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Delegates

The following is a list of the delegates who attended the 2008 SBML Forum meeting.


Richard Adams richard.adams @ ed.ac.uk University of Edinburgh
Edinburgh Pathway Editor, developing import and export of SBML from graphical editor keeping layout data in SBML. (Link to project page)

Kimberly Begley kimberly.lewis @ gmail.com FiSci Consulting, Australia
Assisting in the development of the SBML Test Suite.

Duncan Berenguier duncan @ ebi.ac.uk EMBL-EBI, UK
I am writting a possible SBML extension to include formals models (such as logical models, Petri nets, ...) in SBML. (Link to project page)

Frank Bergmann fbergman @ u.washington.edu Univ. of Washington & Keck Graduate Institute, USA
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, http://sys-bio.org ) 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. (Link to project page)

Eric Billings billings @ helix.nih.gov NIH NHLBI, USA
QBT is a desktop application designed for biologists with proteomic, microarray and other data. QBT provides users with the ability to create their own models, adapt curated models and manage limited data sets within a single application. Users may perform different levels of model validation and conduct simulations for comparison to their data.

Arne Bittig arne.bittig @ uni-rostock.de University of Rostock, Germany

Lutz Brusch lutz.brusch @ tu-dresden.de Dresden University of Technology, Germany
We develop and analyze kinetic, spatio-temporal models of cell biological and developmental processes. We are interested in SBML Level 3's support of spatio-temporal aspects such as advection, diffusion, domain shape and boundary conditions. (Link to project page)

Frank Burden fburden @ fastmail.fm CSIRO Australia

Yo-Cheng Chang markycchang @ gmail.com

Joseph Dada dada @ ieee.org University of Manchester, UK
COPASI project. SBRML, a results markup language proposal. (Link to project page)

Lukas Endler luaks @ ebi.ac.uk EMBL-EBI, UK
Curator of Biomodels Database. (Link to project page)

Adrien Faure faure @ tagc.univ-mrs.fr INSERM U928, France

Akira Funahashi funa @ bio.keio.ac.jp Keio University, Japan
CellDesigner: Modeling tool for biochemical networks (Link to project page)

Ralph Gauges ralph.gauges @ bioquant.uni-heidelberg.de University of Heidelberg, Germany
COPASI (Link to project page)

Martin Golebiewski martin.golebiewski @ eml-r.villa-bosch.de EML Research, Germany
SABIO-RK is a database system offering information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as experimental kinetic data (including rate equations) embedded in their environmental context. The collected data is standardized to a uniform format and structure by using controlled vocabularies and algorithms to unify the data. Entities and expressions are annotated to other resources and biological ontologies. The data can be exported in SBML together with the annotations complying with the MIRIAM standard. SABIO-RK can be accessed by a web-interface or programmatically by web services. (Link to project page)

Jonas Hagmar jonas.hagmar @ fcc.chalmers.se Fraunhofer-Chalmers Centre, Sweden

Noriko Hiroi noriko @ ebi.ac.uk EMBL-EBI, UK
I'm now gathering mathematical model examples of biological problems. They would be the references to consider what should be involved into the next version of SBML.

Sabrina Hoffmann sabrina.hoffmann @ charite.de Berlin Medical University, Germany
Development of a metabolic reconstruction of the hepatocyte which should be made available to modellers using SBML. (Link to project page)

Stefan Hoops shoops @ vbi.vt.edu Virginia Bioinformatics Institute, USA
I work on COPASI. I am also one of the SBML Editors.

Akiya Jouraku jouraku @ bio.keio.ac.jp Keio University, Japan
libSBML, CellDesigner, KEGG2SBML.

Sarah Keating skeating @ caltech.edu Caltech, USA
I am one of the SBML Editors. I am also involved in the development of libSBML, SBMLToolbox and the SBML Test-suite.

Douglas Kell dbk @ manchester.ac.uk University of Manchester, UK
Manchester Centre for Integrative Systems Biology. Also see my group page for links to projects.

