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| - | {{:Team:BCCS-Bristol/Header}}
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| - | == Links ==
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| - | * [[Team:BCCS-Bristol/Modeling/Ideas|Modelling ideas]]
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| - | * [http://code.google.com/p/bsim-bccs/ Google Code subversion repository]
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| - | * [[Team:BCCS-Bristol/Modeling/HowBSimWorks|How BSim Works]]
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| - | * [[Team:BCCS-Bristol/Modeling/ToDo|To do list]]
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| - |
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| - | == Todo list ==
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| - | === Steve ===
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| - | * Wiki
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| - | * Implement Paris GRNs
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| - | * Add paper references to bacterium behaviour and default parameter values (using [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters page from last year])
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| - | * Thread interaction loops; verify performance
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| - | "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)
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| - |
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| - | === Emily ===
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| - | * <s>Issue with bacteria 'escaping' the boundaries</s> r61
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| - | ** When the bacteria have a large enough force and the time step is not small enough the bacteris are able to 'escape' the boundary.
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| - | ** 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.
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| - | ** THIS COULD BE IMPROVED FURTHER - it allows for far greater forces however does not fix this problem in all cases.
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| - |
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| - | * <s>Understand how bacteria "tumble" under magnetic force</s>
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| - | ** 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.
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| - |
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| - | * Implement directed bateria (bacteria under constant magnetic field)
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| - | ** <s>Control only the direction of the bacteria - not the force.</s> r116
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| - | ** Add some variation in the direction of each bacterium
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| - | *** 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]
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| - | *** The interaction of the population with a magnetic field is affected by the temperature.
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| - |
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| - | * Finish coding the magnetic force for variable magnetic force
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| - | ** <s>Code the magnetic force as an additional force on the bacteria along with the internal and external forces.</s> r82
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| - | ** Find realistic values for the magnetic force acting on the bacteria.
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| - |
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| - | * Code half-coated bead
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| - | ** 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).
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| - |
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| - | * Control which objects are affected by the magnetic force
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| - | ** Magnetotactic bacteria in a constant magnetic field
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| - | ** Magnetotactic bacteria in a variable magnetic field
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| - | ** E. coli attaching to a magnetic bead under a variable magnetic field
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| - |
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| - | === Antos ===
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| - | *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]
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| - | *** Update: it works! (r140) Need to run large scale simulation to check for long term synchronization...
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| - | *** 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.
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| - | ** <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]
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| - | ** 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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| - |
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| - | *GRNs and vesicles
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| - | ** 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.
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| - | ** Investigate methods for numerically solving stochastic ODEs.
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| - | === [[Team:BCCS-Bristol/Modeling/Mattia|Mattia]] ===
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| - | ===Tomski===
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| - | * BSimBatch
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| - | ** Update to incorporate refactoring of other classes
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| - | * BSimExport
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| - | ** What information should be output (numerical data, visualisations, etc)
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| - | ** Options for visualisation - multiple output cameras, rotation of single camera, following of BSimParticle
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| - | ** Add options into GUI so that longer simulations can be saved more easily from user interface
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| - | ** Include new parameters in parameter file and BSimParameters
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| - | * Compilation on BlueCrystal
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| - | ** Test jar file generated on BCCS workstation on BC
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| - | ** Find out how to compile code from command line, without dependancy on Eclipse
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