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| - | {{:Team:BCCS-Bristol/Header}}
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| - | == Workflow ==
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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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| - | * 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 [http://code.google.com/p/bsim-bccs/ 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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| - | == Todo list ==
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| - | === Steve ===
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| - | * Abstract for ECCS (1st Sep)
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| - | * Contact Paris team, review gold medal requirements
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| - | * Analyse performance using TPTP, rerun BSim1.0 simulations w/o various collisions to assess statistical importance
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| - | * Identify the most interesting parameters over which to plot a quality function
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| - | * Simplify growth > vesiculation based on P_begin P_end
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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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| - | * Processing export libraries
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| - | * CollisionPhysics > CollisionDetection/CollisionResponse?
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| - | * Study whether 3D implementation of newPosition in BSimBacteriaCreate is reasonable r28
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| - | * Refactor to use Vector and Matrix types from vecmath
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| - | * tumbleSpeed looks a bit suspect
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| - | * 3D diffusion for BSimChemicalField r29
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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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| - | * <s>3D tumbling in BSimBacteria</s> r65
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| - | * <s>Improve knowledge of rigid body collisions</s> [http://chrishecker.com/images/e/e7/Gdmphys3.pdf] [http://www.cs.lth.se/EDA046/lectures/L3.pdf]
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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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| - | * <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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| - | * 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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| - | * 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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| - |
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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! Run large scale simulation to check for long term synchronization...
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| - | *** If Garcia-Ojalvo results can be reproduced, compare chemical field to vesicles.
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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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| - | *** Investigate possibility of using javax/vecmath and matrix ops to maybe make the larger routines more efficient. EDIT: having run ~500 bacteria on RK45, it seems that there are other bottlenecks in performance at the moment so this is a very minor issue.
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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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| - | ** Investigate and implement GRN (ODE) and chemical field interaction.
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| - | *** <s>Study implementation of 3D diffusion in BSim.</s> Seems to work fine
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| - | *** Implement diffusion in/out terms for membrane diffusion.
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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 (eg colour changes, pop-out time series).
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| - | *New and updated BSim documentation?
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| - | *BSim graphics
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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> Done (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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| - | **BSimChemicalField for 3 chemotaxis fields. Low priority as we're not using more than 1 at a time.
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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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