SBML contributors

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,
Comp. Neuroscience Group EMBL-EBI, 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

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 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.