| 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.
|
