Team:Slovenia/Modeling

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<a style="position:absolute; top:0px; left:490px;" href="https://2012.igem.org/Main_Page"><b>iGEM 2012</b></a>
</div>
</div>
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<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
 
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
 
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You <strong>MUST</strong>  have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace. 
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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<!-- start main menu -->
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!align="center"|[[Team:Slovenia|Home]]
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<div id='cssmenu'>
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!align="center"|[[Team:Slovenia/Team|Team]]
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<ul>
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!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Slovenia Official Team Profile]
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<li><a href='https://2012.igem.org/Team:Slovenia'><span>Home</span></a></li>
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!align="center"|[[Team:Slovenia/Project|Project]]
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<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Idea'><span>Idea</span></a>
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!align="center"|[[Team:Slovenia/Parts|Parts Submitted to the Registry]]
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  <ul>
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!align="center"|[[Team:Slovenia/Modeling|Modeling]]
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<li><a href='https://2012.igem.org/Team:Slovenia/IdeaBioTherapy'><span>Biological therapy</span></a></li>
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!align="center"|[[Team:Slovenia/Notebook|Notebook]]
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<li><a href='https://2012.igem.org/Team:Slovenia/IdeaChallenge'><span>Challenge</span></a></li>
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!align="center"|[[Team:Slovenia/Safety|Safety]]
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<li><a href='https://2012.igem.org/Team:Slovenia/Idea'><span>Solution</span></a></li>
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!align="center"|[[Team:Slovenia/Attributions|Attributions]]
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  </ul>
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|}
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</li>
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<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/TheSwitch'><span>The switch</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitch'><span>Overview</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators'><span>Designed TAL regulators</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
 +
  </ul>
 +
</li>
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanisms'><span>Safety mechanisms</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanisms'><span>Overview</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsEscapeTag'><span>Escape tag</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsTermination'><span>Termination</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation'><span>Microcapsule degradation</span></a></li>
 +
  </ul>
 +
</li>
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Implementation'><span>Implementation</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/Implementation'><span>Overview</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationHepatitisC'><span>Hepatitis C</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationIschaemicHeartDisease'><span>Ischaemic heart disease</span></a></li>
 +
 +
  </ul>
 +
</li>
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Modeling'><span>Modeling</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/Modeling'><span>Overview</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingPK'><span>Pharmacokinetics</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMethods'><span>Modeling methods</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel'><span>Quantitative and stability model</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations'><span>Interactive simulations</span></a></li>
 +
  </ul>
 +
</li>
-
If you choose to include a '''Modeling''' page, please write about your modeling adventures here. This is not necessary but it may be a nice list to include.
+
<li><a href='https://2012.igem.org/Team:Slovenia/Parts'><span>Parts</span></a></li>
 +
 +
 
 +
 
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Notebook'><span>Notebook</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/Notebook'><span>Experimental methods</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/NotebookLablog'><span>Lablog</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/NotebookLabSafety'><span>Lab safety</span></a></li>
 +
  </ul>
 +
</li>
 +
 
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Society'><span>Society</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/Society'><span>Human practice</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyScientists'><span>Scientists</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedicalDoctors'><span>Physicians</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyEthics'><span>Ethics, safety and regulations</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyPatients'><span>Patients</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedia'><span>Journalists and general public</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyOutreach'><span>Outreach</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/SocietyQuestionnaire'><span>Questionnaire</span></a></li>
 +
  </ul>
 +
</li>
 +
 
 +
 
 +
<li class='has-sub '><a href='https://2012.igem.org/Team:Slovenia/Team'><span>Team</span></a>
 +
  <ul>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/Team'><span>Team members</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TeamAttributions'><span>Attributions</span></a></li>
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<li><a href='https://2012.igem.org/Team:Slovenia/TeamGallery'><span>Gallery</span></a></li>
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<li><a href='https://2012.igem.org/Team:Slovenia/TeamSponsors'><span>Sponsors</span></a></li>
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<h1>Modeling overview</h1>
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<strong style="font-size:120%;">Modeling summary</strong><br/>
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We constructed deterministic and stochastic models to analyze both of our switches and developed two additional modeling approaches:
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    <li>a quantitative model based on the available experimental data;</li>
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    <li>a new modeling algorithm, called C#Sim, based on object-oriented programming approach.</li>
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All models consistently demonstrate that:
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    <li>the mutual repressor switch is unlikely to exhibit bistability in a realistic experimental setting using monomeric transcription factors;</li>
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    <li>the positive feedback loop switch is, in terms of robustness, far superior to the mutual repressor switch based on non-cooperative orthogonal DNA-binding domains of transcription factors, exhibiting bistability in more demanding (non-ideal) conditions.</li>
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Therefore, we predicted that the mutual repressor switch would not exhibit bistable behavior, while the positive feedback loop switch should be stable. These assessments were confirmed by experimental results, with the positive feedback loop switch clearly exhibiting bistability.
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We also built a pharmacokinetic model of drug distribution to compare our mammalian cell-based therapy with the standard therapy.
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Revision as of 17:19, 25 September 2012


Modeling overview

Modeling summary

We constructed deterministic and stochastic models to analyze both of our switches and developed two additional modeling approaches:

  • a quantitative model based on the available experimental data;
  • a new modeling algorithm, called C#Sim, based on object-oriented programming approach.

All models consistently demonstrate that:

  • the mutual repressor switch is unlikely to exhibit bistability in a realistic experimental setting using monomeric transcription factors;
  • the positive feedback loop switch is, in terms of robustness, far superior to the mutual repressor switch based on non-cooperative orthogonal DNA-binding domains of transcription factors, exhibiting bistability in more demanding (non-ideal) conditions.

Therefore, we predicted that the mutual repressor switch would not exhibit bistable behavior, while the positive feedback loop switch should be stable. These assessments were confirmed by experimental results, with the positive feedback loop switch clearly exhibiting bistability.

We also built a pharmacokinetic model of drug distribution to compare our mammalian cell-based therapy with the standard therapy.

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