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 Monday 7th Aug 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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* 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
 
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* Don't we only need _real_ physics between bacteria and beads..?
 
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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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* 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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=== 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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=== Emily ===
 
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* Fix BSim bug (short description here please :)
 
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* Understand how bacteria "tumble" under magnetic force
 
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* Finish coding the magnetic force
 
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* Code half-coated bead
 
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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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** Implement the solver into BSim.
 
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** Implement other solvers (more efficient) and the ability to choose between them.
 
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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 and implement GRN (ODE) and chemical field interaction.
 
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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