Team:BCCS-Bristol/Modeling

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Revision as of 14:06, 16 July 2009

BCCS-Bristol
iGEM 2009

BSim Analysis

The Modelling Team has spent this week to analyse the BSim behaviour.
The Team made the BSim-UML trying to understand how and where we need to add our features.
After discussing on what is useful to expand in BSim we defined our goals:

Growth and population dynamics

From the 2008 wiki: "It has been assumed that bacteria do not replicate or die in our system. Although valid for short time periods, in simulations of a longer duration population dynamics may become an important factor. Incorporating this behaviour would also make the simulation framework suitable for wider areas of bacteria study, specifically in understanding colony dynamics related to growth and movement."

Implement replication, growth and death of bacteria. Perhaps inherit from a LivingObject class?

Replication: after a random amount of time, duplicate bacteria at the same location. Need to find out the parameters and distribution for replication.

Death: After a random amount of time after cell 'birth', bacteria die.

Growth: is this important? How might it be implemented?

Vesicles

At what rate do bacteria produce vesicles?
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.

Non-motile pattern formation

Can we replicate results like [http://www.nature.com/doifinder/10.1038/368046a0 Generic modelling of cooperative growth patterns in bacterial colonies] and [http://www.pnas.org/content/93/25/14225.full Symmetries in bacterial motility]?
Allow switching of the flagella by external chemicals and a threshold viscosity

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)

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 magnetic beads

Misc

Study functionality of [http://mic.sgmjournals.org/cgi/reprint/144/12/3275.pdf BacSim]
Optimise the performance of the BSimCollisionPhysics class using clever heuristics and approximations
Choice between 2D (for plates & slides) and 3D (for simulation in alternative environments - blood vessels etc)?
Consider use of the Processing language and Java3D for visualisations

@@ Line 2: / Line 2: @@
 == BSim Analysis ==
-The Modelling Team has spent this week to analyse the BSim behaviour.
+The Modelling Team has spent this week to analyse the BSim behaviour.<br/>
-The Team made the [[Team:BCCS-Bristol/Modeling/BSim-UML|BSim-UML]] trying to understand how and where we need to add our features.
+The Team made the [[Team:BCCS-Bristol/Modeling/BSim-UML|BSim-UML]] trying to understand how and where we need to add our features.<br/>
 After discussing on what is useful to expand in BSim we defined our goals:
 *[[Team:BCCS-Bristol/Modeling/Population_Dynamics|Population Dynamics]]