Biomolecular Breadboards:Models: Difference between revisions
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=== TXTL naming conventions === | |||
The TXTL toolbox uses a set of standard names for molecular species and compounds. If new components are added to the system, they must follow these naming conventions. | |||
==== DNA, RNA and protein names ==== | |||
==== Standard species ==== | |||
A number of species are defined by the TXTL library and used to implement core processes: | |||
* RNAP70 [nM]: core RNAP polymerase bound to sigma70 | |||
* Ribo [nM]: Ribosomes | |||
* AA [unit]: amino acid "units". One unit of amino acid is equal to 100 nM. [AA] represents the total amino acid concentration. | |||
* NTP [unit]: necleotide "units". One unit of nucleotide is equal to 100 nM. [NTP] represents the total concentration of nucleotides. | |||
* RecBCD [nM]: exonuclease used to model degradation of linear DNA | |||
==== Standard complexes ==== | |||
=== TXTL toolbox functions === | |||
=== TXTL components === | |||
== Additional Models == | == Additional Models == | ||
Revision as of 08:30, 11 September 2012
| Home | Protocols | DNA parts | Preliminary Data | Models | More Info |
This page contains information about models for simulation and analysis of biomolecular breadboard circuits.
TX-TL Toolbox for MATLAB
The TX-TL toolbox for MATLAB is a set of MATLAB functions that are designed to simplify the modeling of circuits used in the TX-TL 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:
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MATLAB code (plotting commands omitted): % 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);
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TXTL naming conventions
The TXTL toolbox uses a set of standard names for molecular species and compounds. If new components are added to the system, they must follow these naming conventions.
DNA, RNA and protein names
Standard species
A number of species are defined by the TXTL library and used to implement core processes:
- RNAP70 [nM]: core RNAP polymerase bound to sigma70
- Ribo [nM]: Ribosomes
- AA [unit]: amino acid "units". One unit of amino acid is equal to 100 nM. [AA] represents the total amino acid concentration.
- NTP [unit]: necleotide "units". One unit of nucleotide is equal to 100 nM. [NTP] represents the total concentration of nucleotides.
- RecBCD [nM]: exonuclease used to model degradation of linear DNA
Standard complexes
TXTL toolbox functions
TXTL components
Additional Models
In addition to the TX-TL 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.
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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'.
