Delegates List

The 2006 SBML Forum


Nathan Addy
 addy @ molsci.org
Molecular Sciences Institute, USA

Project:     
E-Cell

E-Cell is a simulation platform that can simulate cellular systems by allowing many components driven by different algorithms to coexist in a model. My work consists of adding capabilities for dynamic model structure to E-Cell, in order to add species and reaction generation capabilities to the E-Cell System.

Frank Bergmann
 fbergman @ kgi.edu
Keck Graduate Institute, USA

Project:     
Systems Biology Workbench

The Systems Biology Workbench (SBW) is both a software framework and a collection of tools providing modeling, simulation and analysis capability. The developer of a new application can use these tools as a foundation instead of recreating existing functionality, which allows them to focus on novel tasks. An existing application written in any supported programming language can be modified to interact with SBW with minimal programming overhead. This enables other applications to use its functionality.

Eric Billings
 billings @ helix.nih.gov
Integrative Computational Biology Lab, NHLBI, NIH, USA

Project:     
QBT

QBT is a desktop tool designed for the bench biologist as well as computational biolists. QBT manages models of biological systems that may include elements such as molecular species, sequence features such as binding motifs or SNPs, and cellular structures.

Melanie Courtot
 courtot @ ebi.ac.uk
EMBL-EBI, UK

Project:     
SBO

SBO is the Systems Biology Ontologies project, another cornerstone of the BioModels.net effort. The goal of SBO is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in systems biology, especially in the context of computational modeling.

Emek Demir
 demir @ cbio.mskcc.org
Sloan Kettering Institute, USA

Project:     
BioPAX and Paxtools

BioPAX is a standard language for exchanging pathway information. BioPAX's primary usecases are knowledge representation and integration, and it is a complementary language to SBML. Paxtools is a library for reading and writing BioPAX. Recently Paxtools also started to support a SBML export facility.

Harish Dharuri
 hdharuri @ cds.caltech.edu
Caltech, USA

Project:     
BioModels Database

BioModels Database is an effort to develop a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.

Christopher Dubay
 dubayc @ ohsu.edu
Oregon Health & Sciences University, USA

Project:     
SBML for Pathway modeling in human development


Adrien Faur
 faure @ ibdml.univ-mrs.fr
IBDML, Marseille, France

Project:     
GINsim(Gene Interaction Network simulation)

Our team is working on the qualitative modeling and simulation of genetic regulatory networks. The project involves the development of an export in SBML module for GINsim (Gene Interaction Network simulation), the computer tool developed in the team. As a modeller, biologist by training, I'm not directly involved in the programming, but rather in the testing and feedback phase.

Andrew Finney
 afinney @ cds.caltech.edu
Oxford Computer Consultants, UK

     

Akira Funahashi
 funa @ symbio.jst.go.jp
Kitano Symbiotic Systems Project, Japan

Project:     
CellDesigner

CellDesigner:  a Modeling Tool for Biochemical Networks.
ReCSiP:  a System of Accelerating Biochemical Simulator on Programmable Hardware.

Ralph Gauges
 ralph.gauges @ eml-r.villa-bosch.de
EML Research gGmbH , Germany

Project:     
Render Supplement to the SBML Layout Extension

Although early versions of the SBML Layout Extension included the possibility to specify render information, due to several reasons, the current version does not. Since this sometimes means that part of the information is lost when stored with the SBML Layout Extension, we have developed a supplement to the Layout Extension that allows the users to store render information with their layout. A first implementation as an XSLT stylesheet has also been written which can be used to demonstrate the capabilities of this new supplement.

Sridhar Hariharaputran
 sharihar @ techfak.uni-bielefeld.de
Bielefeld University, Germany

Project:     
SIGNALIGN

Signaling pathways play a major role in many cellular processes. In short from cell birth to cell death, involving lot of complexity but functioning with robustness. Sometimes perturbation in these pathways leads to disease such as cancer. We are interested in modeling and simulation of signaling pathways and would like to know more about their robustness and behavior using different tools and techniques. Also we interested in the alignment and classification of signaling pathways. We have developed a tool, SIGNALIGN (alpha version) for alignment and visualization of signaling pathways. A user interface has been provided to allow them to import and use sbml files of signaling pathways for the alignment and visualization of pathways.

Jan-Hendrik Hofmeyr
 jhsh @ sun.ac.za
University of Stellenbosch, South Africa

Project:     
PySCeS (The Python Simulator for Cellular Systems)


Michael Hucka
 mhucka @ caltech.edu
Caltech, USA

Project:     
SBML

The Systems Biology Markup Language (SBML), a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others.

