BioNetGen: specification and simulation of rule-based models of biochemical systems

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BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. BioNetGen is presently a mixture of Perl, C++, and Python.

References:

James R. Faeder , Michael L. Blinov , and William S. Hlavacek
Rule-Based Modeling of Biochemical Systems with BioNetGen
Systems biology, 2009 - Springer, Ch 5, pp 113–167.

Documentation

Important Notes

Module Name: bionetgen (see the modules page for more information)
Unusual environment variables set
- BIONETGEN_HOME installation directory
- BIONETGEN_BIN executable directory
- BIONETGEN_DATA sample data directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3144 ~]$ module load bionetgen
[+] Loading singularity  3.10.5  on cn4172
[+] Loading git 2.39.2  ...
[+] Loading jupyter
[+] Loading bionetgen 0.7.9  ...

The basdic usage of the bionetgen application is as follows:

[user@cn3144 ~]$ sinteractive
[user@cn3144 ~]$ bionetgen -h
usage: bionetgen [-h] [-d] [-q] [-v] [-req REQUIRE] [-ll LOG_LEVEL]
                 {atomize,graphdiff,info,notebook,plot,run,visualize} ...

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -v, --version         show program's version number and exit
  -req REQUIRE, --require REQUIRE
  -ll LOG_LEVEL, --log-level LOG_LEVEL
                        This option allows you to select a logging level, from quietest to loudest
                        options are: "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG". Default is
                        set to INFO

sub-commands:
  {atomize,graphdiff,info,notebook,plot,run,visualize}
    atomize             SBML to BNGL translator
    graphdiff           A subcommand to compare two contact maps made by BioNetGen. The default
                        mode is "matrix" mode and will generate 4 graphs, two for each individual
                        input recolored, one for input 1 - input 2 and one for input 2 - input 1.
                        This can be used to find differences and communalities between two BNGL
                        models of the same process.
    info                Provides version information for BNG and dependencies
    notebook            Starts a Jupyter notebook to help run and analyze bionetgen models
    plot                Rudimentary plotting of gdat/cdat/scan files
    run                 Runs a given model using BNG2.pl
    visualize           Provides a simple way to get various visualizations of the model.
[user@cn3144 ~]$ cp $BIONETGEN_TESTS/* .
[user@cn3144 ~]$ bionetgen run  -o output_folder -i BP.bngl
BioNetGen version 2.8.4
Reading from file /data/$USER/BioNetGen/test_dir/BP.bngl (level 0)
Read 17 parameters.
Read 4 molecule types.
Read 4 species.
Read 2 observable(s).
Read 2 functions.
Read 4 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to ./BP.xml.
Running NFsim on cn4172
full command: /opt/conda/envs/bionetgen/lib/python3.8/site-packages/bionetgen/bng-linux/bin/NFsim -xml ./BP.xml -o ./BP.gdat -sim 10 -oSteps 100 -cb -gml 1000000 -seed 2123193053
[simulation PID is: 25365]
starting NFsim v1.2.2...

Seeding random number generator with: 2123193053
reading xml file (./BP.xml)
[-------]
preparing simulation...



Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+01 second(s).

