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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


Understanding the mTOR signaling pathway via mathematical modeling

PMCID: 5573916
PMID: 28186392
DOI: 10.1002/wsbm.1379

[…] 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 […]


Predictive Modeling of Drug Treatment in the Area of Personalized Medicine

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

[…] 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, […]


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

PMCID: 4210132
PMID: 25347188
DOI: 10.1371/journal.pone.0111006

[…] after 8 weeks is assumed as a quasi steady state also regarding the quantified metabolite concentrations., 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 […]


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

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

[…] analyzed the data: cr mk af ak tm dd stb sk cw ad acm ck cb. contributed reagents/materials/analysis tools: mk af ak kk bt tm dd stb an tb aw cv kz cw hl ad. wrote the paper: cr mk mrs. provided the pybios modeling system: ak ad cw., mirnas are discussed as diagnostic and therapeutic molecules. however, effective mirna drug treatments with mirnas are, so far, hampered by the complexity […]


A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient Derived Dermal Fibroblasts and iPS Cells

PMCID: 3432516
PMID: 22969728
DOI: 10.3389/fphys.2012.00339

[…] of the disease like glutathione metabolism. based on these pathways and modules a first model prototype of steatosis related processes has been developed employing the modeling and simulation system pybios (wierling et al., ). pybios has an integrated interface to the consensuspathdb facilitating the semi-automatic development of annotated models integrating signaling pathways, metabolic […]


Modeling of miRNA and Drug Action in the EGFR Signaling Pathway

PMCID: 3256223
PMID: 22253908
DOI: 10.1371/journal.pone.0030140

[…] – multiple targets” suggested by wurdinger and costa hoping to open a new avenue for drug development in cancer research., the mirna-egfr signaling model was constructed using the new version of pybios, a web-based modeling and simulation software , ( the model is based on molecular interactions and comprises 1241 reactions and 901 entities. the entities defined […]

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