Team:MIT/Tools/

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<div class="content" id="mcellcontent">
<div class="content" id="mcellcontent">
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= ''mcell'' - A Multicellular Modeling Framework =
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<h1> ''mcell'' - A Multicellular Modeling Framework </h1>
''mcell'' is a small set of Python classes that allows the enterprising modeler to:
''mcell'' is a small set of Python classes that allows the enterprising modeler to:
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''mcell'' is a thin layer on top of the combination of [BionetSolver], which model internal cell states as systems of ODEs, and [CompuCell3D], which models cell shape dynamics using the Glazier-Graner-Hogeweg methos. It was created largely in reaction to inconveniences experienced when using BionetSolver and CompuCell3D as detailed [here]. It is in continuous development.
''mcell'' is a thin layer on top of the combination of [BionetSolver], which model internal cell states as systems of ODEs, and [CompuCell3D], which models cell shape dynamics using the Glazier-Graner-Hogeweg methos. It was created largely in reaction to inconveniences experienced when using BionetSolver and CompuCell3D as detailed [here]. It is in continuous development.
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== Quick ==
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<h3> Quick Links</h3>
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<ul>
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  <li><a href="#install">Why?</a></li>
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  <li><a href="#howitworks">How It Works</a></li>
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  <li><a href="#management">Management of Models</a></li>
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  <li><a href="#analysis">Rendering and Analysis of Runs</a></li>
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</ul>
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== Installation ==
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<h2><a id="install" class="sec"> Installation </a></h2>
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== How it works ==
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<h2><a id="howitworks" class="sec"> How it works </a></h2>
In mcell models, BionetSolver models the internal cell states, and CompuCell3D models the cell dynamics.
In mcell models, BionetSolver models the internal cell states, and CompuCell3D models the cell dynamics.
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=== BionetSolver ===
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<h3> BionetSolver </h3>
BionetSolver reads one or several [SBML] files, each of which define a ''circuit'' as a system of chemical reactions in several containers with given rate laws. SBML models are simply XML files, and can be written with a text editor; however, it is much easier to define them using a graphical designer, like [JDesigner], or using a simple scripting language, like [Jarnac]. (Both of those editors can be obtained by installing the [Synthetic Biology Workbench].
BionetSolver reads one or several [SBML] files, each of which define a ''circuit'' as a system of chemical reactions in several containers with given rate laws. SBML models are simply XML files, and can be written with a text editor; however, it is much easier to define them using a graphical designer, like [JDesigner], or using a simple scripting language, like [Jarnac]. (Both of those editors can be obtained by installing the [Synthetic Biology Workbench].
After loading the circuits, BionetSolver is in posession of a system of ODEs that define the internal state of each modeled cell. To simulate each cell, BionetSolver simply Euler-steps its ODE system forward with a fixed time step. Some of the variables in the ODE model (like, say, the concentration of a protein on the neighboring cells) are actually parameters that are continually updated from the CompuCell3D thread.  
After loading the circuits, BionetSolver is in posession of a system of ODEs that define the internal state of each modeled cell. To simulate each cell, BionetSolver simply Euler-steps its ODE system forward with a fixed time step. Some of the variables in the ODE model (like, say, the concentration of a protein on the neighboring cells) are actually parameters that are continually updated from the CompuCell3D thread.  
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=== CompuCell3D ===
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<h3> CompuCell3D </h3>
CompuCell3D uses  
CompuCell3D uses  
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== Model Management ==
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<h2><a name="management" class="sec"> Model Management </a></h2>
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== Rendering and Analysis ==
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<h2><a name="analysis" class="sec"> Rendering and Analysis </a></h2>
</div>
</div>

Revision as of 02:54, 28 September 2011

Navigation

  • G-Level Assembly
  • Geneious
  • mcell Modeling Platform
assembly stuf
geneious stuff

''mcell'' - A Multicellular Modeling Framework

''mcell'' is a small set of Python classes that allows the enterprising modeler to: * Easily create very flexible models of of multicellular dynamics * Manage the models already created through a simple command-line interface * Easily change defined parameters in models * Render the runs of the models in a convenient, simple way * Analyze the runs of the models through histograms and clustering ''mcell'' is a thin layer on top of the combination of [BionetSolver], which model internal cell states as systems of ODEs, and [CompuCell3D], which models cell shape dynamics using the Glazier-Graner-Hogeweg methos. It was created largely in reaction to inconveniences experienced when using BionetSolver and CompuCell3D as detailed [here]. It is in continuous development.

Quick Links

Installation

How it works

In mcell models, BionetSolver models the internal cell states, and CompuCell3D models the cell dynamics.

BionetSolver

BionetSolver reads one or several [SBML] files, each of which define a ''circuit'' as a system of chemical reactions in several containers with given rate laws. SBML models are simply XML files, and can be written with a text editor; however, it is much easier to define them using a graphical designer, like [JDesigner], or using a simple scripting language, like [Jarnac]. (Both of those editors can be obtained by installing the [Synthetic Biology Workbench]. After loading the circuits, BionetSolver is in posession of a system of ODEs that define the internal state of each modeled cell. To simulate each cell, BionetSolver simply Euler-steps its ODE system forward with a fixed time step. Some of the variables in the ODE model (like, say, the concentration of a protein on the neighboring cells) are actually parameters that are continually updated from the CompuCell3D thread.

CompuCell3D

CompuCell3D uses

Model Management

Rendering and Analysis

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