bioSDP 0.3 – Analysis of uncertain Biochemical Networks via Semidefinite Programming

bioSDP 0.3

:: DESCRIPTION

bioSDP is a Matlab Toolbox for the analysis of uncertain biochemical networks via semidefinite programming.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 bioSDP

:: MORE INFORMATION

Citation

  • Hasenauer, J.; Waldherr, S.; Wagner, K. & Allgöwer, F.: Parameter Identification, Experimental Design and Model Falsification for Biological Network Models Using Semidefinite Programming. IET Systems Biology 4:119-130, 2010.

BN++ 1.1 – Biochemical Network Library

BN++ 1.1

:: DESCRIPTION

BN++ (formerly known as ‘BioMiner’) is a software system in C++ for analyzing and visualizing complex biochemical networks and processes. BN++ was designed to simplify the implementation of tools for answering a broad range of interesting biochemical questions. BN++ is based on a new comprehensive, extensible and reusable data model capable of representing complex and diverse biochemical data in a unified fashion.

DEVELOPER

the Chair for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows  / MacOsX
  • C++ Compiler

:: DOWNLOAD

 BN++

:: MORE INFORMATION

Citation:

Küntzer J, Blum T, Gerasch A, Backes C, Hildebrandt A, Kaufmann M, Kohlbacher O, Lenhof HP:
BN++ -A Biological Information System.
J Integr Bioinformatics 2006, 3(2):34.

ParCorA – Partial Correlation Analysis for the purpose of Biochemical Network Inference

ParCorA

:: DESCRIPTION

ParCorA is a software for partial correlation analysis for the purpose of biochemical network inference from large scale observations, such as obtained with microarrays and metabolic profiling

::DEVELOPER

Mendes Research Group

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 ParCorA

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3565-74. Epub 2004 Jul 29.
Discovery of meaningful associations in genomic data using partial correlation coefficients.
de la Fuente A1, Bing N, Hoeschele I, Mendes P.

SBMLsqueezer 2.1 – Generate Kinetic Equations for Biochemical Networks

SBMLsqueezer 2.1

:: DESCRIPTION

SBMLsqueezer generates kinetic equations for biochemical networks according to context of each reaction. When used as a plugin for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information.

The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action; detailed and generalized enzyme kinetics, various types of Hill equations, S- and H-systems, and additive models for gene regulation. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.

::DEVELOPER

Dr. Andreas Dräger

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBMLsqueezer

:: MORE INFORMATION

Citation

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.
Dräger A, Hassis N, Supper J, Schröder A, Zell A.
BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

COPASI 4.33 – Biochemical Network Simulator

COPASI 4.33

:: DESCRIPTION

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.

::DEVELOPER

COPASI Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

COPASI

:: MORE INFORMATION

Citation

COPASI–a COmplex PAthway SImulator.
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U.
Bioinformatics. 2006 Dec 15;22(24):3067-74.

Methods Mol Biol. 2009;500:17-59. doi: 10.1007/978-1-59745-525-1_2.
Computational modeling of biochemical networks using COPASI.
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U.

CellDesigner 4.4.2 – Biochemical Networks Modeling Tool

CellDesigner 4.4.2

:: DESCRIPTION

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 the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).

::DEVELOPER

Systems Biology Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CellDesigner ; Tutorial

:: MORE INFORMATION

CellDesigner is free to use >> License text

Citation

BioNetCAD 1.1 – Design, Simulation and Experimental Validation of Synthetic Biochemical Networks

BioNetCAD 1.1

:: DESCRIPTION

BioNetCAD ,a CellDesigner plug-in, is a computer assisted design tool for synthetic biology.

::DEVELOPER

BioNetCAD team

:: SCREENSHOTS

BioNetCAD

:: REQUIREMENTS

:: DOWNLOAD

 BioNetCAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Rialle S1, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

SPSens 3.4 – Stochastic Parameter Sensitivity Analysis for Biochemical Networks

SPSens 3.4

:: DESCRIPTION

SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations.

::DEVELOPER

the Control Theory and Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SPSens

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):140-2. doi: 10.1093/bioinformatics/bts642. Epub 2012 Oct 25.
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks.
Sheppard PW, Rathinam M, Khammash M.

ByoDyn 5.12 – Study of Biochemical Networks within the framework of Systems Biology

ByoDyn 5.12

:: DESCRIPTION

ByoDyn is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.

::DEVELOPER

the Computational Biochemistry and Biophysics Lab at GRIB-IMIM/UPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

 ByoDyn

:: MORE INFORMATION

Citation

L. G. A. de Lomana, à. Gómez-Garrido, D. Sportouch, and J. Villà-Freixa,
Optimal Experimental Design in the Modelling of Pattern Formation,”
LNCS, vol. 5101, pp. 610-619, 2008.

Bio-PEPA Workbench 1.0 – Bench of Language for the Modelling & the Analysis of Biochemical Networks

Bio-PEPA Workbench 1.0

:: DESCRIPTION

Bio-PEPA is a language for the modelling and the analysis of biochemical networks.It is based on PEPA, a process algebra originally defined for the performance analysis of computer systems, and extends it in order to handle some features of biochemical networks, such as stoichiometry and different kinds of kinetic laws. A main feature of Bio-PEPA is the possibility to support different kinds of analysis, including stochastic simulation, analysis based on ordinary differential equations (ODEs) and model checking in PRISM.

Bio-PEPA Workbench is an implementation of Bio-PEPA which allows modellers to write models in the Bio-PEPA language and to animate them using stochastic simulation.

::DEVELOPER

Stephen Gilmore , The Centre for Systems Biology at Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bio-PEPA Workbench

:: MORE INFORMATION

Citation

F. Ciocchetta and J. Hillston.
Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks.
Theoretical Computer Science 410 (33-34), pp. 3065-3084, 2009.