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SBML Contributors

Contents

Many people have helped develop SBML as a community standard. This page lists individuals and groups who have made notable contributions to the evolution of SBML and the SBML-using community, 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.

SBML specifications

The following is an attempt to credit everyone (other than the SBML Team) who has developed written proposals and/or specifications for SBML. Please notify sbml-team@googlegroups.com with notices of any omissions, 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 3rd Forum
Eric Mjolsness, Bruce Shapiro Machine Learning Systems NASA Jet Propulsion Lab, USA Support for arrays 3rd Forum
Martin Ginkel, Jörg Stelling Gilles group MPI Magdeburg, Germany Modularity of models 3rd Forum
Nicolas Le Novère, Tom Shimizu Bray Group University of Cambridge, UK Multistate molecules & complex species 3rd Forum
Igor Goryanin, Hugh Spence GlaxoSmithKline UK Miscellaneous SBML extensions proposal 3rd Forum
Naoki Tanimura, Maki Nakayama, Yuichiro Inagaki, Takayuki Saito, Akira Funahashi Systems Biology Institute Japan Representation of graphical diagrams 5th Forum
Sven Sahle, Ralph Gauges, Ursula Rost, Katja Wegner EML Research gGmbH Germany Diagram layout 8th Forum
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry LGPD/IBDM/IML France Logical regulatory networks 9th Forum
Michael Blinov T-10 group Los Alamos National Laboratory, USA Rule-based models 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
Frank Bergmann Sauro Group Keck Graduate Institute, USA Render extension 10th Forum
Karthik Raman Indian Institute of Science India Flux balance models 11th Forum
Ranjit Randhawa, Cliff Shaffer JigCell Group Virginia Tech, USA Model composition ICSB 2006
Stefan Hoops COPASI Team, Virginia Bioinformatics Institute, USA Hierarchical model composition 12th Forum
Anika Oellrich, Nicolas Le Novère Comp. Neuroscience Group EMBL-EBI, UK Multicomponent & multistate species 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 13th Forum
Frank Bergmann, Brett Olivier Univ. of Washington and VU University Amsterdam USA and The Netherlands Flux Balance 14th Forum
Dagmar Waltemath, Neil Swainston, Allyson Lister University of Rostock, University of Manchester and Newcastle University Germany and the UK Annotations 2010 workshop
Chris Myers University of Utah USA (1) Arrays and (2) dynamical structures COMBINE 2011
Fengkai Zhang Simmune Group, NIH NIAID USA Restarted effort for multicomponent & multistate species COMBINE 2012
Harold Goméz Laboratory of Computational Immunology, Boston University USA Restarted effort for dynamic processes HARMONY 2014

Summer of Code

The SBML effort has benefitted multiple times from Google Summer of Code and NRNB Academy.

Google Summer of Code 2016

In 2016, we have been fortunate to have 5 projects involving SBML. They are listed below in alphabetical order by student's last name.

Person(s) Organization Topic Project blog
Hovakim Grabski Russian-Armenian University, Armenia Java support for Deviser, a code generation system for SBML libraries Blog
Kaito Li Funahashi Lab, Keio University, Japan Interconvertible Layout program for CellDesigner Blog
Devesh Khandelwal Cluster Innovation Centre, University of Delhi SBGN-ML and SBML to Escher Converter Blog
Tramy Nguyen Myers Research Group, University of Utah, USA Interconversion between the systems biology modeling formats SBML and BioPAX Blog
Roman Schulte University of Tuebingen, Tübingen, Germany JSBML Validation System Blog


NRNB Academy 2015

The National Resource for Network Biology runs a year-long program similar to Google Summer of Code, and in 2015, we had the privilege of having a student work on an SBML-related project under NRNB's auspices.

Person(s) Organization Topic Project blog
Matthias König Charité Universitätsmedizin Berlin, Germany Porting cysbml to Cytoscape 3 GitHub


Google Summer of Code 2014

In 2014, we were fortunate to have 3 SBML-related projects. They are listed in alphabetical order by student's last name.

Person(s) Organization Topic Project blog
Victor Kofia Bader Lab, University of Toronto, Canada Redesign the implementation of mathematical formulas in JSBML Blog
Ibrahim Y. Vazirabad Milwaukee School of Engineering, USA Improving the plug-in interface for CellDesigner Blog
Leandro Watanabe Myers Research Group, University of Utah, USA Arrays package for JSBML Blog


SBML Events

Organizing and hosting community events that involve SBML is a large effort. It requires funding, resources, and personal time investment by the organizers. The SBML community owes a large debt to the people who have made these events happen.

