Finding attractors

[yzongy]

A previous discussion solved the model checking problem, which was raised by pyboolnet.attractors.compute_attractors(primes, "synchronous") :
[https://github.com//issues/93]

Though this error was solved by manually calling the model_checking function, how do we get the attractors under synchronous update with a given Boolean network(example: BottomStrain_GoldStandardGRNbased.txt) ?

[hklarner]

• so what's the output of compute_attractors(primes, "synchronous")?
• by the way you can add a file name to save the result (useful if computation time is long)

[yzongy]

It came back with a model_checking exception:

INFO attractors.completeness(..)
INFO created /var/folders/8t/qrykd8w57pggdyvkp5c5nl_c0000gn/T/pyboolnet_ti93zc77
INFO no
INFO working on minimal trapspace 1/32: 10011111110100101101010011011111111101111111110111111111111111111001000111001011111111110111110001111111100011011111111111100000111111001111111111111110111111110001111111111111001110011111100111111111111111111011111011111101101011111111111101101111101111111011111111111100011111111111111011101010111111111011101110011111000110111000111111111111101111100111110111011111101111101110111101101001001011111110101111100011001111111010111101111100001110111010100111111111000010100010101111101111101010111111101110010111111111110111111110111011101010111100111101111111111111101111101101110011000110111011011101111011111110111010111111111111001110110111111111011110001111100111111110101111111101111110011011101100101111101001111101110001111110101111111110111111011110101111110101000110111001110001101101111010001011111111110110111011111111001101101110100110000111111111101101001111111111111110011011111110110111111101111101101001111100111011111010110111011111000010111110111111101111110010110011100011111100010111011111111111001011101001111110111010110111111111111101111111111111101100111101111111010011111111011110111111111111101111111111110111111011100111011010011111110111111111111111111110011111011111110010110101011111001110111111111111100111111111011011001111111110110011111111110111111110100110111101111110100011100100000111101111111110111110110111111011011101011011110110111011101101111111110011101111110101011100001111110010011111111111111111101011000101110110111111111011110111010111011111011111110011111111101111011
INFO attractors.univocality(..)
INFO yes
INFO attractors.faithfulness(..)
INFO yes
INFO attractors.find_attractor_state_by_randomwalk_and_ctl(..)
INFO find_attractor_state_by_randomwalk_and_ctl(..)
INFO len(primes)=1517, update=synchronous, length=15170, attempts=10
INFO trial 0
INFO start: 10011111110100101101010011011111111101111111110111111111111111111001000111001011111111110111110001111111100011011111111111100000111111001111111111111110111111110001111111111111001110011111100111111111111111111011111011111101101011111111111101101111101111111011111111111100011111111111111011101010111111111011101110011111000110111000111111111111101111100111110111011111101111101110111101101001001011111110101111100011001111111010111101111100001110111010100111111111000010100010101111101111101010111111101110010111111111110111111110111011101010111100111101111111111111101111101101110011000110111011011101111011111110111010111111111111001110110111111111011110001111100111111110101111111101111110011011101100101111101001111101110001111110101111111110111111011110101111110101000110111001110001101101111010001011111111110110111011111111001101101110100110000111111111101101001111111111111110011011111110110111111101111101101001111100111011111010110111011111000010111110111111101111110010110011100011111100010111011111111111001011101001111110111010110111111111111101111111111111101100111101111111010011111111011110111111111111101111111111110111111011100111011010011111110111111111111111111110011111011111110010110101011111001110111111111111100111111111011011001111111110110011111111110111111110100110111101111110100011100100000111101111111110111110110111111011011101011011110110111011101101111111110011101111110101011100001111110010011111111111111111101011000101110110111111111011110111010111011111011111110011111111101111011
INFO end: 10011111110100101101010011011111111101111111110111111111111111111001000111001011111111110111110001111111100011011111111111100000111111001111111111111110111111110001111111111111001110011111100111111111111111111011111011111101101011111111111101101111101111111011111111111100011111111111111011101010111111111011101110011111000110111000111111111111101111100111110111011111101111101110111101101001001011111110101111100011001111111010111101111100001110111010100111111111000010100010101111101111101010111111101110010111111111110111111110111011101010111100111101111111111111101111101101110011000110111011011101111011111110111010111111111111001110110111111111011110001111100111111110101111111101111110011011101100101111101001111101110001111110101111111110111111011110101111110101000110111001110001101101111010001011111111110110111011111111001101101110100110000111111111101101001111111111111110011011111110110111111101111101101001111100111011111010110111011111000010111110111111101111110010110011100011111100010111011111111111001011101001111110111010110111111111111101111111111111101100111101111111010011111111011110111111111111101111111111110111111011100111011010011111110111111111111111111110011111011111110010110101011111001110111111111111100111111111011011001111111110110011111111110111111110100110111101111110100011100100000111101111111110111110110111111011011101011011110110111011101101111111110011101111110101011100001111110010011111111111111111101011000101110110111111111011110111010111011111011111110011111111101111011
INFO created /var/folders/8t/qrykd8w57pggdyvkp5c5nl_c0000gn/T/pyboolnet_8xy2f1ir
ERROR nusmv did not respond with return code 0: cmd=/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/binaries/NuSMV-a/NuSMVa_mac64 -dcx -dynamic -df -coi /var/folders/8t/qrykd8w57pggdyvkp5c5nl_c0000gn/T/pyboolnet_8xy2f1ir, return_code=-11 output=*** This is NuSMV-A (compiled on Wed Sep 14 14:04:57 2016)
*** NuSMV-A is an extension of NuSMV 2.6.0
*** For more information on NuSMV-A see http://github.com/hklarner/NuSMV-A
*** Enabled addons are: compass
*** For more information on NuSMV see http://nusmv.fbk.eu/
*** or email to nusmv-users@list.fbk.eu.
*** Please report bugs to <Please report bugs to nusmv-users@fbk.eu>

*** Copyright (c) 2010-2014, Fondazione Bruno Kessler

*** This version of NuSMV is linked to the CUDD library version 2.4.1
*** Copyright (c) 1995-2004, Regents of the University of Colorado

*** This version of NuSMV is linked to the MiniSat SAT solver.
*** See http://minisat.se/MiniSat.html
*** Copyright (c) 2003-2006, Niklas Een, Niklas Sorensson
*** Copyright (c) 2007-2010, Niklas Sorensson

, error=b''
Traceback (most recent call last):
File "/Users/yzongy/BooleanNetworks/findTopStrainAttractors.py", line 31, in
pyboolnet.attractors.compute_attractors(primes, "synchronous")
File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/attractors.py", line 109, in compute_attractors
state = find_attractor_state_by_randomwalk_and_ctl(primes=primes, update=update, initial_state=mints)
File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/attractors.py", line 242, in find_attractor_state_by_randomwalk_and_ctl
if model_checking(primes, update, init, spec):
File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/model_checking.py", line 108, in model_checking
answer = model_checking_smv_file(
File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/model_checking.py", line 170, in model_checking_smv_file
raise Exception
Exception

[hklarner]

I would try a different tool, for example this one:

• https://people.kth.se/~dubrova/bns.html

[hklarner]

you can use the function primes2bns to create a bns file.