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friedland1

friedland1

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r0

ara > ∅

r10a

∅ > mT3cr

r10b

mT3cr > ∅

r11

∅ > pT3

r12

pT3 > ∅

r1a

∅ > taRNA

r1b

taRNA > ∅

r2a

∅ > mT7cr

r2b

mT7cr > ∅

r3a

∅ > mGFPcr

r3b

mGFPcr > ∅

r6

∅ > pT7

r7

∅ > pGFP

r8

pT7 > ∅

r9

pGFP > ∅

Parameters

Global parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

pulse3_start = pulse2_start + pulse2_length + pulse_interval

pulse2_start = pulse1_start + pulse1_length + pulse_interval

Function definitions

Events

pulse_start1

Trigger: and(geq(time, pulse1_start), leq(time, pulse1_start + pulse1_length))

Delay:

Assignments:

  • ara = pulse_conc
  • pulse_flag = 1

pulse_start3

Trigger: and(geq(time, pulse3_start), leq(time, pulse3_start + pulse3_length))

Delay:

Assignments:

  • ara = pulse_conc
  • pulse_flag = 1

pulse_end3

Trigger: gt(time, pulse3_start + pulse3_length)

Delay:

Assignments:

  • pulse_flag = 0

pulse_start2

Trigger: and(geq(time, pulse2_start), leq(time, pulse2_start + pulse2_length))

Delay:

Assignments:

  • ara = pulse_conc
  • pulse_flag = 1

pulse_end2

Trigger: and(lt(time, pulse3_start), gt(time, pulse2_start + pulse2_length))

Delay:

Assignments:

  • pulse_flag = 0

pulse_end1

Trigger: and(lt(time, pulse2_start), gt(time, pulse1_start + pulse1_length))

Delay:

Assignments:

  • pulse_flag = 0

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


Species:

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Synthetic gene networks that count.

  • Ari E Friedland
  • Timothy K Lu
  • Xiao Wang
  • David Shi
  • George Church
  • James J Collins
Science 2009; 324 (5931): 1199-1202
Abstract
Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000301) Biomodels notes: Reproduction of fig S5 in the supplement of the reference publication. The simulation was performed with Copasi 4.6. The curves display the pGFP concentration at each time point minus the steady state concentration of pGFP. To simulate to pulses the length of the third pulse was set to -1. The values for the pulses were: pulse1_start = 0.01, pulse_interval = 20 three pulses: pulse1_length = pulse2_length = 11, pulse3_length = 22 two pulses: pulse1_length = pulse2_length = 22, pulse3_length = -1 JWS Online curation: This model was curated by reproducing figure S5 two pulses.