Team:BCCS-Bristol/Modeling/BSim Features

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''In Progress...''
''In Progress...''
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In this section we outline the main features available in BSim 2.0.
 
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* Complete physical and biological plausibility
 
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* Heavily referenced/tied to the available literature
 
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* All constants and parameters in scaled, physical units
 
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* Well commented, documented and easy to use
 
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* Versatile and adaptable, modular components
 
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* Everything can be logged and specified by the user
 
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* Has already been used in other projects (agent based repressilators, microtubules!)
 
== Simulation Features ==
== Simulation Features ==

Revision as of 15:20, 25 September 2009

BCCS-Bristol
iGEM 2009

Contents

BSim Features

In Progress...

Simulation Features

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 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."

  • ODE(s) can be attached to bacteria
  • Can interact with chemical fields etc

Magnetotaxis

  • an alternative to chemotaxis?
    • Allow tuning of the field strength and direction
    • Include both naturally magnetic bacteria and/or magnetic beads
    • Include both uniform magnetic field and/or also variable magnetic field (to affect motion as well as orientation)

Other Features

Separate the physical and biological aspects of features into 2 sections?

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