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| - | {{:Team:BCCS-Bristol/Header}}
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| - | = How BSim works =
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| - | In this section we discuss the new structure of BSim simulations and the improvements made in how they are specified. We present a walkthrough of creating a fully-featured simulation of hundreds of bacteria exhibiting a classic run-and-tumble motion. All examples presented here are included with the BSim 2.0 distribution (''To be uploaded soon...'').
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| - | == The new structure ==
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| - | 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.
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| - | == A short tutorial ==
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| - | Here we present a short tutorial example which will walk you through the main steps of creating a simulation in BSim.
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| - | === Example 1 ===
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| - | == Concept - how BSim Simulations should work ==
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| - | ''Moved to end temporarily - do we still want this here?''
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| - | <pre>
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| - | scene.particles.add(
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| - | new Bacterium(position: 0 1 0, radius: 1),
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| - | new Bacterium(position: 0 1 0, radius: 1),
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| - | new Bacterium(position: 0 1 0, radius: 1),
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| - | new Bead(position: 0 1 0),
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| - | );
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| - | b = new Bacterium()
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| - | b.grn(new GRN(dy/dx = -2x; dx/dz = y^2))
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| - | scene.particles.add(b);
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| - | scene.chemicalFields.add(
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| - | new ChemicalField(chemical: aspartate),
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| - | new ChemicalField(chemical: AHL)
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| - | )
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| - | scene.boundaries(..)
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| - | scene.dt(..)
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| - | scene.simulationTime(..)
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| - | app.renderer(new ProcessingRenderer())
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| - | app.exporters.add(
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| - | new FileExporter(),
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| - | new MovieExporter(),
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| - | new ScreenshotExporter()
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| - | )
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| - | app.gui()
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| - | </pre>
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Latest revision as of 00:12, 21 October 2009
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