Publications

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38 Publications visible to you, out of a total of 38

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 (Expand)

Research projects such as the international COVID-19 Disease Map initiative and the German COVID-19 study hub of NFDI are supported by de.NBI-SysBio tools and services in organizing and sharing research data ’FAIRly‘. This is done via the data management platform FAIRDOMHub/SEEK which is quickly adapted to the users' needs. COVID-19 related literature is manually curated and used for basic research about the curation process of SABIO-RK to provide the research community with high quality kinetics data.

Authors: Maja Rey, Andreas Weidemann, Ulrike Wittig, Dorotea Dudas, Sucheta Ghosh, Martin Golebiewski, Xiaoming Hu, Wolfgang Müller

Date Published: 2021

Publication Type: Booklet

Abstract

Not specified

Authors: Mark-Christoph Müller, Sucheta Ghosh, Maja Rey, Ulrike Wittig, Wolfgang Müller, Michael Strube

Date Published: 2020

Publication Type: InProceedings

Abstract

Not specified

Authors: Carolina B. Moraes, Gesa Witt, Maria Kuzikov, Bernhard Ellinger, Theodora Calogeropoulou, Kyriakos C. Prousis, Stefano Mangani, Flavio Di Pisa, Giacomo Landi, Lucia Dello Iacono, Cecilia Pozzi, Lucio H. Freitas-Junior, Bruno dos Santos Pascoalino, Claudia P. Bertolacini, Birte Behrens, Oliver Keminer, Jennifer Leu, Markus Wolf, Jeanette Reinshagen, Anabela Cordeiro-da-Silva, Nuno Santarem, Alberto Venturelli, Stephen Wrigley, Deepa Karunakaran, Bethlehem Kebede, Ina Pöhner, Wolfgang Müller, Joanna Panecka-Hofman, Rebecca C. Wade, Martina Fenske, Joachim Clos, José María Alunda, María Jesús Corral, Elisa Uliassi, Maria Laura Bolognesi, Pasquale Linciano, Antonio Quotadamo, Stefania Ferrari, Matteo Santucci, Chiara Borsari, Maria Paola Costi, Sheraz Gul

Date Published: 1st Mar 2019

Publication Type: Journal

Abstract

Not specified

Authors: Sucheta Ghosh, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 2019

Publication Type: Journal

Abstract

Not specified

Authors: Pasquale Linciano, Cecilia Pozzi, Lucia dello Iacono, Flavio di Pisa, Giacomo Landi, Alessio Bonucci, Sheraz Gul, Maria Kuzikov, Bernhard Ellinger, Gesa Witt, Nuno Santarem, Catarina Baptista, Caio Franco, Carolina B. Moraes, Wolfgang Müller, Ulrike Wittig, Rosaria Luciani, Antony Sesenna, Antonio Quotadamo, Stefania Ferrari, Ina Pöhner, Anabela Cordeiro-da-Silva, Stefano Mangani, Luca Costantino, Maria Paola Costi

Date Published: 17th Oct 2018

Publication Type: Journal

Abstract

Not specified

Authors: Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller

Date Published: 4th Jan 2018

Publication Type: Journal

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