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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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| - | == Todo list ==
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| - |
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| - | === Steve ===
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| - | * Thread interaction loops
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| - | * Wiki
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| - | * Define parameters and the scene in a main loop a la AgentCell - minimal constructors - lots of sets(), the main() loops should be human-readable!! BSim is gonna be super fast to prototype.
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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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| - | * http://vyshemirsky.blogspot.com/2007/11/sample-from-gamma-distribution-in-java.html
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| - | * Microtubules
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| - | * Change to private access control to discourage getters and setters
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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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| - | * 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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| - | * 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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| - | === Antos ===
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| - | *BSim GRNs
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| - | ** BSimChemicalField generalisation and better integration with scene, rendering etc.
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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>Java implementation of Runge-Kutta 4th order solver.</s> r70
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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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| - | ** <s>Implement the solvers into BSim.</s> Done for single bacterium
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| - | ** <s>Implement other solvers (more efficient).</s> r70
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| - | *** <s>The ability to choose between solvers.</s> This will be in a parameter file or some equivalent settings when importing an ODE file.
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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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| - | ** Interface BSim with external parameters (maybe similar to current parameter files) used to define an ODE system.
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| - | *** <s>Investigate the feasibility of SBML parameters or a similar XML based format.</s> SBML may be overcomplicated for our current needs. Low priority for now.
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| - | *** Similarly investigate the format used by XPP (may be more succinct, also is specifically for ODEs).
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| - | *** If we use JYaml for parameters this may be possible through that.
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| - | ** <s>Investigate and implement GRN (ODE) and chemical field interaction.</s> r139
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| - | *** <s>Study implementation of 3D diffusion in BSim.</s> Seems to work fine
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| - | *** <s>Implement diffusion in/out terms for membrane diffusion.</s> r139 - diffusion in/out based on the two relative concentrations
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| - | ** GRN interaction with vesicle budding and chemical transport (on the surface of the vesicle and inside it).
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| - | ** Incorporate a method for seeing the effects of GRN activity.
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| - | *** <s>Colour changes</s> works but needs reimplementation in new renderer
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| - | *** Time series: could have pop-out, need to fix the data export to allow exporting a time series.
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| - | *New and updated BSim documentation?
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| - | *BSim graphics
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| - | **<s>New rendering framework</s> r182
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| - | *** Add boundaries when they're implemented again.
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| - | *** Re-implement chemical field(s).
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| - | **<s>Rod shape rotation.</s> r125
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| - | **<s>Basic BSimChemicalField drawing in 3D - will help with grns with a diffusing chemical.</s> r124
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| - | *** <s>but needs to be improved in terms of speed</s> Done (removed lighting on chemical field :-s) this is pretty much the limit of optimisations possible without more in depth OpenGL work.
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| - | **<s>GRN/quorum field</s> Done, but needs visual improvements due to high dynamic range of chemical levels.
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| - | **<s>Investigate (OpenGL?) volume rendering (Tom - Vidi?) maybe better for arbitrary (GRN diffusion) chemical fields</s> A definite possibility in OpenGL, probably possible in P3D for (large?) speedups.
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| - | *GRNs and vesicles
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| - | ** Read more about the mechanics of different GRNs (specifically switches).
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| - | ** Find out how they interact with the external environment.
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| - | ** <s>Investigate the possiblity of using a different time-step to the fixed one in BSim.</s> Can use a longer or shorter time-step if required, however need to finish other parts to see if this would be relevant/important.
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| - | ** Investigate the effect of different time steps (GRNs operate on a time scale relatively long compared to that of BSim).
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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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