WikiPathways

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<analytics uacct="UA-1605246-1" ></analytics>
 
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{|  
{|  
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<!-- Special Notice Section-->
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<!--
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|<div class="frontPagePanel blueBg" style="width:95%;margin:1em;width=100%">
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|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel blueFg">Welcome to WikiPathways <sup>BETA</sup></h2>
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<h2 class="frontPagePanel yellowFg">11 April 2019: Scheduled Downtime</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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<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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<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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<!-- TECHNICAL DIFFICULTIES -->
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<h2 class="frontPagePanel yellowFg">How To Find a Pathway</h2>
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<!--
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:There are many ways to find your pathways of interest. You can search by:
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|-valign="top"
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:* Name of the pathway
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|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
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:* Browse by species
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<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
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:* Browse by pathway categories
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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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:* Search by gene name (google search)
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-->
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<h2 class="frontPagePanel yellowFg">Viewing Pathways</h2>
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<!-- ANNOUNCEMENTS -->
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:<big>'''Image'''</big>
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<!--
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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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|-valign="top" align="center"
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:<big>'''Text'''</big>
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|colspan="8"|<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
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:Each Pathway Page has a text description, itemized gene list, references and relevant links.
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<h2 class="frontPagePanel redFg">Share your pathway knowledge in the fight against COVID-19</h2>  
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:<big>'''Data'''</big>
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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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: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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-->
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<h2 class="frontPagePanel yellowFg">Editing Pathways</h2>
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<!-- Page Content -->
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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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|<div class="frontPagePanel greenBg" style="width:95%;margin:1em;width=100%">
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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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</font></div>
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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 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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|-
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|colspan="7"|
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|}
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:'''Also see the [[Help:Contents |Help pages]]'''
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<h2 class="frontPagePanel blueFg">Get Pathways</h2>
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</div>
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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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|rowspan="1" align="center" style="width:25%;"|
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|-
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|colspan="7"|
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|}
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<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel blueFg">Edit Pathways</h2>
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<h2 class="frontPagePanel redFg">''UNDER CONSTRUCTION''</h2>
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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'''This site is undergoing rigorous beta testing. 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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|-
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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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|rowspan="1" align="center" style="width:25%;"|
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|-
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|colspan="7"|
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|}
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If you have any questions or suggestions, you can post them to the [http://groups.google.com/group/wikipathways-user WikiPathways-Users Google Group], or email them directly to us:
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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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|-
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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 greenBg" style="width:90%;margin:1em;width=100%;">
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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" 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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<h2 class="frontPagePanel greenFg">New!</h2>
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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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New AJAX editor embedded into every WikiPathways page. Edit pathways without opening an external editor!
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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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[[Download Pathways|Batch download page]]: download all pathways as an archive of image or data files with a single click!
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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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<h2 class="frontPagePanel greenFg">Coming Soon...</h2>
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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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* Additional Species:
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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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** Fruit Fly
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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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** Zebrafish
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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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** C.elegans
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&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Updates|more...]]
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** Yeast
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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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* Visual comparison of different pathway versions
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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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* Improved pathway editor
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<h2 class="frontPagePanel greenFg">Contents</h2>
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<!-- hide old search
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<inputbox>
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type=search
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searchbuttonlabel=Search
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width=30
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break=no
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</inputbox>
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-->
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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 14:58, 11 April 2024

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

Host-pathogen interaction of human coronaviruses - interferon induction (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/e/e9/WP4880_7025.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/e/e9/WP4880_7025.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), 'Host-pathogen i...', 'https://classic...', 'Host-pathogen i...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4880', '300', 'center', 'Host-pathogen i...', 'pathway', 'Host-pathogen i...')
  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), 'Friday 17 May 2...', '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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