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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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| - | * 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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| - |
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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:
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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:
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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
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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
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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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| - | === 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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| - |
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| - | === Antos ===
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