Portal:CIRM

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Pathway Initiative

In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. We encourage the stem cell community to edit or annotate existing pathways or create new pathways. You can also recommend additional pathways to be included in the stem cell portal.

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CIRM Activities

Press Releases

• Stem Cell Agency Awards More than $42 million in New Research and Leadership Funding
• Stem Cell Agency Board Member and Researcher Honored by ALS Association
• Pitch Perfect Performances Win Stem Cell Agency’s Elevator Pitch Challenge

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Featured Pathway

ESC Pluripotency Pathways (Mus musculus)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/4/43/WP339_40136.svg:
Status:255
Message:[ 0.026] Info: Preferences file /var/www/.PathVisio/.PathVisio doesn't exist, using defaults Error: Unable to read inputfile: /var/www/wikipathways/images/0/09/WP339_40136.gpml GPML Converter Usage: java Converter <input filename> [<output filename>]

Converts between GPML format and several other formats: - GPML (.gpml/.xml) <-> GenMAPP (.mapp) - GPML (.gpml/.xml) -> SVG (.svg) - GPML (.gpml/.xml) -> PNG (.png) - GPML (.gpml/.xml) -> TIFF (.tiff) - GPML (.gpml/.xml) -> PDF (.pdf) The conversion direction is determined from the extension of the input file. Return codes: 0: OK -1: Parameter or file error -2: Conversion error

Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways/images/0/09/WP339_40136.gpml" "/var/www/wikipathways/images/4/43/WP339_40136.svg" 2>&1
' in /var/www/wikipathways/wpi/Pathway.php:1117 Stack trace:

1. 0 /var/www/wikipathways/wpi/Pathway.php(1092): Pathway::convert('/var/www/wikipa...', '/var/www/wikipa...')
2. 1 /var/www/wikipathways/wpi/Pathway.php(1023): Pathway->saveConvertedCache('svg')
3. 2 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(100): Pathway->updateCache('svg')
4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(50): makeThumbLinkObj(Object(Pathway), 'ESC Pluripotenc...', 'http://wikipath...', 'ESC Pluripotenc...', 'center', 'pwthumb', '300')
5. 4 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP339', '300', 'center', 'ESC Pluripotenc...', 'pathway', 'ESC Pluripotenc...')
6. 5 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
7. 6 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
8. 7 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
9. 8 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
10. 9 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
11. 10 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
12. 11 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
13. 12 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay.php(59): Parser->recursiveTagParse('{{Template:Toda...')
14. 13 [internal function]: getPathwayOfTheDay(Object(Parser), 'Saturday 25 May...', 'Curation:CIRM_R...', 'true')
15. 14 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
16. 15 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
17. 16 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
18. 17 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
21. 20 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
22. 21 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
23. 22 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
24. 23 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
25. 24 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
26. 25 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
27. 26 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
28. 27 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
29. 28 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
30. 29 /var/www/wikipathways/includes/Article.php(3406): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 40136)
31. 30 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('{{{{FULLPAGENAM...', false)
32. 31 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
33. 32 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
34. 33 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
35. 34 {main}

View all Featured Pathways for this Portal

Download all CIRM pathways by species:

• Danio rerio
• Homo sapiens
• Mus musculus
• Rattus norvegicus