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Software

Name(s) Software/project(s) Description
Ben Bornstein libSBML LibSBML is a library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It is not an application itself, but rather a library suitable for embedding into an application. The library supports both SBML Level 1 (version 1 and 2) and SBML Level 2. LibSBML is written in ISO C and C++ and currently provides an API for the languages C, C++, Java, Python, Lisp, Perl and MATLAB. LibSBML is known to run on Linux, Windows, and MacOS X, but is portable and support for other platforms should be straightforward to implement.
Norihiro Kikuchi and Tsuyoshi Kobayashi Cell Designer  
Tom Radivoyevitch SBMLR SBMLR maps SBML models to and from a similar list of lists structure defined in R. It includes a function getIncidenceMatrix for extracting reaction network incidence matrices, and a function fderiv which uses such incidence matrices to compute state derivates. fderiv is used by lsoda of R's odesolve package to simulate systems. I'm using SBMLR in my research in deoxynucleotide metabolism. As part of NCI's Integrative Cancer Biology Program, I will also use SBMLR to teach oncology fellows basic math and programming skills in the context of cancer-relevant models; the added value of using R for this mission is that these same fellows are also learning R to carry out statistical analyses. R usage is further motivated by Bioconductor, and by price (it's free!).
Ann Chasson and Robert Phair ProcessDB ProcessDB is a scalable tool for managing the modeling process in the context of individual laboratories or research groups focused on experimental molecular cell biology. ProcessDB provides 1) a flexible, user-defined database of model components: molecules, molecular complexes, cellular locations, and cellular processes; 2) tools for assembling models as collections of processes; 3) automatic conversion of models to systems of non-linear ordinary differential equations based on principles of chemical kinetics; 4) tools to capture a wide variety of experimental protocols and automatically run these experiments on selected models; and 5) tools to export the resulting models-of-experiments to solver and optimization software (currently, Berkeley Madonna, and ultimately any SBML-compatible solver/analysis package) for direct comparison to experimental data. Most ProcessDB modeling projects have involved protein dynamics in living cells followed using GFP fusion proteins (e.g. secretory pathway, chromatin proteins, antigen processing), but ProcessDB has also been used in studies of the MLCK/MLCP signaling cascade as well as a recent study of human folate metabolism. Development is supported by a Phase II SBIR grant from the US National Institutes of Health.
Bin Hu E-CELL E-CELL supports multi-algorithm simulation. ODE and stochastic can coexist simutaneously in one model. Most people use it for metabolic pathway simulation. Some people use it for singal transduction simulation. Also a few people are using it for both purposes.
Naoki Tanimura CellDesigner A graphical tool to model detailed pathways of gene regulation, signal transduction, and metabolism with description about modification and interaction of proteins.
Akira Funahashi CellDesigner, KEGG2SBML CellDesigner: Biochemical network editor KEGG2SBML: Converter which converts KEGG metabolic pathway to SBML
John J. Salama Biomolecular Interaction Network Database (BIND) BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. The BIND database is accessible through a web interface at http://bind.ca, as well as through a SOAP API at http://soap.bind.ca.
Stephanie Taylor BioSens BioSens performs sensitivity analysis on ODE models. It accepts SBML level 2. At some point in the future, we plan to create tools for performing stochastic sensitivity analysis as well.
Karthik Raman PathwayAnalyser PathwayAnalyser is a command-line tool, basically for performing Flux Balance Analysis (FBA) and systematic gene deletion studies for a reaction system. It also can interface with the Taylor program (http://www.ma.utexas.edu/~mzou/taylor/) for high-precision simulation. The program currently parses a reaction list and writes out an SBML file, as well as reports gene deletion analysis and allows simulation using Taylor. The program essentially handles only metabolic models. More support for SBML is intended. It is also desired to incorporate flux annotations into SBML output. MOMA for perturbation analysis will also be incorporated in future. A GUI will also be developed. Intended uses are FBA, MOMA, perturbation analysis and high-precision simulation of pathways.
