WikiPathways

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
(updated curator of the week)
(197 intermediate revisions not shown.)
Line 1: Line 1:
-
__NOEDITSECTION__ <!-- Turn off section editing -->
 
-
__NOTOC__ <!-- Turn off Table of Contents  -->
 
-
 
{|  
{|  
<!-- Special Notice Section-->
<!-- Special Notice Section-->
-
<!--|-valign="top"
+
<!--
 +
|-valign="top"
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
-
<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
+
<h2 class="frontPagePanel yellowFg">11 April 2019: Scheduled Downtime</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>-->
+
<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"
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
|colspan="8"|<div class="frontPagePanel yellowBg" style="width:95%;margin:1em;width=100%">
-
<h2 class="frontPagePanel yellowFg">WikiPathways Survey</h2>
+
<h2 class="frontPagePanel yellowFg">2015-Sep-01: Technical issues.</h2>
-
<font size=2>'''How do you use WikiPathways?  A quick survey to help us focus development and renew funding. [https://www.surveymonkey.com/r/wikipathways https://www.surveymonkey.com/r/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 blueBg" style="width:95%;margin:1em;width=100%">
 +
<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>
 +
-->
 +
 
 +
<!-- Page Content -->
|-valign="top"
|-valign="top"
-
|<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
+
|<div class="frontPagePanel greenBg" style="width:95%;margin:1em;width=100%">
-
<h2 class="frontPagePanel redFg">Welcome to WikiPathways <sup>BETA</sup></h2>
+
<h2 class="frontPagePanel greenFg">Welcome to WikiPathways</h2>
-
<font size=2>'''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>'''WikiPathways is a database of biological pathways maintained by and for the scientific community.'''
 +
''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%">
-
<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 26: Line 38:
|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 38: Line 50:
|}
|}
-
<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 53: Line 65:
|}
|}
-
<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>'''Convert'''</big>{{#imgLink:RequestForm2.png|210|center||external|https://goo.gl/forms/PqBXnKXAjI1hnQMQ2|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]]
+
 
-
* [http://wikipathways.tumblr.com/ Selected publications using WikiPathways].
+
<!-- SURVEY -->
-
'''For more information see the [[Help:Contents |Help pages]]'''
+
{|style="width:100%;margin-top:3em;" border="0" cellspacing="2" cellpadding="1" align="center"
-
|rowspan="1" align="center" style="width:1%;"|
+
|-
 +
|<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 79: Line 93:
| 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:FeaturedPathway | true}}
-
<h2 class="frontPagePanel greenFg">News</h2>
+
<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)]
-
* Check out the new [http://dx.doi.org/10.1093/nar/gkv1024 WikiPathways paper] published January 2016 in NAR.
+
<h2 class="frontPagePanel blueFg" style="margin-top:0.5em;">Updates</h2>
-
* Read about the Reactome pathways on this site in this [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004941 PLOS Comput Bio] paper published May 2016.
+
* '''January 2020 Release''': [[Special:RecentPathwayChanges|96 edits]] by [[WikiPathways:Statistics#Contribution_scores|17 contributors]] and [[WikiPathways:NewPathwayReleases#January_2020|9 new pathways]].
-
* And this Resource Description Framework API is described in this [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004989 PLOS Comput Bio] paper published June 2016.
+
* '''December 2019 Release''': [[Special:RecentPathwayChanges|312 edits]] by [[WikiPathways:Statistics#Contribution_scores|19 contributors]] and [[WikiPathways:NewPathwayReleases#December_2019|3 new pathways]].
-
<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...]]
+
* '''November 2019 Release''': [[Special:RecentPathwayChanges|172 edits]] by [[WikiPathways:Statistics#Contribution_scores|19 contributors]] and [[WikiPathways:NewPathwayReleases#November_2019|15 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 Google group wikipathways-discuss]
+
* '''October 2019 Release''': 728 edits by 16 contributors and 5 new pathways
-
<h2 class="frontPagePanel greenFg">Activity</h2>
+
* '''September 2019 Release''': 905 edits by 15 contributors and 5 new pathways
-
* Check our [[Special:TissueAnalyzer|TissueAnalyzer page]] to study pathway activity in different tissues.
+
* '''August 2019 Release''': 416 edits by 13 contributors and 8 new pathways
-
* Want to add your ORCID id to your WikiPathways account? [http://wikipathways.org/index.php/Template:User_ORCID Find out how to do it!]
+
* '''July 2019 Release''': 284 edits by 21 contributors and 18 new pathways
-
* [[PathwayWidget|Include an interactive pathway image]] on your own blog/website
+
* '''June 2019 Release''': 270 edits by 29 contributors and 4 new pathways
-
* [[WikiPathways:Statistics|Curation statistics]]
+
&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 greenFg">Community Interest</h2>
+
<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]
-
Portals within WikiPathways for communities with focused pathway interests:
+
-
* [[Portal:WormBase|WormBase]] pathways
+
-
* [[Portal:ExRNA|ExRNA]] related pathways
+
-
 
+
-
Want to start your own Portal? [[Contact_Us|Contact us!]]
+
</div>
</div>
|}
|}
 +
 +
__NOEDITSECTION__ <!-- Turn off section editing -->
 +
__NOTOC__ <!-- Turn off Table of Contents  -->

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

Tumor suppressor activity of SMARCB1 (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/3/37/WP4204_90146.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/3/37/WP4204_90146.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), 'Tumor suppresso...', 'https://www.wik...', 'Tumor suppresso...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4204', '300', 'center', 'Tumor suppresso...', 'pathway', 'Tumor suppresso...')
  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


Personal tools