Tag: Systems Biology

SBW 2.12.2 – Systems Biology Workbench

SBW 2.12.2

:: DESCRIPTION

SBW ( Systems Biology Workbench), is an open source framework connecting heterogeneous software applications.

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to communicate and use each others’ capabilities via a fast binary encoded-message system.

SBW goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.

::DEVELOPER

Sauro Lab at University of Washington

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX/Linux

:: DOWNLOAD

SBW

:: MORE INFORMATION

Citation

Sauro, Hucka, Finney, Wellock, Bolouri, Doyle, Kitano.
“Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.”
OMICS. 2003 Winter;7(4):355-72.

DOTcvpSB 2010_E4 – Matlab Toolbox for Dynamic Optimization in Systems Biology

DOTcvpSB 2010_E4

:: DESCRIPTION

DOTcvpSB is a software toolbox which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 DOTcvpSB

:: MORE INFORMATION

Citation:

T. Hirmajer, E. Balsa-Canto and J. R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinformatics 2009, 10:199

SensSB 20120926 – Development and Sensitivity Analysis of Systems Biology Models

SensSB 20120926

:: DESCRIPTION

SensSB (Sensitivity Analysis for Systems Biology) is an easy to use, MATLAB-based software toolbox, which integrates several local and global sensitivity methods that can be applied to a wide variety of biological models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

SensSB

:: MORE INFORMATION

Citation:

M. Rodriguez-Fernandez and J. R. Banga (2010)
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.
Bioinformatics 26(13):1675-1676

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1 – Systems Biology Library for R

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1

:: DESCRIPTION

The package SyBiL is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks.

The R-package sybilSBML provides support for models written in SBML format.

The R-package sybilFCF computes extreme pathways and coupled reaction sets.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SyBiL / sybilSBML  / sybilFCF

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Nov 13;7:125. doi: 10.1186/1752-0509-7-125.
Sybil–efficient constraint-based modelling in R.
Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ.

Facile 0.53 – Network Compiler for Systems Biology

Facile 0.53

:: DESCRIPTION

Facile was created to automate this process of translating a system of chemical equations into a machine readable form. Starting from a simple textual description of the biochemical system, Facile can generate simulation and analysis scripts for Mathematica, Matlab, XPP, EasyStoch, AUTO and Maple.

::DEVELOPER

CENTRE for SYSTEMS BIOLOGY at EDINBURGH

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Facile ; Manual

:: MORE INFORMATION

Citation:

Facile: a command-line network compiler for systems biology ,Siso-Nadal et al., BMC Syst Biol 1 (2007) 36

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.

Cell Illustrator 5.0 – Platform for Systems Biology

Cell Illustrator 5.0

:: DESCRIPTION

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

DEVELOPER

Human Genome Center, Institute of Medical Science, The University of Tokyo

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java

:: DOWNLOAD

 Cell Illustrator

:: MORE INFORMATION

Citation

Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S,
Cell Illustrator 4.0: A computational platform for systems biology,
In Silico Biol, 2010; 10:0002