Revision as of 15:17, 25 September 2009

BCCS-Bristol
iGEM 2009

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
All constants and parameters in scaled, physical units
Well commented, documented and easy to use
Versatile and adaptable, modular components
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
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?

@@ Line 4: / Line 4: @@
 ''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
+* All constants and parameters in scaled, physical units
 * Well commented, documented and easy to use
-* Versatile and adaptable
+* Versatile and adaptable, modular components
 * Everything can be logged and specified by the user
 * Has already been used in other projects (agent based repressilators, microtubules!)
@@ Line 17: / Line 19: @@
 * 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 ===
-* At what rate do bacteria produce vesicles?
+* Small, but size based on growth
-* How long do they stick around?
+* Size and creation rate based on rate of change of surface area [ref - steve?]
-* Where are they produced relative to the bacterium?
+* Vesicle movement - brownian motion in a viscous fluid environment
-* Vesicle movement - brownian motion?
+* Interaction can be specified
-* 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.
+=== Chemical Fields ===
-* Compare vesicle-packaged protein communication with raw protein communcation? See Ollie's email
+* diffusion
+* decay
+* physical units
 === 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."
+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."
-Use a GRN (with delay?) to control vesicle production
+* ODE(s) can be attached to bacteria
-Interface with SBML models (SimBiology toolkit in MATLAB, CellDesigner)?
+* Can interact with chemical fields etc
-Allow switching of the flagella by external chemicals and a threshold viscosity
 === Magnetotaxis ===
-* Implement magnetotaxis as an alternative to chemotaxis.
+* an alternative to chemotaxis?
-** Allow tuning of the field strength and direction via the GUI?
+** 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?''

Team:BCCS-Bristol/Modeling/BSim Features

From 2009.igem.org