This repository contains assorted files that are used to work with COPASI. I wrote these files to aid in my own work and make them available for anyone else to use/modify.

A utility previously called MEC.py is now called model_replicator and has been moved to its own repository.

• copasiplot2gnuplot.pl - PERL script to convert a file saved from a COPASI plot window with several runs (eg from parameter scan) to a data file that gnuplot can index the various runs (this basically just substitutes lines that have no numbers into two blank lines).

• normalize_sequences.pl - PERL script to convert a report file from COPASI parameter estimation or optimization to a regularly spaced file (in terms of function evaluations). More detailed information in the comments at the top of the file.

• progress_of_fit_stats.pl - PERL script to calculate statistics on files containing several parameter estimation or optimization results which have been normalized to contain regular intervals (eg processed with normalize_sequences.pl). More detailed information in the comments at the top of the file.

• run_pe_cps.sh - BASH script to run a series of repeated COPASI parameter estimations (or optimizations) calculating their statistics. Useful for comparing algorithms. Uses PERL scripts normalize_sequences.pl and progress_of_fit_stats.pl. More details in the comments at the top of the file.

• poptbench - BASH script to benchmark a parallel optimization algorithm against the serial version. Requires full path to serial and parallel versions of CopasiSE.

• profilecopasi - BASH script to profile CPU, memory, and I/O features of a CopasiSE run. Requires setting path to CopasiSE executable and uses the audria package. Writes out a CSV file with the data of one or several runs.

• model_report.py - Python script to write a text summary of the model file (either in COPASI or SBML formats). Requires the pandas and html2text packages.