Preventing print-outs when simulating a bionetgen model

[TorkelE]

Hello, I am simulating BioNetGen models in python. The workflow is something like:

import bionetgen
model = bionetgen.bngmodel('model.bngl')
result = bionetgen.run(model);

The "model.bngl" file basically declares the model and then runs a simulate({method=>"ode",t_end=>10,n_steps=>1000}).

Each time I simulate it I get a print-out like:

BioNetGen version 2.7.0
Reading from file /tmp/tmphkgb6zd0/multistate.bngl (level 0)
Read 9 parameters.
Read 3 molecule types.
Read 3 species.
Read 4 observable(s).
Read 4 reaction rule(s).
ACTION: simulate( method=>"cvode" )
ACTION: generate_network( multistate )
Iteration   0:     3 species      0 rxns  0.00e+00 CPU s
Iteration   1:     5 species      2 rxns  0.00e+00 CPU s
Iteration   2:     6 species      6 rxns  0.00e+00 CPU s
Iteration   3:     7 species      9 rxns  0.00e+00 CPU s
Iteration   4:     9 species     12 rxns  0.00e+00 CPU s
Iteration   5:     9 species     18 rxns  1.00e-02 CPU s
Cumulative CPU time for each rule
Rule   1:     6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn
Rule   2:     8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn
Rule   3:     1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn
Rule   4:     3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn
Total   :    18 reactions 1.00e-02 CPU s 5.56e-04 CPU s/rxn
Wrote network in net format to ./multistate.net.
Network simulation using cvode
WARNING: writeFile(): Overwriting existing file ./multistate.net.
Wrote network in net format to ./multistate.net.
Running run_network on slpc385
full command: /home/torkelloman/anaconda3/lib/python3.7/site-packages/bionetgen/bng-linux/bin/run_network -o ./multistate -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./multistate.net ./multistate.net 0.01 1000
[simulation PID is: 20404]
run_network 3.0
Read 9 parameters from ./multistate.net
Read 9 species from ./multistate.net
Read 4 group(s) from ./multistate.net
Read 0 function(s) from ./multistate.net
Read 18 reaction(s) from ./multistate.net
18 reaction(s) have nonzero rate
Initialization took 0.00 CPU seconds
Propagating with cvode using dense LU
Time course of concentrations written to file ./multistate.cdat.
Time course of groups written to file ./multistate.gdat.
Propagation took 0.00e+00 CPU seconds
Program times:  0.00 CPU s 0.00 clock s
Updating species concentrations from ./multistate.cdat
CPU TIME: simulate 0.02 s.
Finished processing file /tmp/tmphkgb6zd0/multistate.bngl.
CPU TIME: total 0.02 s.

when I make several simulations, this generates a lot of text, clogging up my jupyter notebook. Is there some way to prevent this from being generated?

[ASinanSaglam]

Hi,

First, it's not too important but you probably want to post any future python related issues on PyBioNetGen repo instead.

Second, yes there is a way to suppress the output. The documentation is lagging behind development, sorry about the delay. Try doing:

r = bionetgen.run('model.bngl', suppress=True)

run method currently accepts 1 arg, 3 kwargs input, output=None, suppress=False and timeout=None where timeout is in seconds.

Please let me know if it works for you, I'll close the issue after if it does.

[TorkelE]

Thanks, when I add the supress kwarg the run errors. I do

import bionetgen
model = bionetgen.bngmodel('model.bngl')

if I do

result = bionetgen.run(model);

everything is fine, however,

result = bionetgen.run(model, suppress=True);

gives this error:

BioNetGen version 2.7.1
Reading from file /tmp/tmpgcizzo9z/multistate.bngl (level 0)
Read 9 parameters.
Read 3 molecule types.
Read 3 species.
Read 4 reaction rule(s).
Read 4 observable(s).
Wrote model in xml format to ./multistate.xml.
Finished processing file /tmp/tmpgcizzo9z/multistate.bngl.
CPU TIME: total 0.01 s.
Couldn't run the simulation
'NoneType' object has no attribute 'decode'
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<timed exec> in <module>

~/anaconda3/lib/python3.7/site-packages/bionetgen/modelapi/runner.py in run(inp, out, suppress, timeout)
     31             cli = BNGCLI(inp, out, conf["bngpath"], suppress=suppress, timeout=timeout)
     32             try:
---> 33                 cli.run()
     34                 os.chdir(cur_dir)
     35             except Exception as e:

~/anaconda3/lib/python3.7/site-packages/bionetgen/tools/cli.py in run(self)
    138             raise RuntimeError(
    139                 "Failed to run your BNGL file, there might be an issue with your model!",
--> 140                 out.stdout.decode("UTF-8"),
    141                 out.stderr.decode("UTF-8"),
    142             )

AttributeError: 'NoneType' object has no attribute 'decode'

(also, thanks for pointing me to https://github.com/RuleWorld/PyBioNetGen/issues, will use that in the future)

[ASinanSaglam]

I'm looking into it now, can you tell me which OS you are using this on? Also can you run bionetgen info in the command line and give me the output?

[ASinanSaglam]

Actually, I figured out the issue, there will be a new PyBioNetGen version with the patch in 10-15 minutes.

[ASinanSaglam]

OK, PyBioNetGen version 0.7.0 is out, Try updating with pip install bionetgen --upgrade and if that doesn't work try pip install bionetgen==0.7.0. Please let me know if that fixes your problem.

[TorkelE]

That worked! Thanks a lot for the quick help :)

[ASinanSaglam]

I'm glad that's solved and that you for posting it as an issue 👍