How BSim works

The new structure

When we set out to restructure BSim it was decided that it should be made much more versatile and adaptable, and that as much as possible of the physics and coding should effectively be behind the scenes. This would allow stronger focus on the biological aspects of the simulation. To this end BSim has now been rebuilt as an environment where the user takes various functionalities already in place and uses them to create a simulation tailored to their specific requirements.

Concept - how BSim Simulations should work

scene.particles.add(
  new Bacterium(position: 0 1 0, radius: 1),
  new Bacterium(position: 0 1 0, radius: 1),
  new Bacterium(position: 0 1 0, radius: 1),
  new Bead(position: 0 1 0),
);

b = new Bacterium()
b.grn(new GRN(dy/dx = -2x; dx/dz = y^2))
scene.particles.add(b);

scene.chemicalFields.add(
  new ChemicalField(chemical: aspartate),
  new ChemicalField(chemical: AHL)
)

scene.boundaries(..)
scene.dt(..)
scene.simulationTime(..)

app.renderer(new ProcessingRenderer())
app.exporters.add(
  new FileExporter(),
  new MovieExporter(),
  new ScreenshotExporter()
)
app.gui()

Team:BCCS-Bristol/Modeling/HowBSimWorks

From 2009.igem.org

How BSim works

The new structure

Concept - how BSim Simulations should work