WikiPathways

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
Current revision (14:58, 11 April 2024) (view source)
(April data release)
 
(460 intermediate revisions not shown.)
Line 1: Line 1:
-
__NOEDITSECTION__ <!-- Turn off section editing -->
 
-
__NOTOC__ <!-- Turn off Table of Contents  -->
 
-
 
{|  
{|  
 +
<!-- Special Notice Section-->
 +
<!--
 +
|-valign="top"
 +
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
 +
<h2 class="frontPagePanel yellowFg">11 April 2019: Scheduled Downtime</h2>
 +
<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>
 +
-->
 +
<!-- TECHNICAL DIFFICULTIES -->
 +
<!--
|-valign="top"
|-valign="top"
-
|<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
+
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
-
<h2 class="frontPagePanel redFg">Welcome to WikiPathways <sup>BETA</sup></h2>
+
<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
-
<font size=2>'''In the new tradition of [[wikipedia:Main_Page|Wikipedia]], WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. [[WikiPathways:About|More about WikiPathways...]]'''</font></div>
+
<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>
 +
-->
 +
 
 +
<!-- ANNOUNCEMENTS -->
 +
<!--
 +
|-valign="top" align="center"
 +
|colspan="8"|<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
 +
<h2 class="frontPagePanel redFg">Share your pathway knowledge in the fight against COVID-19</h2>  
 +
<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>
 +
-->
 +
 
 +
<!-- Page Content -->
 +
|-valign="top"
 +
|<div class="frontPagePanel greenBg" style="width:95%;margin:1em;width=100%">
 +
<h2 class="frontPagePanel greenFg">Try the New WikiPathways</h2>
 +
<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.
 +
</font></div>
<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
-
<h2 class="frontPagePanel blueFg">Finding Pathways</h2>
+
<h2 class="frontPagePanel blueFg">Find Pathways</h2>
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
|-
|-
Line 17: Line 39:
|rowspan="2" align="center" style="width:25%;"|
|rowspan="2" align="center" style="width:25%;"|
|rowspan="2" align="center" style="width:25%;"|
|rowspan="2" align="center" style="width:25%;"|
-
|rowspan="2" align="center" valign="top"|<big>'''Browse'''</big>{{#imgLink:Browse_thumb_200.jpg|200|center||special|BrowsePathwaysPage|Browse}}
+
|rowspan="2" align="center" valign="top"|<big>'''Browse'''</big>{{#imgLink:Browse_thumb.png|200|center||special|BrowsePathwaysPage|Browse}}
'''Browse by species and category'''
'''Browse by species and category'''
|rowspan="2" align="center" style="width:25%;"|
|rowspan="2" align="center" style="width:25%;"|
Line 29: Line 51:
|}
|}
-
<h2 class="frontPagePanel blueFg">Contributing New Pathways</h2>
+
<h2 class="frontPagePanel blueFg">Get Pathways</h2>
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
|-
|-
|rowspan="1" align="center" style="width:25%;"|
|rowspan="1" align="center" style="width:25%;"|
-
|align="center" valign="top"|<big>'''Create'''</big>{{#imgLink:Create_thumb_160.jpg|160|center||special|CreatePathwayPage|Create}}
+
|align="center" valign="top"|<big>'''Download'''</big>{{#imgLink:Download_label.png|215|center|||Download_Pathways|Download}}
-
'''Create a new pathway page'''
+
'''Multiple formats and methods'''
|rowspan="1" align="center" style="width:25%;"|
|rowspan="1" align="center" style="width:25%;"|
|rowspan="1" align="center" style="width:25%;"|
|rowspan="1" align="center" style="width:25%;"|
-
|rowspan="1" align="center" valign="top"|<big>'''Suggest'''</big>{{#imgLink:Wishlist_thumb_200.jpg|200|center||special|SpecialWishList|Wish list}}
+
|rowspan="1" align="center" valign="top"|<big>'''Growth'''</big>{{#imgLink:Wp_growth_label.png|200|center|||WikiPathways:Statistics|Growth}}
-
'''Add a pathway to the wish list'''
+
'''New pathways added each month'''
|rowspan="1" align="center" style="width:25%;"|
|rowspan="1" align="center" style="width:25%;"|
|-
|-
Line 44: Line 66:
|}
|}
-
<h2 class="frontPagePanel blueFg">Sample Pathway Pages</h2>
+
<h2 class="frontPagePanel blueFg">Edit Pathways</h2>
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
|-
|-
-
|rowspan="1" align="center" style="width:4%;"|
+
|rowspan="1" align="center" style="width:25%;"|
-
|rowspan="1" align="center" valign="top" style="width:45%;"|<big>'''Sandbox'''</big>{{#imgLink:Sandbox_thumb_200.jpg|200|center||pathway|WP4|Sandbox}}
+
|align="center" valign="top"|<big>'''Learn'''</big>{{#imgLink:AcademyPath.png|200|center||external|http://academy.wikipathways.org|WikiPathways Academy}}
'''Play with the editor tools'''
'''Play with the editor tools'''
-
|rowspan="1" align="center" style="width:4%;"|
+
|rowspan="1" align="center" style="width:25%;"|
-
|rowspan="1" align="center" style="width:1%;"|
+
|rowspan="1" align="center" style="width:25%;"|
-
|align="left" valign="top" style="width:45%;"|
+
|align="center" valign="top"|<big>'''Request'''</big>{{#imgLink:RequestForm2.png|210|center||external|https://github.com/wikipathways/pathway-curation-tasks/issues|Figure Conversion}}
-
'''Check out the following pages:'''<br>
+
'''Queue figures for conversion'''
-
* [[Special:RecentPathwayChanges | Show recent changes]]
+
|rowspan="1" align="center" style="width:25%;"|
-
* [[Special:NewPathwaysPage | Show new pathways]]
+
|-
-
* [[Special:MostEditedPathwaysPage | Show most edited pathways]]
+
|colspan="7"|
-
* [[Special:PopularPathwaysPage | Show most viewed pathways]]
+
|}
-
* [[Special:SpecialWishList | Show pathway wish list]]
+
 
