"
Team:MIT/Tools/
From 2011.igem.org
| Line 1: | Line 1: | ||
{{MIT-header}} | {{MIT-header}} | ||
{{MIT-style}} | {{MIT-style}} | ||
| + | <script> | ||
| + | $(document).ready(function(){ | ||
| + | $('.content').css('display','none'); | ||
| + | $('.content:first').css('display','block'); | ||
| + | $('.col_list li').css('cursor','pointer'); | ||
| + | $('a').css('color', 'black'); | ||
| + | $('a').css('text-decoration', 'none'); | ||
| + | |||
| + | $('.col_list li').hover(function() { | ||
| + | $(this).css('background-color','#91A3ED'); | ||
| + | }, function() { | ||
| + | $(this).css('background-color','#E3E3E3'); | ||
| + | }); | ||
| + | $('.col_list li').click(function () { | ||
| + | $('.content').hide(); | ||
| + | var name = $(this).attr('id'); | ||
| + | $('#'+name+'content').fadeIn(500); | ||
| + | |||
| + | }); | ||
| + | }); | ||
| + | </script> | ||
<!-- NAV --> | <!-- NAV --> | ||
| Line 8: | Line 29: | ||
<h2>Navigation</h2> | <h2>Navigation</h2> | ||
<ul> | <ul> | ||
| - | <li id=" | + | <li id="assembly">G-Level Assembly</li> |
| - | <li id=" | + | <li id="geneious">Geneious</li> |
| - | <li id=" | + | <li id="mcell">mcell Modeling Platform</li> |
| - | + | ||
</ul> | </ul> | ||
</div> | </div> | ||
| Line 19: | Line 39: | ||
<div id="col_left"> | <div id="col_left"> | ||
| - | <div class="content" id=" | + | <div class="content" id="assemblycontent"> |
| + | |||
| + | </div> | ||
| + | |||
| + | <div class="geneiouscontent"> | ||
| + | |||
| + | </div> | ||
| + | |||
| + | <div class="content" id="mcellcontent"> | ||
= ''mcell'' - A Multicellular Modeling Framework = | = ''mcell'' - A Multicellular Modeling Framework = | ||
| Line 30: | Line 58: | ||
''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. | ||
| + | |||
| + | == Quick == | ||
== Installation == | == Installation == | ||
Revision as of 02:44, 28 September 2011
<script>
$(document).ready(function(){
$('.content').css('display','none');
$('.content:first').css('display','block');
$('.col_list li').css('cursor','pointer');
$('a').css('color', 'black');
$('a').css('text-decoration', 'none');
$('.col_list li').hover(function() {
$(this).css('background-color','#91A3ED');
}, function() {
$(this).css('background-color','#E3E3E3');
});
$('.col_list li').click(function () {
$('.content').hide();
var name = $(this).attr('id');
$('#'+name+'content').fadeIn(500);
});
});
</script>
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
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
