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simPATHy specifications


Unique identifier OMICS_14087
Name simPATHy
Alternative name simulating PATHways
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A graph and a covariance matrix associated to a reference condition.
Output data A dataset of observations coming from two conditions (reference and dysregulated) simulated from a multivariate normal distribution, covariance matrices of the two conditions, a summary of the parameters used for dysregulation.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.2
Stability Stable
stats, graphics, grDevices, rmarkdown, knitr, mvtnorm, graph, R.utils, igraph, htmlwidgets, shiny, qpgraph, shinydashboard, R(≥3.0), gRbase, ggm, clipper, topologyGSA
Source code URL
Maintained Yes


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  • person_outline Chiara Romualdi <>

Publication for simulating PATHways

simPATHy in publications

PMCID: 5695766
PMID: 29155870
DOI: 10.1371/journal.pone.0188348

[…] on the management of inappropriate polypharmacy and promoting appropriate polypharmacy in older people, focus on the implementation and sustainability of systems and processes is also warranted., simpathy (stimulating innovation management of polypharmacy and adherence in the elderly) was a pan-european initiative, funded by the european commission to help address the issue of inappropriate […]

PMCID: 5445126
PMID: 28603717
DOI: 10.3389/fvets.2017.00074

[…] and potential resistance risks, but the link to phenotypic and clinical resistance and, thus, importance for public health remain to be elucidated., mathematical modeling is a valuable tool in simulating pathways and identifying ways of reducing resistance. however, the relationship between reducing consumption of antibiotics and reducing resistance is not necessarily linear and still […]

PMCID: 4814833
PMID: 27029508
DOI: 10.1038/srep23194

[…] the static representation of the temporal network is provided by the adjacency matrix . each directed edge within astatic defines a node. the connection strength between nodes is now obtained by simulating pathways of a random walk process on the temporal network as follows. a walker is initially randomly assigned to a node. at every time step the walker waits until at least one edge […]

PMCID: 4719073
PMID: 26420781
DOI: 10.1093/bib/bbv087

[…] analysis. pathway analysis can be either quantitative or qualitative and is a key focus of the growing field of systems biology. quantitative pathway analysis uses dynamic mathematical models for simulating pathways and can be especially useful in drug discovery and the development of patient-specific dosage guidelines []. some examples of techniques used in this form of analysis include […]

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simPATHy institution(s)
Department of Biology, University of Padova, Padova, Italy; Department of Statistical Sciences, University of Padova, Padova, Italy
simPATHy funding source(s)
This work was supported by Italian Association for Cancer Research (IG17185), by the University of Padova and by the Italian Ministry of Education, University and Research.

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