Portal:BiGCaT

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BiGCaT at WikiPathways BETA

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Welcome to the BiGCaT Portal, a portal for the BiGCaT Bioinformatics group at Maastricht University.

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News

  • April 17 2008: The BiGCaT portal is open!

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Users

 

Featured Pathway

Mismatch repair (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/9/9c/WP531_11609.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/9/99/WP531_11609.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/9/99/WP531_11609.gpml" "/var/www/wikipathways/images/9/9c/WP531_11609.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), 'Mismatch repair', 'http://wikipath...', 'Mismatch repair', 'center', 'pwthumb', '300')
  5. 4 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP531', '300', 'center', 'Mismatch repair', 'pathway', 'Mismatch repair')
  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...', 'Portal:BiGCaT/F...')
  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, 11609)
  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}

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