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Abstracts

Presentation Abstracts - The 9th Forum on Software Platforms for Systems Biology

(Alphabetical by First Author)




BioNetGen: Software for Rule-Based Reaction Network Generation

Michael Blinov
Los Alamos National Laboratory, USA
mblinov @ lanl.gov

ABSTRACT
General-purpose software BioNetGen allows a user to create a network of molecular species that characterizes the dynamics of a signal transduction system and that accounts comprehensively and precisely for specified activities and interactions of the domains of signaling molecules. The output provides functions that relate model variables to experimental readouts, and can be exported into SBML. Models are relevant for rational drug discovery, analysis of proteomic data, and mechanistic studies of signal transduction.


Graph-Based Rule-Based Approach to SBML Level 3

Michael Blinov
Los Alamos National Laboratory, USA
mblinov @ lanl.gov

ABSTRACT
Recently we have developed BioNetGen software that allows a user to create a network composed of multi-component species, accounting for activities and interactions of the domains of signaling molecules. We introduce XML description that is based on experience gained with BioNetGen. It utilizes a rule-based approach for specifying multi-component species as graphs, and their activities and interactions as graphs rewriting.


libSBML: Recent Developments and Future Directions

Ben Bornstein
California Institute of Technology and NASA JPL, USA
ben.bornstein @ jpl.nasa.gov

ABSTRACT
LibSBML hides the details of SBML I/O, allowing reaction networks and equations to be manipulated as domain-specific programming language objects. The library is written in ISO C/C++ with APIs for Lisp, Fortran, MATLAB, Java, Perl, Python, and SBW. It runs on Linux, Mac OS X, and Windows. First, I'll provide an overview of recent libSBML developments, including nascent model consistency checking capabilities. Next, I'll describe ways to make libSBML more amenable to upcoming SBML extensions. A group discussion to determine future library capabilities will follow.


From Logical Regulatory Networks to Petri Nets to SBML

Claudine Chaouiya, Elisabeth Remy and Denis Thieffry
IBDM and IML, Luminy, France
chaouiya @ esil.univ-mrs.fr

ABSTRACT
Petri Nets offer a rigorous framework to analyse large systems, and have been successfully applied to the modelling of metabolic networks. In the case of genetic networks, logical models are more easily derived. To combine the two approaches, we have defined a systematic rewriting of logical models into standard PN. While some groups have worked on SBML to PNML (standard for PN), we will discuss the prospects opened by the conversion of logical models into PN for the representation of logical regulatory models into SBML.


MesoRD: A Software for Stochastic Reaction Diffusion Simulation

Johan Elf and Johan Hattne
Dept. of Cell & Molecular Biology, Uppsala University, Sweden
johan.elf @ icm.uu.se

ABSTRACT
MesoRD is an open source software (http://mesord.sourceforge.net) written in C++ that implements the Next Subvolume Method. MesoRD reads a SBML level C++ 2 system description, including the geometry of the compartments and diffusion rate constants of different species in annotations.


Multicomponent Species: A Proposal for SBML Level 3

Andrew Finney
University of Hertfordshire, UK
afinney @ caltech.edu

ABSTRACT
SBML Levels 1 and 2 encode models using a scheme consisting of biochemical entities linked by reactions to form networks. Entities are indivisible. Reactions only apply to specific entities. The proposed representation enables models to describe generalized operations on parts of entities which are described as an assemblies of smaller components. This approach avoids the enumeration of species and reactions when encoding models such as signalling pathways.


The SBML Semantic Test Suite

Andrew Finney
University of Hertfordshire, UK
afinney @ caltech.edu

ABSTRACT
We have recently developed the SBML Semantic Test suite, a facility for testing the quality of SBML support by simulation software. The suite consists of SBML models each with documentation and simulation output. The suite comes with customizable portable automation scripts that enable a suitably 'wrapped' simulator to be tested against the suite. A beta version of the suite is available at http://www.cds.caltech.edu/~afinney/semantic-test-suite.tar.gz.


CellDesigner and Hardware Accelerated Simulator

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

ABSTRACT
We have developed CellDesigner2.0, which is a modeling tool of biochemical networks with graphical user interface. CellDesigner2.0 is SBW-enabled and SBML-compliant (Level 1 and Level 2) application which runs on Windows, MacOSX and Linux. Also, we're planning to implement SBML-compliant hardware accelerated simulator. Simulation core (ODE solver and stochastic part) has already been implemented on FPGA. From the evaluation, this hardware executes a simulation 20 to 100 times faster than a software based simulator on Pentium3/AthlonXP PC.


