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Attendees and projects at the 2009 SBML Forum Meeting

Project descriptions were provided by the individuals when filling out the attendance survey form.

Name Institution Project(s)
Frank Bergmann University of Washington, USA SBW
Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW, ) is a software framework that allows heterogeneous application components to communicate and re-use each others' capabilities. SBW is a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW is also a collection of tools for Systems Biology encompassing the areas of modeling, simulation and visualization of biochemical networks. Main applications include: Jarnac, JDesigner for modeling and analysis and roadRunner for high performance simulations. I am also one of the SBML Editors.
Brian Drawert

Lukas Endler EMBL-EBI, UK BioModels Database

Akira Funahashi Keio University, Japan CellDesigner
CellDesigner: A modeling tool for biochemical networks.
Joshua Havumaki Plectix BioSystems, USA Cellucidate
We are developing a web-based modeling platform on which users can build models cell signaling cascades using a biologist-friendly GUI that encourages collaboration. The platform employs a context-free and semantic rule-based modeling method based on the Kappa language.
William Heath

Andreas Hellander

Noriko Hiroi Keio University, Japan CellDesigner
ReCSiP, libSSA, CellDesigner.
Stefan Hoops Virginia Tech, USA COPASI, SBML
COPASI. I am also one of the SBML Editors.
Bin Hu Los Alamos National Laboratory, USA BioNetGen
BioNetGen is a rule-based modeling software for studying complex biological system. It has its own model definition language. We are contributing to the development of the multistate multicomponent species package of the coming SBML level 3. Hopefully this new package can provide a new option for modelers to share rule-based models.
Michael Hucka California Institute of Technology, USA SBML,
I lead the the SBML Team and am Chair of the SBML Editors. My main work involves developing SBML, supporting SBML development and the SBML community, evangelizing SBML, organizing SBML-related workshops, maintaining all aspects of, working on software (including libSBML, the SBML Test Suite and the SBML Demonstrator), and other activities.
Akiya Jouraku Keio University, Japan libSBML, CellDesigner, KEGG2SBML
libSBML, CellDesigner, KEGG2SBML.
Sarah Keating EMBL-EBI, UK SBML
SBML, libSBML, SBML Test Suite, SBMLToolbox, SBML demonstrator. I am also one of the SBML Editors.
Nicolas Le Novère EMBL-EBI, UK SBML, BioModels Database, MIRIAM, SBO,
SBML Level 3 packages (multi, qual); MIRIAM resources; SBO; BioModels DB.
Catherine Lloyd University of Auckland, New Zealand CellML
CellML has evolved as a solution to the problems of inconsistencies between computational and published models. CellML offers an unambiguous method of defining models of cellular function in a format that is both human and machine readable. It allows models to be exchanged across the Web, and shared among modellers, independent of modelling software. The CellML project started in 1999 – around the same time as SBML. The range of models described in CellML overlaps with those described in SBML, however the languages have different emphases: •  “SBML is designed for representing models of biochemical reaction networks”. ( •  “The purpose of CellML is to store and exchange computer-based mathematical models”. (
Curtis Madsen University of Utah, USA iBioSim
I am involved with the development of iBioSim. iBioSim has been developed for the analysis of biochemical reaction network models. While the primary target of iBioSim is models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed.
Chris Myers University of Utah, USA iBioSim
We are developing the iBioSim tool for the modeling, analysis, and design of genetic circuits.
Anika Oellrich EMBL-EBI, UK StochSim
SBML multi package & StochSim.
Brett Olivier VU University Amsterdam, The Netherlands PySCeS
My current project involves extension of constraint based modelling to ecosystems. I also continue to maintain PySCes.
Robert Phair Integrative Bioinformatics Inc., USA Integrative Bioinformatics
Our company is a scientific consulting firm specialized in kinetic modeling of biological systems from single cells to human physiology. Our NIH-supported software, ProcessDB, is designed as an interface between experimentalists and modelers. It supports SBML import so that our clients can leverage existing models from the BioModels database.
Nicolas Rodriguez EMBL-EBI, UK SBMLeditor
SBMLeditor - a very simple, but complete tool, to create models in the SBML format. Biomodels database - a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. SBML converters - a set a tools to convert an SBML file to XPP, BioPax, Scilab, CellML, dot or SVG.
Takeshi Sakurada Keio University, Japan E-Cell
E-Cell IDE (Integrated Development Environment) is a GUI application that aims to support development of diverse biological models. It consists of three major components, pathway designer, simulator and analytical toolkit that are tightly integrated with each other.
Sven Sahle University of Heidelberg, Germany COPASI
COPASI. I am also one of the SBML Editors.
Jim Schaff University of Connecticut Health Center, USA VCell
VCell (Virtual Cell) is a <mostly> SBML compliant modeling/simulation tool for compartmental and spatial modeling of biochemical/electrophysiological systems. Our group is active in the Hierarchical Modeling, Multicomponent, and Spatial modeling Level 3 extensions.
Kai Schallau

Lucian Smith University of Washington, USA Antimony
Antimony is a modular (or 'hierarchical') model definition language intended to be both human-readable and human-writable. libAntimony provides an API that allows other programs to read and convert antimony files and strings. Our latest development is QTAntimony, an editor for translating antimony to SBML and visa-versa.
Ty Thomson Plectix BioSystems, USA Cellucidate
We are developing a web-based modeling platform called Cellucidate for rule-based modeling biochemical systems. Cellucidate offers on online collaborative environment for building, simulating and publishing models, where all computation is done via a cloud computing infrastructure.
Darren Wilkinson Newcastle University, UK CaliBayes
CaliBayes: Bayesian calibration and validation of deterministic and stochastic SBML models using time course data. I am also one of the SBML Editors.

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