Cytoscape 3.7.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.7.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

PPIevo – Protein-protein Interaction Prediction from PSSM based Evolutionary Information

PPIevo

:: DESCRIPTION

PPIevo is a software of protein-protein interaction prediction from PSSM based evolutionary information

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

PPIevo

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 PPIevo

:: MORE INFORMATION

Citation:

Genomics. 2013 Oct;102(4):237-42. doi: 10.1016/j.ygeno.2013.05.006. Epub 2013 Jun 6.
PPIevo: protein-protein interaction prediction from PSSM based evolutionary information.
Zahiri J1, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A.

Paintomics 3 v0.4.5 – Painting Omics Data in Biological Pathways

Paintomics 3 v0.4.5

:: DESCRIPTION

 Paintomics is a web tool for the integration and visualization of transcriptomics and metabolomics data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):137-9. Epub 2010 Nov 23.
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
García-Alcalde F, García-López F, Dopazo J, Conesa A.

Predictionet 1.28.0 – Inference for Predictive Networks designed for Genomic data

Predictionet 1.28.0

:: DESCRIPTION

Predictionet contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

  Predictionet

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jan;40(Database issue):D866-75. doi: 10.1093/nar/gkr1050. Epub 2011 Nov 16.
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Haibe-Kains B1, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J.

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.

Blast2GO 5.2 – Functional Annotation Tool

Blast2GO 5.2

:: DESCRIPTION

Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Blast2GO

:: MORE INFORMATION

Citation

A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles.
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research“,
Bioinformatics, Vol. 21, September, 2005, pp. 3674-3676.

mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems

mlegp 3.1.4

:: DESCRIPTION

 mlegp (Maximum Likelihood Estimates of Gaussian Processes) is an R package to analyze computer models of complex systems.

::DEVELOPER

Bioinformatics Laboratory at Eastern Connecticut State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows / MacOsX
  • R Package

:: DOWNLOAD

 mlegp

:: MORE INFORMATION

Citation

Dancik GM, Dorman KS (2007)
mlegp: statistical analysis for computer models of biological systems using R.
Bioinformatics (2008) 24 (17): 1966-1967.

LocFuse – Human protein-protein Interaction Prediction

LocFuse

:: DESCRIPTION

LocFuse is a novel ensemble learning method of human protein-protein interaction prediction via classifier fusion using protein localization information.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 LocFuse

:: MORE INFORMATION

Citation

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.
Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A.
Genomics. 2014 Dec;104(6 Pt B):496-503. doi: 10.1016/j.ygeno.2014.10.006.

PANDA v2 / PyPanda / PandaR 1.4.2 – Passing Attributes between Networks for Data Assimilation

PANDA v2 / PyPanda / PandaR 1.4.2

:: DESCRIPTION

PANDA is a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast.

PandaR is an alternate implementation of PANDA in R

PyPanda is a python implementation of PANDA

::DEVELOPER

The Glass Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Python / C Compiler / R

:: DOWNLOAD

 PANDA / PyPanda / PandaR

:: MORE INFORMATION

Citation:

PLoS One. 2013 May 31;8(5):e64832. doi: 10.1371/journal.pone.0064832. Print 2013.
Passing messages between biological networks to refine predicted interactions.
Glass K1, Huttenhower C, Quackenbush J, Yuan GC.

PyPanda: a Python package for gene regulatory network reconstruction.
van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML.
Bioinformatics. 2016 Jul 10. pii: btw422.

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.