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| - | {{:Team:BCCS-Bristol/Header}}
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| - | == Workflow ==
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| - |
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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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| - |
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| - | == Todo list ==
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| - |
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| - | === Steve ===
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| - |
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| - | * Meet Sean Davies 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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| - | * Identify what batch simulations we wish to carry out asap. See [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Batch_Simulations].
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| - | * Study whether 3D implementation of newPosition in BSimBacteriaCreate is reasonable r28
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| - | * 3D tumbling in BSimBacteria r30
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| - | * 3D diffusion for BSimChemicalField r29
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| - | * 3D boundaries r34
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| - | * If our paradigm is particle dynamics, interactions with solid boundaries (that have a shape) are making things more complicated than neccesary.. traer physics is proving a big inspiration, it's beautifully simple - following its lead I believe we could decrease the complexity of the bsim physics engine
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| - | * We are going to have to implement collision detection for vesicles - once it's in, perhaps we should use it for bact-bact and bact-bound too.. we probably only need _real_ physics for bact-bead? In any case there seems to be a redundancy with both definition of potential functions and raw 'size' parameters
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| - | * Remove author, date from headers?
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| - | * Further refactoring to achieve clear and consistent class-package naming: make toolbar a nested class of app?
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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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| - | * <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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| - |
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| - | === Mattia ===
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| - | *Last Year Bug Fixing:
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| - | **<s>New solution for reading gammaVals.txt (Old Problem: In Windows Vista semeed to be some reading problems)</s>
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| - | **<s>Mathematic corrections in calcDistFromBoundary(Wrong Mathematics)</s>
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| - | *BSim 3D:
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| - | **Update Class BSimParticle r28 r51
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| - | ***<s>Class parameters</s>
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| - | ***<s>Constructor</s>
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| - | ***<s>setPosition</s>
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| - | ***<s>setCentrePos</s>
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| - | ***<s>setDirection</s>
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| - | ***<s>normalise3DVector</s>
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| - | **Update Class BSimChemicalField r29 r35
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| - | ***<s>Class parameters</s>
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| - | ***<s>Constructor</s>
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| - | ***<s>setAsLinear</s>
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| - | ***<s>redraw</s>
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| - | ***<s>updateField</s>
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| - | ***Update Class BSimChemicalFieldThread
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| - | ****<s>Class parameters</s>
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| - | ****<s>Constructor</s>
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| - | ****<s>run</s>
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| - | ***<s>addChemical</s>
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| - | ***<s>getConcentration</s>
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| - | ***<s>getField</s>
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| - | **Update Class BSImBacterium r30 r50 r55
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| - | ***<s>iterateBacterium</s>
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| - | ***iterateTumble
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| - | ***<s>startNewPhase</s>
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| - | ***<s>doRun</s>
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| - | **Update Class BSImBacteriaCreate r31 r48
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| - | ***<s>createBacteriaSet</s>
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| - | ***<s>createBacterium</s>
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| - | **Update Class BSimDeadBacterium r32
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| - | ***<s>runLogic</s>
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| - | **Update Class BSimBeadsCreate r33
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| - | ***<s>createBeadSet</s>
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| - | ***<s>createBead</s>
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| - | **Update Class BSimChemicalFieldCreate r36
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| - | ***<s>createChemicalField</s>
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| - | **Update Class BSimCollisionPhysics r37 r39 r46
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| - | ***<s>Class parameters</s>
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| - | ***<s>updateProperties</s>
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| - | ***Update Class BSimCollisionPhysicsThread
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| - | ****<s>run</s>
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| - | ****<s>distBetweenPoints</s>
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| - | ****<s>resolveExternalForces</s>
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| - | ****<s>linearMotion</s>
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| - | ****<s>force2Velocity3D</s>
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| - | **Update Class BSimParameters r38 r41 r42 r58
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| - | ***<s>Class parameters</s>
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| - | ***<s>createNewSolid[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Mattia/box Box]BoundariesVec</s>
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| - | ***<s>createNewWrap[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Mattia/box Box]BoundariesVec</s>
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| - | **Update Class BSimScene r40 r56
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| - | ***<s>resetScene</s>
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| - | ***<s>runAllUpdates</s>
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| - | **<s>New Class BSimPlaneBoundaryCreate</s> r43 r 54
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| - | **<s>New Class BSimSolidPlaneBoundary</s> r44 r49 r53
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| - | **Update Class BSim[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Mattia/parameter Parameters]Loader r47 r57
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| - | ***<s>processLine</s>
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| - | **<s>New Class BSimWrapPlaneBoundary</s> r52
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| - |
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| - | === Emily ===
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| - |
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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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| - | ** Control only the direction of the bacteria - not the force.
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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>
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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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| - | *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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| - | ** Investigate the possiblity of using a different time-step to the fixed one in BSim.
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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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| - |
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| - | *BSim GRNs
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| - | ** <s>Java implementation of Runge-Kutta 4th order solver.</s>
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| - | *** Refactor ODEs from an interface to an abstract class if necessary.
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| - | ** 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)
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| - | ** Implement the solvers into BSim.
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| - | ** <s>Implement other solvers (more efficient).</s>
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| - | *** The ability to choose between them (in BSim).
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| - | *** Investigate possibility of using javax/vecmath and matrix ops to maybe make the larger routines more efficient.
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| - | ** Extend to Stochastic ODEs.
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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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| - | *** Investigate the feasibility of SBML parameters or a similar XML based format.
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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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| - | *** Study implementation of 3D diffusion in BSim.
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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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