Frank T. Bergmann

According to our database1, Frank T. Bergmann authored at least 39 papers between 2005 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Links

Online presence:

On csauthors.net:

Bibliography

2023
BASICO: A simplified Python interface to COPASI.
J. Open Source Softw., November, 2023

SBML level 3 package: spatial processes, version 1, release 1.
J. Integr. Bioinform., March, 2023

2022
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR, 2022

2021
PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.
J. Integr. Bioinform., 2021

CoRC: the COPASI R Connector.
Bioinform., 2021

2020
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.
J. Integr. Bioinform., 2020

Systems biology graphical notation markup language (SBGNML) version 0.3.
J. Integr. Bioinform., 2020

2019
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
J. Integr. Bioinform., 2019

2018
SBML Level 3 Package: Flux Balance Constraints version 2.
J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
J. Integr. Bioinform., 2018

SBML Level 3 package: Render, Version 1, Release 1.
J. Integr. Bioinform., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
J. Integr. Bioinform., 2018

A portable structural analysis library for reaction networks.
Biosyst., 2018

2017
SED-ML web tools: generate, modify and export standard-compliant simulation studies.
Bioinform., 2017

2016
Toward Community Standards and Software for Whole-Cell Modeling.
IEEE Trans. Biomed. Eng., 2016

Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation.
CoRR, 2016

SBtab: a flexible table format for data exchange in systems biology.
Bioinform., 2016

Piecewise parameter estimation for stochastic models in COPASI.
Bioinform., 2016

2015
The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.
J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.
J. Integr. Bioinform., 2015

COMBINE Archive Specification Version 1.
J. Integr. Bioinform., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
J. Integr. Bioinform., 2015

2014
COMBINE archive: One File To Share Them All.
CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
BMC Bioinform., 2014

2012
Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinform., 2012

2011
Minimum Information About a Simulation Experiment (MIASE).
PLoS Comput. Biol., 2011

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.
BMC Syst. Biol., 2011

A Profile of Today's SBML-Compatible Software.
Proceedings of the IEEE 7th International Conference on E-Science, 2011

2010
SBML2TikZ: supporting the SBML render extension in LaTeX.
Bioinform., 2010

2009
Antimony: a modular model definition language.
Bioinform., 2009

2008
Comparing simulation results of SBML capable simulators.
Bioinform., 2008

2006
Supporting the SBML layout extension.
Bioinform., 2006

SBW - a modular framework for systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

2005
Bifurcation discovery tool.
Bioinform., 2005


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