Tag: Systems Biology

3Omics – Web based Systems Biology Visualization tool

3Omics

:: DESCRIPTION

3Omics is a one-click web tool for visualizing and rapidly integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data.

::DEVELOPER

3Omics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Jul 23;7:64. doi: 10.1186/1752-0509-7-64.
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
Kuo TC1, Tian TF, Tseng YJ.

DataRail 1.3 – Analysis of High-throughput data encountered in Systems Biology

DataRail 1.3

:: DESCRIPTION

DataRail is an open source MATLAB toolbox for managing, transforming, visualizing, and modeling data, in particular the high-throughput data encountered in Systems Biology.

::DEVELOPER

Saez-Rodriguez Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 DataRail

:: MORE INFORMATION

Citation:

J. Saez-Rodriguez, A. Goldsipe, J. Muhlich, L. Alexopoulos, B. Millard, D. A. Lauffenburger, P. K. Sorger
Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail.
Bioinformatics, 24:6, 840-847 (2008)

IOCBio 1.2.2 – Open-source Software from the Laboratory of Systems Biology

IOCBio 1.2.2

:: DESCRIPTION

The IOCBio project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

IOCBio

:: MORE INFORMATION

Citation

J Microsc. 2011 Aug;243(2):124-40. doi: 10.1111/j.1365-2818.2011.03486.x. Epub 2011 Feb 15.
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images.
Laasmaa M, Vendelin M, Peterson P.

BioCham 4.5.17 – Modelling Environment for Systems Biology

BioCham 4.5.17

:: 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 1.4.1 – Systems Biology Operational Software DVD ISO Image

SB.OS 1.4.1

:: 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 Team

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable DVD

:: DOWNLOAD

SB.OS

:: MORE INFORMATION

cPath2 pc11 – Pathway Database Designed for Systems Biology Research

cPath2 pc11

:: 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

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 Biology

SBFC Online

::DEVELOPER

SBFC Team

:: 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.

SYSBIONS 04 – Nested Sampling for Systems Biology

SYSBIONS 04

:: DESCRIPTION

SYSBIONS is a computational tool for model selection and parameter inference using nested sampling.

::DEVELOPER

the Theoretical Systems Biology Group at Imperial College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SYSBIONS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 16. pii: btu675. [Epub ahead of print]
SYSBIONS: nested sampling for systems biology.
Johnson R, Kirk P, Stumpf MP.

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.

SBEAMS 0.22.1 – Systems Biology Experiment Analysis Management System

SBEAMS 0.22.1

:: DESCRIPTION

SBEAMS is a framework for collecting, storing, and accessing data produced by a wide variety of experiments. The software provides a customizable framework to meet the needs of modern systems biology research.

SBEAMS – Microarray provides MIAME-compliant Affymetrix GeneChip microarray database functionality under the SBEAMS framework.

SBEAMS-Proteomics is part of the SBEAMS (Systems Biology Experiment Analysis Management System) Project, which is a framework for collecting, storing, and accessing data produced by a variety of different experiments; these experiments can be managed separately but then correlated later under the same framework.

::DEVELOPER

SBEAMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • MySQL

:: DOWNLOAD

  SBEAMS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jun 6;7:286.
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T.