Biomolecular Breadboards:Models

From OpenWetWare
Home Protocols DNA parts Preliminary Data Models More Info

This page contains information about models for simulation and analysis of biomolecular breadboard circuits. Additional information can be found in the following conference paper:

TX-TL Toolbox for MATLAB


Simple example: Gene expression

This example shows constitutive expression of the destabilized enhanced Green Fluorescent Protein (deGFP) from a gene on a plasmid.


Create a tube containing TX-TL extract, 'E6'. The extract contains RNAP, ribosomes, sigma factors exonucleases and RNA-ase.

 tube1 = txtl_extract('E6'); 

Create a tube containing TX-TL buffer, 'E6'. This contains amino acids and nucleotide pairs.

 tube2 = txtl_buffer('E6');

Creat a new tube that will contain the DNA to be expressed, and name it 'circuit'.

 tube3 = txtl_newtube('circuit'); 

Use txtl_add_dna to add custom deGFP DNA to tube3, under control of a constitutive p70 promoter:

 dna_deGFP = txtl_add_dna(tube3, 'p70(50)', 'rbs(20)', 'deGFP(1000)', 4.0, 'plasmid'); 

The numbers in brackets are the lengths of the respective regions in number of base pairs (BP). These are used to calculate reaction rates for transcription, translation and degradation. The number 4.0 specifies that the initial concentration of the DNA (in nM) in the experiment once all the tubes have been combined. The last input argument species that the DNA is placed on a plasmid, and thus is not susceptible to exonuclease action.

Combine the tubes containing the extract, buffer and circuit into a final tube (referred to as Mobj) in a fixed ratio defined in the experimental protocol.

 Mobj = txtl_combine([tube1, tube2, tube3]);

Define simulation time and set the 'StopTime' property of the simulation:

 simulationTime = 15*60*60;
 configsetObj = getconfigset(Mobj, 'active'); 
 set(configsetObj, 'StopTime', simulationTime); 

Every model (tube) has an associated 'configuration set object' used to define how the model is to be simulated, and we can set its proterties as above. Simulate the model:

 [simData] = txtl_runsim(Mobj,configsetObj); 
 t_ode = simData.Time;
 x_ode = simData.Data;

This simulates the model object using the associated configuration set, and returns the time evolution of the concentration of the species in the model. Produce a standard plot:


TXTL naming conventions


DNA, RNA and protein names


  • mRNA: [RNA utr--gene]
  • Protein: [protein gene]


Standard species


  • RNAP70 [nM]: core RNAP polymerase bound to sigma70
  • Ribo [nM]: Ribosomes

Standard complexes



TXTL toolbox functions



TXTL components


  • p70 - default constitutive promoter
  • ptet - promoter repressed by TetR


  • rbs - default ribosome binding site


  • tetR - TetR, including sequestration reaction with aTc

Additional Models


GamS modeling


GamS-protsynt81bis 05Sep12.png
