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<li><a href="home.htm">Home</a></li>
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<li><a href="rhodofactory.htm">Rhodofactory</a></li>
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<li><a href="promoterselection.htm">Promoter selection </a></li>
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<li><a href="results.htm">results </a></li>
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  </tr>
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<li><a href="perspectives.htm">Perspectives</a></li>
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<li class="active"><a href="Modelling.htm">Modeling</a></li>
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<li><a href="aboutus.htm">About us</a> </li>
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<li><a href="outreach.htm">outreach</a></li>
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<h1><a href="#"></a></h1>  
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<div id="page">
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<div id="context">
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<h1><em>Modeling Biological Systems!</em></h1>
 +
            <p>Characterization of biological systems has reached an unparalleled level of detail. To
 +
organize this detail and arrive at a better fundamental understanding of life processes, it is
 +
essentialthat powerful conceptual tools from mathematics and computer science be applied to the
 +
frontier problems in biology.<br>
 +
<br>
 +
Modeling is evolving into an important partner of experimental work. They attempt to predict
 +
and understand the behavior of complex biological systems before they are actually created. Also
 +
models can help to simplify the complexity of data and interactions involved into a more concise
 +
form with some measure of predictive ability. This can provide valuable insights into the working
 +
and general principles of organization of biological systems. Also it may suggest novel experiments
 +
for testing hypotheses, based on the modeling experiences.
 +
</p>
 +
            <hr>
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  <tr>
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<p id="refe"> References used through this section.<br>
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  <td><img src="https://static.igem.org/mediawiki/2012/6/68/LOGOPRIN.jpg" width="240" height="178" alt="Logo Principal" /></td>
+
 
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  <td bgcolor="01A79D"><ul class="nav">
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1. Oh JI, Kaplan S. (2001) <strong>Generalized approach to the regulation and integration of gene expression.</strong> Mol
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<li>
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Microbiol.<br>
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<a href="/Team/CINVESTAV-IPN-UNAM_MX/home.htm">Home<span class="flecha">&#9660;</span></a>
+
 
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</li>
+
2.Zeilstra-Ryalls JH, Kaplan S. (1995) <strong>Aerobic and anaerobic regulation in Rhodobacter sphaeroides</strong>2.4.1: the
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<li>
+
role of the fnrL gene. J Bacteriol.<br>
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<a href="#">Rhodofactory<span class="flecha">&#9660;</span></a>
+
 
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<ul>
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3.Shinji MasudaandCarl E. Bauer. (2002)<strong>AppA Is a Blue Light Photoreceptor that Antirepresses
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<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Overview.htm">Overview<span class="flecha">&#9660;</span></a></li>
+
Photosynthesis Gene Expression in Rhodobacter sphaeroides.</strong> Cell Press.<br>
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+
 
