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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.

The SBML Editors and the Chair

The SBML Editors are devoted experts who write official specification documents, correct errata, assess proposals, and manage revisions to SBML. They are elected by the SBML community and serve for 3-year terms as volunteers. There are five Editors plus one Chair. The Chair is the leader of the SBML Team (described below), and acts as overall coordinator.


(''Chair'') [http://www.cds.caltech.edu/~mhucka Michael Hucka]

(Chair) Michael Hucka (Ph.D. in Computer Science and Engineering) is a Member of the Professional Staff at Caltech. He has Chaired the SBML Editors and SBML Team since 2003. He works on all aspects of SBML and is involved with BioModels.net consortium efforts such as BioModels Database.

[http://frank-fbergmann.blogspot.com/ Frank Bergmann]

Frank Bergmann (Ph.D. in Computation & Systems Biology) is a Research Fellow in the department for modeling of biological processes at the University of Heidelberg and a member of the SBML Team. He is the lead software developer for the Systems Biology Workbench and is also one of the programmers on COPASI.

[http://drupal.lenoverelab.org/perso/lenov/index.html Nicolas Le Novère]

Nicolas Le Novère (Ph.D. in Molecular Pharmacology) is group leader at the Babraham Institute and visiting group leader at the EBI. His interests include signal transduction and computational modeling of biological processes. He develops BioModels Database, MIRIAM Registry Identifiers.organd SBO.

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

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.

Sven Sahle

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's 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.

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

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 (SEMS). Dagmar is also a SED-ML Editor, and is working on improved semantic annotations for all COMBINE formats.


Past SBML Editors have been 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), 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.

The SBML Partners

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


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.

The 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

Michael Hucka is the SBML Team leader. 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.

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 the upcoming new SBML Reference Implementation project.

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.

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 EBI, 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.

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.


Past Members of the SBML Team

The SBML effort has greatly benefitted from the involvement of many talented individuals over the years. Some are still active in SBML; others have moved on to other exciting work.

  • Hamid Bolouri was the leader of the Caltech SBML & SBW Team from 1999 until 2003, as well as the University of Hertfordshire SBML Team for several years. In addition to Hamid's roles in the initial development of SBML, his group developed several SBML-related software resources (including the first SBML model repository and online SBML validator), and was the alma mater of Maria Schilstra, Sarah Keating, Joanne Matthews, and others. He continues to perform research in systems biology, and recently published two new books (Computational Modeling of Gene Regulatory Networks—A Primer and Personal Genomics and Personalized Medicine).
  • Andrew M. Finney was a member of the SBML Team from the very beginning. Until his return to industry, he was one of SBML's chief architects and greatest contributors.
  • Herbert M. Sauro was another original member of the SBML Team and the implementor of the earliest SBML-aware simulation software, Jarnac and JDesigner. He is now faculty at the University of Washington.
  • Maria J. Schilstra developed the original CellML2SBML and the first NetBuilder, the latter being one of the first applications to understand SBML when SBML was first introduced. Maria also created the first SBML model repository, the contents of which seeded the very first instantiation of BioModels Database. She has also made many other contributions to SBML over the years. Maria is currently the group leader of the Biological and Neural Computation Laboratory at the University of Hertfordshire, UK.
  • Ben Bornstein is a software engineer at the NASA Jet Propulsion Laboratory. He is the architect of libSBML and for a long time was its primary developer; he also developed the second generation of the SBML online validator. At NASA he's been even more productive, and in 2011, one of his projects (where he was a technical lead) won NASA's 2011 Software of the Year award.
  • Akira Funahashi, Ph.D. in Computer Science, co-developed KEGG2SBML and CellDesigner (née SBEdit), as well as contributed to libSBML, and has been involved with such things as SBGN from the very beginning. At the beginning of the SBML project, Akira was a researcher in the Kitano Symbiotic Systems Project and The SBI. Today he is an Associate Professor in the Dept. of Biosciences and Informatics at Keio University.
  • Ben Kovitz is a freelance software engineer who worked on many things in SBML and SBW, including having written the wiki engine that ran the sbml.org website from 2002 to 2008, parts of libSBML, and RFC 3823 defining the MIME type for SBML. He is now pursuing a Ph.D. at Indiana University.
  • Joanne Matthews was a research programmer at the University of Hertfordshire, UK, in Maria Schilstra's group. Among other things, she worked on CellML2SBML as well as the first generation of the SBML.org online tools.
  • Enuo He was a visiting student in the BNMC during 2007. She worked on both developing test cases for the SBML Test Suite and on curating models for BioModels Database. She is now at the University of Oxford pursuing her Ph.D.
  • Kimberly Begley worked as a consultant during 2008 on the SBML Test Suite. She has degrees in both Computer Science and Biology and is a Bioinformatics Consultant working in Australia. She has over a decade of experience developing database and XML systems for groups including QFAB, MDS Proteomics, Blueprint, and Lilly Systems Biology.
  • Akiya Jouraku was a member of SBML Team from 2007 to 2010 while he was a Research Assistant in the Dept. of Biosciences and Informatics at Keio University, Japan. He developed several aspects of libSBML, including the plug-in system for libSBML 5 and the file compression capability. He also co-developed CellDesigner and KEGG2SBML. His research interests include systems biology, interconnection networks, and parallel processing.
  • Bruce E. Shapiro is now the director of the BNMC, focusing on computational morphodynamics. Bruce developed the Mathematica-based MathSBML package which served for several years as the package used to generate reference simulation results for the SBML Test Suite. Today he continues to develop and support Cellerator and related plugins and extensions. His interests include computational morphodynamics, computational neuroscience, and modeling of signal transduction networks.

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)

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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