http://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&feed=atom&action=historyTeam:Groningen/Modeling - Revision history2024-03-29T00:00:20ZRevision history for this page on the wikiMediaWiki 1.16.0http://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=154410&oldid=prevJaap: Blanked the page2011-09-21T15:22:22Z<p>Blanked the page</p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">'''Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local Artifitial Inteligence (AI) department and has significant experience in modeling in matlab.'''</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">==Methods==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">First of all we have to decide in what enviorment we want to model in. There is a lot of different software out there. Our 2009 team did a large survey on modeling packages used in Igem [https://2009.igem.org/Team:Groningen/Brainstorm/Modelling]. Our whitebook also included several biomodeling packages that we should look at:</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*[[Team:Groningen/Modeling/SynBioSS|SynBioSS]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*[[Team:Groningen/Modeling/CellDesigner|CellDesigner]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*[[Team:Groningen/Modeling/COPASI|COPASI]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*[[Team:Groningen/Modeling/Matlab with SimBiology|Matlab with SimBiology]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">Although COPASI and SimBiology seemed really nice (be sure to look at it when in doubt) we decided to go with matlab for the following reasons:</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Freedom of programming: Although the matlab programming syntax is rather cumborsome (espcially when using OOP) we are sure it can produce anything we want. </del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Popularety: There is a very large userbase for matlab and plenty of support for it. Many other iGEM teams use it so it will be easy to share our finings and models.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Great plotting and visalisation option: this will allow us to see what is going on without the hassle of exporting and importing the data to other packages.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Familiarety of the team: Not having to learn using a program from the beginning is a big advantage. Some of our members have years of experience with matlab and have no problem implementing anything in matlab.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">==Library==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">We are currently developing our own modeling library and hopefully we will be able to finish it in time for other teams to use it. It will be geared towards beginning/intermediate matlab users who want to model single cell processes. </del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">==Modules==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">We decided to build our model in the samen modules as the cloners will use. Because of the fragilety of the by stable switches these should be modeled first.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*[[Team:Groningen/Modeling/Module 1|Module 1]]</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">==Modeling blog==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">You can check our modeling progress on our [[Team:Groningen/Modeling/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.</del></div></td><td colspan="2"> </td></tr>
</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=131480&oldid=prevRodrigoperez at 13:06, 18 September 20112011-09-18T13:06:52Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local Artifitial Inteligence (AI) department and has significant experience in modeling in matlab.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local Artifitial Inteligence (AI) department and has significant experience in modeling in matlab.'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Methods==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Methods==</div></td></tr>
</table>Rodrigoperezhttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=131479&oldid=prevRodrigoperez at 13:06, 18 September 20112011-09-18T13:06:27Z<p></p>
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</table>Rodrigoperezhttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=131477&oldid=prevRodrigoperez at 13:06, 18 September 20112011-09-18T13:06:07Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">''</ins>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local <ins class="diffchange diffchange-inline">Artifitial Inteligence (</ins>AI<ins class="diffchange diffchange-inline">) </ins>department and has significant experience in modeling in matlab.<ins class="diffchange diffchange-inline">''</ins></div></td></tr>
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</table>Rodrigoperezhttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=81617&oldid=prevJaap at 10:16, 19 August 20112011-08-19T10:16:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modeling blog==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modeling blog==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>You can check our modeling progress on our [[Team:Groningen/Modeling/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>You can check our modeling progress on our [[Team:Groningen/Modeling/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">!align="center"|[[Team:Groningen|Home]]</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Groningen Official Team Profile]</del></div></td><td colspan="2"> </td></tr>
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</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=80174&oldid=prevJaap at 09:36, 18 August 20112011-08-18T09:36:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.</div></td></tr>
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</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=80011&oldid=prevJaap at 07:43, 18 August 20112011-08-18T07:43:46Z<p></p>
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<tr><td colspan="2"> </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;">{{HeaderGroningen2011}} </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.</div></td></tr>
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</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=9751&oldid=prevJaap at 13:55, 2 June 20112011-06-02T13:55:23Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Methods==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Methods==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>First of all we have to decide in what enviorment we want to model in. There is a lot of different software out there. Our 2009 team did a large survey on modeling packages used in Igem [https://2009.igem.org/Team:Groningen/Brainstorm/Modelling]. Our <del class="diffchange diffchange-inline">[[Whitebook|</del>whitebook<del class="diffchange diffchange-inline">]] </del>also included several biomodeling packages that we should look at:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>First of all we have to decide in what enviorment we want to model in. There is a lot of different software out there. Our 2009 team did a large survey on modeling packages used in Igem [https://2009.igem.org/Team:Groningen/Brainstorm/Modelling]. Our whitebook also included several biomodeling packages that we should look at:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/SynBioSS|SynBioSS]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/SynBioSS|SynBioSS]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/CellDesigner|CellDesigner]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/CellDesigner|CellDesigner]]</div></td></tr>
</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=7872&oldid=prevJaap at 08:17, 24 May 20112011-05-24T08:17:12Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/Matlab with SimBiology|Matlab with SimBiology]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Team:Groningen/Modeling/Matlab with SimBiology|Matlab with SimBiology]]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Alothough </del>COPASI seemed really nice (be sure to look at it when in doubt) we decided to go with matlab for the following reasons:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Although </ins>COPASI <ins class="diffchange diffchange-inline">and SimBiology </ins>seemed really nice (be sure to look at it when in doubt) we decided to go with matlab for the following reasons:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Freedom of programming: Although the matlab programming syntax is rather cumborsome (espcially when using OOP) we are sure it can produce anything we want. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Freedom of programming: Although the matlab programming syntax is rather cumborsome (espcially when using OOP) we are sure it can produce anything we want. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Popularety: There is a very large userbase for matlab and plenty of support for it. Many other iGEM teams use it so it will be easy to share our finings and models.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Popularety: There is a very large userbase for matlab and plenty of support for it. Many other iGEM teams use it so it will be easy to share our finings and models.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Great plotting and visalisation option: this will allow us to see what is going on without the hassle of exporting and importing the data to other packages.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Great plotting and visalisation option: this will allow us to see what is going on without the hassle of exporting and importing the data to other packages.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Familiarety of the team: Not having to learn using a program from the beginning is a big advantage. Some of our members have years of experience with matlab and have no problem implementing anything in matlab.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Familiarety of the team: Not having to learn using a program from the beginning is a big advantage. Some of our members have years of experience with matlab and have no problem implementing anything in matlab.</div></td></tr>
<tr><td colspan="2"> </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"> </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;">==Library==</ins></div></td></tr>
<tr><td colspan="2"> </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;">We are currently developing our own modeling library and hopefully we will be able to finish it in time for other teams to use it. It will be geared towards beginning/intermediate matlab users who want to model single cell processes. </ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modules==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modules==</div></td></tr>
</table>Jaaphttp://2011.igem.org/wiki/index.php?title=Team:Groningen/Modeling&diff=6928&oldid=prevJaap: /* Modeling blog */2011-05-19T11:18:11Z<p><span class="autocomment">Modeling blog</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modeling blog==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Modeling blog==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>You can check our modeling progress on our <del class="diffchange diffchange-inline">[</del>[[Team:Groningen/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>You can check our modeling progress on our [[Team:Groningen<ins class="diffchange diffchange-inline">/Modeling</ins>/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.</div></td></tr>
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</table>Jaap