Henning Schmidt MATLAB Systems Biology Toolbox The toolbox allows simulation and analysis of ODE based models of biochemical systems. Supported analysis methods are bifurcation analysis, parameter sensitivity analysis, etc. Coming methods are methods for parameter identification, metabolic control analysis, network identification, handling and analysis of measurement data, and capabilities for in-silico experiments. Models can be build by importing SBML models (algebraic rules, events, and the 'piecewise' operator are not supported yet), textual description of a model in a certain toolbox-own format, and by command line commands. Basic export functionality from the toolbox' model representation to SBML is implemented. The toolbox can be used for the simulation and analysis of a great variety of biochemical models and is not limited to a certain type of model (as long as it is possible to describe the system by ODEs).
Christoph Flamm SBML ODE Solver, libSBML Perl bindings The SBML ODE Solver is a command-line oriented tool and programming library for construction and numerical integration of a system of ordinary differential equations (ODE) from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI C, provides bindings for a variety of scripting languages and is currently distributed under the GPL license. The package uses the libSBML for parsing SBML models and construction of ODE systems, and CVODE for numerical integration. Optional data visualization modules based on XMGrace and Graphviz allow a quick inspection of the model's structure and dynamics, providing a low-level interface to SBML models, which is especially useful for education purposes. The SBML ODE Solver offers itself both as a stand-alone tool and as a simple and reliable programming library, that provides a powerful platform-independent integration back-end for higher-level SBML analysis or visualization tools. Thus the SBML ODE Solver is targeted at biomathematicians, 'command-line friendly' biochemists and biologists, and at application developers, respectively. As SBML is able to represent not only reaction networks but arbitrary ODE systems, the tool can be considered as a general ODE solver, or as an interface to the established and well tested CVODE environment for solving non-stiff and stiff ODE systems.
Ralph Gauges SBML layout extension It implements the proposed layout extension on top of libsbml. (For the proposal see http://projects.eml.org/bcb/sbml/) The extension allows programs to store information about the layout of the biochemical networks within SBML files.
Brett Olivier PySCeS, JWS Online Both PySCeS (http://pysces.sourceforge.net) and JWS Online (http://jjj.biochem.sun.ac.za) are ODE based modelling applications that can be used to analyse and model cellular and metabolic systems. PySCeS is a Python, console based, interactive modelling environment which (amongst other things): - calculates time simulations - solves for steady states - performs metabolic control analysis - does parameter continuation - calculates elementary modes - reads/writes SBML level 2 JWS Online is a Mathematica based, online, interactive repository of models which currently: - calculates time simulations - solves for steady states - performs metabolic control analysis
Sven Sahle copasi, sbml layout extension general tool for modeling, simulation (ODE and stochastic) and analysis of biochemical reaction networks. See www.copasi.org
Nicolas Rodriguez SBMLeditor Editing of SBML files any level.
Wayne Rindone BioSPICE debugging the bug use case SBML is used to store and communicate flux balance metabolic networks between tools that help make the model complete and accurate and tools that produce the flux analysis predictions. The tools for preparing, performing, and displaying the predictions use special flux annotations.
Colin Gillespie BASIS BASIS is currently a web-service based modelling system. Software already developed include a stochastic simulator (in C) and various bits and pieces in Python (eg visualisation, swig interface to the simulator,...)
Zheng Li TERANODE Design Suite Currently support ODE models. Visual modeling environment. Import and export support for SBML. Import of KEGG pathway models. Export to MATLAB format.
Jan Cerveny Systems Biology of Photosynthesis in Dynamic Light Environment We construct a web-based platform for modeling and reverse engineering of photosynthetic reactions and regulations in a dynamic light environment. Detailed knowledge of photosynthetic rate constants allows formulation of ODE system that reflects accurately primary photosynthetic processes. Current modeling effort focuses on regulatory feedbacks that are largely unknown. In contrast to many other biological systems, photosynthetic processes can be monitored accurately and non-invasively by optical techniques, leading to an effective verification of newly proposed regulatory motifs. We anticipate that the regulatory motifs found and confirmed in photosynthesis will be relevant also in other biological systems operating in a dynamic environment and requiring a rapid response.
