Team:BCCS-Bristol/Modeling

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Revision as of 18:03, 9 August 2009 by Mattia.fazzini (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 Monday 7th Aug 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].


  • 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
  • Study whether 3D implementation of newPosition in BSimBacteriaCreate is reasonable r28
  • 3D tumbling in BSimBacteria r30
  • 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

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

| Example of the box used for the boundary

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

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