Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/Practical 1

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Synthetic Biology (Spring2008): Computer Modelling Practicals

Home        CellDesigner Tutorial        Practical 1        Practical 2        Practical 3        Schedule        Back to Synthetic Biology Course       

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Practical 1 (3h)


Objectives:

  • Learning how to use a computational modelling tool for biochemical reaction simulations.
    • Building biochemical networks
    • Simulating the time evolution of the reactions
  • Exploring the properties of simple biochemical reactions.
    • A --> B --> C model
    • Synthesis-Degradation model
    • Michaelis-Menten model

Deliverables

  • A report is expected by ... (Word or PDF format, sent to XXX@XXX)
  • When you find in the text (illustration needed), it means that you will have to provide an image export of your simulation results in your report.


Part I: Introduction to Computer Modelling

  • presentation slides

Part II: Getting to know CellDesigner

  • Check tutorial
  • Open a sample file
  • Select items, move them around, delete, undo.


Part III: Building Your First Model: A --> B --> C

Model CellDesigner Instructions
[math]\displaystyle{ A -(k_{1})-\gt B -(k_{2})-\gt C }[/math]
  • Open a NEW document.
  • Create 3 compounds A, B, and C (help).
  • Create Reaction_1 linking 'A' to 'B' (help).
  • Create Reaction_2 linking 'B' to 'C'
  • Save your model
Dynamical system, Law of Mass action:
  • [math]\displaystyle{ \frac{d[A]}{dt} = - k_{1}*[A] }[/math]
  • [math]\displaystyle{ \frac{d[B]}{dt} = k_{1}*[A] }[/math]
  • [math]\displaystyle{ \frac{d[C]}{dt} = k_{2}*[B] }[/math]
  • Edit Reaction_1, Create a NEW local parameter called K1, value equals 1.0 (help).
  • Create a kinetic law for Reaction_1, according to the dynamical system (help).
  • Edit Reaction_2, Create a NEW local parameter called K2, value equals 10.0
  • Create a kinetic law for Reaction_2, according to the dynamical system.
  • Save your model.
Simulate the dynamical behaviour
  • Open Simulation Panel (help)
  • set time for the simulation to be 10 seconds
  • press Execute, and check results.
  • Questions:
    • describe the time evolution of A, B and C, with the default parameters.
    • Using 'Parameter Scan' function, investigate how K1 and K2 influence the production of C
    • find the set of parameters (k1, k2), within the range, so that B is maximal

Part IV: Synthesis-Degradation Model

Model CellDesigner Instructions
[math]\displaystyle{ 0 -(k_{1})-\gt A -(k_{2})-\gt 0 }[/math]
  • Open a NEW document.
  • Create a 'Source', and a 'A' compounds
  • Create a Reaction_1 linking 'Source' to 'A'
  • Create a Reaction_2, as a 'degradation reaction', linked to 'A'
  • Save your file.
Dynamical system, Law of Mass action:
  • [math]\displaystyle{ \frac{d[A]}{dt} = k_{1} - k_{2}*[A] }[/math]
  • Edit Reaction_1, and create a new parameter k_1 = 1.0, and create the kinetic law according to the ODE system.
  • Edit Reaction_2, and create a new parameter k_2 = .01, and create the kinetic law according to the ODE system.
  • Save your model.
Simulate the dynamical behaviour
  • Open Simulation Panel
  • Set time for the simulation to be 10 seconds, 1000 points.
  • Press Execute, and check results.
  • Questions:
    • Run a simulation over t=1000s, comment on the time evolution of 'A'(illustration needed).
    • Using the dynamical system, define what is the steady state level of 'A' with regards to the parameters synthesisRate and degradationRate.
    • Using the parameter scan, illustrate the influence of both parameters on the steady state level of 'A' (illustration needed).
  • Resources:

Part V: Michaelis-Menten Model

Model CellDesigner Instructions
[math]\displaystyle{ E + S \lt -(k_{1}/k_{2})-\gt ES -(k_{3})-\gt P }[/math]
  • ...
Dynamical system, Law of Mass action: [math]\displaystyle{ a }[/math]
  • [math]\displaystyle{ \frac{d[E]}{dt} = k_{2}*[ES] - k_{1}*[E][S] }[/math]
  • [math]\displaystyle{ \frac{d[S]}{dt} = k_{2}*[ES] - k_{1}*[E][S] }[/math]
  • [math]\displaystyle{ \frac{d[ES]}{dt} = k_{1}*[E][S] - k_{2}*[ES] }[/math]
  • [math]\displaystyle{ \frac{d[P]}{dt} = k_{3}*[E][S] }[/math]
Simulate the dynamical behaviour
  • Open Simulation Panel
  • set time for the simulation to be 10 seconds
  • press Execute, and check results.
  • Questions:
    • What is the influence of each parameter on how quickly the Product is formed ?
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