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PottersWheel specifications

Information


Unique identifier OMICS_20237
Name PottersWheel
Alternative name PW
Software type Application/Script, Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 4.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Thomas Maiwald

Additional information


Tutorial: http://www.potterswheel.de/Pages/tutorials.php

Publications for PottersWheel

PottersWheel citations

 (32)
library_books

Modelling and simulation of biased agonism dynamics at a G protein coupled receptor

2018
J Theor Biol
PMCID: 5811930
PMID: 29337260
DOI: 10.1016/j.jtbi.2018.01.010

[…] d PTX cells were fitted simultaneously, using optimisation algorithms to minimise the squared error between simulation and data points. The methods used were the trust region algorithm implemented in PottersWheel (), followed by a genetic algorithm routine implemented in MATLAB . A subset of the kinetic parameters were varied; for each reversible reaction, we fixed one rate constant (typically for […]

library_books

Correlated receptor transport processes buffer single cell heterogeneity

2017
PLoS Comput Biol
PMCID: 5659801
PMID: 28945754
DOI: 10.1371/journal.pcbi.1005779

[…] All ODE models were implemented with the MATLAB toolbox PottersWheel that was used for parameter calibrations (http://www.potterswheel.de) []. Model analysis and simulations were performed with custom MATLAB scripts. As a measure for the goodness of fit, w […]

library_books

Systems modelling ageing: from single senescent cells to simple multi cellular models

2017
PMCID: 5869859
PMID: 28698310
DOI: 10.1042/EBC20160087

[…] many types of identifiability analyses such as the parameter profile likelihood approach []. Various software packages exist that compute the parameter profile likelihoods including Data2Dynamics [], PottersWheel [] and COPASI [] with PyCoTools (https://github.com/CiaranWelsh/PyCoTools). Other routine types of analyses that are used in systems modelling include a global sensitivity analysis which […]

library_books

A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes

2017
PeerJ
PMCID: 5582613
PMID: 28879062
DOI: 10.7717/peerj.3703

[…] r relevance with individual data.As shown in , the saturation hypothesis (line 1) cannot be explained with the family of parameters identified by the fitting procedure. Indeed, all models reported by PottersWheel toolbox procedure had a p-value lower than 1, which is too low to be considered as relevant. An explanation can be found in the study of local Chi2-scores involved in the computation of t […]

call_split

A systems study reveals concurrent activation of AMPK and mTOR by amino acids

2016
Nat Commun
PMCID: 5121333
PMID: 27869123
DOI: 10.1038/ncomms13254
call_split See protocol

[…] estimated parameters. A legend of all the names (for example, species, parameters, observables and so on) used in the model is provided in . A complete list of ODEs is provided in .The Matlab Toolbox PottersWheel and the PottersWheel identifiability toolboxes MOTA and PLE were used for designing and calibrating the kinetic rate constants of the models. Each reaction contained a kinetic rate consta […]

library_books

Model Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages

2016
PLoS Comput Biol
PMCID: 4963125
PMID: 27464342
DOI: 10.1371/journal.pcbi.1005018

[…] The gene expression model is based on ordinary differential equations (ODEs) and mass action kinetics. It was implemented using the MATLAB Toolbox PottersWheel [] and comprises 23 species and 47 parameters. The model setup is explained in [], a short summary is given in as well as a list of model equations and parameter values. The ODE system i […]

Citations

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PottersWheel institution(s)
Freiburg Center for Data Analysis and Modeling, Freiburg University, Freiburg, Germany; Institute of Physics, Freiburg University, Freiburg, Germany
PottersWheel funding source(s)
Supported by the HepatoSys initiative of the German Federal Ministry of Education and Research (BMBF, 0313074D), the European project of Computational Systems Biology of Cell Signalling (COSBICS, LSHG-CT-2004- 512060), the German Federal Ministry for Economy and the European Social Fund (BMWi, ESF, 03EGSBW-004).

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