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.
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 ...
[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: 8.300000e+00 CPU time (total): 5.285080e-01s events (step): 418
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Sim time: 8.500000e+00 CPU time (total): 5.446180e-01s events (step): 406
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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.
[user@cn3111 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$