Rainer Machne SBML ODE Solver, libSBML Perl bindings The SBML ODE Solver is a command-line oriented tool and programming library for construction and numerical integration of a system of ordinary differential equations (ODE) from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI C, provides bindings for a variety of scripting languages and is currently distributed under the GPL license. The package uses the libSBML for parsing SBML models and construction of ODE systems, and CVODE for numerical integration. Optional data visualization modules based on XMGrace and Graphviz allow a quick inspection of the model's structure and dynamics, providing a low-level interface to SBML models, which is especially useful for education purposes. The SBML ODE Solver offers itself both as a stand-alone tool and as a simple and reliable programming library, that provides a powerful platform-independent integration back-end for higher-level SBML analysis or visualization tools. Thus the SBML ODE Solver is targeted at biomathematicians, 'command-line friendly' biochemists and biologists, and at application developers, respectively. As SBML is able to represent not only reaction networks but arbitrary ODE systems, the tool can be considered as a general ODE solver, or as an interface to the established and well tested CVODE environment for solving non-stiff and stiff ODE systems.
Bruce Shapiro MathSBML MathSBML is a full-featured package for using SBML in Mathematica. It includes facilities for reading, simulating, writing, manipulating and translating SBML models.
Michael Blinov BioNetGen BioNetGen is a software for generating mathematical models that account for the full spectrum of molecular species implied by user-specified activities, potential modifications and interactions of the domains of signaling molecules. BioNetGen exports model in SBML, and we would like to achieve the full compatibility of exported SBML files with tools that can import SBML. Tyically, models generated with BioNetGen are very large, accounting for many thousands of species and reactions. SBML file for such system takes several MB's of disk space. Thus, exported files can can be used by other tools to verify handling of very large SBML files.
Fedor Kolpakov BioUML BioUML is open source extensible Java workbench for visual modeling of biological systems (http://www.biouml.org). Content of databases on biological pathways, SBML and CellML models can be expressed in terms of the BioUML meta model and visualized by the workbench. BioUML workbench completely supports SBML level 1 and 2. It provides two alternative simulation engines that passed 100% SBML semantic tests (http://www.biouml.org/sbml_tests/overview.html) : 1) Java simulation engine - automatically generates and compiles Java code. For simulation we have adopted odeToJava library that provides solvers both for stiff and non-stiff models. For solving algebraic equations Newton solver is used. 2) MATLAB simulation engine automatically generates code for MATLAB and invokes MATLAB engine to simulate a model behavior. Code generators support events, delays, rules, algebraic rules and piecewise functions so the generated code is not trivial. Plug-in based architecture (Eclipse plug-in runtime is used, http://www.eclipse.org) provides the workbench extensibility and possibility of seamless integration with other tools (MATLAB, SBW, GinSIM, JavaScript). The module concept allows developers to incorporate their databases into the workbench. There are modules for GeneNet, TRANSPATH and KEGG/pathways databases. BioUML technology is also used for development of new database - Biopath (code name, http://biopath.biouml.org), now it contains about 200 diagrams on biological pathways and about 20 cell cycle models.
Cliff Shaffer, Nick Allen, Ranjit Randhawa JigCell Because the cell cycle underlies the growth, development, and reproduction of all living organisms, knowledge about its control is central to cell biology and has potential applications in the health care and pharmaceutical industries. We want to develop novel, computational tools, with user-friendly interfaces, for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular. Our primary results are of two types. We create and distribute models of the cell cycle. And we create and distribute software that supports modelers of biochemical reaction pathways. Our tools (JigCell) currently include a model builder, run manager, comparator, and automatic parameter estimator. We hope to soon add a numerical bifurcation analysis package. Our team provides a unique synergy between biologists and computer scientists. Our philosophy is that this synergy is an important driver for advancing the state-of-the-art in systems biology. By creating advanced software tools, computer scientists can help biologists to become more productive. By having the computer scientists work directly with practicing biology modelers, the biologists can guide the computer scientists to write software that is worthwhile.
Frank Bergmann SBW The Systems Biology Workbench (SBW) provides a framework that allows to loosely couple applications of different domain. This combination happens dynamically and seamlessly at the runtime of the different applications. For example simulators can be incorporated into model designers as demonstrated by Jarnac / JDesigner (reference OMICS paper). SBW provides application developers with binding libraries for a large variety of programming languages: C/C++, Delphi, and Java to name just a few of them. A new binding library is also in a test phase that allows every .NET language access to SBW. And so SBW actively encourages code-reuse. Instead of porting whole applications towards a new programming language, the programmer just implements a few calls to SBW to access/provide the desired functionality.

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