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Delegates

Delegates List

2007 SBML Forum


Frank Bergmann

University of Washington, USA

Project: Systems Biology Workbench
With the Systems Biology Workbench (SBW), we provide a modular framework that allows applications to share their capabilities. With the framework we include a wide variety of modules (popular applications such as: JDesigner or Jarnac), building blocks that new applications can use to perform frequent tasks such as modeling, bifurcation analysis, frequency analysis, deterministic and stochastic simulation, network layout and 3D visualization. This allows developers to focus on novel tasks.

Michael Blinov

University of Connecticut Health Center, USA

Project: http://vcell.org/bionetgen
The number of protein complexes and modification states that potentially can be generated during the response to a signal is large, because proteins contain multiple modifications sites and interact with multiple binding partners. Manually specifying each term of a mathematical model may no longer work. A solution is provided by 1) automatic extraction from pathway databases re-usable model, using BioPAX ontology, and 2) specifying rules of interaction based on protein modularity, implemented in BioNetGen software.

Akira Funahashi

Keio University, Japan

Project: CellDesigner
CellDesigner: A modeling tool for biochemical networks. CellDesigner is software for modeling and simulation of biochemical and gene regulatory networks. While CellDesigner itself is a sophisticated structured diagram editor, it enables users to directly integrate various tools, such as built-in SBML ODE Solver and SBW-powered simulation/analysis modules. CellDesigner runs on various platforms such as Windows, MacOS X and Linux, and is freely available from our website at http://celldesigner.org.

Stefan Hoops

VBI, USA

Project: SBML Editor; COPASI

Michael Hucka

California Institute of Technology, USA

Project: SBML, SBGN, BioModels Database, BioModels.net, libSBML, SBO, MIRIAM, ICSB 2007

Sarah Keating

California Institute of Technology, USA

Project: libSBML/SBMLToolbox/SBML Test Suite

Douglas Kell

University of Manchester, UK

Project: www.mcisb.org, www.dbkgroup.org
Integrating a variety of software elements into workflows for performing integrative systems biology. See e.g. [1] Kell, D. B. (2006). Metabolomics, modelling and machine learning in systems biology: towards an understanding of the languages of cells. The 2005 Theodor Bücher lecture. FEBS J 273, 873-894; [2] Kell, D. B. (2006). Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Disc Today 11, 1085-1092.

Dagmar Koehn

EMBL-EBI, UK

Project: I have been working with Adj. Prof. Lena Stroembaeck (Linkoepings University, Sweden) on Standard Comparison during my diploma thesis (2006) and then moved to the dIEM oSiRiS project at Rostock University, Germany (Prof. Lin Uhrmacher) where I am concentrating on XML model storage (SBML being one of the formats). Currently I am a Marie Curie Research Fellow at the EMBL-EBI in Nicolas Le Novère's group. (Hinxton, UK). We are working on a classification of simulation algorithms and aim at developing a "Minimum Information" standard for information about simulation runs.

Fedor Kolpakov

Institute of Systems Biology

Project: BioUML
I would like to discuss two topics: 1) Embedding formal graphic notations into SBML models We have developed XML fromat that allows formally describe graphical notation. The description includes: - object types, that can be used - object properties - how objects should be visualised - semantic rules for diagram editing. As an example we have represented in this format Cell Designer 3.5 graphic notation. We have suggested simple format for annotations in SBML format that allows bind components of SBML model with graphic notation. General idea is quite simple: all additional information is stored as property-value, and possible properties are defined by graphic notation. 2) Models composition We have implemented initial solution for digarams composition in BioUML workbench. I would like to present some details of this approach that can be usefull for SBML. I also would like to discuss approach with models inheritance - when somebody incorporate submodel in bigger model it may be needed to modify it. We suggest set of rules that describes possible modifications: - changing in parameters and initial values - removing model components - adding new components

Camille Laibe

EMBL-EBI

Project: MIRIAM, SBO, BioModels Database

Anuradha Lakshminarayana

University of Connecticut Health Center, USA

Project: Developer in the Virtual Cell Project, SBML translations to and from Virtual Cell

Nicolas Le Novère

EMBL-EBI, UK

Project: SBML; BioModels Database, MIRIAM Resources; SBO; SBMLeditor; StochSim

Paul-Jean Letourneau

Wolfram Research Manchester


James Lu

Johann Radon Institute for Computational and Applied Mathematics, Austria

Project: Inverse extensions for the SBML ODE Solver Library Inverse eigenvalue analysis using MathSBML

Pontus Melke

Lund University

Project: Member of Henrik Jonsson's group, working with multicellular modeling etc.

Ion I. Moraru

University of Connecticut Health Center, USA

Project: The Virtual Cell

Brett Olivier

University of Stellenbosch, South Africa

Project: PySCeS
PySCeS, the Python Simulator for Cellular Systems</b>
Developing Python based systems biology software such as PySCeS.