Sim time: 0.000000e+00  CPU time (total): 4.400000e-05s  events (step): 0
Sim time: 1.000000e-01  CPU time (total): 2.315000e-03s  events (step): 127
Sim time: 2.000000e-01  CPU time (total): 4.583000e-03s  events (step): 133
Sim time: 3.000000e-01  CPU time (total): 7.367000e-03s  events (step): 174
Sim time: 4.000000e-01  CPU time (total): 1.054300e-02s  events (step): 197
Sim time: 5.000000e-01  CPU time (total): 1.416000e-02s  events (step): 217
Sim time: 6.000000e-01  CPU time (total): 1.698200e-02s  events (step): 182
Sim time: 7.000000e-01  CPU time (total): 2.073700e-02s  events (step): 226
Sim time: 8.000000e-01  CPU time (total): 2.422700e-02s  events (step): 224
Sim time: 9.000000e-01  CPU time (total): 2.793900e-02s  events (step): 245
Sim time: 1.000000e+00  CPU time (total): 3.218600e-02s  events (step): 249
Sim time: 1.100000e+00  CPU time (total): 3.649500e-02s  events (step): 239
Sim time: 1.200000e+00  CPU time (total): 4.071200e-02s  events (step): 264
Sim time: 1.300000e+00  CPU time (total): 4.510700e-02s  events (step): 280
Sim time: 1.400000e+00  CPU time (total): 5.074200e-02s  events (step): 306
Sim time: 1.500000e+00  CPU time (total): 5.536500e-02s  events (step): 282
Sim time: 1.600000e+00  CPU time (total): 6.066200e-02s  events (step): 312
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Sim time: 1.800000e+00  CPU time (total): 7.121000e-02s  events (step): 289
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Sim time: 2.000000e+00  CPU time (total): 8.162400e-02s  events (step): 278
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Sim time: 4.200000e+00  CPU time (total): 2.089880e-01s  events (step): 365
Sim time: 4.300000e+00  CPU time (total): 2.156030e-01s  events (step): 370
Sim time: 4.400000e+00  CPU time (total): 2.218300e-01s  events (step): 356
Sim time: 4.500000e+00  CPU time (total): 2.283790e-01s  events (step): 366
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Sim time: 5.300000e+00  CPU time (total): 2.910690e-01s  events (step): 394
Sim time: 5.400000e+00  CPU time (total): 2.975890e-01s  events (step): 338
Sim time: 5.500000e+00  CPU time (total): 3.049480e-01s  events (step): 389
Sim time: 5.600000e+00  CPU time (total): 3.122370e-01s  events (step): 394
Sim time: 5.700000e+00  CPU time (total): 3.188870e-01s  events (step): 357
Sim time: 5.800000e+00  CPU time (total): 3.263640e-01s  events (step): 399
Sim time: 5.900000e+00  CPU time (total): 3.344340e-01s  events (step): 425
Sim time: 6.000000e+00  CPU time (total): 3.431630e-01s  events (step): 421
Sim time: 6.100000e+00  CPU time (total): 3.514830e-01s  events (step): 407
Sim time: 6.200000e+00  CPU time (total): 3.595950e-01s  events (step): 416
Sim time: 6.300000e+00  CPU time (total): 3.667240e-01s  events (step): 365
Sim time: 6.400000e+00  CPU time (total): 3.742360e-01s  events (step): 392
Sim time: 6.500000e+00  CPU time (total): 3.812160e-01s  events (step): 358
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Sim time: 7.500000e+00  CPU time (total): 4.611030e-01s  events (step): 446
Sim time: 7.600000e+00  CPU time (total): 4.694120e-01s  events (step): 432
Sim time: 7.700000e+00  CPU time (total): 4.777980e-01s  events (step): 426
Sim time: 7.800000e+00  CPU time (total): 4.868270e-01s  events (step): 379
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Sim time: 8.000000e+00  CPU time (total): 5.030150e-01s  events (step): 405
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Sim time: 8.200000e+00  CPU time (total): 5.207430e-01s  events (step): 453
Sim time: 8.300000e+00  CPU time (total): 5.285080e-01s  events (step): 418
Sim time: 8.400000e+00  CPU time (total): 5.366710e-01s  events (step): 416
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Sim time: 8.700000e+00  CPU time (total): 5.608180e-01s  events (step): 397
Sim time: 8.800000e+00  CPU time (total): 5.686940e-01s  events (step): 404
Sim time: 8.900000e+00  CPU time (total): 5.764850e-01s  events (step): 414
Sim time: 9.000000e+00  CPU time (total): 5.858260e-01s  events (step): 413
Sim time: 9.100000e+00  CPU time (total): 5.947840e-01s  events (step): 448
Sim time: 9.200000e+00  CPU time (total): 6.038400e-01s  events (step): 426
Sim time: 9.300000e+00  CPU time (total): 6.127030e-01s  events (step): 412
Sim time: 9.400000e+00  CPU time (total): 6.222660e-01s  events (step): 483
Sim time: 9.500000e+00  CPU time (total): 6.310190e-01s  events (step): 454
Sim time: 9.600000e+00  CPU time (total): 6.406940e-01s  events (step): 463
Sim time: 9.700000e+00  CPU time (total): 6.496990e-01s  events (step): 439
Sim time: 9.800000e+00  CPU time (total): 6.576430e-01s  events (step): 403
Sim time: 9.900000e+00  CPU time (total): 6.661630e-01s  events (step): 435
Sim time: 1.000000e+01  CPU time (total): 6.748340e-01s  events (step): 435

You just simulated 35638 reactions in 6.748580e-01s
( 5.280815e+04 reactions/sec, 1.893647e-05 CPU seconds/event )
Null events: 1   (1.893700e-05 CPU seconds/non-null event )

done.  Total CPU time: 2.25732s

WARNING: system state was not retrieved following simulate_nf. To retreive system state, call simulate_nf with option: get_final_state=>1.
CPU TIME: simulate 2.34 s.
Finished processing file /data/$USER/BioNetGen/test_dir/BP.bngl.
CPU TIME: total 2.35 s.

End the interactive session:

[user@cn3111 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$