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<li><a href="home.htm">Home</a></li>
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  <td><img src="images/spacer.gif" width="240" height="1" alt="" /></td>
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<li><a href="rhodofactory.htm">Rhodofactory</a></li>
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  <td><img src="images/spacer.gif" width="710" height="1" alt="" /></td>
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<li><a href="promoterselection.htm">Promoter selection </a></li>
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  <td><img src="images/spacer.gif" width="1" height="1" alt="" /></td>
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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>
 +
<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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<h1><a href="#"></a></h1>  
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<!-- end #header -->
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<div id="page">
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<div id="context">
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<h1><em>Some of the tools that we used during the <br /><br />modeling process.!</em></h1>
 +
<p id="text2">Wolfram Research Mathematica</p>
 +
            <p>Mathematica is a general computer software system and language intended for mathematical and
 +
other applications. You can use Mathematica as: A numerical and symbolic calculator where you
 +
type in questions, and Mathematica prints out answers, a visualization system for functions and
 +
data, a high-level programming language in which you can create programs, large and small ones.
 +
and a modeling and data analysis environment.</p>
 +
<p id="text2">Rule-Based Modeling of Biochemical Systems with BioNetGen</p>
-
 
+
<p>Rule-based modeling involves the representation of molecules as structured objects and molecular
-
<tr>
+
interactions as rules for transforming the attributes of these objects.The approach is notable in that
-
  <td><img src="https://static.igem.org/mediawiki/2012/6/68/LOGOPRIN.jpg" width="240" height="178" alt="Logo Principal" /></td>
+
it allows one to systematically incorporate site-specific details about protein-protein interactions into
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  <td bgcolor="01A79D"><ul class="nav">
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a model. BioNetGen allows a user to create a computational model that characterizes the dynamics
-
<li>
+
of a signal transduction system, and that accounts comprehensively and precisely for specified
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<a href="/Team/CINVESTAV-IPN-UNAM_MX/home.htm">Home<span class="flecha">&#9660;</span></a>
+
enzymatic activities, potential post-translational modifications and interactions of the domains of
-
</li>
+
signaling molecules. The output defines and parameterizes the network of molecular species that
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<li>
+
can arise during signaling and provides functions that relate model variables to experimental
-
<a href="#">Rhodofactory<span class="flecha">&#9660;</span></a>
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readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis
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<ul>
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of proteomic data and mechanistic studies of signal transduction.
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<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Overview.htm">Overview<span class="flecha">&#9660;</span></a></li>
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</p>
-
           
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<p>For further details go to:</p>
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Light Response.htm">Light Response<span class="flecha">&#9660;</span></a></li>
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<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" width="200" height="200" id="botonwolfman" align="middle">
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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Oxigen Response.htm">Oxigen Response<span class="flecha">&#9660;</span></a></li>
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<param name="allowScriptAccess" value="sameDomain" />
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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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            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Perspective.htm">Perspective<span class="flecha">&#9660;</span></a></li>
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</object>
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<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" width="218" height="139" id="vcell" align="middle">
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</ul>
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<param name="allowScriptAccess" value="sameDomain" />
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<li>
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</object>
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<a href="">Results<span class="flecha">&#9660;</span></a>
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<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" width="535" height="112" id="bionetgen" align="middle">
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<ul>
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<param name="allowScriptAccess" value="sameDomain" />
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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>
+
</div>
-
            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/palustris response.htm">R. palustris response<span class="flecha">&#9660;</span></a></li>
+
<div id="sidebar">
-
            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/sphaeroides response.htm">R. sphaeroides response<span class="flecha">&#9660;</span></a></li>
+
  <div id="updates" class="orangebox">
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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>
-
<li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Construction.htm">Construction<span class="flecha">&#9660;</span></a></li>
+
<li><a href="Differential.htm">Differential equations modeling</a></li>
-
           
+
<li><a href="Rule-Based.htm">Rule-Based model</a></li>
-
            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Metods.htm">Metods<span class="flecha">&#9660;</span></a></li>
+
<li><a href="Cellular.htm">Cellular Automata</a></li>
-
            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Results.htm">Results<span class="flecha">&#9660;</span></a></li>
+
</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">Modelling<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>
+
-
            <li><a href="/Team/CINVESTAV-IPN-UNAM_MX/Labs.htm">Labs<span class="flecha">&#9660;</span></a></li>
+
-
            <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="Human Practice.htm">Human Practice<span class="flecha">&#9660;</span></a></li>
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            <li><a href="Safety.htm">Safety<span class="flecha">&#9660;</span></a></li>
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</ul>
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  <div style="clear: both;">&nbsp;</div>
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<div id="bodys_r2_c2"></div>
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<div id="piep">
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<p align="center"> <strong>Rhodofactory 2012</strong> </p>
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    <div class="Text">
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<div id="sponsors">
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      <p><strong>Wolfram  Research Mathematica</strong></p>
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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>
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      <p><br />
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</div>
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        Mathematica is a general computer  software system and language intended for mathematical and other applications. You  can use Mathematica as: A numerical and symbolic calculator where you type in  questions, and Mathematica prints out answers, a visualization system for  functions and data, a high-level programming language in which you can create  programs, large and small ones. and a modeling and data analysis environment.</p>
+
<div id="sponsors">
-
      <p><br />
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  <div align="center"><img src="https://static.igem.org/mediawiki/2012/6/67/Osli.png" alt="osli" width="88" height="46" /></div>
-
        <strong>Rule-Based  Modeling of Biochemical Systems with BioNetGen</strong><br />
+
</div>
-
      </p>
+
-
      <p>Rule-based modeling involves the  representation of molecules as structured objects and molecular interactions as  rules for transforming the attributes of these objects.  The approach is notable in that it allows one  to systematically incorporate site-specific details about protein-protein  interactions into a model. BioNetGen allows a user to create a computational  model that characterizes the dynamics of a signal transduction system, and that  accounts comprehensively and precisely for specified enzymatic activities,  potential post-translational modifications and interactions of the domains of  signaling molecules. The output defines and parameterizes the network of  molecular species that can arise during signaling and provides functions that  relate model variables to experimental readouts of interest. Models that can be  generated are relevant for rational drug discovery, analysis of proteomic data  and mechanistic studies of signal transduction.</p>
+
<div id="sponsors">
-
       
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  <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><br />
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</div>
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        <strong>For further details go to:</strong></p>
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<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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        <p><a href="http://bionetgen.org" target="_blank"><strong>http://bionetgen.org</strong><img src="images/mate2.jpg" width="75" height="62" /></a></p>
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Latest revision as of 00:29, 27 October 2012

Rho

Some of the tools that we used during the

modeling process.!

Wolfram Research Mathematica

Mathematica is a general computer software system and language intended for mathematical and other applications. You can use Mathematica as: A numerical and symbolic calculator where you type in questions, and Mathematica prints out answers, a visualization system for functions and data, a high-level programming language in which you can create programs, large and small ones. and a modeling and data analysis environment.

Rule-Based Modeling of Biochemical Systems with BioNetGen

Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects.The approach is notable in that it allows one to systematically incorporate site-specific details about protein-protein interactions into a model. BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities, potential post-translational modifications and interactions of the domains of signaling molecules. The output defines and parameterizes the network of molecular species that can arise during signaling and provides functions that relate model variables to experimental readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction.

For further details go to:

 

Rhodofactory 2012

icytdf
osli
bio
fermentAS
cinestav
genscript
unam
gto
quimica
valaner
ipn

Retrieved from "http://2012.igem.org/Team/CINVESTAV-IPN-UNAM_MX/Tools.htm"