https://wiki.biouml.org/index.php?action=history&feed=atom&title=BioNetGen_language_format 2026-04-23T12:19:21Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=BioNetGen_language_format&diff=7024&oldid=prev 2017-02-13T12:01:00Z

<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 12:01, 13 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:BioNetGen language format (*.bngl)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:BioNetGen language format (*.bngl)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Element type</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Element type</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:{{Type link|<del class="diffchange diffchange-inline">diagram</del>}}</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:{{Type link|<ins class="diffchange diffchange-inline">Diagram</ins>}}</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.bionetgen (plugin)|biouml.plugins.bionetgen (Support for BioNetGen)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.bionetgen (plugin)|biouml.plugins.bionetgen (Support for BioNetGen)]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=BioNetGen_language_format&diff=6752&oldid=prev 2015-08-25T06:06:25Z

<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 06:06, 25 August 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># simulate (simulate_ode, simulate_ssa).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># simulate (simulate_ode, simulate_ssa).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Syntax and parameters for BioNetGen actions. 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Multi-valued parameters may be either arrays or hashes. &#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>{|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>{| <ins class="diffchange diffchange-inline">class=&quot;wikitable&quot;</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Action/parameter&lt;sup&gt;1&lt;/sup&gt;'''</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Action/parameter&lt;sup&gt;1&lt;/sup&gt;'''</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Default'''</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Default'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|'''generate_network'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|colspan=&quot;2&quot;</ins>|'''generate_network'''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|'''Generate species and reactions through iterative application of rules to seed species'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|colspan=&quot;2&quot;</ins>|'''Generate species and reactions through iterative application of rules to seed species'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|max_agg</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|max_agg</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 66:</td> <td colspan="2" class="diff-lineno">Line 66:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|'''simulate_ode/simulate_ssa/simulate'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|colspan=&quot;2&quot;</ins>|'''simulate_ode/simulate_ssa/simulate'''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|'''Simulation parameters for current model/network'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|colspan=&quot;2&quot;</ins>|'''Simulation parameters for current model/network'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|t_end</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>|t_end</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=BioNetGen_language_format&diff=6459&oldid=prev 2015-08-25T05:20:43Z

<p>Automatic synchronization with BioUML</p> <a href="https://wiki.biouml.org/index.php?title=BioNetGen_language_format&amp;diff=6459&amp;oldid=5839">Show changes</a>

WikiBot https://wiki.biouml.org/index.php?title=BioNetGen_language_format&diff=5839&oldid=prev 2014-12-11T09:18:09Z

<p>Protected &quot;<a href="/index.php/BioNetGen_language_format" title="BioNetGen language format">BioNetGen language format</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 09:18, 11 December 2014</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=BioNetGen_language_format&diff=5838&oldid=prev 2014-12-11T09:18:06Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;File format title<br /> :BioNetGen language format (*.bngl) (with deploying to full network)<br /> ;Element type<br /> :{{Type link|diagram}}<br /> ;Plugin<br /> :[[Biouml.plugins.bionetgen (plugin)|biouml.plugins.bionetgen (Support for BioNetGen)]]<br /> <br /> == BioNetGen language format (*.bngl) (with deploying to full network) ==<br /> BioNetGen importer (imports .bngl file to dml-diagram, deploys model to full reaction network)<br /> <br /> ==== Parameters: ====<br /> <br /> * '''File to import''' – Specify file from your computer<br /> * '''Target''' – Path in repository to put imported file to<br /> * '''Properties''' – Additional importer parameters<br /> <br /> [[Category:File formats]]<br /> [[Category:Autogenerated pages]]</div>

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