Moriyoshi Koizumi mozo @ sfc.keio.ac.jp Keio University, Japan
I am currently involved in E-Cell project, whose aim is to develop methods of efficient simulation of biological phenomena in various levels of abstraction. In addition, I maintain the LibSBML package for the debian-med project. (Link to project page)

Fedor Kolpakov fedor @ biouml.org Institute of Systems Biology, Russia
BioUML. (Link to project page)

Yutaro Kumagai ykumagai @ biken.osaka-u.ac.jp

Nicolas Le Novère lenov @ ebi.ac.uk EMBL-EBI, UK
I am an SBML editor. I also coordinate BioModels.net (SBO, MIRIAM, BioModels.net). (Link to project page)

Chen Li chenli @ ebi.ac.uk EMBL-EBI, UK
BioModels Database is a free resource for storing, viewing and retrieving published, peer-reviewed quantitative models of biochemical and cellular systems. Models are thoroughly curated and the model elements are annotated with terms from controlled vocabularies and links to relevant data resources. The model can be downloaded in various formats, which are SBML, CellML, BioPAX, SciLab, XPP and VCell. Enhanced web interface provides more explicit view of each model and online tool to generate sub-model. As a supplement, the Web Services of BioModels Database allows third-party software to directly access up-to-date data of models. (Link to project page)

Catherine Lloyd c.lloyd @ auckland.ac.nz The University of Auckland, New Zealand
The CellML Model Repository (http://www.cellml.org/models) is a database providing free access to over 330 biological models derived from published, peer-reviewed papers. These models describe a wide range of biological processes, including signal transduction pathways, metabolic pathways, electrophysiology, immunology, the cell cycle, muscle contraction, mechanical models and constitutive laws. CellML and the CellML Model Repository are an integral part of the IUPS Physiome Project. As the CellML community grows, there will be more users submitting their CellML models to the repository, and model curation and annotation will become essential to the maintenance of the CellML Model Repository as a useful resource. (Link to project page)

Saeedeh Maleki-Dizaji s.maleki-dizaji @ dcs.shef.ac.uk Sheffield University, UK

Patrick May may @ mpimp-golm.mpg.de Max-Planck Institute, Germany

Pedro Mendes pedro.mendes @ manchester.ac.uk University of Manchester, UK, & VBI, USA
COPASI modelling and simulation software. Submitted a proposal for a Results markup language (SBRML). (Link to project page)

Stuart Moodie stuart.moodie @ ed.ac.uk University of Edinburgh
Edinburgh Pathway Editor. (Link to project page)

Ion Moraru moraru @ panda.uchc.edu University of Connecticut Health Center, USA
SBML L3 extensions - modularity, composition, spatial. SBML - VCML translation. All things VCell. (Link to project page)

Jeremy Muhlich jmuhlich @ gmail.com Harvard Medical School, USA
DataRail/SB-Pipeline; informatics support for modelers in my lab. (Link to project page)

Chris Myers myers @ ece.utah.edu University of Utah, USA
We are developing iBioSim, a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models, and the design of synthetic genetic circuits. Models can be created using our SBML editor that support virtually all of SBML L2V3 including reactions, rules, events, constraints, etc. iBioSim also includes an efficient analysis engine that supports ODE, stochastic, and Markov chain methods. Finally, iBioSim has a graphical editor for visualizing analysis results. iBioSim has been applied to numerous projects including an analysis of the phage lambda decision circuit, the E. coli Fim switch, and the design of a synthetic genetic Muller C-element. (Link to project page)

Aurelien Naldi naldi @ tagc.univ-mrs.fr INSERM U928, France
GINsim is a software for the logical (qualitative) modelling of gene regulatory networks. Our main interest is the qualitative extension for SBML 3. (Link to project page)

Kedar Nath Natarajan kedar @ ebi.ac.uk EMBL-EBI, UK
Converters for SBML.

Tolstykh Nikita tolstyh @ biouml.org Institute of Systems Biology, Russia
BioUML. (Link to project page)

Anika Oellrich anika @ ebi.ac.uk EMBL-EBI, UK
Proposal for L3M extension of SBML, StochSim.

