BSim Features

In Progress... In this section we outline the main features available in BSim 2.0.

Complete physical and biological plausibility
Heavily referenced/tied to the available literature
Well commented, documented and easy to use
Versatile and adaptable
Everything can be logged and specified by the user
Has already been used in other projects (agent based repressilators, microtubules!)

Simulation Features

Bacteria

Heavy basis on literature

Vesicles

At what rate do bacteria produce vesicles?
How long do they stick around?
Where are they produced relative to the bacterium?
Vesicle movement - brownian motion?
Interaction with bacteria/chemicals/boundaries/etc.
Vesicles should be able to carry different proteins and express their effects, starting with GFP and RFP. Perhaps at first GreenVesicle and RedVesicle classes are sufficient, but later we might want to implement a Vesicle class and a separate Protein class.
Compare vesicle-packaged protein communication with raw protein communcation? See Ollie's email

GRN modelling

"Each of the modelling approaches 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."

Use a GRN (with delay?) to control vesicle production Interface with SBML models (SimBiology toolkit in MATLAB, CellDesigner)? Allow switching of the flagella by external chemicals and a threshold viscosity

Magnetotaxis

Implement magnetotaxis as an alternative to chemotaxis.
- Allow tuning of the field strength and direction via the GUI?
- 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)

Team:BCCS-Bristol/Modeling/BSim Features

From 2009.igem.org

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