Past 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. The following list is in alphabetical order:

  • 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. She is now the Managing Director, Chronic Pain Network at McMaster University.
  • Frank Bergmann worked on many software systems and services, including the online SBML validator, the SBML Test Suite, the SBML Test Suite Database, libSBML, and more.
  • Christoph M. Blessing was a graduate student at the Computational Systems Biology Group at the University of Tübingen working with the SBML Team during 2017–2018. He worked on SBML hierarchical model flattening in JSBML.
  • 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).
  • 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.
  • Lisa Falk was an undergraduate student at the Computational Systems Biology Group at the University of Tübingen working with the SBML Team during 2017–2018. She worked on the SBML validation system in JSBML for qualitative models.
  • 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.
  • 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.
  • Harold Gómez is a coauthor of MOCCASIN. He was a Bioinformatics graduate student in the Brown University Laboratory of Computational Immunology and is now in the Department of Biosystems Science and Engineering at ETH Zurich.
  • Thomas M. Hamm was a Ph.D. student at the Computational Systems Biology Group at the University of Tübingen. He is a co-developer of JSBML.
  • 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.
  • 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.
  • 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.
  • Onur Özel was a graduate student at the Computational Systems Biology Group at the University of Tübingen working on JSBML during 2019–2020.
  • Anton Rabe was a graduate student at the Computational Systems Biology Group at the University of Tübingen working on JSBML-related software during 2018–2019.
  • Mahdi Sadeghi was a Ph.D. student at the Neuro-Cognitive Modeling Group at the University of Tübingen who worked on JSBML during 2019–2020.
  • 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.
  • Roman Schulte was a student with the Computational Systems Biology group at the University of Tübingen. He has contributed to multiple parts of the SBML project, especially JSBML and the SBML validation system in JSBML.
  • Bruce E. Shapiro is 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.
  • Linda Taddeo provided administrative support at Caltech related to SBML activities, including travel and workshop organization. She also helped in the maintenance of the SBML website, in managing financial arrangements, and other activities.
  • Thorsten Tiede was a Ph.D. student at the Applied Bioinformatics Group at the University of Tübingen who worked on and with JSBML during 2019–2020.
  • David E. Vetter was a graduate student at the Computational Systems Biology Group at the University of Tübingen on JSBML during 2019–2020.
  • Thomas J. Zajac was an undergraduate student at the Computational Systems Biology Group at the University of Tübingen on the SBML Team during 2017–2018. He worked on migrating SBML source repositories from SourceForge to GitHub, as well as developed parts of JSBML.