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Team:BCCS-Bristol/Modeling-BSim Parameter File
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== BSim Parameter File == | == BSim Parameter File == | ||
| + | |||
| + | === Introduction === | ||
| + | Simulations in BSim are defined in 'parameter files'. These files set the properties of all variables, controls the visual outputs and tells the program where to save data. [https://static.igem.org/mediawiki/2008/0/06/BSimExp-Density_1600.txt This file ] defines the simulation of 1600 bacteria following the chemotatic gradient. Within the simulation there is one particle. | ||
=== How To Use The File === | === How To Use The File === | ||
| - | + | Parameter files are run as an argument to the BSimBatch program: | |
| - | + | java bsim.BSimBatch ./Parameter_Files/BSimExp-Adhesion_3_Control.txt | |
| - | + | Or opened within BSimApp using the 'Load simulation' button. | |
=== Option Definitions === | === Option Definitions === | ||
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CREATE_BACTERIA_SET: p1x p1y width height number type diameter(0=default) | CREATE_BACTERIA_SET: p1x p1y width height number type diameter(0=default) | ||
Creates a set of uniformly random distributed bacteria within a rectangular region defined by an upper left point, p1, and a width and height. If you wish the bacteria to be the default size then the diameter value should be 0, otherwise enter the size in microns. There are 5 types of bacteria: | Creates a set of uniformly random distributed bacteria within a rectangular region defined by an upper left point, p1, and a width and height. If you wish the bacteria to be the default size then the diameter value should be 0, otherwise enter the size in microns. There are 5 types of bacteria: | ||
| - | # Basic | + | # Basic |
| - | # Sensing | + | # Sensing |
| - | # Co-ordinated | + | # Co-ordinated |
| - | # Recruit | + | # Recruit |
| - | # Dead | + | # Dead |
CREATE_PARTICLE_SET: p1x p1y width height number type diameter(0=default) | CREATE_PARTICLE_SET: p1x p1y width height number type diameter(0=default) | ||
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FIELD_RECRUIT_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate | FIELD_RECRUIT_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate | ||
FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) | FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) | ||
| - | The chemical field is defined by an upper left point p1 with width and height. Boxes define the resolution of the gradient. The threshold is the smallest difference in the chemotactic gradient that a bacteria can sense. The | + | * The chemical field is defined by an upper left point ''p1'' with ''width'' and ''height''. |
| + | * ''Boxes'' define the resolution of the gradient. | ||
| + | * The ''threshold'' is the smallest difference in the chemotactic gradient that a bacteria can sense. | ||
| + | * The '''type'' of field can either be fixed or diffuse being 1 and 2 respectively. | ||
| + | * The ''boundary'' defines whether the chemical signal can diffuse out of the boundary or whether the chemicals are retained within, 1 is a fixed boundary whereas 2 is a leaky boundary. | ||
| + | * The ''rate'' sets how quickly the chemcial can diffuse. | ||
==== Visual Aids ==== | ==== Visual Aids ==== | ||
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VISUAL_AID_PARTICLE_TRACE: StepsSkipped | VISUAL_AID_PARTICLE_TRACE: StepsSkipped | ||
VISUAL_AID_CLOCK: AlwaysLeaveAs1 | VISUAL_AID_CLOCK: AlwaysLeaveAs1 | ||
| + | |||
| + | * ''StepsSkipped'' is the number of time steps that are skipped between points on the traces. | ||
| + | * If a visual aid is not required, simply remove the relevant line from the parameter file. | ||
==== Simulation View ==== | ==== Simulation View ==== | ||
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SCREEN_HEIGHT: pixels | SCREEN_HEIGHT: pixels | ||
SCREEN_WIDTH: pixels | SCREEN_WIDTH: pixels | ||
| - | SCREEN_ZOOM: xZoom | + | SCREEN_ZOOM: xZoom |
SCREEN_MOVE: xTrans yTrans | SCREEN_MOVE: xTrans yTrans | ||
| + | * ''xZoom'' is the magnification level of the simulation view. When xZoom = 1, 1 Pixel = 1 Micron, when xZoom = 2, 1 Pixel = 1/2 Micron and so on. | ||
| + | * ''xTrans'' and ''yTrans'' are a vector that the simulation view is moved by. | ||
==== Batch Settings ==== | ==== Batch Settings ==== | ||
Latest revision as of 15:35, 28 October 2008
Contents |
BSim Parameter File
Introduction
Simulations in BSim are defined in 'parameter files'. These files set the properties of all variables, controls the visual outputs and tells the program where to save data. This file defines the simulation of 1600 bacteria following the chemotatic gradient. Within the simulation there is one particle.
How To Use The File
Parameter files are run as an argument to the BSimBatch program:
java bsim.BSimBatch ./Parameter_Files/BSimExp-Adhesion_3_Control.txt
Or opened within BSimApp using the 'Load simulation' button.
Option Definitions
General Simulation Options
DT: 0.005
The time step (in seconds) used by the simulation. This should be small enough that you do not get objects moving through each other or that two objects get so close in a single time step that the reactive force pushes them too far apart.
VISCOSITY: 0.001
The viscosity of the medium in Pa.s. This effects the speed of movement of the bacteria. The force of the bacteria should be selected based on this.
