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1579 Publications visible to you, out of a total of 1579

Abstract

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Author: Giulio Belletti

Date Published: 1st Feb 2021

Publication Type: Journal

Abstract (Expand)

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

Authors: L. Schmiester, Y. Schalte, F. T. Bergmann, T. Camba, E. Dudkin, J. Egert, F. Frohlich, L. Fuhrmann, A. L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos, S. Merkt, W. Muller, D. Pathirana, E. Raimundez, L. Refisch, M. Rosenblatt, P. L. Stapor, P. Stadter, D. Wang, F. G. Wieland, J. R. Banga, J. Timmer, A. F. Villaverde, S. Sahle, C. Kreutz, J. Hasenauer, D. Weindl

Date Published: 27th Jan 2021

Publication Type: Journal

Abstract

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Authors: Lorenz Braun, Sotirios Nikas, Chen Song, Vincent Heuveline, Holger Fröning

Date Published: 21st Jan 2021

Publication Type: Journal

Abstract

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Authors: Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis

Date Published: 17th Jan 2021

Publication Type: Journal

Abstract

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Authors: Outi M. H. Salo-Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo Vargas Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela-Kakkonen, Anders Støttrup Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes-Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert

Date Published: 2021

Publication Type: Journal

Abstract

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Author: Michael Strube

Date Published: 2021

Publication Type: InBook

Abstract

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Authors: F. R. N. Schneider, Ph. Podsiadlowski, B. Müller

Date Published: 2021

Publication Type: Journal

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