Frank Bergmann
Keck Graduate Institute, USA
| fbergman @ kgi.edu
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- Project: Systems Biology Workbench
- 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-written in diverse programming languages and running on different platforms - to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.
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Ben Bornstein
Caltech, USA
| ben.bornstein @ jpl.nasa.gov
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- Project: libSBML
- LibSBML is a library designed to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with many example programs), but rather a library you can embed in your own applications. LibSBML is written in ISO C and C++ but as a library it may be used from a number of programming languages. In fact, we strive to adhere to the natural idioms of each particular language to make the libSBML programming experience seamless. For example, SBML elements behave like lists and sequences in Python, but vectors in Matlab. Also, the C and C++ interfaces are completely distinct (it's possible to program in pure C), but in C++ the C APIs may be called without sacrifcing type safety. The LibSBML code is very portable and is supported on Linux, Windows (native), and Mac OS X.
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Jan Cervený
Czech Technical University, Czech Republic
| Jan.Cerveny @ fs.cvut.cz
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- Project: Reduction of dimensionality in dynamic biological models
- Detailed dynamic models of networks of coupled biochemical reactions are hard to apply without extensive reduction of their dimensionality. We aim at designing an algorithm that would lead to internally consistent reduction corresponding to a particular time resolution.
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William Denney
University of Pennsylvania, USA
| denney @ seas.upenn.edu
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Harish Dharuri
Caltech, USA
| hdharuri @ cds.caltech.edu
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- 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.
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Andrew Finney
University of Hertfordshire, UK
| afinney @ cds.caltech.edu
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- Project: SystemCell
- Event driven framework for simulating large scale heirarcical models of biological systems. The Initial focus is on developing a tumor model based on an existing model of the cell cycle.
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Christoph Flamm
University of Vienna, Austria
| xtof @ tbi.univie.ac.at
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- Project: SBML ODE Solver Library (SOSlib)
- The SBML ODE Solver Library (SOSlib) is both a programming library and a command-line application for construction, symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the terms of the GNU Lesser General Public License (LGPL). The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. SUNDIALS' version of CVODE is incorporated for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems.
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Akira Funahashi
Kitano Symbiotic Systems Project, Japan
| funa @ symbio.jst.go.jp
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- Project: CellDesigner
- A modeling/simulation tool for biochemical networks. CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using SBML. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
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Ralph Gauges
EML, Germany
| ralph.gauges @ eml-r.villa-bosch.de
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- Project: SBML Layout Extension
- The SBML Layout Extension is an extension to the SBML file format that allows the storage of graphical layout information on reaction networks within an SBML file. We are currently working on complementing the layout extension with render information to make it applicable to a wider range of graph types.
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Colin Gillespie
University of Newcastle, UK
| c.gillespie @ ncl.ac.uk
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- Project: BASIS
- BASIS is a new Project developing web-based services for quantitative study of the biology of ageing.
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Damon Hachmeister
The MathWorks, USA
| dhachmei @ mathworks.com
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Stefan Hoops
Virginia Bioinformatics Institute, USA
| shoops @ vbi.vt.edu
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- Project: Copasi
- Copasi is a software application for simulation and analysis of biochemical networks.
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Michael Hucka
Caltech, USA
| mhucka @ caltech.edu
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- 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.
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Akiya Jouraku
Kitano Symbiotic Systems Project, Japan
| jouraku @ symbio.jst.go.jp
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- Project: CellDesigner
- A modeling/simulation tool for biochemical networks. CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using SBML. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
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Sarah Keating
University of Hertfordshire, UK
| skeating@caltech.edu
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- Project: libSBML/SBMLToolbox
- SBMLToolbox is a package for working with SBML models in MATLAB. The toolbox currently includes functions for reading and writing SBML models, converting SBML models into MATLAB data structures, viewing and manipulating those structures, converting them to MATLAB symbolic format, and simulating them using MATLAB's ODE solvers.
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Nicolas Le Novère
EMBL-EBI, UK
| lenov @ ebi.ac.uk
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- 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.
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Lu Li
EMBL-EBI, UK
| luli @ ebi.ac.uk
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- 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.
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Rainer Machne
University of Vienna, Austria
| raim @ tbi.univie.ac.at
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- Project: SBML ODE Solver Library
- A C/C++ library for symbolic and fast numerical analysis of SBML encoded biochemical reaction networks.
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Ladislav Nedbal
Institute of Systems Biology and Ecology, Czech Republic
| nedbal @ greentech.cz
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- Project: Reduction of dimensionality in dynamic biological models
- Detailed dynamic models of networks of coupled biochemical reactions are hard to apply without extensive reduction of their dimensionality. We aim at designing an algorithm that would lead to internally consistent reduction corresponding to a particular time resolution.
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Yasunori Osana
Keio University, Japan
| osana @ am.ics.keio.ac.jp
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- Project: CellDesigner
- A modeling/simulation tool for biochemical networks. CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using SBML. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
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Emanuele Raineri
EMBL, Germany
| emanuele.raineri @ embl.de
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- Project: Smartcell
- General purpose simulation software, which includes links to a variety of pathway/reaction databases and different computational approaches (Gillespie, ODE, tau-leap). It is also possible to specify the localization of species and reactions and the number and characteristic of diffusion processes.
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Nicolas Rodriguez
European Bioinformatics Institute, UK
| rodrigue @ ebi.ac.uk
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- Project: SBMLeditor
- 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.
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Sven Sahle
EML, Germany
| sven.sahle @ eml.org
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- Project: Copasi
- A tool for modeling, simulation and analysis of biochemical pathways.
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Jim Schaff
University of Connecticut Health Center, USA
| schaff @ neuron.uchc.edu
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- Project: Virtual Cell Project
- A spatially oriented modeling and simulation problem solving enviroment for cell biology.
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Marvin Schulz
Max Planck Institute for Molecular Genetics, Germany
| schulzma @ molgen.mpg.de
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- Project: SBMLmerge
- 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.
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Kalai Selvi Shanmugam
German Cancer Research Center, Germany
| k.shanmugam @ dkfz-heidelberg.de
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Bruce Shapiro
Caltech, USA
| bshapiro @ caltech.edu
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- Project: Caltech Biological Network Modeling Center (BNMC)
- The goal of the BNMC is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems.
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Mahesh Visvanathan
University of Medical and Health Informatics and Technology, Austria
| mahesh.visvanathan @ umit.at
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- Project: Model Integrator
- The aim of this Project is to combine various form of clinical, micro array, MS data sets which are avilable in different XML formats and to extract those information required for doing simulation and present it in the SBML. The current version is SBML Level2 version 1 format and do simulation and store that information in a dataware house. The task would be interesting to implement it in SBML Level2 and Version 2.
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Witold Eryk Wolski
Newcastle University School of Mathematics and Statistics, UK
| w.e.wolski @ ncl.ac.uk
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- Project: Calibayes
- Integration of GRID-based post-genomic data resources through Bayesian calibration of biological simulators.
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