https://wiki.biouml.org/index.php?action=history&feed=atom&title=Modular_modeling 2026-04-16T07:35:45Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Modular_modeling&diff=4271&oldid=prev 2013-06-07T09:16:23Z

<p></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 09:16, 7 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*graphic notation - provides rules for graphical presentation of modular models;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*<ins class="diffchange diffchange-inline">[[</ins>graphic notation<ins class="diffchange diffchange-inline">]] </ins>- provides rules for graphical presentation of modular models;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[flattening algorithm]] - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[flattening algorithm]] - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[agent based modeling]] - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[agent based modeling]] - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.</div></td></tr> </table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=Modular_modeling&diff=982&oldid=prev 2013-04-16T08:13:03Z

<p>+<a href="/index.php/Category:Modular_modeling" title="Category:Modular modeling">Category:Modular modeling</a></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 08:13, 16 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[Modular model of the human CVS v.1|version 1]], [[Modular model of the human CVS v.2|version 2]]).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[Modular model of the human CVS v.1|version 1]], [[Modular model of the human CVS v.2|version 2]]).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</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;"></ins></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;">[[Category:Modular modeling]]</ins></div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=Modular_modeling&diff=81&oldid=prev 2013-04-03T18:16:41Z

<p></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 18:16, 3 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[modular model of apoptosis]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[modular model of apoptosis]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*[[overall circulation model]] created by Guyton</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*[[overall circulation model]] <ins class="diffchange diffchange-inline">originally </ins>created by <ins class="diffchange diffchange-inline">professor </ins>Guyton <ins class="diffchange diffchange-inline">et al.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[Modular model of the human CVS v.1|version 1]], [[Modular model of the human CVS v.2|version 2]]).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[Modular model of the human CVS v.1|version 1]], [[Modular model of the human CVS v.2|version 2]]).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</div></td></tr> </table>

Axec@dote.ru https://wiki.biouml.org/index.php?title=Modular_modeling&diff=71&oldid=prev 2013-04-03T08:48:08Z

<p></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 08:48, 3 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[modular model of apoptosis]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[modular model of apoptosis]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[overall circulation model]] created by Guyton</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[overall circulation model]] created by Guyton</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[<del class="diffchange diffchange-inline">version1</del>]], [[<del class="diffchange diffchange-inline">version2</del>]]).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*modular model of cardio-vascular system ([[<ins class="diffchange diffchange-inline">Modular model of the human CVS v.1|version 1</ins>]], [[<ins class="diffchange diffchange-inline">Modular model of the human CVS v.2|version 2</ins>]]).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>All these models are freely available via the web interface provided by the BioUML platform.</div></td></tr> </table>

Axec@dote.ru https://wiki.biouml.org/index.php?title=Modular_modeling&diff=67&oldid=prev 2013-04-03T07:01:55Z

<p></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 07:01, 3 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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;">[[File:notation.png|thumb|Modular model notation]]</ins></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;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Modular approach to modeling of biological systems has been rapidly developing in recent years. It implies system decomposition into subsystems, each of which can be modeled and validated independently. Model of the whole system is given as a combination of the subsystem models (modules).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Modular approach to modeling of biological systems has been rapidly developing in recent years. It implies system decomposition into subsystems, each of which can be modeled and validated independently. Model of the whole system is given as a combination of the subsystem models (modules).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>This approach makes the structure of complex hierarchic models more explicit by allocation of functional units and their interconnections.It also allows incorporating models developed by different authors, focusing on different parts of the system and utilizing different scales and even formalisms into complex models.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>This approach makes the structure of complex hierarchic models more explicit by allocation of functional units and their interconnections.It also allows incorporating models developed by different authors, focusing on different parts of the system and utilizing different scales and even formalisms into complex models.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*<del class="diffchange diffchange-inline">[[</del>graphic notation<del class="diffchange diffchange-inline">]] </del>- provides rules for graphical presentation of modular models;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*graphic notation - provides rules for graphical presentation of modular models;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[flattening algorithm]] - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[flattening algorithm]] - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[agent based modeling]] - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[agent based modeling]] - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.</div></td></tr> </table>

Axec@dote.ru https://wiki.biouml.org/index.php?title=Modular_modeling&diff=66&oldid=prev 2013-04-03T06:52:24Z

<p>Created page with &quot;Modular approach to modeling of biological systems has been rapidly developing in recent years. It implies system decomposition into subsystems, each of which can be modeled a...&quot;</p> <p><b>New page</b></p><div>Modular approach to modeling of biological systems has been rapidly developing in recent years. It implies system decomposition into subsystems, each of which can be modeled and validated independently. Model of the whole system is given as a combination of the subsystem models (modules).<br /> This approach makes the structure of complex hierarchic models more explicit by allocation of functional units and their interconnections.It also allows incorporating models developed by different authors, focusing on different parts of the system and utilizing different scales and even formalisms into complex models.<br /> <br /> The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:<br /> <br /> *[[graphic notation]] - provides rules for graphical presentation of modular models;<br /> *[[flattening algorithm]] - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;<br /> *[[agent based modeling]] - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.<br /> We have developed a number of examples demonstrating application of this approach:<br /> <br /> *[[modular model of apoptosis]]<br /> *[[overall circulation model]] created by Guyton<br /> *modular model of cardio-vascular system ([[version1]], [[version2]]).<br /> All these models are freely available via the web interface provided by the BioUML platform.</div>

Axec@dote.ru