M. Wilayat Hussain
 m_wilayat_hussain @ yahoo.com
Mohammad Ali Jinnah University Islamabad, Pakistan

     


Henrik Jonsson
 henrik @ thep.lu.se
Lund University, Sweden

Project:     
Modeling of pathways and multicellular systems with focus on plants and cell colonies


Akiya Jouraku
 jouraku @ symbio.jst.go.jp
Kitano Symbiotic Systems Project, JST, Japan

Project:     
CellDesigner



Sarah Keating
 s.m.keating @ herts.ac.uk
University of Hertfordshire, UK

Project:     
libSBML/SBMLToolbox

Development of:
SBMLToolbox - a MATLAB toolbox to facilitate the use of SBML models within the MATLAB environment.
libSBML - in particular implementation of support for units and model validation.

Fedor Kolpakov
 fedor @ biouml.org
Institute of Systems Biology, Novosibirsk, Russia

Project:     
BioUML

BioUML is integrated extensible open source Java workbench that adopts visual modeling approach for formal description and simulation of complex biological systems. Its core is metamodel that provides an abstract layer for comprehensive formal description of wide range of biological systems. Content of databases on biological pathways, SBML and CellML models can be expressed in terms of the metamodel. BioUML workbench provides Java and MATLAB simulation engines. Both engines passed 100% SBML semantic test suite. Test details are available at: http://www.biouml.org/sbml_tests/overview.html. BMOND (http://BMOND.biouml.org) - database on Biological Models and Diagrams - is developed using BioUML technology.

Nicolas Le Novère
 lenov @ ebi.ac.uk
EMBL-EBI, UK

Project:     
BioModels Database; MIRIAM; SBO; SBML spatial extension; SBML complex species extension


Allen Lee
 allen.lee @ mathworks.com
The MathWorks, USA

Project:     
SimBiology


Chen Li
 chenli @ ebi.ac.uk
EMBL-EBI, UK

Project:     
BioModels Database


Peter Li
 Peter.Li @ manchester.ac.uk
University of Manchester, UK

Project:     
Taverna

The Manchester Centre for Integrative Systems Biology is investigating how workflows can provide a loosely coupled approach for integrating distributed data in the life sciences. Using Taverna (http://taverna.sourceforge.net), we have designed workflows which can automatically construct biological pathways using data from databases such as KEGG and BIND in a generic and ad hoc fashion. Pathway models were created in SBML which were visualized from within Taverna using GraphViz and an interactive graph viewer called SharkView.

James Lu
 james.lu @ oeaw.ac.at
Johann Radon Institute for Computational and Applied Mathematics, Austria

Project:     
SBML ODE Solver and others

Parameter identification package for biology and chemistry using regularization methods.   Incorporation of adjoint equation solver within the SBML ODE Solver Library.   Inverse Bifurcation Toolbox for SBML models using MathSBML and Matlab-based bifurcation analysis software MATCONT.

Rainer Machne
 raim @ tbi.univie.ac.at
University of Vienna, Austria

Project:     
SBML ODE Solver Library

A C/C++ library for fast and efficient numerical and symbolic analysis of SBML-based biochemical reaction networks.

Johannes Mandel
 johannes.mandel @ fh-weihenstephan.de
University of Ulster, UK

Project:     
Narrator

Narrator is a graph-based software tool for modeling biochemical transformation and information processing. Information processing is modelled with computed logical entities and their graphical representation can be used to for example describe exogenous variables (events)in the diagram.

Pontus Melke
 pontus @ thep.lu.se
Lund University, Sweden

Project:     
Modeling of single cell signal transduction pathways, with focus on the TGF-beta pathway, and multicellular systems like plants and growing cell colonies.


Pedro Mendes
 mendes @ vbi.vt.edu
Virginia Bioinformatics Institute, USA

Project:     
COPASI

COPASI is a package for modeling and simulation of biochemical networks. COPASI uses ODEs and/or stochastic methods to simulate dynamics of biochemical networks and has several tools for nonlinear dynamics analysis, optimization, and parameter estimation.

Eric D. Mjolsness
 emj @ ics.uci.edu
University of California, Irvine, USA

Project:     
The Computable Plant

Using the study of meristem development in Arabidopsis thaliana, Eric Mjolsness, a computer scientist at UCI, and Elliot Meyerowitz, a plant developmental biologist at Caltech, are working together to provide a quantitative and cellular description of plant development.

Ion I. Moraru
 moraru @ panda.uchc.edu
UCHC, USA

Project:     
The Virtual Cell


Dylan Morris
 dmorris @ caltech.edu
Caltech, USA

Project:     
Development of spatial models in systems biology


Stefan Mueller
 stefan.mueller @ oeaw.ac.at
RICAM, Austrian Academy of Sciences, Austria

Project:     
SOSlib (SBML ODE Solver library)


Joanna Murakami
 murakami @ caltech.edu
Caltech, USA

Project:     
Mathematica conversion of xCellerator reactions into SBML


Aurélien Naldi
 naldi @ ibdml.univ-mrs.fr
Developmental Biology Institute of Marseille-Luminy (IBDML), France

Project:     
GINsim

Our team is working on qualitative models of regulatory networks, developing GINsim, a tool to build and analyse such models. We have investigated using SBML as exchange format with other tools. While doing this, we encountered some semantic problems with the current version of SBML (level 2). The presentation aims to highlight these problems and to propose an extension to solve them.

