Testimonials
"Your program is unique in its attempt to focus on data integration."
(Prof. at Queen's University, Kingston, Canada)
"It is the software I've been searching for and hoping for, for years! A truly excellent program!"
(Prof. at Georgia Tech, Atlanta, USA)
"PottersWheel optimization still works even with my huge model of 863 reactions."
(PhD student from
University of Tsukuba, Japan)
"We are pleased about the focus on model creation and parameter estimation based on noisy data. In our opinion, this software has the potential of becoming a standard for modeling approaches in the Systems Biology community."
(Anonymous referee 1 of the PottersWheel Bioinformatics publication.)
"Potterswheel aims to help in an essential task in systems biology, namely the calibration of dynamic models based on experimental data. The toolbox is the most comprehensive for this task to the best of our knowledge, covering nearly all steps involved in the dynamic simulation of biological processes (model set up, simulation, parameter estimation, comparsion of models, report generation, etc)."
(Anonymous referee 2 of the PottersWheel Bioinformatics publication.)
"Please find below references to a published paper making use of Potterswheel.
Thank you very much for this marvelous toolbox."
(Research fellow, Karlsruhe Institute of Technology)
Publications using PottersWheel
[9] Gas Phase Fullerene Anions Hydrogenation by Methanol Followed by IRMPA Dehydrogenation
J.F. Greisch, B. Leyh, F. Reemacle, E. De Pauw
Journal of the American Society for Mass Spectrometry 21 (2010), pp. 117-126
[8] Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions.
M. Schilling, T. Maiwald, S. Hengl, D. Winter, C. Kreutz, W. Kolch, W.D. Lehmann, J. Timmer, U. Klingmüller.
Molecular Systems Biology , 2009, in press
[7] Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction
M.N Costa, K. Radhakrishnan, B.S. Wilson, D.G. Vlachos, J.S. Edwards
PLoS One. 2009 Jul 23;4(7):e6316.
[6] Mechanism of PP2A-mediated IKKbeta dephosphorylation: a systems biological approach
J. Witt, S. Barisic, E. Schumann, F. Allgower, O. Sawodny, T. Sauter, D. Kulms
BMC Systems Biology 2009, 3:71
[5] Systems-level interactions between insulin - EGF networks amplify mitogenic signaling
N. Borisov, E. Aksamitiene, A. Kiyatkin, S. Legewie, J. Berkhout, T. Maiwald, N. Kaimachnikov, J. Timmer, J. Hoek, B. Kholodenko
Molecular Systems Biology 2009, 5:256
[4] Small RNAs establish delays and temporal thresholds in gene expression
S. Legewie, D. Dienst, A. Wilde, H. Herzel, I.M. Axmann
Biophys J, 2008, 95(7):3232-8
[3] Developing Optimal Experimental Design Strategies in Cancer Systems Biology with Applications to Microfluidics Device Engineering
F. Menolascina, D. Bellomo, T. Maiwald, V. Bevilacqua, C. Ciminelli, A. Paradiso, and S. Tommasi , BMC Bioinformatics 2009, in press.
[2] Data-based identifiability analysis of nonlinear dynamical models
S. Hengl, C. Kreutz, J. Timmer, T Maiwald
Bioinformatics 2007, 23, 2612-2618
[1] Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, J. Timmer
Bioinformatics 2009, 25(15):1923-1929