PESCADOR – Extract and Analyse a Network of Gene and Protein Interactions from a set of Medline abstracts

PESCADOR

:: DESCRIPTION

PESCADOR (Platform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships) is a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva A1, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA.

HIPPIE 2.2 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 2.2

:: DESCRIPTION

HIPPIE (Human Integrated Protein-Protein Interaction rEference) is a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

HIPPIE

:: MORE INFORMATION

Citation

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH.
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH1, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.

NetPathMiner 1.22.0 – R package for Network Path Mining through Gene Expression

NetPathMiner 1.22.0

:: DESCRIPTION

NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.

::DEVELOPER

NetPathMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/MacOsX
R
BioConductor

:: DOWNLOAD

NetPathMiner

:: MORE INFORMATION

Citation

NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.
Bioinformatics. 2014 Jul 28. pii: btu501.

NetSeed – Identify the Seed sets of Networks

NetSeed

:: DESCRIPTION

NetSeed is a software package for identifying the seed sets of networks

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

NetSeed

:: MORE INFORMATION

Citation

Rogan Carr and Elhanan Borenstein (2012)
NetSeed: A network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.
Bioinformatics. doi: 10.1093/bioinformatics/btr721.

lpNet 2.18.0 – Linear Programming Model for Network Inference

lpNet 2.18.0

:: DESCRIPTION

lpNet aims at infering biological networks, in particular signaling and gene networks.

::DEVELOPER

Lars Kaderali

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R
BioConductor

:: DOWNLOAD

lpNet

:: MORE INFORMATION

Citation

lpNet: a linear programming approach to reconstruct signal transduction networks.
Matos MR, Knapp B, Kaderali L.
Bioinformatics. 2015 May 29. pii: btv327

WordCloud 3.1.3 – Cytoscape plugin to Generate a Visual Summary of a Network

WordCloud 3.1.3

:: DESCRIPTION

The WordCloud plugin is a Cytoscape plugin that generates a visual summary of a network. It displays string attributes associated with nodes in the network as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurence in a phrase can be visualized by arranging words in clusters or as a network.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java
Cytoscap

:: DOWNLOAD

WordCloud

:: MORE INFORMATION

Citation

Source Code Biol Med. 2011 Apr 7;6:7.
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.
Oesper L, Merico D, Isserlin R, Bader GD.

MCODE 1.5.1 – Cytoscape plugin that finds Clusters in a Network

MCODE 1.5.1

:: DESCRIPTION

MCODE is a Cytoscape plugin that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.

::DEVELOPER

Bader Lab

:: SCREENSHOTS