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.
Contributors to 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 SBML Forum |
Eric Mjolsness, Bruce Shapiro |
Machine Learning Systems, NASA Jet Propulsion Lab, USA |
Support for arrays |
3rd SBML Forum |
Martin Ginkel, Jörg Stelling |
Gilles group, MPI Magdeburg, Germany |
Modularity of models |
3rd SBML Forum |
Nicolas Le Novère, Tom Shimizu |
Bray Group, University of Cambridge, UK |
Multistate molecules & complex species |
3rd SBML Forum |
Igor Goryanin, Hugh Spence |
GlaxoSmithKline, UK |
Miscellaneous SBML extensions proposal |
3rd SBML Forum |
Naoki Tanimura, Maki Nakayama, Yuichiro Inagaki, Takayuki Saito, Akira Funahashi |
Systems Biology Institute, Japan |
Representation of graphical diagrams |
5th SBML Forum |
Sven Sahle, Ralph Gauges, Ursula Rost, Katja Wegner |
EML Research gGmbH, Germany |
Diagram layout |
8th SBML Forum |
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry |
LGPD/IBDM/IML, France |
Logical regulatory networks |
9th SBML Forum |
Michael Blinov |
T-10 group, Los Alamos National Laboratory, USA |
Rule-based models |
9th SBML Forum |
Colin Gillespie, Darren Wilkinson, Richard Boys, Carole Proctor, Daryl Shanley, Tom Kirkwood, Stuart Moodie, Maciej Swat |
BASIS Group, Newcastle University, UK, |
Distributions |
May '05 |
Frank Bergmann |
Sauro Group, Keck Graduate Institute, USA |
Render extension |
10th SBML Forum |
Karthik Raman |
Indian Institute of Science, India |
Flux balance models |
11th SBML 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 SBML Forum |
Anika Oellrich, Nicolas Le Novère |
Comp. Neuroscience Group, EMBL-EBI, UK |
Multicomponent & multistate species |
13th SBML Forum |
Duncan Berenguier, Nicolas Le Novère, Martijn van Iersel, Claudine Chaouiya |
Comp. Neuroscience Group, EMBL-EBI, UK, and Inst. Gulbenkian de Ciência, Oeiras, Portugal |
Qualitative models |
13th SBML Forum |
Frank Bergmann, Brett Olivier |
Univ. of Washington and VU University Amsterdam, USA and The Netherlands |
Flux Balance |
14th SBML 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 |
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 students
The SBML effort has benefitted multiple times from Google Summer of Code and NRNB Academy.
Google Summer of Code 2020
In 2020, we were fortunate to have had three projects involving SBML. They are listed below in alphabetical order by the students’ last names.
| Person | Organization | Topic | Project blog |
|---|---|---|---|
| Medha Bhattacharya | Indira Gandhi Delhi Technical University for Women, India | Development of a system that generates spatial SBML models using deep learning | Blog |
| Hemil Panchiwala | Indian Institute of Technology, Roorkee, India | Simulation of systems biology models in Java: support for new features | Blog |
| Hemant Yadav | Indian Institute of Technology, Roorkee, India | Implementation of SBML-JSON converter and SBML-JSON scheme | Blog |
Google Summer of Code 2019
In 2019, we were fortunate to have had three projects involving SBML.
| Person | Organization | Topic | Project blog |
|---|---|---|---|
| Nikhil Ghodke | Vishwakarma Institute of Technology, Pune, India | New Build System for InSilico | Blog |
| Bhavye Jain | Indian Institute of Technology Roorkee, Uttarakhand, India | Validation of spatial systems biology models in Java | Blog |
| Kaustubh Trivedi | Indian Institute of Technology Roorkee, Uttarakhand, India | Extending ModelPolisher to a universal annotation tool | Blog |
Google Summer of Code 2018
In 2018, we were fortunate to have had another project involving SBML.
| Person | Organization | Topic | Project blog |
|---|---|---|---|
| Shalin Shah | Duke University, USA | Simulating systems biology models in Java | Blog |
Google Summer of Code 2017
In 2017, we were fortunate to have had 2 projects involving SBML. They are listed below in alphabetical order by student’s last name.
| Person | Organization | Topic | Project blog |
|---|---|---|---|
| Takahiro Yamada | Keio University, Japan | Web App for SBML Model Analysis | Blog |
| Haoran Yu | University of British Columbia, Canada | Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic | Blog |
Google Summer of Code 2016
In 2016, we were fortunate to have had 5 projects involving SBML. They are listed below in alphabetical order by student’s last name.
| Person | Organization | Topic | Project blog |
|---|---|---|---|
| Hovakim Grabski | Russian-Armenian University, Armenia | Java support for Deviser, a code generation system for SBML libraries | Blog |
| Kaito Ii | 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 | Organization | Topic | Project blog |
|---|---|---|---|
| Matthias König | Charité Universitätsmedizin Berlin, Germany | Porting cysbml to Cytoscape 3 | Blog |
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 | 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 history
A brief history of the beginnings of SBML is provided on a separate page.