Team:BCCS-Bristol/Modeling

From 2009.igem.org

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== [[Team:BCCS-Bristol/Modeling/Population_Dynamics|Growth and population dynamics]]==
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== Workflow ==
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[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid From the 2008 wiki]:
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* Study [[Team:BCCS-Bristol/Modeling/Ideas]] to understand high level development goals (you can add stuff to that page!)
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"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."
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* Decide the specifics of what needs to be done and add items to your to-do list. Ideally the items added should read like commit messages
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* Commit to the subversion repository and <s>strike out</s> the item on your to-do list, adding a reference to the commit number if possible e.g:
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** <s>Rename BSimObject to BSimParticle</s> r19
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Implement replication, growth and death of bacteria. Perhaps inherit from a LivingObject class?
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== Todo list ==
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Replication: after a random amount of time, duplicate bacteria at the same location. Need to find out the parameters and distribution for replication.
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=== Steve ===
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Death: After a random amount of time after cell 'birth', bacteria die.
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* Meet Sean Davies Monday 7th Aug re: beads - try to bring some polystyrene beads
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* Learn something more about bioscaffolds
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* Contact Paris team re:video
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* Decide whether we are talking at the synbio conference, if so, who is talking
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Growth: is this important? How might it be implemented?
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* Rename bsimapp > bsimgui, logic > internalforce?
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* Delete author, date from headers?
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* Make toolbar a nested class of app
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* Further refactoring to achieve clear and consistent class - package naming
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* Are PART_PART, PART_BACT, PART_BEAD really neccesary?
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* Add paper references to parameter values in the code using [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters|a page from last year]
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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]?
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=== Mattia ===
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== Vesicles ==
 
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* At what rate do bacteria produce vesicles?
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=== Emily ===
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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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== 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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=== Antos ===
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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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== Batch simulations ==
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* Implement magnetotaxis as an alternative to chemotaxis.  
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We should identify what batch simulations we wish to carry out asap. See [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Batch_Simulations|last year's page].
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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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== Misc ==
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== BSim Subversion repository ==
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* Optimise the [[Team:BCCS-Bristol/Modeling/Performance|performance]] of the BSimCollisionPhysics class using clever heuristics and approximations
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[http://code.google.com/p/bsim-bccs/ The BSim svn repository] is hosted on Google Code.
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* Choice between 2D (for plates & slides) and 3D (for simulation in alternative environments - blood vessels etc)?
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* Consider use of the Processing language and Java3D for visualisations
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* 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]
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Revision as of 14:05, 7 August 2009

BCCS-Bristol
iGEM 2009

Contents

Workflow

  • Study Team:BCCS-Bristol/Modeling/Ideas to understand high level development goals (you can add stuff to that page!)
  • Decide the specifics of what needs to be done and add items to your to-do list. Ideally the items added should read like commit messages
  • Commit to the subversion repository and strike out the item on your to-do list, adding a reference to the commit number if possible e.g:
    • Rename BSimObject to BSimParticle r19

Todo list

Steve

  • Meet Sean Davies Monday 7th Aug re: beads - try to bring some polystyrene beads
  • Learn something more about bioscaffolds
  • Contact Paris team re:video
  • Decide whether we are talking at the synbio conference, if so, who is talking
  • Rename bsimapp > bsimgui, logic > internalforce?
  • Delete author, date from headers?
  • Make toolbar a nested class of app
  • Further refactoring to achieve clear and consistent class - package naming
  • Are PART_PART, PART_BACT, PART_BEAD really neccesary?
  • Add paper references to parameter values in the code using page from last year

Mattia

Emily

Antos

Batch simulations

We should identify what batch simulations we wish to carry out asap. See year's page.

BSim Subversion repository

[http://code.google.com/p/bsim-bccs/ The BSim svn repository] is hosted on Google Code.

Retrieved from "http://2009.igem.org/Team:BCCS-Bristol/Modeling"