Team:BCCS-Bristol/Modeling

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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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* Meet Sean Davies re: beads - try to bring some polystyrene beads
 
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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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* 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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* 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>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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* 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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* HOWEVER.. 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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=== 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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*BSim Population Dynamics:
 
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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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** Control only the direction of the bacteria - not the force.
 
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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> r66
 
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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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*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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*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).
 

Latest revision as of 23:53, 20 October 2009