SBMLToolbox Release 1.0

Sarah M. Keating
University of Hertfordshire, UK
skeating@caltech.edu

ABSTRACT
SBMLToolbox is an open-source MATLAB toolbox that uses libSBML to provide MATLAB users with functions for reading, writing and manipulation SBML models. Version 1.0 works on Windows, Linux, and MacOS. SBMLToolbox supports reading and writing of SBML Levels 1 and 2 and the simulaton of models using MATLAB's ODE functions. In this presentation, I will summarize the features available in the current release and features planned for upcoming releases, and discuss using SBMLToolbox with the SBML Semantic Test Suite.


BioUML: Open Source Extensible Workbench for Systems Biology

Fedor Kolpakov
Design Technological Institute of Digital Techniques, Russia
fkolpakov @ academ.org

ABSTRACT
Core of BioUML is meta model providing an abstract layer for formal description of biological and other complex systems. Content of databases on biological pathways (TRANSPATH, KEGG/pathways, GeneNet, GeneOntology) as well as SBML and CellML models can be expressed in terms of the meta model and used by BioUML workbench. Plug-in based architecture provides the workbench extensibility. There are plug-ins for database access, diagram editing, graph layout, simulation and for integration with MATLAB and SBW.


Merging and Visualisation of SBML Models

Karthik Raman and Nagasuma R. Chandra
Supercomputer Education and Research Centre, Indian Institute of Science, India
karthik @ rishi.serc.iisc.ernet.in

ABSTRACT
For the simulation of genomic scale systems, it is required to generate SBML models by merging several small pathway models, available in public databases such as KEGG. We created a genomic scale model of Mycobacterium tuberculosis for modeling and simulating the effect of various drugs, by merging these pathway models. SBML is an ideal platform for these models, as it lends itself to easy merging as well as visualisation using simple tools.


PySCeS: Python Simulator for Cellular Systems

Johann M. Rohwer, Brett G. Olivier and Jan-Hendrik S. Hofmeyr
Department of Biochemistry, Stellenbosch University, South Africa
jr @ sun.ac.za

ABSTRACT
Computer modelling has become indispensable in the analysis and understanding of cellular processes. Here we describe PySCeS, the Python Simulator for Cellular Systems, a new open-source modelling tool. PySCeS is extremely flexible and user-extensible, has been developed in Python (www.python.org) and uses the SciPy (www.scipy.org) scientific libraries. It operates on both win32 and posix operating systems. PySCeS comprises a "toolkit" of high-level modules in a standard Python environment, allowing for interactive command line use or execution of programme scripts.


SBML Support in E-Cell Simulation Environment Version 3.1.103

Takeshi Sakurada
Institute for Advanced Biosciences, Keio University, Japan
sakurada @ sfc.keio.ac.jp

ABSTRACT
E-Cell3 is a new software platform for the cell simulation developed by E-Cell project and collaborators. It has three major components, simulation environment, modelling environment and analysis tools. The E-Cell Simulation Environment (E-Cell SE) version 3.1.103 is the latest beta toward next stable release. In this short presentation, I would like to show the updates of current developments of E-Cell system, especially the ver. 3.1.103 and SBML support.


Modularization of Systems Biology Markup Language Using Hierarchical UML Models

David Schröder and Jörg R. Weimar
Technical University at Braunschweig, Germany
J.Weimar @ tu-bs.de

ABSTRACT
Since many tools partially support SBML, we specify a modularization of SBML into modules which consist of those elements or attributes which can be deleted from the specification independently of others. We identified syntactic and semantic dependencies between the modules and provide UML models for all consistent subsets of modules. In this way, one can specify for each tool which modules are supported. XSD schemata are created automatically for each subset, and SBML files can be analyzed for the occurrence of the modules.


SBML Arrays in MathSBML and the Computable Plant Project

Bruce E. Shapiro
California Institute of Technology and NASA JPL, USA
bshapiro @ jpl.nasa.gov

ABSTRACT
The SBML Level 3 arrays proposal was partially implemented in the MathSBML Model Builder to support the computable plant project. A variety of functions allow easy generation of array-based SBML model segments, notably the dimensions, index, foreach, variableLink, and initialAssignmentRule features of the Array Proposal, as well as MathML vector and matrix assignments. In addition, the Computable Plant Project has introduced the connectionRule to describe different networks of connectivity between cells.


Model Integration in SBML Using the BioPAX Ontology

Jeremy Zucker
Dana-Farber Cancer Institute, Harvard Medical School, USA
zucker @ research.dfci.harvard.edu

ABSTRACT
Model integration requires not only data, but data about data, or metadata. Because the BioPAX ontology was developed by the biopathways community to enable database integration, it seems a natural fit to use BioPAX as metadata in SBML to enable model integration. We give a brief overview of the BioPAX ontology, recommend best practices for using BioPAX, and provide some clear, well-developed examples which incorporate BioPAX into SBML models using the CellML metadata standard.


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