Tag: Biological Network

GEDEVO / GEDEVO-M / CytoGEDEVO 1.0.3.1 – Global Alignment of Biological Networks with Cytoscape

GEDEVO / GEDEVO-M / CytoGEDEVO 1.0.3.1

:: DESCRIPTION

GEDEVO (Graph Edit Distance + EVOlution) is a software tool for solving the network alignment problem.

GEDEVO-M is an extension of the idea implemented in GEDEVO to multiple input networks.

CytoGEDEVO is a Cytoscape plugin that implements the GEDEVO  method for pairwise global network alignment.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

CytoGEDEVO

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 GEDEVO /  GEDEVO-M / CytoGEDEVO

:: MORE INFORMATION

Citation

Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach:
GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment.
GCB 2013:68-79

CytoGEDEVO – Global alignment of biological networks with Cytoscape.
Malek M, Ibragimov R, Albrecht M, Baumbach J.
Bioinformatics. 2015 Dec 14. pii: btv732

SimBioNeT 1.2.16 – Simulator of Biological Network Topology

SimBioNeT 1.2.16

:: DESCRIPTION

SimBioNeT is a biological network topology simulator, in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired degree distribution, e.g. scale free, and a clustering coefficient constant with the number of nodes in the network, a typical characteristic of biological networks.

::DEVELOPER

Barbara Di Camillo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • R package

:: DOWNLOAD

  SimBioNeT

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2). doi: 10.1109/TCBB.2011.116. Epub 2011 Aug 18.
SimBioNeT: A Simulator of Biological Network Topology.
Di Camillo B, Falda M, Toffolo G, Cobelli C.

CentiBiN 1.4.3 – Centralities in Biological Networks

CentiBiN 1.4.3

:: DESCRIPTION

CentiBiN is an application for the calculation and visualization of centralities for biological networks.

::DEVELOPER

Bioinformatics @ IPK Gatersleben

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CentiBiN

:: MORE INFORMATION

Citation

Björn H. Junker, Dirk Koschützki and Falk Schreiber (2006):
Exploration of biological network centralities with CentiBiN.
BMC Bioinformatics, 7:219

RESQUE 1.0 – REduction-based scheme using Semi-Markov scores for networkQUEing

RESQUE 1.0

:: DESCRIPTION

RESQUE is an efficient algorithm for querying large-scale biological networks.

::DEVELOPER

Mohammad Ebrahim Sahraeian and Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python / Matlab

:: DOWNLOAD

 RRESQUE

:: MORE INFORMATION

Citation

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Bioinformatics, 28 (16): 2129-2136, 2012. doi:10.1093/bioinformatics/bts341

Cerebral 2.8.2 – Cytoscape Plugin for Layout of and Interaction with Biological Networks

Cerebral 2.8.2

:: DESCRIPTION

Cerebral (Cell Region-Based Rendering And Layout)  is a plugin for the open-source Cytoscape biomolecular interaction viewer. It uses subcellular localization and functional information to automatically generate a more pathway-like layout of a network diagram.

::DEVELOPER

The Cerebral team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Cerebral

:: MORE INFORMATION

Citation:

Barsky A, Gardy JL, Hancock REW, Munzner T.
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
Bioinformatics 2007 Apr 15;23(8):1040-2. PMID: 17309895

Medusa 3.0 – Visualization and Clustering Analysis of Biological Network

Medusa 3.0

:: DESCRIPTION

Medusa is a java standalone application for visualization and clustering analysis of biological networks in 2D. It is highly interactive and it supports weighted and multi-edged graphs where each edge between two bioentities can represent a different biological concept. Comparing to previous versions, it is currently enriched with a variety of layout and clustering methods for more intuitive visualizations. It is easy to integrate with web application since it is offered as an applet.

::DEVELOPER

Medusa Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Medusa

:: MORE INFORMATION

Citation

Medusa: a simple tool for interaction graph analysis.
Hooper SD, Bork P
Bioinformatics. 2005 Dec 15; 21(24): 4432-3. Epub 2005 Sep 27; PubMed: 16188923.

GEOMI 07 – Visual Analytic tool for Biological Networks

GEOMI 07

:: DESCRIPTION

GEOMI (Geometry for Maximum Insight) is a visual analytic tool being developed by NICTA  for the visualisation and analysis of large and complex networks such as social networks and biological networks. Such visual analytic tools involve taking advantage of the graphics capabilities of computers to support analysis of network structure.

::DEVELOPER

Joshua Ho

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  GEOMI , Source Code.

:: MORE INFORMATION