Category: System Biology & Modeling

SigTran 3.0.4 – Cell Signaling Simulation Software

SigTran 3.0.4

:: DESCRIPTION

SigTran is a modeling environment especially designed to enable biological researchers to carry out large scale simulations and analysis of complex signal transduction networks. SigTran is being used by the UW/CSI modeling team to aid in their systems biology research into T cell signal tranduction events.

SigTran has incorporated some of the latest developments in the field of stochastic simulation of biological networks. Some of these major developments include the Firth-Bray algorithm with molecular complexes treated as software objects with multistate functionality , Shimizu’s work on spatial organization of cell signaling pathways and the algorithmic enhancements of Gibson and others to the Gillespie algorithm.

::DEVELOPER

The Cell Systems Initiative

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

SigTran

:: MORE INFORMATION

SigTran is freely available for downloading and testing. Questions and comments should be directed to the Modeling Group at Cell Systems Initiative modeling@cellsystems.org.

BALSA – Cell Systems Modeling Environment

BALSA

:: DESCRIPTION

BALSA (Biological Abstraction Layer for Simulation Analysis) is a prototype cell systems modeling environment written in Java.

features:

  • a Bioglyphics software editor
  • a Bioglyphics to SBML compiler
  • automated cartoon generation
  • seamless integration with SigTran for SBML models

::DEVELOPER

The Cell Systems Initiative

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • Java

:: DOWNLOAD

please contact:Paul Loriaux (ploriaux@washington.edu )

:: MORE INFORMATION

PRESENTATIONS

modelMaGe 1.0 beta – Automatic Model Management & Generation

modelMaGe 1.0 beta

:: DESCRIPTION

modelMaGe is a computational tool for automatic model management and generation. It can help you to create and manage different versions of a model you are working on. One of the main advantages is that the user only has to specify one single model structure and a set of directives that detail the family of candidate models.

  • automatically generates SBML or Copasi candidate models by removing specified model components from a given master model,
  • automatically documents candidate models,
  • automatically fits candidate models to data using CopasiSE,
  • provides a ranking of candidate models fits based on the AIC.

::DEVELOPER

modelMaGe Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

modelMaGe ; Manual

:: MORE INFORMATION

modelMaGe web version.

modelMaGe is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version.

Citation:

Moleculizer 1.1.3 – Cellular Reaction Network Stochastic Simulator

Moleculizer 1.1.3

:: DESCRIPTION

Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.It was designed to enable a researcher to simulate the behavior of intracellular signaling systems over time and in response to defined perturbations. The outcomes of the simulations can then be tested experimentally.  A unique feature of Moleculizer is that it generates species and reactions, as they are needed. This ‘on- the-fly’ mode saves time by increasing computational speed and reducing manual input by the researcher. Moleculizer uses Monte Carlo methods to simulate the reactions. Moleculizer models can be exported as SBML files that can be subsequently imported into other modeling and simulation software such as ECell.

::DEVELOPER

Larry Lok

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Moleculizer

:: MORE INFORMATION

Moleculizer is available to the public under the Lesser GNU Public License.

References:
Lok, L and Brent, R.   Automatic generation of cellular reaction networks with Moleculizer 1.0. Nature Biotechnology, 1:131-136 (2005).

HillSim 1.0 – Signaling System Analyzer

HillSim 1.0

:: DESCRIPTION

HillSim is a computer program for analyzing and optimizing signaling system models.  HillSim analyzes and optimizes models of biological signaling networks. An input, nodes, and arrows comprise signaling system models: the input is typically some extra-cellular chemical, such as the alpha-factor pheromone for the yeast pheromone response system; nodes typically represent signaling proteins, and have activities that can vary from fully inactive to fully active; and arrows create causal links between the nodes so that signaling proteins can activate or inactivate each other.  Arbitrarily complex network topologies can be modeled, including those with feedbacks, feedforwards, or arrows that multiply the activities of multiple nodes.

::DEVELOPER

Steve Andrews

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

HillSim for Mac/Linux ; for Win

:: MORE INFORMATION

Citation:

Andrews, Steven S., Yu, Richard. C., and Brent, Roger.  (2008).  Cell signaling dose response alignment may arise from cooperativity or pull-up/pull-down mechanisms.  Molecular Systems Biology, submitted.

STOCHSIM 1.4 – Stochastic Simulator for Biochemical Reactions

STOCHSIM 1.4

:: DESCRIPTION

STOCHSIM is a stochastic simulator for (bio)chemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. In STOCHSIM simple two-dimensional spatial structures have been implemented, in which nearest-neighbour interactions of molecules can be simulated.

STOCHSIM provides a general purpose biochemical simulator in which individual molecules or molecular complexes are represented as individual software objects. Reactions between molecules occur stochastically, according to probabilities derived from known rate constants. An important feature of the program is its ability to represent multiple post-translational modifications and conformational states of protein molecules.

::DEVELOPER

Bray Group: Computer Models of Bacterial Chemotaxis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Perl/Tk

:: DOWNLOAD

STOCHSIM

:: MORE INFORMATION

Complementary information about the program is available on the website of Nicolas Le Novère .

BCT 4.4 – Bacterial Chemotaxis Modelling & Simulator

BCT 4.4

:: DESCRIPTION

BCT is a text-based, deterministic simulator of the chemotaxis signal transduction pathway in E. coli. The BCT (bacterial chemotaxis) model is built from units representing the molecular components in the pathway, almost all of which can be assigned experimentally determined intracellular concentrations and enzymatic rate or binding constants.

::DEVELOPER

Bray Group: Computer Models of Bacterial Chemotaxis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

BCT

:: MORE INFORMATION

N/A

SME 1.8 – Sigmoid Model Explorer

SME 1.8

:: DESCRIPTION

SME (Sigmoid Model Explorer) is a Graphical User Interface of the Sigmoid Project. It is a front end that provides access to the web services of the pathway databases and Cellerator, the module responsible for simulations. Some of SME’s features are:

  • Query and retrieval of Cellerator Models in Sigmoid Database via web service
  • Graphical view of Cellerator Models with customizable icons
  • Custom selection and editing of model parameters
  • Remote simulation of customized models in Cellerator via web service

::DEVELOPER

SME Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SME

:: MORE INFORMATION

Register to become a SIGMOID user.

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net

KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML

KEGG2SBML 1.5.0

:: DESCRIPTION

KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML’s capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.

::DEVELOPER

Akiya Jouraku, Nobuyuki Ohta and Akira Funahashi , Dept. of Biosciences and Informatics at Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

KEGG2SBML

:: MORE INFORMATION

Citations

  1. Converting KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).
  2. Converting the KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    5th International Conference on Systems Biology (ICSB 2004), October, 2004.

KEGG2SBML License