Biomolecular Breadboards:Models
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This page contains information about models for simulation and analysis of biomolecular breadboard circuits.  This page contains information about models for simulation and analysis of biomolecular breadboard circuits.  
  ==  +  == TXTL Toolbox for MATLAB == 
  +  The TXTL toolbox for MATLAB is a set of MATLAB functions that are designed to simplify the modeling of circuits used in the TXTL cell free expression system. The source code for the toolbox is available via [http://sourceforge.net/projects/txtl SourceForge].  
+  
+  === Simple example ===  
+  The following code sets up a simple simulation of a negatively autoregulated gene in the TXTL system:  
+  [[Image:txtlnegautoreg.pngright200px]]  
+  % Set up the standard TXTL tubes  
+  tube1 = txtl_extract('e1');  
+  tube2 = txtl_buffer('b1');  
+  
+  % Set up a tube that will contain our DNA  
+  tube3 = txtl_newtube('circuit');  
+  dna_tetR = txtl_dna(tube3, 'ptet', 'rbs', 'tetR', 100, 'linear');  
+  dna_gamS = txtl_dna(tube3, 'p70', 'rbs', 'gamS', 10, 'plasmid');  
+  
+  % Mix the contents of the individual tubes and add some inducer  
+  Mobj = txtl_combine([tube1, tube2, tube3], [6, 2, 2]);  
+  txtl_addspecies(Mobj, 'aTc', 0.1);  
+  
+  % Run a simulaton  
+  [t_ode, x_ode, names] = sbiosimulate(Mobj, configsetObj);  
+  
+  == Additional Models ==  
+  
+  In addition to the TXTL toolbox, several additional models have been developed for individual breadboard projects.  
=== GamS modeling ===  === GamS modeling === 
Revision as of 11:17, 11 September 2012
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This page contains information about models for simulation and analysis of biomolecular breadboard circuits.
Contents 
TXTL Toolbox for MATLAB
The TXTL toolbox for MATLAB is a set of MATLAB functions that are designed to simplify the modeling of circuits used in the TXTL cell free expression system. The source code for the toolbox is available via SourceForge.
Simple example
The following code sets up a simple simulation of a negatively autoregulated gene in the TXTL system:
% Set up the standard TXTL tubes tube1 = txtl_extract('e1'); tube2 = txtl_buffer('b1'); % Set up a tube that will contain our DNA tube3 = txtl_newtube('circuit'); dna_tetR = txtl_dna(tube3, 'ptet', 'rbs', 'tetR', 100, 'linear'); dna_gamS = txtl_dna(tube3, 'p70', 'rbs', 'gamS', 10, 'plasmid'); % Mix the contents of the individual tubes and add some inducer Mobj = txtl_combine([tube1, tube2, tube3], [6, 2, 2]); txtl_addspecies(Mobj, 'aTc', 0.1); % Run a simulaton [t_ode, x_ode, names] = sbiosimulate(Mobj, configsetObj);
Additional Models
In addition to the TXTL toolbox, several additional models have been developed for individual breadboard projects.
GamS modeling
For linear DNA, GamS can be used to reduce the rate of degradation of DNA and increase the expression level (see preliminary data for more information). The figure below shows the results of a preliminary model that we are developing to capture the affects of gamS.

Figure 1. Protein expression as a function of gamS concentration. The simulation results show the output of the model in 'protsynt81bis.m', generated with the script 'gamS_plot.m'.