Revision as of 23:04, 7 July 2009 by Sr8243 (Talk | contribs)

iGEM 2009


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?


  • 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

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)


  • 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


  • Study functionality of 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