Team:BCCS-Bristol/Modeling
From 2009.igem.org
BCCS-Bristol
iGEM 2009
iGEM 2009
Contents |
Workflow
- Study Team:BCCS-Bristol/Modeling/Ideas to understand high level development goals (you can add stuff to that page!)
- 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
- Commit to the [http://code.google.com/p/bsim-bccs/ subversion repository] and
strike outthe item on your to-do list, adding a reference to the commit number if possible e.g:-
Rename BSimObject to BSimParticler19
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Todo list
Steve
- Meet Sean Davies re: beads - try to bring some polystyrene beads
- Learn something more about bioscaffolds
- Contact Paris team re:video
- Decide whether we are talking at the synbio conference, if so, who is talking
- Identify what batch simulations we wish to carry out asap. See [1].
- Study whether 3D implementation of newPosition in BSimBacteriaCreate is reasonable r28
- Refactor to use Vector and Matrix types from vecmath
- 3D diffusion for BSimChemicalField r29
- 3D boundaries r34
- Remove author, date from headers?
- Further refactoring to achieve clear and consistent class-package naming: make toolbar a nested class of app?
- Are PART_PART, PART_BACT, PART_BEAD really neccesary?
- Add paper references to parameter values in the code using page from last year
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3D tumbling in BSimBacteriar65 -
Improve knowledge of rigid body collisions[http://chrishecker.com/images/e/e7/Gdmphys3.pdf] [http://www.cs.lth.se/EDA046/lectures/L3.pdf]
- 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
- 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
Mattia
- Last Year Bug Fixing:
New solution for reading gammaVals.txt (Old Problem: In Windows Vista semeed to be some reading problems)Mathematic corrections in calcDistFromBoundary(Wrong Mathematics)
- BSim 3D:
- Update Class BSimParticle r28 r51
Class parametersConstructorsetPositionsetCentrePossetDirectionnormalise3DVector
- Update Class BSimChemicalField r29 r35
Class parametersConstructorsetAsLinearredrawupdateField- Update Class BSimChemicalFieldThread
Class parametersConstructorrun
addChemicalgetConcentrationgetField
- Update Class BSImBacterium r30 r50 r55
iterateBacterium- iterateTumble
startNewPhasedoRun
- Update Class BSImBacteriaCreate r31 r48
createBacteriaSetcreateBacterium
- Update Class BSimDeadBacterium r32
runLogic
- Update Class BSimBeadsCreate r33
createBeadSetcreateBead
- Update Class BSimChemicalFieldCreate r36
createChemicalField
- Update Class BSimCollisionPhysics r37 r39 r46
Class parametersupdateProperties- Update Class BSimCollisionPhysicsThread
rundistBetweenPointsresolveExternalForceslinearMotionforce2Velocity3D
- Update Class BSimParameters r38 r41 r42 r58
- Update Class BSimScene r40 r56
resetScenerunAllUpdates
New Class BSimPlaneBoundaryCreater43 r 54New Class BSimSolidPlaneBoundaryr44 r49 r53- Update Class BSimParametersLoader r47 r57
processLine
New Class BSimWrapPlaneBoundaryr52
- Update Class BSimParticle r28 r51
Emily
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Issue with bacteria 'escaping' the boundariesr61- When the bacteria have a large enough force and the time step is not small enough the bacteris are able to 'escape' the boundary.
- 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.
- THIS COULD BE IMPROVED FURTHER - it allows for far greater forces however does not fix this problem in all cases.
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Understand how bacteria "tumble" under magnetic force- 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.
- Implement directed bateria (bacteria under constant magnetic field)
- Control only the direction of the bacteria - not the force.
- Finish coding the magnetic force for variable magnetic force
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Code the magnetic force as an additional force on the bacteria along with the internal and external forces. - Find realistic values for the magnetic force acting on the bacteria.
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- Code half-coated bead
- 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).
- Control which objects are affected by the magnetic force
- Magnetotactic bacteria in a constant magnetic field
- Magnetotactic bacteria in a variable magnetic field
- E. coli attaching to a magnetic bead under a variable magnetic field
Antos
- GRNs and vesicles
- Read more about the mechanics of different GRNs (specifically switches).
- Find out how they interact with the external environment.
- Investigate the possiblity of using a different time-step to the fixed one in BSim.
- Investigate the effect of different time steps (GRNs operate on a time scale relatively long compared to that of BSim).
- Investigate the mechanics of our GRNs with respect to vesicle budding and communication.
- Investigate methods for numerically solving stochastic ODEs.
- BSim GRNs
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Java implementation of Runge-Kutta 4th order solver.- Refactor ODEs from an interface to an abstract class if necessary.
- 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)
- Implement the solvers into BSim.
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Implement other solvers (more efficient).- The ability to choose between them (in BSim).
- Investigate possibility of using javax/vecmath and matrix ops to maybe make the larger routines more efficient.
- Extend to Stochastic ODEs.
- Interface BSim with external parameters (maybe similar to current parameter files) used to define an ODE system.
- Investigate the feasibility of SBML parameters or a similar XML based format.
- Similarly investigate the format used by XPP (may be more succinct, also is specifically for ODEs).
- Investigate and implement GRN (ODE) and chemical field interaction.
- Study implementation of 3D diffusion in BSim.
- Implement diffusion in/out terms for membrane diffusion.
- GRN interaction with vesicle budding and chemical transport (on the surface of the vesicle and inside it).
- Incorporate a method for seeing the effects of GRN activity (eg colour changes, pop-out time series).
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