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CC3D WS 6.4: Parameter Files, Best Practice, Parameter Scans [James Sluka] August 3, 2024
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CompuCell3D Workshop: Module 6.4: Best Practices, Parameter Files and Basic Parameter Scans, August 3, 2024
Presented by Dr. James Sluka
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA
*Contents*
Hints and tricks for simulating with CC3D
Use one extra MCS step, e.g., 10001
Using multiple CPU’s (thread, cores)
Effective use of steppables
Define the basic units of the model (time, length, …)
Best Practices
Version tracking
Biological description
Parameters
Collect parameters at top of one of the project files
Logging parameters
Multiple parameter sets
Parameter Scans (PSCAN)
Adding a metric to the CC3D project to judge results of changin parameters
Adding the parameter scan
Running the parameter scan
Locating the output
Slides, exercises and demos for all videos available here:
Please consider subscribing to our CC3D-related channels:
Presented by Dr. James Sluka
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA
*Contents*
Hints and tricks for simulating with CC3D
Use one extra MCS step, e.g., 10001
Using multiple CPU’s (thread, cores)
Effective use of steppables
Define the basic units of the model (time, length, …)
Best Practices
Version tracking
Biological description
Parameters
Collect parameters at top of one of the project files
Logging parameters
Multiple parameter sets
Parameter Scans (PSCAN)
Adding a metric to the CC3D project to judge results of changin parameters
Adding the parameter scan
Running the parameter scan
Locating the output
Slides, exercises and demos for all videos available here:
Please consider subscribing to our CC3D-related channels:
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