Computational Methods in Systems Biology

PINT: A Static Analyzer for Transient Dynamics of Qualitative Networks 315

In the next major release, we plan to add full support for synchronized
local transitions, i.e., transitions that modify simultaneously the state of sev-
eral automata. This improvement will allow to import any safe (1-bounded)
Petri nets, broadening the class of supported dynamical models.

References

1. Abou-Jaoud ́e, W., Monteiro, P.T., Naldi, A., Grandclaudon, M., Soumelis, V.,
   Chaouiya, C., Thieffry, D.: Model checking to assess t-helper cell plasticity. In:
   Front. Bioeng. Biotechnol. 2 , January 2015


2. Antao, T.: Bioinformatics with Python cookbook. Packt Publishing Ltd.,
   Birmingham (2015)


3. Baral, C.: Knowledge Representation, Reasoning and Declarative Problem Solving.
   Cambridge University Press, New York (2003)


4. Calzone, L., Fages, F., Soliman, S.: Biocham: an environment for modeling bio-
   logical systems and formalizing experimental knowledge. Bioinformatics 22 (14),
   1805–1807 (2006)


5. Cimatti, A., Clarke, E., Giunchiglia, E., Giunchiglia, F., Pistore, M., Roveri, M.,
   Sebastiani, R., Tacchella, A.: NuSMV 2: an opensource tool for symbolic model
   checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, pp.
   359–364. Springer, Heidelberg (2002). doi:10.1007/3-540-45657-0 29


6. Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Fried-
   berg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de Hoon, M.J.L.: Biopython:
   freely available python tools for computational molecular biology and bioinformat-
   ics. Bioinformatics 25 (11), 1422–1423 (2009)


7. Fages, F., Martinez, T., Rosenblueth, D.A., Soliman, S.: Influence systems vs reac-
   tion systems. In: Bartocci, E., Lio, P., Paoletti, N. (eds.) CMSB 2016. LNCS, vol.
   9859, pp. 98–115. Springer, Cham (2016). doi:10.1007/978-3-319-45177-0 7


8. Fitime, L.F., Roux, O., Guziolowski, C., Paulev ́e, L.: Identification of bifurcations
   in biological regulatory networks using answer-set programming. In: Constraint-
   Based Methods for Bioinformatics Workshop (2016)


9. Folschette, M., Paulev ́e, L., Magnin, M., Roux, O.: Sufficient conditions for reacha-
   bility in automata networks with priorities. Theor. Comput. Sci. 608 , 66–83 (2015).
   Part 1, From Computer Science to Biology and Back


10. Gonzalez, A.G., Naldi, A., S ́anchez, L., Thieffry, D., Chaouiya, C.: Ginsim: A
    software suite for the qualitative modelling, simulation and analysis of regulatory
    networks. Biosystems 84 (2), 91–100 (2006). Dynamical Modeling of Biological Reg-
    ulatory Networks


11. Grieco, L., Calzone, L., Bernard-Pierrot, I., Radvanyi, F., Kahn-Perl`es, B., Thi-
    effry, D.: Integrative modelling of the influence of MAPK network on cancer cell
    fate decision. PLoS Comput. Biol. 9 (10), e1003286 (2013)


12. Grunberg, R., Nilges, M., Leckner, J.: Biskit – a software platform for structural
    bioinformatics. Bioinformatics 23 (6), 769–770 (2007)


13. Helikar, T., Kowal, B., McClenathan, S., Bruckner, M., Rowley, T., Madrahimov,
    A., Wicks, B., Shrestha, M., Limbu, K., Rogers, J.A.: The cell collective: toward
    an open and collaborative approach to systems biology. BMC Syst. Biol. 6 (1), 96
    (2012)


14. Klarner, H., Streck, A., Siebert, H.: PyBoolNet: a python package for the gener-
    ation, analysis and visualization of boolean networks. Bioinformatics 33 , 770–772
    (2016)