— the global portal for all things SBML


The following is the current list of known attendees at the 2010 Hackathon. We update this list periodically based on the attendance survey results. If you are not listed here and are planning on coming,

please fill out the attendance survey

so that we can add you to the list and make appropriate arrangements.

Name Institution Project URL
Steve Andrews Fred Hutchinson Cancer Research Center
I work on Smoldyn, a particle-based biochemical simulator.
James Bassingthwaighte University of Washington, US
I work on JSim, a simulation system for the modeling analysis of data on biophysical, biochemical, and physiological systems using both spatially distributed and lumped compartmental systems.
Frank Bergmann University of Washington, US
I work on the Systems Biology Workbench and related projects like libSedML, RoadRunner, SBML Layout and Ben(Zai)Ten. I am also one of the SBML editors.
Michael Blinov University of Connecticut Health Center, US
Lukas Endler European Bioinformatics Institute, UK
I am a curator for BioModels Database, a database of quantitative kinetic models.
Juergen Eils DFKZ (German Cancer Research Center), DE,
As provider for experimental databases, we are interested in connecting experiments to their associated modles and vice versa. In particular we are interested in storing models and SBML and related databases.
Ron Henkel University of Rostock, Germany
Bill Hlavacek Los Alamos National Laboratory, US
I work on software and methods for rule-based modeling of biochemical systems.
Michael Hoehl DFKZ (German Cancer Research Center), DE
Bin Hu Los Alamos National Laboratory, US
Mike Hucka Caltech, US
I work on almost all areas of SBML development, and a little bit on efforts too.
Sarah Keating European Bioinformatics Institute, UK
I work on many areas of SBML software including libSBML, the SBML Test Suite, and SBMLToolbox.
Camille Laibe European Bioinformatics Institute, UK
I work on (more specifically: BioModels Database, MIRIAM, MIRIAM Resources and SBO).
Nicolas Le Novère European Bioinformatics Institute, UK,
I work on building software infrastructure for model exchange and reuse.
Curtis Madsen University of Utah, US
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. iBioSim includes the following tools: - GCM Editor - a tool to create a model using the Genetic Circuit Model (GCM) format. - SBML Editor - a tool to create a model using the Systems Biology Markup Language (SBML). - reb2sac - an abstraction-based ODE, Monte Carlo, and Markov analysis tool. - GeneNet - a tool to learn a GCM from time series data (TSD). - TSD Graph Editor- a tool to visualize TSD files. - Probability Graph Editor - a tool to visualize probability data.
Ion Moraru University of Connecticut Health Center, US
Chris Myers University of Utah, US
Our research group is developing the iBioSim tool for systems and synthetic biology.
David Nickerson University of Auckland, NZ
I work on CellML and associated technologies.
Anika Oellrich European Bioinformatics Institute, UK
Nicolas Rodriguez European Bioinformatics Institute, UK
I work on SBMLEditor, SBML converters, Biomodels Database, and jsbml.
Sven Sahle University of Heidelberg, DE
I work on COPASI, a tool for creating, editing, simulating and analyzing biochemical reaction networks. I also work on the SBML layout/render extension and other SBML related topics.
James Schaff University of Connecticut Health Center, US
I work on Virtual Cell, a modeling and simulation framework for computational cell biology.
Herbert Sauro University of Washington, US
Lucian Smith University of Washington, USA
Neil Swainston University of Manchester, UK
In the MCISB we generate kinetic models of metabolism, initially focussing on yeast. In doing so we fuse experimental analyses with modelling, and are growing increasingly interested in automating this procedure. This involves the development of a loosely-coupled informatics infrastructure for experimental data analysis and dissemination, and model generation and simulation, relying heavily on semantic annotation of both data and models.
Dagmar Waltemath University of Rostock, DE
I am investigating two questions currently: 1) How can model similarities be determined based on the given annotations of a model, particularly an SBML model? To answer that question, we try to apply similarity functions (coming from Information Retrieval research) on model representations, focusing on the model annotations. A framework for sophisticated testing, Sombi, is under development. 2) How can simulation experiments be described in a standardised and reproducible way? The proposed XML format I am participating in working on is the Simulation Experiment Description Markup Language (SED-ML).
Darren Wilkinson University of Newcastle, UK
I work on CaliBayes, a system for carrying out fully Bayesian inference for both determinstic and stochastic SBML models using time course data.

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