https://wiki.biouml.org/index.php?action=history&feed=atom&title=Find_longest_connected_chains_%28analysis%29 2026-04-13T08:45:40Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Find_longest_connected_chains_(analysis)&diff=7805&oldid=prev 2019-03-12T09:33:57Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:33, 12 March 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 27:</td> <td colspan="2" class="diff-lineno">Line 27:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score cutoff''' – Molecules with Score lower than specified will be excluded from the result</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score cutoff''' – Molecules with Score lower than specified will be excluded from the result</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Search collection''' – Collection containing reactions</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Search collection''' – Collection containing reactions</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Custom search collection''' – Path to the custom search collection</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Species''' – Species to which analysis should be confined</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Species''' – Species to which analysis should be confined</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Decorators''' – Decorators</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Decorators''' – Decorators</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Find_longest_connected_chains_(analysis)&diff=7054&oldid=prev 2017-02-13T12:01:27Z

<p>Protected &quot;<a href="/index.php/Find_longest_connected_chains_(analysis)" title="Find longest connected chains (analysis)">Find longest connected chains (analysis)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 12:01, 13 February 2017</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Find_longest_connected_chains_(analysis)&diff=7041&oldid=prev 2017-02-13T12:01:22Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Molecular-networks-Find-longest-connected-chains-icon.png]] Find longest connected chains<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> ;Class<br /> :{{Class|biouml.plugins.keynodes.LongestChainFinder}}<br /> ;Plugin<br /> :[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]]<br /> <br /> ==== Description ====<br /> Goal of this analysis is to find longest ''chains'' which contains as many elements from '''input collection''' as possible. Here ''chain'' means a path which starts and ends with the elements from the '''input collection'''. In this path length between two elements from the '''input collection''' is limited by '''maximal search radius'''.<br /> <br /> Analysis uses Dijkstra search algorithm to find all possible chains. Then short chains, or long chains which contains just a few elements from '''input collection''' are cut off using '''score''' parameter. Let ''N&lt;sub&gt;start&lt;/sub&gt;'' be a number of elements from the '''input collection''' in the chain, ''N&lt;sub&gt;total&lt;/sub&gt;'' be a total number of elements in the chain, then score is obtained using following formula:<br /> <br /> :: [[File:Molecular-networks-Find-longest-connected-chains-longestChainScore.gif]]<br /> <br /> where ''coef'' is value of '''score coefficient'''.<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Molecules collection''' – Input the collection of molecules/genes<br /> * '''Limit input size''' (expert) – Limit size of input list<br /> * '''Input size''' (expert) – Size of input list<br /> * '''Search direction''' – Direction to perform search in (either upstream, downstream reactions or both directions)<br /> * '''Max radius''' – Maximal search radius<br /> * '''Max depth for Dijkstra''' – Maximal depth which will be used in Dijkstra search algorithm<br /> * '''Score cutoff''' – Molecules with Score lower than specified will be excluded from the result<br /> * '''Search collection''' – Collection containing reactions<br /> * '''Species''' – Species to which analysis should be confined<br /> * '''Decorators''' – Decorators<br /> * '''Output table''' – Path to the result table<br /> * '''Score coefficient''' (expert) – Parameter which is used to evalueate score<br /> <br /> [[Category:Analyses]]<br /> [[Category:Molecular networks (analyses group)]]<br /> [[Category:GeneXplain analyses]]<br /> [[Category:Autogenerated pages]]</div>

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