![](bg5.png)
we present an evolution of the tool that enables
stochastic simulations and biological noise analysis
in the context of those simulations. Stochastic simula-
tions are significantly more complex in computational
terms and require longer CPU times to conclude than
analogous deterministic simulations. Nevertheless,
this type of simulations accurately describes the dy-
namic behavior of systems with a small number of
molecules, something that deterministic simulations
can not always do.
This new prototype of EasyModel 1.1 is now be-
ing tested before it is rolled out to replace the cur-
rent 1.0 production version. Once this task is done
we will implement additional functionality to enable
user-friendly ways to merge individual models, to
scan parameter values and independent variables, and
to perform bifurcation analysis.
ACKNOWLEDGEMENTS
This work was partially supported by Minis-
terio de Economia, Industria y Competitividad
[TIN2017-84553-C2-2-R]; Ministerio de Educacion
[PRX18/00142]; and by Bridge Grants from Univer-
sitat de Lleida and INSPIRES.
REFERENCES
Alves, R., Antunes, F., and Salvador, A. (2006). Tools for
kinetic modeling of biochemical networks. Nature
Biotechnology, 24(6):667–672.
Ascher, U. M. and Petzold, L. R. (1997). Computer
Methods for Ordinary Differential Equations and
Differential-Algebraic Equations.
Ballet, P., Rivi
`
ere, J., Pothet, A., Theron, M., Pichavant,
K., Abautret, F., Fronville, A., and Rodin, V. (2016).
Modelling and simulating complex systems in biol-
ogy: Introducing NetBioDyn - a pedagogical and in-
tuitive agent-based software. In Multi-Agent-Based
Simulations Applied to Biological and Environmental
Systems, pages 128–158. IGI Global.
Bartolome, J., Alves, R., Solsona, F., and Teixido, I. (2019).
EasyModel: user-friendly tool for building and analy-
sis of simple mathematical models in systems biology.
Bioinformatics.
Benque, D., Bourton, S., Cockerton, C., Cook, B., Fisher, J.,
Ishtiaq, S., Piterman, N., Taylor, A., and Vardi, M. Y.
(2012). Bio Model Analyzer: Visual Tool for Mod-
eling and Analysis of Biological Networks. LNCS,
7358:686–692.
Dr
¨
ager, A., Rodriguez, N., Dumousseau, M., D
¨
orr, A., Wr-
zodek, C., Le Nov
`
ere, N., Zell, A., and Hucka, M.
(2011). JSBML: a flexible Java library for working
with SBML. Bioinformatics, 27(15):2167–2168.
Goldbeter, A. (1991). A minimal cascade model for the
mitotic oscillator involving cyclin and cdc2 kinase.
Proceedings of the National Academy of Sciences,
88(20):9107–9111.
Helikar, T., Kowal, B., McClenathan, S., Bruckner, M.,
Rowley, T., Madrahimov, A., Wicks, B., Shrestha, M.,
Limbu, K., and Rogers, J. A. (2012). The Cell Col-
lective: toward an open and collaborative approach to
systems biology. BMC systems biology, 6:96.
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle,
J. C., Kitano, H., and Forum, t. r. o. t. S. (2003). The
systems biology markup language (SBML): a medium
for representation and exchange of biochemical net-
work models. Bioinformatics, 19(4):524–531.
Le Nov
`
ere, N., Bornstein, B., Broicher, A., Courtot, M.,
Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra,
M., Shapiro, B., Snoep, J. L., and Hucka, M. (2006).
{BioModels Database}: a free, centralized database
of curated, published, quantitative kinetic models of
biochemical and cellular systems. Nucleic Acids Re-
search, 34(Database issue):D689—-D691.
Maarleveld, T. R., Olivier, B. G., and Bruggeman, F. J.
(2013). StochPy: A comprehensive, user-friendly tool
for simulating stochastic biological processes. PLoS
ONE, 8(11).
Paulsson, J. (2004). Summing up the noise in gene net-
works.
Peters, M., Eicher, J. J., van Niekerk, D. D., Waltemath, D.,
and Snoep, J. L. (2017). The JWS online simulation
database. Bioinformatics, 33(10):btw831.
SBML.org (2019). SBML Software Ma-
trix http://sbml.org/SBML
Software Guide/
SBML Software Matrix (12-12-2019).
Sorribas, A., Hern
´
andez-Bermejo, B., Vilaprinyo, E., and
Alves, R. (2007). Cooperativity and saturation in bio-
chemical networks: A saturable formalism using Tay-
lor series approximations. Biotechnology and Bio-
engineering, 97(5):1259–1277.
Wolfram Research Inc. (2108). WebMathematica
3.4.3. www.wolfram.com/products/webmathematica
(5/6/19).
EasyModel 1.1: User-friendly Stochastic and Deterministic Simulations for Systems Biology Models
149