PHYSICS_WELL_WIDTH_BACT_BACT: 0.0 PHYSICS_WELL_DEPTH_BACT_BACT: 0.0 PHYSICS_WELL_WIDTH_BACT_PART: 0.0 PHYSICS_WELL_DEPTH_BACT_PART: 0.0 PHYSICS_WELL_WIDTH_PART_PART: 0.0 PHYSICS_WELL_DEPTH_PART_PART: 0.0 PHYSICS_WELL_WIDTH_PART_BDRY: 0.0 PHYSICS_WELL_DEPTH_PART_BDRY: 0.0 PHYSICS_WELL_WIDTH_BACT_BDRY: 0.0 PHYSICS_WELL_DEPTH_BACT_BDRY: 0.0 PHYSICS_REACT_FORCE: 15.0
All interactions between bacteria, particles and boundaries are handled by a potential function. Each of these options specifies the relevant options for the linear piece-wise function. The same reaction force (when objects overlap) is shared by all objects.
BACTERIA_RADIUS: 0.7
The default radius of a bacterium in microns.
BACTERIA_FORCE_DOWN: 0.41 BACTERIA_FORCE_UP: 0.4387
The force (in pN) that a bacterium exerts when moving up and down an Aspartate chemotactic gradient.
UP_RUN_LENGTH: 1.6 DOWN_RUN_LENGTH: 0.7 ISO_RUN_LENGTH: 0.86
The mean run length up and down an Aspartate chemotatic gradient (in seconds). Also the run length when in an isotropic region is given. This mean is for the exponential distribution used to model the run length distribution.
PARTICLE_RADIUS: 10.0
The default radius of a particle in microns.
Bacteria, Particle and Boundary Sets
CREATE_BACTERIUM_SINGLE: x y diameter(0=default)
CREATE_PARTICLE_SINGLE: x y diameter(0=default)
CREATE_BACTERIA_SET: p1x p1y width height number type diameter(0=default)
Creates a set of uniformly random distributed bacteria within a rectangular region defined by an upper left point, p1, and a width and height. If you wish the bacteria to be the default size then the diameter value should be 0, otherwise enter the size in microns. There are 5 types of bacteria:
- Basic
- Sensing
- Co-ordinated
- Recruit
- Dead
CREATE_PARTICLE_SET: p1x p1y width height number type diameter(0=default)
Creates a set of uniformly random distributed particles within a rectangular region defined by an upper left point, p1, and a width and height. At present there is only one type of particle and so this should be left as 0. If you wish the particle to be the default size then the diameter value should be 0, otherwise enter the size in microns.
CREATE_BOUNDARY_SOLID: p1x p1y p2x p2y
Creates a straight solid boundary between two points.
CREATE_BOUNDARY_WRAP: p1x p1y p2x p2y pOffsetX pOffsetY
Creates a straight wrapping boundary between two points (p1, p2) with an offset vector that is used to place objects that cross the boundary.
Chemical Fields
FIELD_GOAL_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) FIELD_COORD_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_COORD_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) FIELD_RECRUIT_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero)
- The chemical field is defined by an upper left point p1 with width and height.
- Boxes define the resolution of the gradient.
- The threshold is the smallest difference in the chemotactic gradient that a bacteria can sense.
- The 'type of field can either be fixed or diffuse being 1 and 2 respectively.
- The boundary defines whether the chemical signal can diffuse out of the boundary or whether the chemicals are retained within, 1 is a fixed boundary whereas 2 is a leaky boundary.
- The rate sets how quickly the chemcial can diffuse.
Visual Aids
VISUAL_AID_BACTERIA_TRACE: StepsSkipped VISUAL_AID_AVG_BACTERIA_TRACE: StepsSkipped VISUAL_AID_PARTICLE_TRACE: StepsSkipped VISUAL_AID_CLOCK: AlwaysLeaveAs1
- StepsSkipped is the number of time steps that are skipped between points on the traces.
- If a visual aid is not required, simply remove the relevant line from the parameter file.
Simulation View
SCREEN_HEIGHT: pixels SCREEN_WIDTH: pixels SCREEN_ZOOM: xZoom SCREEN_MOVE: xTrans yTrans
- xZoom is the magnification level of the simulation view. When xZoom = 1, 1 Pixel = 1 Micron, when xZoom = 2, 1 Pixel = 1/2 Micron and so on.
- xTrans and yTrans are a vector that the simulation view is moved by.
Batch Settings
VIDEO_FRAMES_SKIP: FramesToSkipInVideo(OnlyUsedWhenRunByBSimBatch) RECORD_VIDEO: FlagToRecordVideo(1=true)(OnlyUsedWhenRunByBSimBatch) DATA_FRAMES_SKIP: FramesToSkipInTextOutput(OnlyUsedWhenRunByBSimBatch) SIMULATION_LENGTH: NumberOfTimeSteps(OnlyUsedWhenRunByBSimBatch) SIMULATION_RUNS: NumberOfRuns(OnlyUsedWhenRunByBSimBatch) EXPORT_DIR: DirectoryPath(MustExist)(OnlyUsedWhenRunByBSimBatch)