Yasunori Osana

Keio University, Japan

Project: ReCSiP
ReCSiP, a reconfigurable hardware based biochemical simulator. We have both deterministic and stochastic implementation, and continuing effort to support SBML.

Michael Pedersen

University of Edinburgh, UK

Project: I am a PhD student designing a high-level formal language of biological systems (LBS). LBS includes notions of species modification sites, complexes, parameterised modules and associated type systems. I believe these notions do not currently feature in SBML, but they could be addressed in future developments. LBS can be given semantics in terms of Petri nets, but can also be translated to SBML. Work on translation tools is currently in progress.

Vlad Petyuk

Pacific Northwest National Lab, USA

Project: http://ncrr.pnl.gov/
Extensively involved in analysis of mass spectrometry based proteomics data. Plan to use SBML for interpreting the shotgun proteomics data in the context of biological models.

Robert Phair

Integrative Bioinformatics Inc., USA

Project: ProcessDB
Integrative Bioinformatics Inc (IBI), an NIH-supported startup, is developing ProcessDB, a software tool for organizing and managing the modeling process. ProcessDB manages collections of molecules, molecular complexes, processes, models, quantitative models, experiments, and models of experiments. ProcessDB supports import and export of SBML, facilitates model combination and comparison and allows simultaneous testing against any number of experiments. Our consulting practice has used ProcessDB to support several very cool papers and two recently funded NIH proposals.

Nicolas Rodriguez

European Bioinformatics Institute, UK

Project: SBMLeditor
SBMLeditor, an editor for models in the Systems Biology Markup Language</b>
The SBMLeditor provides a simple, low level editor of SBML files of any level. 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. SBMLeditor provides the ability to use the new annotation framework introduce in SBML level 2v2 based on RDF and dublin core dc:creator and dc:relation or dcterms:xxx elements. Some functions provided by libSBML are available if the library is setup properly on the system. A visual MathML equation editor is also provided to speed up the writing of the mathML parts of SBML.

Sven Sahle

University of Heidelberg, Germany

Project: COPASI
COPASI - a modeling and simulation tool for biochemical systems. SBML Layout Extension - An SBML Level 3 feature for storing the layout of a graphical model representation

Patrik Sahlin

University of Lund, Sweden

Project: I am a member of the Computational Biology & Biological Physics Group at Lund University. We are developing a simulator to solve problems within systems biology. We are interested if and how we can incorporate SBML into our software.

Herbert Sauro

University of Washington, USA

Project: Systems Biology Workbench (SBW)
With the Systems Biology Workbench (SBW), we provide a modular framework that allows applications to share their capabilities. With the framework we include a wide variety of modules (popular applications such as: JDesigner or Jarnac), building blocks that new applications can use to perform frequent tasks such as modeling, bifurcation analysis, frequency analysis, deterministic and stochastic simulation, network layout and 3D visualization. This allows developers to focus on novel tasks.

Jim Schaff

University of Connecticut Health Center, USA

Project: Virtual Cell
VCell "Virtual Cell" (vcell.org), a spatially oriented modeling and simulation framework for cell physiology (ode,pde,stochastic - spatial, nonspatial - biological/mathematical modeling). We are currently expanding our SBML support to be nearly complete and are interested in extending SBML to handle spatial modeling as well.

Maria Schilstra

University of Hertfordshire, UK

Project: NetBuilder
We are developing NetBuilder, a general modeling and simulation (stochastic, deterministic, hybrid) tool for biochemical reaction systems, with extensions that facilitate the modeling of genetic and other regulatory networks.

Bruce Shapiro

California Institute of Technology, USA

Project: MathSBML, SBML

Evangelos Simeonidis

MCISB, University of Manchester

Project: My main responsibility at the Manchester Centre for Integrative Systems Biology (MCISB) is the mathematical modelling of biological systems. The MCISB is pioneering the development of new technologies in Systems Biology. We are developing a number of techniques for the study of the metabolism of Saccharomyces cerevisiae.

Irena Spasic

University of Manchester

Project: Manchester Centre for Integrative Systems Biology

Hugh Spence

GlaxoSmithKline, UK


Neil Swainston

Manchester Centre for Integrative Systems Biology

Project: Systems biology of yeast metabolism. Data management in systems biology: experimental and modelling.

Alice Villeger

University of Manchester, UK


May D. Wang

Georgia Tech, USA


Katja Wegner

University of Hertfordshire, UK

Project: NetBuilder
We are developing NetBuilder, a general modeling and simulation (stochastic, deterministic, hybrid) tool for biochemical reaction systems, with extensions that facilitate the modeling of genetic and other regulatory networks.

Hongseok Yun

MBEL, KAIST, Korea

Project: MetaFluxNet - MFAML - WebCell

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