- Guzzi R (2012) Introduction to inverse meth-
ods with applications to geophysics and remote
sensing (in Italian). Earth sciences and geogra-
phy series. Springer, New York.http://www.
springer.com/it/book/9788847024946 - Ambrosio L, Dal Maso G (1990) A general
chain rule for distributional derivatives. Proc
Am Math Soc 108:691–702. doi:10.1090/
S0002-9939-1990-0969514-3 - Li C, Donizelli M, Rodriguez N et al (2010)
BioModels database: an enhanced, curated and
annotated resource for published quantitative
kinetic models. BMC Syst Biol 4:92.
doi:10.1186/1752-0509-4-92 - Hucka M, Finney A, Sauro HM, Bolouri H,
Doyle JC et al (2003) The systems biology
markup language (SBML): a medium for rep-
resentation and exchange of biochemical net-
work models. Bioinformatics 19:524–531.
doi:10.1093/bioinformatics/btg015 - Orr HA (2006) The distribution of fitness
effects among beneficial mutations in Fisher’s
geometric model of adaptation. J Theor Biol
238:279–285. doi:10.1016/j.
jtbi.2005.05.001 - Waterfall JJ (2006) Universality in multiparam-
eter fitting: sloppy models. Ph.D. thesis, Cor-
nell University, Ithaca, New York - White A, Tolman M, Thames HD, Withers
HR, Mason KA, Transtrum MK (2016) The
limitations of model-based experimental
design and parameter estimation in sloppy sys-
tems. PLoS Comput Biol 12:e1005227.
doi:10.1371/journal.pcbi.1005227 - Tyson JJ (1991) Modeling the cell division
cycle: cdc2 and cyclin interactions. Proc Natl
Acad Sci USA 88:7328–7332 - Bellu G, Saccomani MP, Audoly S, D’Angio`L
(2007) DAISY: a new software tool to test
global identifiability of biological and physio-
logical systems. Comput Methods Prog
Biomed 88:52–61. doi:10.1016/j.
cmpb.2007.07.002- Song C, Phenix H, Abedi V, Scott M, Ingalls
BP, Kaern M, Perkins TJ (2010) Estimating the
stochastic bifurcation structure of cellular net-
works. PLoS Comput Biol 6. doi:10.1371/
journal.pcbi.1000699 - Lu J, Engl HW, Schuster P (2006) Inverse
bifurcation analysis: application to simple gene
systems. Algorithms Mol Biol 1:11.
doi:10.1186/1748-7188-1-11 - Villaverde AF, Banga JR (2014) Reverse engi-
neering and identification in systems biology:
strategies, perspectives and challenges. J R Soc
Interface 11. doi:10.1098/rsif.2013.0505 - Paci P, Colombo T, Fiscon G, Gurtner A,
Pavesi G, Farina L (2017) SWIM: a computa-
tional tool to unveiling crucial nodes in com-
plex biological networks. Sci Rep 7:44797.
doi:10.1038/srep44797 - Villaverde A, Henriques D, Smallbone K,
Bongard S, Schmid J, Cicin-Sain D,
Crombach A, Saez-Rodriguez J, Mauch K,
Balsa-Canto E, Mendes P, Jaeger J, Banga JR
(2015) BioPreDyn-bench: a suite of bench-
mark problems for dynamic modelling in sys-
tems biology. BMC Syst Biol 9:8.
doi:10.1186/s12918-015-0144-4 - Press WH, Teukolsky SA, Vetterling WT, Flan-
nery BP (2007) Numerical recipes: the art of
scientific computing, 3rd edn. Cambridge Uni-
versity Press, Cambridge - Haselgrove CB (1961) The solution of nonlin-
ear equations and of differential equations with
two-point boundary conditions. Comput J
4:255–259 - Gillespie DT (2007) Stochastic simulation of
chemical kinetics. Annu Rev Phys Chem
58:35–55. doi:10.1146/annurev.
physchem.58.032806.104637
94 Rodolfo Guzzi et al.