Brett Olivier
 bgoli @ sun.ac.za
Stellenbosch University, South Africa

Project:     
PySCeS - the Python Simulator for Cellular Systems

We have developed PySCeS as a flexible, Python based, modelling tool for exploring cellular processes. PySCeS includes modules for analysing the structural, time dependent and steady state properties (e.g. MCA) of ODE based kinetic models. While basic SBML reading/writing has been implemented, we are expanding our support with the aim of using SBML as an exchange format thus allowing PySCeS to more easily interact with other systems biology software.

Yasunori Osana
 osana @ dna.bio.keio.ac.jp
Keio University, Japan

Project:     
CellDesigner / ReCSiP

CellDesigner: a graphical SBML modeling tool
ReCSiP: a hardware accelerated biochemical simulator

Jean Peccoud
 peccoud @ vt.edu
Virginia Tech / Virginia Bioinformatics Institute, USA

Project:     
Dynamic partitioning for hybrid simulation of molecular networks

We present a hybrid simulation algorithm that dynamically partitions systems of coupled chemical equations into subsets of continuous and discrete reactions, approximates the continuous reactions deterministically as a system of ordinary differential equations (ODE), and uses a Monte Carlo method for generating discrete reaction events according to a time-dependent propensity. We are working on making this simulation engine SBML compliant.

Karthik Raman
 karthik @ rishi.serc.iisc.ernet.in
Indian Institute of Science, India

Project:     
PathwayAnalyser

PathwayAnalyser is a tool for systems biologists for analysis of metabolic pathways, particularly by Flux Balance Analysis. PA interfaces with the GNU Linear Programming Toolkit (GLPK) for linear programming and OOQP is used for quadratic programming/MoMA. It can give a comprehensive report on gene deletions from the SBML Model input. It is currently a command-line tool but a GUI may be added soon. The current focus is to make it computationally efficient and handle genome-scale models.

Nicolas Rodriguez
 rodrigue @ ebi.ac.uk
European Bioinformatics Institute, UK

Project:     
SBMLeditor, an editor for models in the Systems Biology Markup Language

SBMleditor is a tool to facilitate the quick creation and edition of models encoded in the Systems Biology Markup language (SBML) in any levels or versions. SBMLeditor tries to provide 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.

Sven Sahle
 sven.sahle @ eml-r.villa-bosch.de
EML Research, Germany

Project:     
COPASI and SBML

A short overview of new features of COPASI, especially assignment and ODE rules, and how they interact with SBML.

Jim Schaff
 schaff @ neuron.uchc.edu
University of Connecticut Health Center, USA

Project:     
Virtual Cell

We are developing the Virtual Cell (vcell.org), a spatially oriented web accessible platform for cell modeling and simulation. We continue to improve our SBML inport/export capabilities especially regarding Units and multicompartmental modeling. We are also interested in extending SBML to support spatial modeling.

Henning Schmidt
 henning @ fcc.chalmers.se
Fraunhofer Chalmers Centre, Sweden

Project:     
Systems Biology Toolbox for MATLAB

SBMLmerge is a tool for combining several SBML files into one and for detecting conflicts that prevent their combination. SBMLmerge can also create network graphs showing the models before and after merging.

Falk Schreiber
 schreibe @ ipk-gatersleben.de
IPK Gatersleben, Germany

Project:     
Modelling, analysis, simulation and visualisation of biological networks in the context of plant biological problems


Bruce Shapiro
 bshapiro @ caltech.edu
Caltech, USA

Project:     
MathSBML, SBML


Hugh Spence
 hugh.d.spence @ gsk.com
GlaxoSmithKline, UK

Project:     
Pathway Modeling Factory (PMF)


Lafras Uys
 lafras @ sun.ac.za
Stellenbosch University, South Africa

Project:     
Storing SBML in the Berkeley DB XML database for rapid searching, retrieval and construction of biological models

We are investigating Berkeley DB XML (www.sleepycat.com) to manage SBML. BDB DB XML can store SBML documents whole or as nodes. SBML stored as nodes allows efficient indexing and searching. Complex queries can be executed with the BDB XML XQuery implementation. We hope that this will lead to easier creation of new models from existing reaction descriptions. Where different versions of the same model exists, storing SBML in a database can avoid redundant XML.

Steven Watterson
 watterss @ maths.tcd.ie
University of Edinburgh, UK