SED-ML Editors

The SED-ML specification is written by an editorial board consisting of five editors. They are elected by the SED-ML community (members of the sed-ml-discuss mailing list) and serve for 3-year terms as volunteers. SED-ML editors are responsible for hosting all material relevant to SED-ML, coordinating the SED-ML development, maintaining the SED-ML website and the SED-ML specification documents.

Eran Agmon

Eran Agmon (2023-2025)

Eran Agmon is an Assistant Professor at the Center for Cell Analysis and Modeling at University of Connecticut Health. As the primary developer of Vivarium, Eran has been developing software for integrating heterogeneous modeling methods to build multi-algorithmic, multi-scale simulations. He is interesting in building models of microbiomes that span molecular to multi-cellular and ecological scales.

Weiwei Ai

Weiwei Ai (2024-2026)

Weiwei Ai (PhD in Electrical and Electronic Engineering) is a Research Fellow at the Auckland Bioengineering Institute, New Zealand. Her research areas include multiscale modeling, machine learning applications in computational physiology, and modeling software design. Employing standards such as CellML, SEDML, and semantic annotation, she automates model processes from construction, integration, and reduction to system analysis. She is also interested in incorporating prior knowledge and structured standards into machine learning techniques to integrate knowledge graphs from research literature, biological ontologies, annotated models, and simulation results, along with experimental data.

Matthias König

Matthias König (2024-2026; 2020-2022; 2017-2019)

Matthias König (PhD. in Biophysics) leads an junior research group for Systems Biology and Systems Medicine of the liver at the Humboldt University Berlin. His research areas include computational modeling, data science, development of bioinformatics methods and machine learning based on biological, medical and clinical data. He has been actively involved in the development of SBML, SED-ML and software supporting these standards: Lead-developer of cy3sbml and sbmlutils; contributor of the SBML simulation software libroadrunner and tellurium.

David Nickerson

David Nickerson (2023-2025; 2019-2021; 2015-2017; 2011-2013)

David Nickerson (PhD in Bioengineering) is a Senior Research Fellow in the Auckland Bioengineering Institute where he leads the Auckland Physiome Group, working on several projects addressing reproducibility, discoverability, and reusability in computational physiology. David is also involved in many aspects of the CellML project as well as various cardiac modeling projects. He also develops several CellML-related software tools and is the current CellML delegate to the COMBINE coordination group.

Lucian Smith

Lucian Smith (2022-2024; 2016-2018)

Lucian Smith (PhD. in Biochemistry) works as a Research Scientist for both the University of Washington with the Sauro lab, and for Caltech with the SBML Team. He is the co-creator of Antimony and, more recently, of phraSED-ML, and has been an SBML editor, working extensively with the SBML Hierarchical Model Composition specification.

Editorial board meetings

The editors meet regularly in online meetings and during the yearly COMBINE and HARMONY meetings.


Meeting in Seattle, WA, US during HARMONY2017. Getting ready for the L1V3 release.

Past members of the SED-ML editorial board

Richard Adams
Richard Adams (2011-2012)
Richard Adams (Ph.D. in Cell Biology) is software project manager at the Centre for Systems Biology, Edinburgh. He works on the SBSI systems biology software framework, SED-ML tools and the jlibsedml Java library for SED-ML.
Frank Bergmann
Frank Bergmann (2020-2022; 2011-2014)
Frank T. Bergmann (PhD. in Computational and Systems Biology) is a researcher at the University of Heidelberg where he is one of the core developers of COPASI, a simulation and modeling environment supporting the COMBINE standards. He also maintains several open source projects, supporting the use of the COMBINE standards.
Jonathan Cooper
Jonathan Cooper (2012-2015)
Jonathan Cooper is a Research Fellow in Computational Science based in the Computational Biology Group at the University of Oxford, with a background in computer science, software engineering, and computational biology. He has been working with biological markup languages (notably CellML) since 2005, is a core developer of the Chaste computational biology software, and is currently developing the concept of "functional curation", building on SED-ML.
Alan Garny
Alan Garny (2018-2020)
Alan Garny (DPhil in Computational Physiology) is the project manager and lead developer of OpenCOR, a CellML-based modelling environment that relies on COMBINE standards (incl. SED-ML). He is also involved in the CellML project, of which he is currently an editor, and in cardiac electrophysiological modelling.
Tomas Helikar
Tomas Helikar (2021-2023)
Dr. Helikar is an Associate Professor in the Department of Biochemistry at the University of Nebraska - Lincoln. His research expertise is in computational systems biology, technology development, and STEM education.
Jonathan Karr
Jonathan Karr (2021-2023)
Jonathan Karr is an Assistant Professor in the Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai. The goal of Jonathan's research is to develop comprehensive whole-cell models of all of the biochemical activity inside cells to enable a predictive foundation for medicine and bioengineering analogous to the Newtonian foundation for mechanical engineering.
Nicolas Le Novère
Nicolas Le Novère (2011-2013)
Nicolas Le Novère is a group leader at the EMBL-European Bioinformatics Institute. His research unfolds along two axis: 1) modelling neuronal signalling, at the molecular, sub-cellular and cellular levels, and 2) developing tools and resources for systems biology, in particular including standards.
Andrew Miller
Andrew Miller (2011-2012)
Andrew Miller is a researcher at the Auckland Bioengineering Institute. His research interests focus around the representation of mathematical models; he is involved in the development of tools for processing CellML models, including SProS, a SED-ML processing service that forms part of the CellML API.
Ion Moraru
Ion Moraru (2014-2016)
Ion Moraru (M.D., Ph. D.) is a Professor of Cell Biology in the Richard D. Berlin Center for Cell Analysis and Modeling at the University of Connecticut.
Brett Olivier
Brett Olivier (2015-2017)
Brett G. Olivier (Ph.D. in Biochemistry) is a Researcher in the Systems Bioinformatics group at the VU University Amsterdam . His interests range from fundamental theoretical research (metabolic regulation analysis, control analysis, constraint based modelling) to software design and development (CBMPy, PySCeS, JWS Online) and the development and implementation of open modelling standards.
Sven Sahle
Sven Sahle (2014-2016)
Sven Sahle (Ph. D. in Theoretical Chemistry) is a junior group leader in the department for modeling of biological processes at the University of Heidelberg. He is one of the lead software engineers of COPASI. His interests include kinetic modeling of signaling and metabolic processes with a focus on dynamic properties of biochemical models.
Herbert Sauro
Herbert Sauro (2018-2020)
Herbert Sauro (PhD in Systems Biology) is a Professor in the University of Washington, Department of Bioengineering. Herbert has been involved in standards and software development in systems biology for a long time and was one of the founding members of the original SBML team. The Tellurium Python modeling platform which has been developed with his collaborators and students, supports the current SED-ML and COMBINE standards.
Dagmar Waltemath
Dagmar Waltemath (2017-2019; 2011-2014)
Dagmar Waltemath (Ph.D. in Computer Science) is a professor in medical informatics at the University Medicine Greifswald. Dagmar works on strategies for biomedical research data management and develops concepts for the integration of that data with computational models describing biology and disease. She has been actively involved in the development of SED-ML, SBML, and the COMBINE Archive format.

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