SubNet 2.0 – Subnetwork Extraction

SubNet 2.0

:: DESCRIPTION

SubNet is a Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes.

::DEVELOPER

ZDZ lab

:: SCREENSHOTS

SubNet

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java

:: DOWNLOAD

 SubNet

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2509-11. doi: 10.1093/bioinformatics/btt430. Epub 2013 Aug 13.
SubNet: a Java application for subnetwork extraction.
Lemetre C1, Zhang Q1, Zhang ZD.

capDSD – Confidence, Augmented Pathway Diffusion State Distance

capDSD

:: DESCRIPTION

capDSD is an extension of DSD  that takes in to account a measure of interaction confidence while also incorporating directed pathway data.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 capDSD

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jun 15;30(12):i219-i227. doi: 10.1093/bioinformatics/btu263.
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence.
Cao M, Pietras CM, Feng X, Doroschak KJ, Schaffner T, Park J, Zhang H, Cowen LJ, Hescott BJ.

NetGestalt / NetSAM 1.32.0 – Integrating Multidimensional Omics data over Biological Networks

NetGestalt / NetSAM 1.32.0

:: DESCRIPTION

NetGestalt is a data integration framework that allows simultaneous presentation of large-scale experimental and annotation data from various sources in the context of a biological network to facilitate data visualization, analysis, interpretation, and hypothesis generation.

NetSAM (Network Seriation and Modularization) is an R package that takes an edge-list representation of a network as an input and generates files that can be used as an input for the one-dimensional network visualization tool NetGestalt  or other network analysis.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 NetSAM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):597-8. doi: 10.1038/nmeth.2517.
NetGestalt: integrating multidimensional omics data over biological networks.
Shi Z, Wang J, Zhang B.

pathClass 0.9.4 – Classification using Biological Pathways as prior knowledge

pathClass 0.9.4

:: DESCRIPTION

pathClass is a collection of classification methods that use information about feature connectivity in a biological network as an additional source of information. This additional knowledge is incorporated into the classification a priori. Several authors have shown that this approach significantly increases the classification performance.

::DEVELOPER

pathClass team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 pathClass

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1442-3. doi: 10.1093/bioinformatics/btr157. Epub 2011 Mar 30.
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.
Johannes M1, Fröhlich H, Sültmann H, Beissbarth T.

FindPath – in silico Design of Synthetic Metabolic Pathways

FindPath

:: DESCRIPTION

FindPath is an unified system predicting and ranking the possible pathways according to their metabolic efficiency in cellular context. This tool rely on chemical reactions database to generate all possible metabolic pathways and exploits constraint-based models (CBMs) to identify the synthetic pathway that is the most effective for achieving a desired metabolic function in a given host microorganism.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • MatLab

:: DOWNLOAD

 FindPath

:: MORE INFORMATION

Citation

FindPath: A Matlab solution for in silico design of synthetic metabolic pathways.
Gilles V, Marc C, Jean-Charles P, Stéphanie H.
Bioinformatics. 2014 Jul 3. pii: btu422.

Systrip 1.0 – Investigation of Time-series data in the context of Metabolic Networks

Systrip 1.0

:: DESCRIPTION

Systrip is a visual environment for the analysis of time-series data in the context of biological networks. Systrip gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process.

::DEVELOPER

Romain Bourqui

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Systrip

:: MORE INFORMATION

Cloud-COPASI 2020 – Biochemical Simulation and Analysis using Cloud Computing

Cloud-COPASI 2020

:: DESCRIPTION

Cloud-COPASI is a web-based tool for running computationally intensive simulation and analysis tasks in parallel on a high-throughput computing pool.

::DEVELOPER

Mendes Research Group

:: REQUIREMENTS

:: DOWNLOAD

 Cloud-COPASI

:: MORE INFORMATION

MetaViz – Visualization software for Metabolic Network

MetaViz

:: DESCRIPTION

MetaViz enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways.

::DEVELOPER

Romain Bourqui

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MetaViz

:: MORE INFORMATION

Citation

Romain Bourqui , Ludovic Cottret , Vincent Lacroix , David Auber , Patrick Mary , Marie-France Sagot and Fabien Jourdan
Metabolic network visualization eliminating node redundance and preserving metabolic pathways
BMC Systems Biology 2007, 1:29doi:10.1186/1752-0509-1-29

Ometer 0.6 – Multivariate Data Analysis

Ometer 0.6

:: DESCRIPTION

Ometer is software for multivariate analysis of functional genomics and systems biology data (it can be used for other types of data, too). Ometer is driven by a plain command line interface, which allows it to be called directly from scripts.

ometer can provide:

  • correlation analysis
  • partial correlation analysis
  • principal component analysis (PCA), including biplot display
  • linear multiple discriminant analysis (MDA),
  • linear multiple discriminant analysis with genetic algorithm variable selection – 2 different algorithms (GA-DFA and GA-DFA2).
  • non-negative matrix factorization (NMF)
  • factor analysis with varimax rotation (FA)

::DEVELOPER

Mendes Research Group

:: SCREENSHOTS

Command line

:: REQUIREMENTS

  • Windows / Linux/ MacOsX

:: DOWNLOAD

Ometer

:: MORE INFORMATION

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.