Tag: Network

CIPHER – Correlating Protein Interaction Network and Phenotype Network to predict Disease Genes

CIPHER

:: DESCRIPTION

CIPHER, which stands for Correlating interactome and phenome networks to predict disease genes, is a computational framework we proposed to prioritize human disease genes. It was one of the first studies to explore interactome-phenome wide gene-disease relationships, and generated the first comprehensive genetic landscape of human disease,connecting 5080 human disease phenotypes with 14433 human genes.

::DEVELOPER

Wu Lab @ Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

NO

 :: MORE INFORMATION

Citation:

Mol Syst Biol. 2008;4:189. doi: 10.1038/msb.2008.27. Epub 2008 May 6.
Network-based global inference of human disease genes.
Wu X1, Jiang R, Zhang MQ, Li S.

GeneStitch 1.2.1 – Network Matching Algorithm to Gene Assembly

GeneStitch 1.2.1

:: DESCRIPTION

GeneStitch is a tool to assemble genes using network matching algorithm. Given an already-assembled dataset, it is capable of assembling contigs together to form more complete genes with the help of a reference gene set. Currently the assembly software that GeneStitch support is SOAPdenovo.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  GeneStitch

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Wu YW, Rho M, Doak TG, Ye Y.

CytoscapeRPC 1.8 – Create, Query and Modify Cytoscape Networks

CytoscapeRPC 1.8

:: DESCRIPTION

CytoscapeRPC is a Cytoscape plug-in which allows users to create, query and modify Cytoscape networks. This means that you can automate your Cytoscape tasks from any programming language which supports XML-RPC

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CytoscapeRPC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2451-2. Epub 2011 Jun 27.
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.
Bot JJ, Reinders MJ.

PIANA 1.47 – Protein Interactions And Network Analysis tool

PIANA 1.47

:: DESCRIPTION

PIANA (Protein Interactions And Network Analysis) is a software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks.

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • MySQL

:: DOWNLOAD

 PIANA

:: MORE INFORMATION

Citation

R. Aragues, D. Jaeggi and B. Oliva
“PIANA: Protein Interactions and Network Analysis”
Bioinformatics. 2006 Apr 15;22(8):1015-7 (2006)

PSN – Protein Pocket Similarity Networks

PSN

:: DESCRIPTION

the PSN (Pocket Similarity Networks) is a software to describe the similarity among these pockets with different thresholds, which are the measurements of the similarity. In order to explore the relationship between the pocket similarity and the GO terms similarity, we statistics the percentage of proteins with similar pockets corresponding to identical GO terms and semantic similarity of the GO functions. Then, the topology structure of the network is used to predict functions. The closest neighbors of pocket and the connected components of the networks would be used to predict a target protein’s functions (GO terms) by a scoring scheme. We test the performance of the method by cross-validated experiments on large scale proteins come from different families. We also predicted the GO functions of some un-annotated proteins.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PSN

:: MORE INFORMATION

Citation

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, and Xiang-Sun Zhang.
Predicting gene ontology functions from protein’s regional surface structures.
BMC Bioinformatics, Vol. 8, 475, 2007

IBRENA 1.0 – In silico Biochemical Reaction Network Analysis

IBRENA 1.0

:: DESCRIPTION

IBRENA (Insilico Biochemical REaction Network Analysis) is a software to aid the analysis of complex biological reaction networks. In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis.

::DEVELOPER

Sriram Neelamegham 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 IBRENA

:: MORE INFORMATION

Citation

Liu, G. and S. Neelamegham,
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks.
Bioinformatics (2008) 24 (8): 1109-1111.

 

JNets 1.0 – Visualise, Manipulate and Analyze Networks by Overlaying Annotation

JNets 1.0

:: DESCRIPTION

JNets is a network visualization and analysis tool. JNets was primarily designed for visualizing and analyzing protein interaction networks, but is flexible enough to be used for any type of network. JNets is available as a stand alone application or an applet. Using the applet, interactive networks can be deployed from web pages.

::DEVELOPER

Jamie MacPherson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 JNets 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Mar 26;10:95.
JNets: exploring networks by integrating annotation.
Macpherson JI, Pinney JW, Robertson DL.

NePhe 1.0 – Network RNAi Phenotype Score

NePhe 1.0

:: DESCRIPTION

NePhe （Network RNAi Phenotype） is intended to implement a network-based integrative approach to prioritize reliable hits in genome-wide screens

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NePhe

:: MORE INFORMATION

Citation

Wang L, Tu Z, Sun FZ (2009)
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.
BMC Genomics 10:220.

EM-NM – Network Motif Identification in Stochastic Networks

EM-NM

:: DESCRIPTION

EM-NM is intended to implement the methodology for network motif identification in stochastic networks.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 EM-NM

:: MORE INFORMATION

Citation

Rui Jiang, Zhidong Tu, Ting Chen, and Fengzhu Sun.
Network Motif Identification in Stochastic Networks
Proc. Natl. Acad. Sci. USA, Vol.103, No.25, 9404~9409, 2006.