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Light Response.htm">Light Response<span class="flecha">&#9660;</span></a></li>
+
4.Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. (2004)<strong>BioNetGen: software for rule-based modeling of
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Oxigen Response.htm">Oxigen Response<span class="flecha">&#9660;</span></a></li>
+
signal transduction based on the interactions of molecular domains.</strong> Bioinformatics.</p>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Chassis.htm">Chassis<span class="flecha">&#9660;</span></a></li>
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</div>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Perspective.htm">Perspective<span class="flecha">&#9660;</span></a></li>
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<div id="sidebar">
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  <div id="updates" class="orangebox">
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</ul>
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</li>
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<li>
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<a href="">Results<span class="flecha">&#9660;</span></a>
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<ul>
+
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<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Biobricks.htm">Biobricks<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Notebook.htm">Notebook<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Protocol.htm">Protocol<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/palustris response.htm">R. palustris response<span class="flecha">&#9660;</span></a></li>
+
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/sphaeroides response.htm">R. sphaeroides response<span class="flecha">&#9660;</span></a></li>
+
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</ul>
+
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</li>
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<li>
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    <h2>Modeling</h2>
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<a href="#">IGEM Contribution<span class="flecha">&#9660;</span></a>
+
<ul>
-
<ul>
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<li><a href="Tools.htm" target="_parent">Tools we used</a></li>
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<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Construction.htm">Construction<span class="flecha">&#9660;</span></a></li>
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<li><a href="Differential.htm">Differential equations modeling</a></li>
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<li><a href="Rule-Based.htm">Rule-Based model</a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Metods.htm">Methods<span class="flecha">&#9660;</span></a></li>
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<li><a href="Cellular.htm">Cellular Automata</a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Results.htm">Results<span class="flecha">&#9660;</span></a></li>
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</ul>
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+
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</ul>
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</li>
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<li>
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<a href="/Team/CINVESTAV-IPN-UNAM_MX/Modelling.htm">Modeling<span class="flecha">&#9660;</span></a>
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</li> 
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    <li>
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<a href="#">Team<span class="flecha">&#9660;</span></a>
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<ul>
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<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Members.htm">Members<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Institute.htm">Institute<span class="flecha">&#9660;</span></a></li>
+
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Labs.htm">Labs<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Sponsor.htm">Sponsor<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Acknowledgments.htm">Acknowledgments<span class="flecha">&#9660;</span></a></li>
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</ul>
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</li>
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    <li>
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<a href="#">Outreach<span class="flecha">&#9660;</span></a>
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<ul>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Human Practice.htm">Human Practices<span class="flecha">&#9660;</span></a></li>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Safety.htm">Safety<span class="flecha">&#9660;</span></a></li>
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  <div style="clear: both;">&nbsp;</div>
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<div id="bodys_r2_c2"></div>
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<p align="center"> <strong>Rhodofactory 2012</strong> </p>
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    <div class="Text"><strong>
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<div id="sponsors">
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      Importance of Modeling and Simulation
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  <div align="center"><img src="https://static.igem.org/mediawiki/2012/8/8a/Icytdf.png" alt="icytdf" width="90" height="82" /></div>
-
      </strong>
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</div>
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      <p>&nbsp;</p>
+
<div id="sponsors">
-
      <p>Characterization of  biological systems has reached an unparalleled level of detail. To organize  this detail and arrive at a better fundamental understanding of life processes,  it is essential   that powerful conceptual tools from  mathematics and computer science be applied to the frontier problems in  biology. </p>
+
  <div align="center"><img src="https://static.igem.org/mediawiki/2012/6/67/Osli.png" alt="osli" width="88" height="46" /></div>
-
      <p><br />
+
</div>
-
        Modeling of biological systems is  evolving into an important partner of experimental work. They attempt to predict and understand  the behavior of complex biological systems before they are actually created. Also  models can help to simplify the complexity of data and interactions involved  into a more concise form with some measure of predictive ability. This can provide valuable insights into the working and general  principles of organization of biological systems. Also it may suggest novel  experiments for testing hypotheses, based on the modeling experiences.</p>
+
-
      <p><a href="Tools.htm"><strong>Some of  the tools that we used during the modeling process.</strong></a></p>
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<div id="sponsors">
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      <p><strong><a href="Model.htm">Construction  of Model</a></strong></p>
+
  <div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fb/Bio.png" alt="bio" width="80" height="97" /></div>
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      <p><strong><a href="intercellular.htm">Modeling  the intercellular signaling process during regulation of PS genes expression in  BioNetGEn.</a></strong></p>
+
</div>
-
      <p><strong><a href="equations.htm">Differential  equations modeling the interactions between AppA and PpsR. </a></strong><a href="equations.htm"><br />
+
<div id="sponsors"><img src="https://static.igem.org/mediawiki/2012/d/d6/Fermentas.png" alt="fermentAS" width="82" height="45" /></div>
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          <strong>Modeling  Steady State</strong></a><strong></strong></p>
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<div id="sponsors">
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<p><a href="automata.htm"><strong>Cellular  automata approaches to biological modeling.</strong></a></p>
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  <div align="center"><img src="https://static.igem.org/mediawiki/2012/a/a3/Cinestav.png" alt="cinestav" width="74" height="91" /></div>
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<p><strong>References  used through this section.</strong></p>
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</div>
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<ol>
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<div id="sponsors"><img src="https://static.igem.org/mediawiki/2012/9/9b/Genscript.png" alt="genscript" width="83" height="45" /></div>
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  <li>Oh JI, Kaplan S. (2001) <strong>Generalized approach to the regulation and integration of gene  expression. </strong>Mol Microbiol. </li>
+
<div id="sponsors">
-
</ol>
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  <div align="center"><img src="https://static.igem.org/mediawiki/2012/1/16/Unam.png" alt="unam" width="83" height="93" /></div>
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<ol>
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</div>
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  <li>Zeilstra-Ryalls JH,  Kaplan S. (1995) <strong>Aerobic and anaerobic regulation in Rhodobacter sphaeroides</strong> 2.4.1: the role of the fnrL gene. J Bacteriol. </li>
+
<div id="sponsors"><img src="https://static.igem.org/mediawiki/2012/c/c9/Gto.png" alt="gto" width="84" height="46" /></div>
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</ol>
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    <div id="sponsors">
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<p>&nbsp;</p>
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      <div align="center"><img src="https://static.igem.org/mediawiki/2012/f/fa/Qimica.png" alt="quimica" width="80" height="72" /></div>
-
<ol>
+
-
  <li>Rakesh Pandey,  Dietrich Flockerz. (2011) <strong>Modeling the Light- and Redox-Dependent Interaction  of PpsR/AppA in Rhodobacter sphaeroides. </strong>Cell Press.</li>
+
-
</ol>
+
-
<ol>
+
-
  <li>Shinji Masuda&nbsp;and&nbsp;Carl E. Bauer. (2002) <strong>AppA Is a Blue Light Photoreceptor  that Antirepresses Photosynthesis Gene Expression in Rhodobacter sphaeroides.</strong> Cell Press.</li>
+
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</ol>
+
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<ol>
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Latest revision as of 00:09, 27 October 2012

Rho

Modeling Biological Systems!

Characterization of biological systems has reached an unparalleled level of detail. To organize this detail and arrive at a better fundamental understanding of life processes, it is essentialthat powerful conceptual tools from mathematics and computer science be applied to the frontier problems in biology.

Modeling is evolving into an important partner of experimental work. They attempt to predict and understand the behavior of complex biological systems before they are actually created. Also models can help to simplify the complexity of data and interactions involved into a more concise form with some measure of predictive ability. This can provide valuable insights into the working and general principles of organization of biological systems. Also it may suggest novel experiments for testing hypotheses, based on the modeling experiences.

References used through this section.
1. Oh JI, Kaplan S. (2001) Generalized approach to the regulation and integration of gene expression. Mol Microbiol.
2.Zeilstra-Ryalls JH, Kaplan S. (1995) Aerobic and anaerobic regulation in Rhodobacter sphaeroides2.4.1: the role of the fnrL gene. J Bacteriol.
3.Shinji MasudaandCarl E. Bauer. (2002)AppA Is a Blue Light Photoreceptor that Antirepresses Photosynthesis Gene Expression in Rhodobacter sphaeroides. Cell Press.
4.Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. (2004)BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics.

 

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