-
'''For more information see the [[Help:Contents |Help pages]]'''
+
<!-- SURVEY -->
-
|rowspan="1" align="center" style="width:1%;"|
+
{|style="width:100%;margin-top:3em;" border="0" cellspacing="2" cellpadding="1" align="center"
 +
|-
 +
|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
 +
<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>
|-
|-
|colspan="7"|
|colspan="7"|
Line 69: Line 94:
| valign="top"|
| valign="top"|
-
<div class="frontPagePanel greenBg" style="width:90%;margin:1em;width=100%;">
+
<div class="frontPagePanel blueBg" style="width:90%;margin:1em;width=100%;">
-
<h2 class="frontPagePanel greenFg">Today's Featured Pathway</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:FeaturedPathway | true}}
+
<h2 class="frontPagePanel blueFg">Today's Featured Pathway</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:CurrentHighlight | true}}
-
<h2 class="frontPagePanel greenFg">Latest edits</h2><recentChanges class="greenBg" style="border:none" namespace='102' limit='1'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Edits|more...]]
+
<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
-
<h2 class="frontPagePanel greenFg">Latest discussions</h2><recentChanges class="greenBg" style="border:none" namespace='90' limit='3'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Discussions|more...]]
+
* '''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].
-
<h2 class="frontPagePanel greenFg">Forum</h2><rss>http://groups.google.com/group/wikipathways-discuss/feed/rss_v2_0_msgs.xml|short|max=3</rss>&nbsp;&nbsp;&nbsp;&nbsp;[http://groups.google.com/group/wikipathways-discuss more...]
+
* '''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].
-
<h2 class="frontPagePanel greenFg">New!</h2>
+
* '''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].
-
* Interactive pathway viewer, [[Pathway:WP4|try it here!]]
+
* '''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].
-
* [[PathwayWidget|Include an interactive pathway image]] on your own blog/website
+
* '''December 2023 Release''': [[Special:RecentPathwayChanges|120 edits]] by [[WikiPathways:Statistics#Contribution_scores|12 contributors]].
-
* [[WikiPathways:Statistics|Curation statistics]]
+
* '''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].
 +
* '''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].
 +
* '''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].
 +
* '''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].
 +
&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Updates|more...]]
 +
<h2 class="frontPagePanel blueFg">Discussions</h2><recentChanges class="blueBg" style="border:none" namespace='90' limit='2'></recentChanges>&nbsp;&nbsp;&nbsp;&nbsp;[[WikiPathways:Discussions|more...]]
 +
<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]
-
<h2 class="frontPagePanel greenFg">Community Interest</h2>
 
-
Portals within WikiPathways for communities with focused pathway interests:
 
-
* [[Portal:CIRM|CIRM]] stem cell pathways
 
-
* [[Portal:Micronutrient|Micronutrient initiative]] nutrition pathways
 
-
* [[Portal:GenMAPP|GenMAPP]] analysis pathways
 
-
* [[Portal:BiGCaT|BiGCaT]] contributed pathways
 
-
 
-
Want to start your own Portal? [[Contact_Us|Contact us!]]
 
-
 
-
<h2 class="frontPagePanel greenFg">Statistics</h2>{{ #siteStats: class="greenBg" style="border: 0;"}}
 
</div>
</div>
|}
|}
 +
 +
__NOEDITSECTION__ <!-- Turn off section editing -->
 +
__NOTOC__ <!-- Turn off Table of Contents  -->

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

SARS coronavirus and innate immunity (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/5/5c/WP4912_44494.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/5/5c/WP4912_44494.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), 'SARS coronaviru...', 'https://classic...', 'SARS coronaviru...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4912', '300', 'center', 'SARS coronaviru...', 'pathway', 'SARS coronaviru...')
  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 3 May 20...', '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


    Retrieved from "https://classic.wikipathways.org/index.php/WikiPathways"
    Personal tools