Tutorials

Documentation for SPARCED

• Jupyter Notebook
• SPARCED Hands-On Primer Tutorial
  • Prerequisites
  • Running Python Scripts
    • Model Compilation
    • Simulation Execution
    • Benchmark Generation
    • Benchmark Validation
    • Visualization
  • Key Examples
  • Additional Resources
  • Questions or Issues?
• Using the SPARCED Command Line Interface (CLI)
  • Getting Started
  • Common Commands
    • General Usage
    • Available Commands
  • Advanced Options
  • Examples
  • MPI Support
  • Troubleshooting
• Building and Running the SPARCED Singularity Container
  • Building the Container
    • 1. Prerequisites
    • 2. Clone the SPARCED Repository
    • 3. Build the Container
    • 1. Shell into the Container
    • 2. Run the Container Directly
    • 3. Bind Directories (Optional)
    • 4. Execute Specific Commands
• SPARCED input file format specification
  • General Principles
  • File Organization
  • Species table
    • Detailed field descriptions
  • Ratelaws Table
  • Detailed Field Descriptions
    • Notes for Users
  • Compartments Table
  • Detailed Field Descriptions
    • Notes for Users
  • Observables table
    • Detailed field descriptions
    • Usage
  • OmicsData Table
    • Detailed field descriptions
    • Notes for Users
  • GeneReg table
    • Detailed field descriptions
    • Usage
    • Guidelines for Extension
  • Initializer file (Optional)
    • Detailed field descriptions
    • Usage
• Species Naming Conventions
  • General Principles
  • Naming Structure
  • Where:
    • Examples
  • Prefixes
  • Suffixes
  • Guidelines for Complexes
    • Examples:
  • Potential Pitfalls
  • Regex Validation
  • Automating Naming