microbial-dynamics - Model and analyze microbial population dynamics
Models and analyzes microbial populations using growth-curve fitting, community dynamics, stochastic simulation, biofilm and CFU analysis, genome annotation, and anaerobic digestion modeling.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Fit bacterial growth curves
- Extract growth parameters
- Model community interactions
- Simulate stochastic populations
- Quantify crystal violet biofilms
- Calculate CFU concentrations
- Annotate bacterial genomes
- Model anaerobic digestion
Inputs
- OD600 time-series data
- Growth model selection
- Community interaction parameters
- Initial population sizes
- Stochastic reaction definitions
- Crystal violet assay replicates
- Serial dilution plate counts
- Bacterial genome sequences
- Anaerobic digestion parameters
Outputs
- Growth model parameters
- Community population trajectories
- Stochastic simulation trajectories
- Biofilm analysis tables
- CFU/mL estimates
- Genome annotations
- Gene statistics
- Anaerobic digestion model results
Requirements
- Python environment
- SciPy
- NumPy
- Pandas
- Matplotlib
- Prokka for genome annotation