WikiPathways

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
Current revision (14:58, 11 April 2024) (view source)
(April data release)
 
(609 intermediate revisions not shown.)
Line 1: Line 1:
-
<analytics uacct="UA-1605246-1" ></analytics>
+
{|
 +
<!-- 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>
 +
-->
-
= WikiPathways =
+
<!-- TECHNICAL DIFFICULTIES -->
-
=== A Wiki for Biological Pathways ===
+
<!--
-
''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.''
+
|-valign="top"
 +
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
 +
<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
 +
<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>
-
<big>'''UNDER CONSTRUCTION'''</big>
+
<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
 +
<h2 class="frontPagePanel blueFg">Find Pathways</h2>
 +
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
 +
|-
 +
|rowspan="2" align="center" style="width:25%;"|
 +
|align="center" valign="top"|<big>'''Search'''</big><BR>{{#searchPathwaysBox:}}
 +
|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.png|200|center||special|BrowsePathwaysPage|Browse}}
 +
'''Browse by species and category'''
 +
|rowspan="2" align="center" style="width:25%;"|
 +
|-
 +
|align="left" valign="top"|'''You can search by:'''
 +
*Pathway name ''(Apoptosis)''
 +
*Gene or protein name ''(p53)''
 +
*Any page content ''(cancer)''
 +
|-
 +
|colspan="7"|
 +
|}
-
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!
+
<h2 class="frontPagePanel blueFg">Get Pathways</h2>
 +
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
 +
|-
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|align="center" valign="top"|<big>'''Download'''</big>{{#imgLink:Download_label.png|215|center|||Download_Pathways|Download}}
 +
'''Multiple formats and methods'''
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|rowspan="1" align="center" valign="top"|<big>'''Growth'''</big>{{#imgLink:Wp_growth_label.png|200|center|||WikiPathways:Statistics|Growth}}
 +
'''New pathways added each month'''
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|-
 +
|colspan="7"|
 +
|}
-
Thomas Kelder: Thomas.Kelder[AT]BIGCAT[DOT]unimaas[DOT]nl
+
<h2 class="frontPagePanel blueFg">Edit Pathways</h2>
-
<br>
+
{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
-
Alex Pico: apico[AT]gladstone[DOT]ucsf[DOT]edu
+
|-
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|align="center" valign="top"|<big>'''Learn'''</big>{{#imgLink:AcademyPath.png|200|center||external|http://academy.wikipathways.org|WikiPathways Academy}}
 +
'''Play with the editor tools'''
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|align="center" valign="top"|<big>'''Request'''</big>{{#imgLink:RequestForm2.png|210|center||external|https://github.com/wikipathways/pathway-curation-tasks/issues|Figure Conversion}}
 +
'''Queue figures for conversion'''
 +
|rowspan="1" align="center" style="width:25%;"|
 +
|-
 +
|colspan="7"|
 +
|}
-
<big>'''UNDER CONSTRUCTION'''</big>
+
<!-- SURVEY -->
 +
{|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"|
 +
|}
-
{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} }}
+
</div>
-
==== TEST PAGES: ====
 
-
<inputbox>
+
| valign="top"|
-
type=search
+
<div class="frontPagePanel blueBg" style="width:90%;margin:1em;width=100%;">
-
</inputbox>
+
<h2 class="frontPagePanel blueFg">Today's Featured Pathway</h2>{{ #pathwayOfTheDay: {{LOCALDAYNAME}} {{LOCALDAY}} {{LOCALMONTHNAME}} {{LOCALYEAR}} | Curation:CurrentHighlight | true}}
 +
<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
 +
* '''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].
 +
* '''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].
 +
* '''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].
 +
* '''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].
 +
* '''December 2023 Release''': [[Special:RecentPathwayChanges|120 edits]] by [[WikiPathways:Statistics#Contribution_scores|12 contributors]].
 +
* '''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]
-
[[:Category:Human|Overview of all human pathways]]
+
</div>
 +
|}
-
[[:Category:Mouse|Overview of all mouse pathways]]
+
__NOEDITSECTION__ <!-- Turn off section editing -->
-
 
+
__NOTOC__ <!-- Turn off Table of Contents  -->
-
[[:Category:Rat|Overview of all rat pathways]]
+
-
 
+
-
[[:Category:Cellular Process|Cellular Process category]]
+
-
 
+
-
[[:Category:Metabolic Process|Metabolic Process category]]
+
-
 
+
-
[[:Category:Physiological Process|Physiological Process category]]
+
-
 
+
-
[[:Category:Molecular Function|Molecular Function category]]
+
-
 
+
-
----
+
-
 
+
-
[[Help:LiteratureReferences|Help on literature references]]
+

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/2/2f/WP4799_2054.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/2/2f/WP4799_2054.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


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