Authors: Florian Becker, Simon Fuchs, Lukas Refisch, Friedel Drepper, Wolfgang Bildl, Uwe Schulte, Shuo Liang, Jonas Immanuel Heinicke, Sierra C Hansen, Clemens Kreutz, Bettina Warscheid, Bernd Fakler, Evgeny V Mymrikov, Carola Hunte

Superior Title: eLife, Vol 12 (2023)

Subject Terms: CHP3, NHE1, conformational changes, myristoylation, myristoyl switch, Ca2+-binding proteins, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/83868; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/bdcb900445214a9b841db465955cec1f

Authors: Lukas Refisch, Fabian Lorenz, Torsten Riedlinger, Hannes Taubenböck, Martina Fischer, Linus Grabenhenrich, Martin Wolkewitz, Harald Binder, Clemens Kreutz

Superior Title: BMC Medical Research Methodology, Vol 22, Iss 1, Pp 1-13 (2022)

Subject Terms: COVID-19, Infectious disease models, Input estimation, Ordinary differential equations, Parameter estimation, Nonlinear systems, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2288

Access URL: https://doaj.org/article/b1513cf3ae79452e80ea89648a04a71c

Authors: Leonard Schmiester, Yannik Schälte, Frank T Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R Banga, Jens Timmer, Alejandro F Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

Superior Title: PLoS Computational Biology, Vol 17, Iss 1, p e1008646 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/c3dd6d0bbd004deaba2fc5b1d5df8992

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/journal_contribution/PEtab_specification_/13645165

Availability: https://doi.org/10.1371/journal.pcbi.1008646.s001

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/journal_contribution/PEtab_tutorial_/13645168

Availability: https://doi.org/10.1371/journal.pcbi.1008646.s002

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/figure/Overview_of_PEtab_files_and_the_most_important_features_/13645177

Availability: https://doi.org/10.1371/journal.pcbi.1008646.g002

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/figure/Parameter_hierarchy_and_pre-equilibration_in_PEtab_/13645180

Availability: https://doi.org/10.1371/journal.pcbi.1008646.g003

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/figure/Specifying_parameter_estimation_problems_in_PEtab_/13645174

Availability: https://doi.org/10.1371/journal.pcbi.1008646.g001

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/dataset/Non-exhaustive_overview_of_the_functionality_offered_by_the_different_toolboxes_currently_supporting_the_PEtab_format_/13645186

Availability: https://doi.org/10.1371/journal.pcbi.1008646.t001

Authors: Leonard Schmiester (8327379), Yannik Schälte (10036114), Frank T. Bergmann (10036117), Tacio Camba (10036120), Erika Dudkin (10036123), Janine Egert (10036126), Fabian Fröhlich (848026), Lara Fuhrmann (10036129), Adrian L. Hauber (10036132), Svenja Kemmer (10036135), Polina Lakrisenko (10036138), Carolin Loos (7056845), Simon Merkt (10036141), Wolfgang Müller (420131), Dilan Pathirana (6292544), Elba Raimúndez (8520369), Lukas Refisch (10036144), Marcus Rosenblatt (10036147), Paul L. Stapor (10036150), Philipp Städter (10036153), Dantong Wang (298935), Franz-Georg Wieland (10036156), Julio R. Banga (8131953), Jens Timmer (25170), Alejandro F. Villaverde (8219148), Sven Sahle (222858), Clemens Kreutz (315828), Jan Hasenauer (328495), Daniel Weindl (1844341)

Subject Terms: Genetics, Biotechnology, Evolutionary Biology, Ecology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, SBML, systems biology Reproducibility, model simulation, Systems Biology Markup Language, PEtab problem, parameter estimation problems, tab-separated value files, observation model, parameter estimation toolboxes, systems biology, data-based modeling studies, 20 example parameter estimation pro., Python library, PEtab support, specification

Relation: https://figshare.com/articles/dataset/Overview_of_supported_PEtab_features_in_different_tools_based_on_passed_test_cases_of_the_PEtab_test_suite_/13645192

Availability: https://doi.org/10.1371/journal.pcbi.1008646.t002