Team:BCCS-Bristol/Modeling

From 2009.igem.org

Revision as of 22:22, 10 August 2009 by Sr8243 (Talk | contribs)

BCCS-Bristol
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 out the item on your to-do list, adding a reference to the commit number if possible e.g:
    • Rename BSimObject to BSimParticle r19

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
  • 3D tumbling in BSimBacteria r30
  • 3D diffusion for BSimChemicalField r29
  • 3D boundaries r34
  • 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 dramatically 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?
  • 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
  • Improve knowledge of rigid body collisions [http://chrishecker.com/images/e/e7/Gdmphys3.pdf]

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 parameters
      • Constructor
      • setPosition
      • setCentrePos
      • setDirection
      • normalise3DVector
    • Update Class BSimChemicalField r29 r35
      • Class parameters
      • Constructor
      • setAsLinear
      • redraw
      • updateField
      • Update Class BSimChemicalFieldThread
        • Class parameters
        • Constructor
        • run
      • addChemical
      • getConcentration
      • getField
    • Update Class BSImBacterium r30 r50 r55
      • iterateBacterium
      • iterateTumble
      • startNewPhase
      • doRun
    • Update Class BSImBacteriaCreate r31 r48
      • createBacteriaSet
      • createBacterium
    • Update Class BSimDeadBacterium r32
      • runLogic
    • Update Class BSimBeadsCreate r33
      • createBeadSet
      • createBead
    • Update Class BSimChemicalFieldCreate r36
      • createChemicalField
    • Update Class BSimCollisionPhysics r37 r39 r46
      • Class parameters
      • updateProperties
      • Update Class BSimCollisionPhysicsThread
        • run
        • distBetweenPoints
        • resolveExternalForces
        • linearMotion
        • force2Velocity3D
    • Update Class BSimParameters r38 r41 r42 r58
      • Class parameters
      • createNewSolidBoxBoundariesVec
      • createNewWrapBoxBoundariesVec
    • Update Class BSimScene r40 r56
      • resetScene
      • runAllUpdates
    • New Class BSimPlaneBoundaryCreate r43 r 54
    • New Class BSimSolidPlaneBoundary r44 r49 r53
    • Update Class BSimParametersLoader r47 r57
      • processLine
    • New Class BSimWrapPlaneBoundary r52

Emily

  • Fix BSim bug (short description here please :)
  • Understand how bacteria "tumble" under magnetic force
  • Finish coding the magnetic force
  • Code half-coated bead

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
    • Java implementation of Runge-Kutta 4th order solver.
      • Refactor ODEs from an interface to an abstract class if necessary.
    • Implement the solver into BSim.
    • Implement other solvers (more efficient) and the ability to choose between them.
    • 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).
Retrieved from "http://2009.igem.org/Team:BCCS-Bristol/Modeling"