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

GEMSiRV 20130911 – GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization

GEMSiRV 20130911

:: DESCRIPTION

GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

GEMSiRV

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GEMSiRV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.

DomainGraph 3.01 – Cytoscape Plugin of Analysis and Visualization of Molecular Interaction Networks

DomainGraph 3.01

:: DESCRIPTION

DomainGraph is the successor tool of DomainNetworkBuilder and works as Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin decomposes protein networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using Affymetrix GeneChip microarrays, which supports the analysis of alternative splicing events and the characterization of their effects on protein and domain interaction networks.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  DomainGraph

:: MORE INFORMATION

Citation:

Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, BR., Albrecht, M. (2010)
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic Acids Res. 2010 July 1; 38

GIPro 1.0 – Visualization of High-throughput Genetic and Physical Interaction data

GIPro 1.0

:: DESCRIPTION

GIPro is a Cytoscape plugin developed to allow integrative analysis and visualization of high-throughput genetic and physical interaction data in the context of protein complexes.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GIPro

:: MORE INFORMATION

MSAVis – Multiple Sequence Alignment Visualization system

MSAVis

:: DESCRIPTION

MSAVis is a multiple sequence alignment visualization system that integrates the display of conserved domain data.

:: DEVELOPER

AgBase

:: SCREENSHOTS

MSAVis

:: REQUIREMENTS

  • Windows /Linux/MacOsX
  • Python
  • BioPython
  • wxPython
  • NumPy
  • PyOpenGL

:: DOWNLOAD

 MSAVis

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S7. doi: 10.1186/1471-2105-10-S11-S7.
Exploratory visual analysis of conserved domains on multiple sequence alignments.
Jankun-Kelly TJ, Lindeman AD, Bridges SM.

PACVr 0.9.4 – Plastome Assembly Coverage Visualization in R

PACVr 0.9.4

:: DESCRIPTION

PACVr visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes.

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • R

:: DOWNLOAD

PACVr

:: MORE INFORMATION

Citation

Gruenstaeudl M, Jenke N.
PACVr: plastome assembly coverage visualization in R.
BMC Bioinformatics. 2020 May 24;21(1):207. doi: 10.1186/s12859-020-3475-0. PMID: 32448146; PMCID: PMC7245912.

MarVis Suite 2.0 – Clustering & Visualization of Metabolomic Markers

MarVis Suite 2.0

:: DESCRIPTION

MarVis (Marker Visualization) is designed for intensity-based clustering and visualization of large sets of metabolomic markers.The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

MarVis

:: MORE INFORMATION

Citation

Kaever A, Lingner T, Feussner K, G?bel C, Feussner I, Meinicke P:
MarVis: a tool for clustering and visualization of metabolic biomarkers.
BMC Bioinformatics 2009, 10:92.

miRseqViewer 1.0 – Visualization of Sequence, Structure and Expression for Analysis of microRNA Sequencing data

miRseqViewer 1.0

:: DESCRIPTION

miRseqViewer is a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows.

::DEVELOPER

miRseqViewer team

:: SCREENSHOTS

miRseqViewer

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 miRseqViewer

:: MORE INFORMATION

Citation

miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.
Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S.
Bioinformatics. 2014 Oct 15. pii: btu676.

RINalyzer 2.0 – Cytoscape plugin of Visualization and Analysis of Biomolecular Networks

RINalyzer 2.0

:: DESCRIPTION

RINalyzer is a Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin allows the simultaneous visualization and interactive analysis of residue interaction networks (RINs) together with the corresponding 3D protein structures displayed in UCSF Chimera. It also provides a comprehensive set of topological centrality measures to gain additional insights into the structural and functional role of interacting residues.

::DEVELOPER

RINalyzer team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 RINalyzer

:: MORE INFORMATION

Citation:

Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011):
Analyzing and visualizing residue networks of protein structures.
Trends in Biochemical Sciences, 36(4): 179-182.

LocusZoom 1.3 – Visualization of Genome-wide Association Scan Result

LocusZoom 1.3

:: DESCRIPTION

LocusZoom is a tool to plot regional association results from genome-wide association scans or candidate gene studies.Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LocusZoom

:: MORE INFORMATION

Citation

Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ.
LocusZoom: regional visualization of genome-wide association scan results
Bioinformatics (2010) 26 (18): 2336-2337.