* '''August 2019 Release''': 416 edits by 13 contributors and 8 new pathways
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* '''July 2019 Release''': 284 edits by 21 contributors and 18 new pathways
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* '''June 2019 Release''': 270 edits by 29 contributors and 4 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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Revision as of 19:24, 20 January 2020

Welcome to WikiPathways

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

Read about our 12-year journey so far and official exit from beta.

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

Convert

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

Differentiation Pathway (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/b/b4/WP2848_1.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/b/b4/WP2848_1.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), 'Differentiation...', 'https://www.wik...', 'Differentiation...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP2848', '300', 'center', 'Differentiation...', 'pathway', 'Differentiation...')
  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), 'Monday 24 Febru...', '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/OutputPage.php(405): Parser->parse('{| ?<!-- Specia...', Object(Title), Object(ParserOptions), true, true, 108694)
  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}

Curator of the Week

Denise Slenter (Maastricht University)

Updates

    more...

Discussions

23 February 2020
Welcome new user (5) by Susan Coort
    more...

Forum

    Google group wikipathways-discuss


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