SBML Forum Meetings
Date(s) Event Location Host(s)
Sept. 19–24, 2016 COMBINE 2016 Newcastle University, Newcastle upon Tyne, UK Multiple groups
Oct. 12–16, 2015 COMBINE 2015 University of Utah, Salt Lake City, United States Myers Group
Aug. 18–22, 2014 COMBINE 2014 University of Southern California, Los Angeles, United States Keck School of Medicine of USC
Sep. 16–20, 2013 COMBINE 2013 Institut Curie, Paris, France U900 Computational Systems Biology of Cancer Department
Aug. 15–19, 2012 COMBINE 2012 University of Toronto, Toronto, Ontario, Canada Bader Lab
Sep. 3–7, 2011 COMBINE 2011 Heidelberg Institute for Theoretical Studies, Heidelberg, Germany HITS
Oct. 6–9, 2010 COMBINE 2010 Informatics Forum, University of Edinburgh Multiple groups
Sep. 3–4, 2009 14th SBML Forum Meeting Stanford University, Stanford, California, USA BNMC
Aug. 27–28, 2008 13th SBML Forum Meeting Wallenberg Conference Center, Göteborg, Sweden BNMC
Oct. 5–6, 2007 12th SBML Forum Meeting Long Beach Convention Center, Long Beach, California, USA BNMC
Oct. 12–13, 2006 11th SBML Forum Meeting National Museum of Emerging Science and Technology, Tokyo, Japan BNMC
Oct. 23–24, 2005 10th SBML Forum Meeting Conference Center at Harvard Medical, Boston, Massachusetts, USA SBML Team
Oct. 14–15, 2004 9th SBML Forum Meeting NH Heidelberg Hotel, Heidelberg, Germany SBML Team
Nov. 10, 2003 8th SBML Forum Meeting Chase Park Plaza Hotel, St. Louis, Missouri, USA SBML Team
May 11–12, 2003 7th SBML Forum Meeting Sheraton Ft. Lauderdale Airport, Ft. Lauderdale, Florida, USA SBML Team
Dec. 12, 2002 6th SBML Forum Meeting Karolinska Institutet, Stockholm, Sweden SBML Team
Jul. 8–9, 2002 5th Workshop on Software Platforms for Systems Biology University of Hertfordshire, Hertfordshire, UK SBML Team
Dec. 9, 2001 4th Workshop on Software Platforms for Systems Biology California Institute of Technology, Pasadena, California, USA ERATO Kitano Symbiotic Systems Project
Jun. 1–2, 2001 3rd Workshop on Software Platforms for Systems Biology California Institute of Technology, Pasadena, California, USA ERATO Kitano Symbiotic Systems Project
Nov. 14, 2000 2nd Workshop on Software Platforms for Systems Biology Royal Park Hotel, Tokyo, Japan ERATO Kitano Symbiotic Systems Project
Apr. 28–29, 2000 1st Workshop on Software Platforms for Systems Biology California Institute of Technology, Pasadena, California, USA ERATO Kitano Symbiotic Systems Project
SBML Hackathons
Date(s) Event Location Host(s)
June 7–11, 2016 HARMONY 2016 University of Auckland, Auckland, New Zealand Auckland Bioengineering Institute
April 20–24, 2015 HARMONY 2015 Martin Luther University Halle-Wittenberg, Wittenberg, Germany Schreiber group and Waltemath group
April 22–25, 2014 HARMONY 2014 University of Manchester, Manchester, UK Manchester Institute of Biotechnology
May 20–23, 2013 HARMONY 2013 University of Connecticut Health Center, Connecticut, USA Virtual Cell Group
May 21–25, 2012 HARMONY 2012 Maastricht University, Maastricht, The Netherlands BiGCaT
April 18–22, 2011 HARMONY 2011 Computational Biology Center at MSKCC, New York, US Sander group
May. 1–4, 2010 2010 SBML-BioModels.net Hackathon University of Washington,
Seattle, WA, USA
Sauro Group at UW
Mar. 26–28, 2009 Seventh SBML Hackathon European Bioinformatics Institute, Hinxton, UK Le Novère Group at the EBI
Apr. 6–8, 2008 Sixth SBML Hackathon Stellenbosch University, Stellenbosch, South Africa JJJ Group, Stellenbosch
Jun. 7–8, 2007 Fifth SBML Hackathon University of Newcastle,
Newcastle, UK
BASIS Group
Apr. 7–8, 2006 Fourth SBML Hackathon The Chateau at Nové Hrady,
Nové Hrady, Czech Republic
Institute of Systems Biology and Ecology
May 9–10, 2005 Third SBML Hackathon National Museum of Emerging Science and Innovation,
Tokyo, Japan
SBI
Apr. 30 – May 1, 2004 Second SBML Hackathon European Bioinformatics Institute, Hinxton, UK Le Novère Group at the EBI
Jul. 29–30, 2003 First SBML Hackathon Virginia Bioinformatics Institute, Blacksburg, Virginia, USA Mendes Group at the VBI
SBML Focused Workshops
Date(s) Event Location Host(s)
Jun. 20–22, 2011 Statistical models workshop 2011 Videoconference with main location at EBI, UK Le Novère Group at EMBL-EBI
Oct. 9, 2010 SBML 10th Anniversary Symposium Edinburgh, UK U. Edinburgh School of Informatics
May 19–21, 2010 Annotations package workshop 2010 Videoconference with locations at EBI, U. Rostock, and others N. Swainston, D. Waltemath & A. Lister
May 17–18, 2010 SBML-NeuroML interfacing mini-workshop EBI Le Novère Group at EMBL-EBI
Aug. 12–13, 2008 Alternative modeling frameworks 2008 Videoconference with locations at EBI, U. Rostock, and SIB Le Novère Group at EMBL-EBI
Dec. 6–7, 2007 SBML Multicomponent & Multistate Workshop 2007 Videoconference with locations at EBI, UCHC, University of Pittsburgh, and Virginia Tech Le Novère Group at EMBL-EBI
Sep. 9–10, 2007 SBML Composition Workshop 2007 Videoconference with locations at UCHC, EBI, and Max Planck Institute for Molecular Genetics Virtual Cell Group at UCHC

SBML History

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

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