Team:BCCS-Bristol/Modeling
From 2009.igem.org
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=== Antos === | === Antos === | ||
*BSim GRNs | *BSim GRNs | ||
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** <s>Proof of concept to check functionality.</s> [http://www.pnas.org/content/101/30/10955 Something like this] | ** <s>Proof of concept to check functionality.</s> [http://www.pnas.org/content/101/30/10955 Something like this] | ||
*** Update: it works! (r140) Need to run large scale simulation to check for long term synchronization... | *** Update: it works! (r140) Need to run large scale simulation to check for long term synchronization... | ||
*** Compare chemical field with degradation to vesicular transport. | *** Compare chemical field with degradation to vesicular transport. | ||
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*** <s>Refactor ODEs from an interface to an abstract class if necessary.</s> EDIT: [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] seems sufficient so far, however need to generalise ODEs to just one interface. | *** <s>Refactor ODEs from an interface to an abstract class if necessary.</s> EDIT: [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] seems sufficient so far, however need to generalise ODEs to just one interface. | ||
** <s>Investigate other options in terms of external libraries (eg odeToJava - good but seems overcomplicated for current purposes; hundreds of lines of code for one solver routine)</s>[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos#ODE_Solvers_and_Libraries_already_in_existence done] | ** <s>Investigate other options in terms of external libraries (eg odeToJava - good but seems overcomplicated for current purposes; hundreds of lines of code for one solver routine)</s>[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos#ODE_Solvers_and_Libraries_already_in_existence done] | ||
** <s>Implement the solvers into BSim.</s> Done for single bacterium | ** <s>Implement the solvers into BSim.</s> Done for single bacterium | ||
** <s>Implement other solvers (more efficient).</s> r70 | ** <s>Implement other solvers (more efficient).</s> r70 | ||
- | *** <s>The ability to choose between solvers.</s> | + | *** <s>The ability to choose between solvers.</s> |
** Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria. | ** Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria. | ||
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*GRNs and vesicles | *GRNs and vesicles | ||
- | ** Read more about the mechanics | + | ** Read more about the mechanics switch, bistable and 'counter' GRNs and methods of modelling them. |
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** Investigate the mechanics of our GRNs with respect to vesicle budding and communication. | ** Investigate the mechanics of our GRNs with respect to vesicle budding and communication. | ||
** Investigate methods for numerically solving stochastic ODEs. | ** Investigate methods for numerically solving stochastic ODEs. |
Revision as of 13:38, 15 September 2009
BCCS-Bristol
iGEM 2009
iGEM 2009
Contents |
Links
- Modelling ideas
- [http://code.google.com/p/bsim-bccs/ Google Code subversion repository]
- How BSim Works
Todo list
Steve
- Wiki
- Implement Paris GRNs
- Add paper references to bacterium behaviour and default parameter values (using page from last year)
- Thread interaction loops; verify performance
"Growth curves were measured for all of the mutants, and their log-phase doubling times were calculated. In general, more extreme vesiculation phenotypes corresponded to longer doubling times" (Outer Membrane Vesicle Production by Escherichia coli Is Independent of Membrane Instability)
Emily
-
Issue with bacteria 'escaping' the boundariesr61- When the bacteria have a large enough force and the time step is not small enough the bacteris are able to 'escape' the boundary.
- Fix this by checking the distance and direction of all the bacteria close to the boundary. This will catch those that have crossed the boundary in one time step.
- THIS COULD BE IMPROVED FURTHER - it allows for far greater forces however does not fix this problem in all cases.
-
Understand how bacteria "tumble" under magnetic force- It is believed that the magnetic force causes the bacteria to orientate in line with the field and so the tumble phase will not occur.
- Implement directed bateria (bacteria under constant magnetic field)
-
Control only the direction of the bacteria - not the force.r116 - Add some variation in the direction of each bacterium
- The average alignment of the population is described by Langevin function for classical paramagnetism. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.mi.36.100182.001245]
- The interaction of the population with a magnetic field is affected by the temperature.
-
- Finish coding the magnetic force for variable magnetic force
-
Code the magnetic force as an additional force on the bacteria along with the internal and external forces.r82 - Find realistic values for the magnetic force acting on the bacteria.
-
- Code half-coated bead
- Apply two different potentials to each half of the bead - one side has a potential well (the bacteria attach here) and the other side has no well (the bacteria will interact normally here).
- Control which objects are affected by the magnetic force
- Magnetotactic bacteria in a constant magnetic field
- Magnetotactic bacteria in a variable magnetic field
- E. coli attaching to a magnetic bead under a variable magnetic field
Antos
- BSim GRNs
-
Proof of concept to check functionality.[http://www.pnas.org/content/101/30/10955 Something like this]- Update: it works! (r140) Need to run large scale simulation to check for long term synchronization...
- Compare chemical field with degradation to vesicular transport.
-
Refactor ODEs from an interface to an abstract class if necessary.EDIT: interface seems sufficient so far, however need to generalise ODEs to just one interface.
-
Investigate other options in terms of external libraries (eg odeToJava - good but seems overcomplicated for current purposes; hundreds of lines of code for one solver routine)done -
Implement the solvers into BSim.Done for single bacterium -
Implement other solvers (more efficient).r70-
The ability to choose between solvers.
-
- Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria.
-
- GRNs and vesicles
- Read more about the mechanics switch, bistable and 'counter' GRNs and methods of modelling them.
- Investigate the mechanics of our GRNs with respect to vesicle budding and communication.
- Investigate methods for numerically solving stochastic ODEs.
Mattia
Tomski
- BSimBatch
- Update to incorporate refactoring of other classes
- BSimExport
- What information should be output (numerical data, visualisations, etc)
- Options for visualisation - multiple output cameras, rotation of single camera, following of BSimParticle
- Add options into GUI so that longer simulations can be saved more easily from user interface
- Include new parameters in parameter file and BSimParameters
- Compilation on BlueCrystal
- Test jar file generated on BCCS workstation on BC
- Find out how to compile code from command line, without dependancy on Eclipse