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SBML Core Developers

Contents

This page lists individuals and groups who have (or have had) specific roles, but this short list is not meant to diminish the contributions of the broader community of people and companies developing software systems that use SBML. People's involvements also change over time, and we try to keep this page updated to stay current with the SBML community.

SBML Editors, Coordinator, and Secretary

The SBML Editors are devoted experts who develop SBML specifications, correct errata, assess proposals, and manage revisions to SBML. The five Editors are elected by the SBML community and serve for 3-year terms as volunteers. One of the Editors is nominated by the other Editors to be Coordinator and lead activities such as organizing and chairing Editor meetings, monitoring progress on new SBML developments, and other such work. The SBML Permanent Secretary is not an elected or volunteer position; instead, it is someone from the SBML Team paid to work on SBML activities such as managing community votes, writing documents, etc.


[http://compbio.igc.gulbenkian.pt/nmd/node/14 Claudine Chaouiya] (2017-2019)

Editor

Claudine Chaouiya (2017-2019) (Ph.D. in Computer Science) is a group leader at the Instituto Gulbenkian de Ciência, Oeiras Portugal. Her Network Modelling lab focuses on developing methods and tools to enhance the qualitative modelling of large regulatory networks. The group is also involved in modelling studies of regulatory and signalling networks. Claudine was involved in the definition of the SBML qual package and is member of the Consortium for Logical Models and Tools (CoLoMoTo).

[http://www.ra.cs.uni-tuebingen.de/mitarb/draeger/ Andreas Dräger] (2015-2017)

Editor

Andreas Dräger (2015-2017) (Ph.D. in bioinformatics) is a researcher in the Center for Bioinformatics Tuebingen (ZBIT) of the University of Tuebingen. He is focused on the development of biophysically constrained kinetic models. He has founded several SBML software projects, including JSBML, and the Simulation Core Library.

Sarah M. Keating (2016-2018)

Coordinator

Sarah M. Keating (2016-2018) (Ph.D. in Electrical & Electronic Engineering) is based at the EBI and works on software tools to facilitate the use of SBML. She is the lead developer for libSBML and Deviser and is involved in developing many other tools/facilities provided by the SBML Team, including the SBML Test Suite, RELAX NG schemas for SBML, and more.


[http://lenoverelab.org/members/Nicolas_Le_Novere Nicolas Le Novère] (2016-2018)

Editor

Nicolas Le Novère (2016-2018) (Ph.D. in molecular biology) is a group leader at the Babraham Institute. His research areas include cellular signaling, and he has developed many resources for systems biology including BioModels Database.

[https://www.linkedin.com/in/fengkai-zhang-8aba2018 Fengkai Zhang] (2017-2019)

Editor

Fengkai Zhang (2017-2019) (M.D. and M.Math in Bioinformatics) is a staff scientist at the NIAID/NIH. He is a member of the Laboratory of Systems Biology and one of the core developers of the Simmune project. He is also the lead author of SBML Multi package specification, and the major developer of libSBML-multi.

Lucian Smith

Secretary

Lucian Smith (Ph.D. in Molecular Biology) is a staff scientist at U. Washington. He is the author of Antimony, as well as SBML Level 3 package specifications such as Hierarchical Model Composition. He also works on the SBML Test Suite.



Past SBML Editors have been Dagmar Waltemath (2014–2016), Brett G. Olivier (2014–2016), Frank Bergmann (2009–2011, 2013–2015), Sven Sahle (2008–2010, 2013–2015), Sarah M. Keating (2007–2009, 2011–2013), Chris J. Myers (2011–2013), James C.Schaff (2010–2012), Lucian Smith (2010–2012), Darren Wilkinson (2008–2010), Stefan Hoops (2007–2009), Nicolas Le Novère (2006–2008, 2012–2014), Michael Hucka (2000–2015), Andrew M. Finney (2000–2006), Herbert M. Sauro (2000–2006), and Hamid Bolouri (2000–2006). The SBML effort and community benefited tremendously from their involvement and hard work.

SBML Scientific Advisory Board

The SBML Scientific Advisory Board is composed of scientists and researchers with expertise in topics covered by SBML. The SAB provides guidance to the SBML Editors and the SBML Forum regarding the goals, features, applications, and other aspects of SBML development and use. The current members of the SAB are:

  • Prof. Gary Bader, Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, Canada.
  • Directeur de Recherche Dirk Drasdo, Institut National de Recherche en Informatique et en Automatique (INRIA), France, and associated with Interdisziplinäres Zentrum für Bioinformatik (IZBI) and Institute for Working Environment (IfADo), Germany.
  • (Chair) Dr. Michael Hucka, California Institute of Technology, USA.
  • Prof. Jonathan Karr, Institute for Multiscale Biology & Genomics, Icahn School of Medicine at Mount Sinai, New York, USA.
  • Prof. Douglas Kell, Research Chair in Bioanalytical Sciences, School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, UK.
  • Prof. Dr. Dr. Edda Klipp, Full Professor for Theoretical Biophysics, Humboldt-Universität zu Berlin (HUB), Germany.
  • Prof. Dr. Ursula Kummer, Center for Organismal Studies Heidelberg/Bioquant, Heidelberg University, Germany.
  • Prof. Dr. Bas Teusink, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, Netherlands.

SBML Team

The SBML Team strives to support the SBML community and the development and maintenance of specific SBML infrastructure and facilities. In particular, the team is responsible for (1) maintaining this website, the SBML mailing lists, electronic surveys, and other resources; (2) arranging for the development and support of critical software, including libSBML, the SBML Validator, and the SBML Test Suite; and (3) organizing SBML events, including the SBML Forum Meetings and SBML Hackathons.


Michael Hucka

Team leader.

Michael Hucka He works on all aspects of SBML and contributes to libSBML, the SBML Test Suite, and the Online SBML Validator. He also writes grant proposals, organizes workshops, maintains SBML.org, and does other odd jobs.

Frank Bergmann

Frank Bergmann is currently working on libSBML, the Online SBML Validator, and the SBML Test Suite. He is also one of the SED-ML Editors.

[http://www.ra.cs.uni-tuebingen.de/mitarb/draeger/ Andreas Dräger]

Andreas Dräger is a junior group leader at the Tuebingen Center for Bioinformatics, and is also a co-developer of JSBML and several upcoming software efforts by the SBML Team.

Sarah M. Keating

Sarah M. Keating is the current lead developer for libSBML and the SBMLToolbox. She is also developing the SBML Test Suite, the RELAX NG schemas for SBML, and DEVISER.

Lucian Smith

Lucian Smith leads the development of the SBML Level 3 hierarchical model composition package. He also works on the SBML Test Suite.

Nicolas Rodriguez

Nicolas Rodriguez is a scientific programmer at the Babraham Institute, where he is working in the Le Novère group. He is the main developer of SBMLeditor and the Biomodels DB converters. He is currently co-developing JSBML.

Harold Gómez

Harold Gómez is a Ph.D. student at ETH Zurich in the Computational Biology Group (CoBi). He is the co-developer of the Dynamic Structures draft package for SBML Level 3 as well as the co-author of MOCCASIN.

Thomas M. Hamm

Thomas M. Hamm is a Ph.D. student at the Applied Bioinformatics Group at the University of Tuebingen. He is a co-developer of JSBML.


Linda Taddeo

Linda Taddeo provides administrative support related to SBML activities, including travel and workshop organization. She also aids in the maintenance of the SBML website, in managing financial arrangements, and other activities as needed.


Many people other have been members of the SBML Team in past years. In fact, there have been so many that we have devoted a whole separate page to them!


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This page was last modified 09:38, 16 February 2017.



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