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.

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.

BioPreDyn-Bench v15102014B – Dynamic Modelling in Systems Biology

BioPreDyn-Bench v15102014B

:: DESCRIPTION

BioPreDyn-bench isa suite of benchmark problems for dynamic modelling in systems biology.

::DEVELOPER

BioPreDyn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Matlab

:: DOWNLOAD

 BioPreDyn-Bench

:: MORE INFORMATION

Citation:

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.
BMC Syst Biol. 2015 Feb 20;9:8. doi: 10.1186/s12918-015-0144-4.

SBFC 1.3.7 – Systems Biology Format Converter

SBFC 1.3.7

:: DESCRIPTION

SBFC aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biolog

SBFC Online Version

::DEVELOPER

Computational Systems Neurobiology Group – Systems Biology of Neuronal Signalling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SBFC

:: MORE INFORMATION

Citation

The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N.
BMC Bioinformatics. 2016 Apr 5;17(1):154. doi: 10.1186/s12859-016-1000-2.

BioCham 3.7 – Modelling Environment for Systems Biology

BioCham 3.7

:: DESCRIPTION

BioCham (Biochemical Abstract Machine) is a modelling environment for systems biology, with some unique features for inferring unknown model parameters from temporal logic constraints.
BioCham is mainly composed of :

  • a rule-based language for modeling biochemical systems (compatible with SBML)
  • several simulators (boolean, differential, stochastic),
  • a temporal logic based language to formalize the temporal properties of a biological system and validate models with respect to such specifications,
  • unique features for developing/correcting/completing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints.

::DEVELOPER

The “Contraintes” project-team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BioCham

:: MORE INFORMATION

Citation

ioinformatics. 2006 Jul 15;22(14):1805-7. Epub 2006 May 3.
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge.
Calzone L, Fages F, Soliman S.

SB.OS 0.9 – Systems Biology Operational Software DVD ISO Image

SB.OS 0.9

:: DESCRIPTION

SB.OS is a live bootable DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software. Text and video documentation material, as well as an offline copy of the BioModels.net database, are included.

List of Systems Biology Software is as below:

  • CellDesigner 4.0.1 (including plugin SBMLsqueezer 1.3)
  • COPASI 4.5.30
  • Cytoscape 2.6.3 (including plugin BiNoM)
  • Edinburgh Pathway Editor 1.3.0
  • ISATools 1.1
  • libSBML 3.4.1
  • modelMage 1.0beta
  • OpenAlea
  • SBML2LaTeX 0.9.8
  • SBML-PET 2.3.5
  • SBMLeditor 1.3.4
  • SystemsBiologyWorkbench 2.7.10
  • semanticSBML 1.0.11
  • STSE
  • Taverna 2.1
  • vanted 1.8
  • TiDE 1.2.1
  • Xppaut 6.0

Systems Biology Models

  • BioModels Database
  • Yeast consensus model version 2.0

Convenience Tools

  • gtk-recordMyDesktop
  • XML Copy Editor 1.2.0.6

Python

  • epydoc
  • NumArray
  • NumPy
  • Python 2.5, IPython
  • PyX
  • Soappy
  • SciPy

::DEVELOPER

SB.OS TeamTheoretical BiophysicsHumboldt-Universität zu Berlin

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable DVD

:: DOWNLOAD

SB.OS

:: MORE INFORMATION

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

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

cPath2 v7 – Pathway Database Designed for Systems Biology Research

cPath2 v7

:: DESCRIPTION

cPath is an open-source data management software that runs the Pathway Commons web service.

::DEVELOPER

Computational Biology Center @ Memorial Sloan Kettering Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 cPath

:: MORE INFORMATION

Citation

Ethan G Cerami, Gary D Bader, Benjamin E Gross, and Chris Sander,
cPath: open source software for collecting, storing, and querying biological pathways
BMC Bioinformatics 2006, 7:497

SBEToolbox 1.3.2 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.2

:: DESCRIPTION

SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc…

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBEToolbox

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. eCollection 2013.
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.
Konganti K1, Wang G, Yang E, Cai JJ.