Biosimulators_iBioSim

BioSimulators-compliant command-line interface to the iBioSim simulation program.

Contents

• Installation
• Usage
• License
• Development team
• Questions and comments

Installation

Install Docker image

docker pull paytonco/ibiosim

Local Usage

usage: iBioSim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [--directory DIRECTORY]
               [-p PROPERTIES] [-ti INITTIME] [-tl LIMTIME] [-ot OUTTIME]
               [-pi PRINTINTERVAL] [-m0 MINSTEP] [-m1 MAXSTEP] [-aErr ABSERR]
               [-sErr RELERR] [-sd SEED] [-r RUNS] [-sim SIMULATION] [-v]

BioSimulatiors-compliant command-line interface to the iBioSim simulation program <https://github.com/MyersResearchGroup/iBioSim>.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Arbitrary SBML, SED-ML, or Combine Archive file
  -o OUT_DIR, --out-dir OUT_DIR, -outDir OUT_DIR
                        Where the output should be stored
  --directory DIRECTORY
                        Project directory
  -p PROPERTIES, --properties PROPERTIES
                        Loads a properties file
  -ti INITTIME, --inittime INITTIME
                        Non-negative double initial simulation time
  -tl LIMTIME, --limtime LIMTIME
                        Non-negative double simulation time limit
  -ot OUTTIME, --outtime OUTTIME
                        Non-negative double output time
  -pi PRINTINTERVAL, --printinterval PRINTINTERVAL
                        Positive double for print interval
  -m0 MINSTEP, --minstep MINSTEP
                        Positive double for minimum step time
  -m1 MAXSTEP, --maxstep MAXSTEP
                        Positive double for maximum step time
  -aErr ABSERR, --abserr ABSERR
                        Positive double for absolute error
  -sErr RELERR, --relerr RELERR
                        Positive double for relative error
  -sd SEED, --seed SEED
                        Long for random seed
  -r RUNS, --runs RUNS  Positive integer for number of runs
  -sim SIMULATION, --simulation SIMULATION
                        Simulation type. Options are: ode, hode, ssa, hssa,
                        dfba, jode, jssa
  -v, --version         show program's version number and exit

Usage Through Docker Container

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)"/tests/fixtures,target=/root/in \
  --mount type=bind,source="$(pwd)"/tests/results,target=/root/out \
  paytonco/ibiosim:latest \
    -i /root/in/BIOMD0000000297.omex \
    -o /root/out

License

This package is released under the Apache-2.0

Development Team

This package was developed by the Genetic Logic Lab at the University of Colorado Boulder.

Questions and comments

Please contact the Genetic Logic Lab with any questions or comments.