Shinsuke Ohnuki

Nobuyuki Ohta ohta @ fun.bio.keio.ac.jp Keio University, Japan
KEGG2SBML. (Link to project page)

Brett Olivier bgoli @ sun.ac.za University of Stellenbosch, South Africa
PySCeS: the Python Simulator for Cellular Systems. (Link to project page)

Gopalacharyulu V. Peddinti ext-gopal.peddinti @ vtt.fi VTT Technical Research Center of Finland

Sathish Periyasamy S.Periyasamy @ cs.cardiff.ac.uk Cardiff University, UK

Nicolas Rodriguez rodrigue @ ebi.ac.uk EMBL-EBI, UK
SBMLeditor is a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. I am also developing and maintaining the convertors from SBML to various format (XPP, BioPax, SVG, cellML, SciLab). (Link to project page)

Rune Saetre satre @ idi.ntnu.no University of Tokyo, Japan
PathText is developed to connect Natural Language Processing (NLP) technology to the graphs and diagrams that are used by biologists. The current prototype uses the Payao Web 2.0 community tagging system for biological networks as a web based UI to let the user quickly find text snippets and articles related to the different parts of the Pathway. Text Mining is done by the MEDIE, Facta and KLEIO systems. They rely on many databases and other enabling technologies like the Systems Biology Markup Language (SBML), Graphical Notation (SBGN) and the CellDesigner program which is used to show graphical models. (Link to project page)

Sven Sahle sven.sahle @ bioquant.uni-heidelberg.de University of Heidelberg, Germany
COPASI: a software tool for modeling and simulation biochemical reaction networks. (Link to project page)

Maria Schilstra m.j.1.schilstra @ herts.ac.uk University of Hertfordshire, UK
NetBuilder': Tool for specification and simulation of models of well-stirred (bio)chemical reaction systems, with options facilitating modelling of complex control interactions. Petri-net (to user) and matrix (to simulation engine) model representation. (Link to project page)

Henning Schmidt henning @ hschmidt.de University of Rostock, Germany
Systems Biology Toolbox 2 for MATLAB. (Link to project page)

Daryl Shanley daryl.shanley @ ncl.ac.uk Newcastle University, UK
I develop mathematical models of mechanisms of ageing. I participate in the development of a web service enabled stochastic simulation system, BASIS. (Link to project page)

Bruce Shapiro bshapiro @ caltech.edu Caltech, USA
MathSBML, SBML Team, xCellerator, ComputablePlant

Yong-Jun Shin yshin @ utdallas.edu University of Texas at Dallas, USA
I'm new to SMBL, and I would like to see the forum mainly for learning experience.

Evangelos Simeonidis v.simeonidis @ manchester.ac.uk University of Manchester, UK
I work for the MCISB; my main responsibility is the mathematical modelling of biological systems. The MCISB is pioneering the development of new technologies in Systems Biology, a new conceptual view on biological research that uses complex computational and mathematical analysis to advance traditional methods.We are developing techniques for the study of the metabolism of Saccharomyces cerevisiae. (Link to project page)

Kieran Smallbone kieran.smallbone @ manchester.ac.uk University of Manchester, UK
Modelling: Creation of valid/correctly-annotated SBML models Creation of modelling scripts to interface SBML with MatLab and Octave. (Link to project page)

Anatoly Sorokin asorokin @ inf.ed.ac.uk University of Edinburgh, UK
Edinburgh Pathway Editor. (Link to project page)

Neil Swainston neil.swainston @ manchester.ac.uk University of Manchester, UK
(Link to project page)

Denis Thieffry thieffry @ tagc.univ-mrs.fr INSERM U928 & University of the Mediterranean
Logical modelling of biological regulatory networks. (Link to project page)

Anja Thormann anjath84 @ aol.com FU Berlin, Germany

Susheel Varma susheel.varma @ sheffield.ac.uk University of Sheffield, UK

Alice C. Villeger alice.villeger @ manchester.ac.uk University of Manchester, UK
Arcadia: a visualisation tool for metabolic pathways.

Katja Wegner k.wegner @ herts.ac.uk University of Hertfordshire, UK
NetBuilder' is a tool for building, visualizing, and simulating multi-layered genetic networks, structured as hierarchical Petri-nets. It has a built-in stochastic and deterministic simulators and im-/exports SBML. I am part of the developer team of the layout and rendering extension for SBML. (Link to project page)

Darren Wilkinson d.j.wilkinson @ ncl.ac.uk Newcastle University, UK
SBML for discrete stochastic simulation. SBML-shorthand. SBML Discrete Stochastic Models Test Suite. BASIS system for SBML-based stochastic modelling of the biochemical mechanisms of ageing. Development of CaliBayes web-services platform for SBML model assessment, analysis and calibration against experimental data. (Link to project page)

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