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Team:BCCS-Bristol/Modeling
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| - | == | + | == [[Team:BCCS-Bristol/Modeling/Population_Dynamics|Growth and population dynamics]]== |
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[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid From the 2008 wiki]: | [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid From the 2008 wiki]: | ||
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Growth: is this important? How might it be implemented? | Growth: is this important? How might it be implemented? | ||
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| + | 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]? | ||
== Vesicles == | == Vesicles == | ||
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* Interaction with bacteria/chemicals/boundaries/etc. | * 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. | * 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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== GRN modelling == | == GRN modelling == | ||
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Use a GRN (with delay?) to control vesicle production | Use a GRN (with delay?) to control vesicle production | ||
| - | Interface with SBML models (SimBiology toolkit in MATLAB, CellDesigner) | + | Interface with SBML models (SimBiology toolkit in MATLAB, CellDesigner)? |
| + | Allow switching of the flagella by external chemicals and a threshold viscosity | ||
== Magnetotaxis == | == Magnetotaxis == | ||
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== Misc == | == Misc == | ||
| - | * | + | * Optimise the [[Team:BCCS-Bristol/Modeling/Performance|performance]] of the BSimCollisionPhysics class using clever heuristics and approximations |
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* Choice between 2D (for plates & slides) and 3D (for simulation in alternative environments - blood vessels etc)? | * 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 | * Consider use of the Processing language and Java3D for visualisations | ||
| + | * We created [[Team:BCCS-Bristol/Modeling/BSim-UML|BSim-UML]] to help us understand how and where we need to add new features | ||
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| + | == References == | ||
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| + | * [http://mic.sgmjournals.org/cgi/reprint/144/12/3275.pdf BacSim] | ||
Revision as of 16:23, 3 August 2009
iGEM 2009
Contents |
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?
Can we replicate results like Generic modelling of cooperative growth patterns in bacterial colonies and Symmetries in bacterial motility?
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.
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)
Misc
- 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
- We created BSim-UML to help us understand how and where we need to add new features
