WikiPathways

From 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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{|  
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<!--
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<h2 class="frontPagePanel blueFg">A Wiki for Biological Pathways</h2>
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<font size=2>'''In the “tradition” of <span class=plainlinks>[http://wikipedia.org Wikipedia]</span> 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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<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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<!-- ANNOUNCEMENTS -->
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|colspan="8"|<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
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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:Disease/COVIDPathways|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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<!-- Page Content -->
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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>
<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel yellowFg">How To Find a Pathway</h2>
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<h2 class="frontPagePanel blueFg">Find Pathways</h2>
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:There are many ways to find your pathways of interest. You can search by:
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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:* Name of the pathway
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|-
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:* Browse by species
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|rowspan="2" align="center" style="width:25%;"|
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:* Browse by pathway categories
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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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|-
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|colspan="7"|
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|}
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:Coming soon:
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<h2 class="frontPagePanel blueFg">Get Pathways</h2>
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:*Search by gene name
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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:*Advanced search options, limit by organism or category
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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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<h2 class="frontPagePanel yellowFg">Viewing Pathways</h2>
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<h2 class="frontPagePanel blueFg">Edit Pathways</h2>
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:<big>'''Image'''</big>
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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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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|-
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:<big>'''Text'''</big>
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|rowspan="1" align="center" style="width:25%;"|
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:Each Pathway Page has a text description, itemized gene list, references and relevant links.
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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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:<big>'''Data'''</big>
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'''Play with the editor tools'''
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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].
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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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|rowspan="1" align="center" style="width:25%;"|
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|-
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|colspan="7"|
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<h2 class="frontPagePanel yellowFg">Editing Pathways</h2>
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<!-- SURVEY -->
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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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{|style="width:100%;margin-top:3em;" border="0" cellspacing="2" cellpadding="1" align="center"
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|-
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:'''Try it out in the [[Pathway:Human:Sandbox | Sandbox]] pathway!'''
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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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:'''Also see the [[Help:Contents |Help pages]]'''
 
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<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
 
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<h2 class="frontPagePanel redFg">''UNDER CONSTRUCTION''</h2>
 
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'''This site is undergoing rigorous beta testing through the end of May 2007.  We are still implementing critical features and making major changes to these pages. Nevertheless, feel free to use the site to find, edit and create pathway content.'''
 
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If you have any questions or suggestions, you can add them to the [[CommentsAndSuggestions | Comments and Suggestions]] page, or email them directly to us: 
 
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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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Also see the [http://ftp2.bigcat.unimaas.nl/~martijn.vaniersel/mantis/my_view_page.php PathVisio bug tracker] for WikiPathays and PathVisio related bugs.
 
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<div class="frontPagePanel blueBg" style="width:90%;margin:1em;width=100%;">
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<h2 class="frontPagePanel greenFg">Today's featured pathway</h2>
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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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{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} }}
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<h2 class="frontPagePanel blueFg">Curator of the Week</h2>{{#imgLink:Alexander_Pico.jpg‎‎‎|70|center|||http://www.wikipathways.org/index.php/User:AlexanderPico|Alexander Pico}} [http://www.wikipathways.org/index.php/User:AlexanderPico AlexanderPico(Gladstone Institutes)]
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<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
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* '''June 2020 Release''': [[Special:RecentPathwayChanges|215 edits]] by [[WikiPathways:Statistics#Contribution_scores|18 contributors]] and [[WikiPathways:NewPathwayReleases#June_2020|9 new pathways]]'''.
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* '''May 2020 Release''': [[Special:RecentPathwayChanges|269 edits]] by [[WikiPathways:Statistics#Contribution_scores|16 contributors]] and [[WikiPathways:NewPathwayReleases#May_2020|18 new pathways]]'''.
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* '''April 2020 Release''': [[Special:RecentPathwayChanges|427 edits]] by [[WikiPathways:Statistics#Contribution_scores|20 contributors]] and [[WikiPathways:NewPathwayReleases#April_2020|24 new pathways]], including many '''[[Portal:Disease/COVIDPathways|COVID-19 related pathways]]'''.
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* March 23: Rapidly growing collcetion of [[Portal:Disease/COVIDPathways|COVID-19 related pathways]]
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* '''March 2020 Release''': [[Special:RecentPathwayChanges|167 edits]] by [[WikiPathways:Statistics#Contribution_scores|27 contributors]] and [[WikiPathways:NewPathwayReleases#March_2020|9 new pathways]]
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* '''February 2020 Release''': [[Special:RecentPathwayChanges|193 edits]] by [[WikiPathways:Statistics#Contribution_scores|24 contributors]] and [[WikiPathways:NewPathwayReleases#February_2020|3 new pathways]]
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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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&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 class="frontPagePanel greenFg">Contents</h2>
 
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<inputbox>
 
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searchbuttonlabel=Search
 
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[[:Category:Human|Overview of all human pathways]]
 
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[[:Category:Mouse|Overview of all mouse pathways]]
 
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[[:Category:Rat|Overview of all rat pathways]]
 
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[[:Category:Cellular Process|Cellular Process category]]
 
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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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<h2 class="frontPagePanel greenFg">Statistics</h2>
 
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{{ #siteStats: class="greenBg" style="border: 0;"}}
 
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Revision as of 04:55, 6 July 2020

Share your pathway knowledge in the fight against COVID-19

ACCESS the rapidly growing collection of COVID-19 pathways, CONTRIBUTE your time and domain knowledge about pathway biology as a pathway author, and USE these pathways in your research.

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

Type I Interferon Induction and Signaling During SARS-CoV-2 Infection (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/4/40/WP4868_5616.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/4/40/WP4868_5616.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), 'Type I Interfer...', 'https://www.wik...', 'Type I Interfer...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4868', '300', 'center', 'Type I Interfer...', 'pathway', 'Type I Interfer...')
  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), 'Wednesday 5 Aug...', '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, 111059)
  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

AlexanderPico(Gladstone Institutes)

Updates

    more...

Discussions

Today
Welcome! (20) by Marvin Martens
    more...

Forum

    Google group wikipathways-discuss


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