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PyBioS specifications


Unique identifier OMICS_08768
Name PyBioS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.4
Stability No
Maintained No

PyBioS citations


Models of Models: A Translational Route for Cancer Treatment and Drug Development

PMCID: 5609574
PMID: 28971064
DOI: 10.3389/fonc.2017.00219

[…] al models of the signal transduction networks in cells (or cell collectives), based on the ever-expanding biological knowledge base, e.g., on signaling pathways in human cells. For this, we are using PyBioS, currently in its third iteration (PyBioS3), an integrated software platform for the design, modeling, and simulation of cellular systems (, ). The current model integrates about 50 cancer-rela […]


Understanding the mTOR signaling pathway via mathematical modeling

Wiley Interdiscip Rev Syst Biol Med
PMCID: 5573916
PMID: 28186392
DOI: 10.1002/wsbm.1379

[…] eling approaches can be implemented and simulated using publicly available Systems Biology tools. ODEs and stochastic models can be simulated via user‐friendly tools such as CellDesigner, COPASI, and PyBioS, all of which include methods for parameter estimation and model analysis. Boolean or logic‐based models can be created and simulated by, e.g., CellNetOptimizer, a software suite which allows t […]


Predictive Modeling of Drug Treatment in the Area of Personalized Medicine

Cancer Inform
PMCID: 4671548
PMID: 26692759
DOI: 10.4137/CIN.S1933

[…] s advanced methods for steady-state analysis, metabolic control analysis, parameter scanning, and parameter estimation.More than 10 years ago, we started developing a web-based modeling system called PyBioS (, PyBioS uses an object-oriented design, which allows the generation of large-scale models of cellular interaction networks comprising “objects” (eg, genes, protei […]


Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC Treated Mouse Strains

PLoS One
PMCID: 4210132
PMID: 25347188
DOI: 10.1371/journal.pone.0111006
call_split See protocol

[…] The mathematical model of the arachidonic acid (AA)/eicosanoid pathway was developed in PyBioS , based on information from KEGG and a survey of literature –. Parameter optimization of the mathematical model was performed with COPASI . COPASI provides a number of different algorithms for […]


Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack

Biotechnol J
PMCID: 4314672
PMID: 25074435
DOI: 10.1002/biot.201400109

[…] To be able to develop, manipulate, and execute computer models of biological processes, we have developed PyBioS (, an object oriented modeling platform [, ]. Biological networks representing either the normal biological processes in a specific “normal” cell type, or the modified proc […]


High Throughput miRNA and mRNA Sequencing of Paired Colorectal Normal, Tumor and Metastasis Tissues and Bioinformatic Modeling of miRNA 1 Therapeutic Applications

PLoS One
PMCID: 3707605
PMID: 23874421
DOI: 10.1371/journal.pone.0067461

[…] 1 expression on a system biological scale we used a computer simulation of cancer related cellular signaling pathways , and its down-stream regulated genes. The mathematical model was developed with PyBioS that is a web-based software for the modeling and simulation of cellular reaction systems , , . It provides a framework for the development of computational models using an interface to public […]


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