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CLI Reference

The bionetgen command-line tool exposes the same in-process backend used by the Python API.

bionetgen run

Run a BNGL model simulation.

bionetgen run MODEL [OPTIONS]

Options:

  • -m, --method [ode|ssa|nf|pla|psa] simulation method.
  • -t, --t-end FLOAT end time.
  • -n, --n-steps INT number of output steps.
  • -o, --output PATH write tabular output to a file.
  • -v, --verbose show progress.

Examples:

bionetgen run model.bngl --method ode --t-end 1000 --n-steps 500
bionetgen run model.bngl -m ssa -o results.tsv
bionetgen run model.bngl -m nf -t 50 -v

bionetgen scan

Run a one-dimensional parameter scan.

bionetgen scan MODEL [OPTIONS]

Options:

  • --parameter NAME parameter to scan.
  • --min FLOAT minimum value.
  • --max FLOAT maximum value.
  • --n-points INT number of scan points.
  • --log-scale use logarithmic spacing.
  • --method [ode|ssa|nf|pla|psa] simulation method.
  • --t-end FLOAT end time.
  • --n-steps INT number of output steps.
  • --parallel INT worker process count.
  • -o, --output PATH write a CSV file.

Examples:

bionetgen scan model.bngl --parameter k_on --min 0.01 --max 100 --n-points 50
bionetgen scan model.bngl --parameter k_on --log-scale --output scan.csv

bionetgen sensitivity

Compute local normalized sensitivities.

bionetgen sensitivity MODEL [OPTIONS]

Options:

  • --parameter NAME repeatable; if omitted, all parameters are used.
  • --observable NAME repeatable; if omitted, all observables are used.
  • --method [ode|ssa|nf|pla|psa] simulation method.
  • --t-end FLOAT end time.
  • --n-steps INT number of output steps.
  • --delta FLOAT relative perturbation size.
  • --parallel INT worker process count.
  • -o, --output PATH write a CSV file.

Example:

bionetgen sensitivity model.bngl --parameter k_on --observable AB

bionetgen visualize

Export a visualization graph.

bionetgen visualize MODEL [OPTIONS]

Options:

  • --type [contact_map|regulatory_graph|rule_influence_graph|reaction_network_graph|ruleviz_pattern|ruleviz_operation|process_graph|sbml_multi] graph type.
  • -o, --output PATH write the serialized graph to disk.

Examples:

bionetgen visualize model.bngl --type contact_map -o contact_map.graphml
bionetgen visualize model.bngl --type sbml_multi -o model_multi.xml

bionetgen execute

Execute all actions defined in a BNGL model file.

bionetgen execute MODEL [OPTIONS]

Option:

  • -v, --verbose show progress.

bionetgen check

Parse a BNGL file and report model statistics or syntax errors.

bionetgen check MODEL

Example output:

OK: /path/to/model.bngl
  Parameters:      12
  Molecule types:  4
  Seed species:    6
  Reaction rules:  8
  Observables:     5
  Actions:         2

bionetgen export

Export a model to another format.

bionetgen export MODEL -f FORMAT -o OUTPUT

Formats:

  • xml
  • net
  • bngl
  • sbml
  • matlab
  • latex

Examples:

bionetgen export model.bngl -f sbml -o model.xml
bionetgen export model.bngl -f matlab -o model.m
bionetgen export model.bngl -f net -o model.net
bionetgen export model.bngl -f latex -o model.tex

Environment Variables

Variable Description
BIONETGEN_USE_PERL Set to 1 to use the legacy Perl BNG2.pl path
BNGPATH Path to a legacy BNG2.pl installation for compatibility mode