Team:BCCS-Bristol/Modeling-To Do List

Modelling To Do List

GRN Modelling

BSim Framework

Multi-threading Optimisations

Update the main computational classes to split up work into separate threads. Should improve performance when running on a single computer.

• BSimChemicalField [Done] - Update class to use worker threads when calculating the new diffusion field.
• BSimCollisionPhysics [Done] - Update class to use worker threads when calculating the force matrix.
• BSimCollisionPhysics - Update class to use multithread the call to the runLogic method on each bacterium.

Batch Processing

We need to be able to run batch runs of simulations to get enough results for statistical analysis.

• Parameter File Definition - We need a simple text file defined that allows for all the parameters in the simulation and sets of bacteria, particles and boundaries defined. It should look something like the example below with each line either giving a parameter definition or BSimObject creation details.

Viscosity: 0.0001
Dt: 0.01
CreateBacterium: 10, 10, 3.7, 50
CreateRandomBacteriaSet: 0, 0, 500, 600, 3.7, 50
...

• BSimBatch - Class to read the parameter files and run a set number of simulations, outputting videos and a data file of particle movement.
• Blue Crystal Accounts - Contact university about getting accounts to run some larger scale simulations
• Output Filters - Create new classes that can be attached to a simulation scene, allowing for information about the scene be output, e.g. in the form of text based or movie files. This ties in with the parameters that need to be monitored for the statistical analysis.

BSim Simulations