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| - | {{:Team:BCCS-Bristol/Header}}
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| - | = BSim Features =
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| - | ''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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| - | * Well commented, documented and easy to use
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| - | * Versatile and adaptable
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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!)
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| - | == Simulation Features ==
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| - | === Bacteria ===
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| - | * Heavy basis on literature
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| - | === Vesicles ===
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| - | * At what rate do bacteria produce vesicles?
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| - | * How long do they stick around?
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| - | * Where are they produced relative to the bacterium?
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| - | * Vesicle movement - brownian motion?
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| - | * Interaction with bacteria/chemicals/boundaries/etc.
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| - | * 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.
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| - | * Compare vesicle-packaged protein communication with raw protein communcation? See Ollie's email
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| - | === GRN modelling ===
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| - | "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."
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| - | Use a GRN (with delay?) to control vesicle production
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| - | Interface with SBML models (SimBiology toolkit in MATLAB, CellDesigner)?
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| - | Allow switching of the flagella by external chemicals and a threshold viscosity
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| - | === Magnetotaxis ===
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| - | * Implement magnetotaxis as an alternative to chemotaxis.
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| - | ** Allow tuning of the field strength and direction via the GUI?
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| - | ** Include both naturally magnetic bacteria and/or magnetic beads
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| - | ** Include both uniform magnetic field and/or also variable magnetic field (to affect motion as well as orientation)
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| - | == Other Features ==
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"
