Team:BCCS-Bristol/Modeling/BSim

From 2009.igem.org

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== BSim stochastic simulation etc==
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== BSim Features ==  
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= BSim Features =
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There are many new features available in the new version of BSim:
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In this section we outline the main features available in BSim 2009.
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== Biological Simulation Features ==
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=== Bacteria ===
=== Bacteria ===
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* physical units
* physical units
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=== GRN modelling ===
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=== [[Team:BCCS-Bristol/Modeling/GRN|GRN modelling]] ===
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BSim 2008: "Each of the modelling approaches [''GRNs and agent-based modelling''] have been considered in separate contexts, mainly due to the differing aspects of the system they are concerned with. Now, having working models for each, it would be possible to bring these together with the aim of improving simulation accuracy and allowing for the internal cellular dynamics to be studied in an ever changing physical environment. Such a hybrid model may also help shed light on the critical aspects of project as a whole."
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BSim allows the user to specify complex GRNS based on ODEs and apply these to individual bacteria to analyse GRN effects on a population level. It is now possible to analyse the effects of individual GRNs on a population level, all within the same context.
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BSim 2009 provides a robust implementation of the second and fourth order Runge-Kutta methods for systems of ordinary differential equations. It is possible to easily specify systems of ODEs as objects within the simulation. These ODE systems can be "attached" to objects in the simulation if necessary and can be used to simulate any aspect of the environment to which they are coupled, depending on the user's requirements. An example would be attaching an ODE system to each bacterium and coupling these systems via an external chemical field. See the overview of our ongoing [[Team:BCCS-Bristol/Modeling/quorum_coupled_repressilators|quorum-coupled repressilators]] simulation for an example application of this.
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As a result of the modular nature of the solver implementation it would also be possible to implement stochastic ODEs, and delay differential equations in a similar manner. These features are likely to be implemented soon to assist with the modelling of more complex GRN systems across a population.
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=== [[Team:BCCS-Bristol/Modeling/Magnetotaxis|Magnetotaxis]] ===
=== [[Team:BCCS-Bristol/Modeling/Magnetotaxis|Magnetotaxis]] ===
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Summary of magnetotaxis here with image etc.
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It is now possible to simulate magnetotactic bacteria. These bacteria are sensitive to externally applied magnetic fields and can therefore be influenced to move along the direction of user specified magnetic field lines.
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==References:==
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[1] http://www.calpoly.edu/~rfrankel/magbac101.html
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[2] Blakemore, RP (1982) Magnetotactic bacteria. Annual Reviews of Microbiology 36: 217-238.
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[3] Nicola Ann Spaldin, Magnetic materials: fundamentals and device applications, University Press, Cambridge 2003
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Revision as of 20:09, 18 October 2009

BCCS-Bristol
iGEM 2009


Read more about BSim, our Stochastic agent based modelling framework.


Tutorials
Download
Case Studies
Interested in finding out more about the creation of BSim simulations? Click here for a selection of tutorial examples. Want to use the BSim software yourself? Click here to download the core libraries and source code (available freely under the MIT licence). The BSim platform has already been used in a number of other projects! Read more about these projects here.


Contents

BSim Features

There are many new features available in the new version of BSim:

Bacteria

  • Heavy basis on literature
  • Run and tumble by default (flagellar motor)
  • chemotaxis!
  • brownian motion and fluid forces implemented
  • easily adaptable.

Interactions and actions

  • easily specified and adaptable
  • can do whatever you want:
    • Collision
    • Merging (vesicle/bacterium)
    • GRNs
  • other interactions:
    • Everything can interact! chemical fields, GRNs, vesicles...

Vesicles

  • Small, but size based on growth
  • Size and creation rate based on rate of change of surface area [ref - steve?]
  • Vesicle movement - brownian motion in a viscous fluid environment
  • Interaction can be specified

Chemical Fields

  • diffusion
  • decay
  • physical units

GRN modelling

BSim allows the user to specify complex GRNS based on ODEs and apply these to individual bacteria to analyse GRN effects on a population level. It is now possible to analyse the effects of individual GRNs on a population level, all within the same context.

Magnetotaxis

It is now possible to simulate magnetotactic bacteria. These bacteria are sensitive to externally applied magnetic fields and can therefore be influenced to move along the direction of user specified magnetic field lines.

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