SBML.org — the global portal for all things SBML

About

Contents

SBML is the result of many people's efforts over many years. 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.

A history of the beginnings of SBML is provided on a separate page.

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

Editor

Andreas Dräger (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

Coordinator

Sarah M. Keating (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]

Editor

Nicolas Le Novère (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.

[http://www.bgoli.net/blog/ Brett G. Olivier]

Editor

Brett G. Olivier (Ph.D. in Biochemistry) is a Researcher in the Systems Bioinformatics group at the VU University Amsterdam. His interests range from the kinetic modelling of metabolic regulation and control to the modelling of microbial communities using constraint based methods. He is the lead developer of PySCeS and CBMPy.

[http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/ Dagmar Waltemath]

Editor

Dagmar Waltemath (Ph.D. in Computer Science) is a junior group leader in Systems Biology and Bioinformatics at Rostock University. Her group develops methods and tools for improved management of computational models (SEMS). Dagmar is also a COMBINE Coordinator, and is working on improved semantic annotations for all COMBINE formats.

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 Frank Bergmann (2013–2015), Sven Sahle (2013–2015), Sarah M. Keating (2011–2013), Chris J. Myers (2011–2013), James C.Schaff (2010–2012), Lucian Smith (2010–2012), Darren Wilkinson (2008–2009), Stefan Hoops (2007–2009), Nicolas Le Novère (2006–2008, 2011–2013), 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 Partner Groups

Over the years, a few groups have devoted large portions of their resources, time, and energy, over many years, to support SBML in all ways, in particular by obtaining independent funding for explicit SBML development and hosting members of the SBML Team (described below). The SBML Partners are, in effect, the backbone of the SBML effort.



Hucka Group
California Institute of Technology
Pasadena, California
US




Le Novère Group
Babraham Institute
Babraham Research Campus
Cambrige
UK



BioModels team
(part of the Proteomics Service Team)
European Bioinformatics Institute
Cambrige
UK



Kummer Group
Modeling of Biological Processes, BioQUANT/COS
University of Heidelberg
Heidelberg
Germany



Dräger Group
Center for Bioinformatics (ZBIT)
University of Tuebingen
Tübingen
Germany


Past SBML Partners have been the Kitano group at the Systems Biology Institute (Japan), the Bolouri group at the University of Hertfordshire (UK), and the Brent group at the Molecular Sciences Institute (US). The SBML project began in John Doyle's group at Caltech, with Hamid Bolouri, Andrew Finney, Herbert Sauro and Michael Hucka.

SBML Scientific Advisory Board

The SBML Scientific Advisory Board (SAB) 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 chair of the SBML SAB is Dr. Michael Hucka.

SBML Contributors

Development of SBML specifications is open and proceeds with input from the user community. Many people have spent significant time developing proposals for SBML enhancements and extensions. The following is an attempt to credit everyone who has developed written proposals for SBML changes (other than those by the original SBML Team). We greatly appreciate notices of omissions and other errors (please email sbml-team@caltech.edu) so that we can make this list as accurate as possible.

Person(s) Group Topic First publicized
Daniel Lucio,
James Schaff,
John Wagner
Virtual Cell Team,
Univ. of Connecticut Health Center, USA
Representing spatial geometry Jun. '01 (3rd Forum)
Eric Mjolsness,
Bruce Shapiro
Machine Learning Systems
NASA Jet Propulsion Lab, USA
Support for arrays Jun. '01 (3rd Forum)
Martin Ginkel,
Jörg Stelling
Gilles group
MPI Magdeburg, Germany
Modularity of models Jun. '01 (3rd Forum)
Nicolas Le Novère
Tom Shimizu
Bray Group
University of Cambridge, UK
Multistate molecules & complex species Jun. '01 (3rd Forum)
Igor Goryanin,
Hugh Spence
GlaxoSmithKline
UK
Miscellaneous SBML extensions proposal Jun. '01 (3rd Forum)
Naoki Tanimura,
Maki Nakayama,
Yuichiro Inagaki,
Takayuki Saito,
Akira Funahashi
Systems Biology Institute
Japan
Representation of graphical diagrams Jul. '02 (5th Forum)
Sven Sahle,
Ralph Gauges,
Ursula Rost,
Katja Wegner
EML Research gGmbH
Germany
Diagram layout Nov. '03 (8th Forum)
Claudine Chaouiya,
Elisabeth Remy,
Denis Thieffry
LGPD/IBDM/IML
France
Logical regulatory networks Oct. '04 (9th Forum)
Michael Blinov T-10 group
Los Alamos National Laboratory, USA
Rule-based models Oct. '04 (9th Forum)
Colin Gillespie,
Darren Wilkinson,
Richard Boys,
Carole Proctor,
Daryl Shanley,
Tom Kirkwood

Stuart Moodie
Maciej Swat


BASIS Group
Newcastle University, UK



Comp. Neuroscience Group
EMBL-EBI, UK
Distributions May '05 (sbml-discuss)
Frank Bergmann Sauro Group
Keck Graduate Institute, USA
Render extension Oct. '05 (10th Forum)
Karthik Raman Indian Institute of Science
India
Flux balance models Oct. '06 (11th Forum)
Ranjit Randhawa,
Cliff Shaffer
JigCell Group
Virginia Tech, USA
Model composition Mar. '06 (ICSB 2006)
Stefan Hoops COPASI Team,
Virginia Bioinformatics Institute, USA
Hierarchical model composition Oct. '07 (12th Forum)
Anika Oellrich,
Nicolas Le Novère
Comp. Neuroscience Group
EMBL-EBI, UK
Multicomponent & multistate species Oct. '08 (13th Forum)
Duncan Berenguier,
Nicolas Le Novère
Martijn van Iersel

Claudine Chaouiya

Comp. Neuroscience Group
EMBL-EBI, UK

Inst. Gulbenkian de Ciência
Oeiras, Portugal

Qualitative models Oct. '08 (13th Forum)
Frank Bergmann,
Brett Olivier
Univ. of Washington and VU University Amsterdam
USA and The Netherlands
Flux Balance Oct. '09
Dagmar Waltemath
Neil Swainston
Allyson Lister
University of Rostock, University of Manchester and Newcastle University
Germany and the UK
Annotations Oct. '10 (2010 workshop)
Chris Myers University of Utah
USA
Restart efforts on (1) arrays and (2) dynamical structures Oct. '11 (COMBINE 2011)

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.

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!

Funding

We are grateful for the funding agencies and organizations that have supported SBML in the past and continue to support it today. Without them, SBML would not exist. Our acknowledgments page provides a full list of who they are.

The principal investigator on the project that lead to the development of the first specification of SBML was Hiroaki Kitano, and the PI of the subcontract to Caltech was John C. Doyle. In addition to the JST-funded project, Hiroaki Kitano, John C. Doyle, Hamid Bolouri, and Roger Brent at different times obtained funding from various agencies in the USA, Japan and UK to support staff and meetings aimed at continuing the development of SBML and associated resources. Since 2005, other principal investigators (notably Michael Hucka at Caltech and Nicolas Le Novère at EMBL-EBI) have obtained funding to continue development and support of SBML.

Ownership

No one—not the principal investigators, nor the SBML Editors, nor the SBML Team, nor the funding agencies or anyone else—owns SBML; it is a free and open community effort that extends beyond any single group, and we view ourselves only as organizers and fellow developers.


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