MetDraw 1.0.0 – Automated Metabolic Maps and Data Visualization

MetDraw 1.0.0

:: DESCRIPTION

MetDraw creates visualizations of genome-scale, metabolic models. These “reaction maps” can be used to visualize high-throughput expression data using the companion program MetColor.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 MetDraw

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1327-8. doi: 10.1093/bioinformatics/btt758. Epub 2014 Jan 9.
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Jensen PA1, Papin JA.

BRAGI 20091106 – A Protein Visualization and Modeling Program

BRAGI 20091106

:: DESCRIPTION

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs.

::DEVELOPER

BRAGI Team

:: SCREENSHOTS

BRAGI

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 BRAGI

:: MORE INFORMATION

Citation

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW.
Bioinformatics. 2005 Apr 1;21(7):1291-3. Epub 2004 Nov 16.

PaVESy 20060803 – Pathway Visualization Editing System

PaVESy 20060803

:: DESCRIPTION

 PaVESy allows user-driven, interactive creation and visualization of pathway maps.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 PaVESy

:: MORE INFORMATION

Citation

A. Luedemann, D. Weicht, J. Selbig, J. Kopka (2004)
PaVESy: Pathway Visualization and Editing System.
Bioinformatics 2004 20(16): 2841-2844

ProteinVR 1.0.3 – Browser-based, virtual-reality visualization of Molecular Structures

ProteinVR 1.0.3

:: DESCRIPTION

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ProteinVR

:: MORE INFORMATION

 

VANESA 0.3 – Visualization and Analysis of Networks in System Biology

VANESA 0.3

:: DESCRIPTION

VANESA is a software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

VANESA

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 VANESA

:: MORE INFORMATION

Citation

VANESA – a software application for the visualization and analysis of networks in system biology applications.
Brinkrolf C, Janowski SJ, Kormeier B, Lewinski M, Hippe K, Borck D, Hofestädt R.
J Integr Bioinform. 2014 Jun 23;11(2):239. doi: 10.2390/biecoll-jib-2014-239.

MembraneEditor 2.2.2_2 – Modeling, Visualization and Analysis of PDB-based Membranes

MembraneEditor 2.2.2_2

:: DESCRIPTION

The CELLmicrocosmos MembraneEditor (CmME) interactively generates heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

MembraneEditor

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MembraneEditor

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 May 23;51(5):1165-82. doi: 10.1021/ci1003619. Epub 2011 Apr 19.
CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.
Sommer B1, Dingersen T, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz KJ.

Eyediagram – Visualization Probabilistic Decompositions

Eyediagram

:: DESCRIPTION

The eyediagram visualization can be used to illustrate associations between entities, as found by probabilistic component models, such as topic models.

::DEVELOPER

Probabilistic Machine Learning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

 Eyediagram

:: MORE INFORMATION

Citation

Probabilistic retrieval and visualization of biologically relevant microarray experiments
José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma and Samuel Kaski
Bioinformatics (2009) 25 (12): i145-i153.

gseaLda – Probabilistic Retrieval and Visualization of Biologically Relevant Microarray Experiments

gseaLda

:: DESCRIPTION

gseaLda is a r package for probabilistic retrieval and visualization of biologically relevant microarray experiments

::DEVELOPER

Probabilistic Machine Learning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

 gseaLda

:: MORE INFORMATION

Citation

Probabilistic retrieval and visualization of biologically relevant microarray experiments
José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma and Samuel Kaski
Bioinformatics (2009) 25 (12): i145-i153.

Haploview 4.2 – Analysis & Visualization of LD & Haplotype Maps

Haploview 4.2

:: DESCRIPTION

Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.

::DEVELOPER

The Analytic and Translational Genetics Unit(AUGT),The Broad Institute,

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Haploview

:: MORE INFORMATION

Citation

Barrett JC, Fry B, Maller J, Daly MJ.
Haploview: analysis and visualization of LD and haplotype maps.
Bioinformatics. 2005 Jan 15 [PubMed ID: 15297300]

RuleBender 2.3 – Biological Rule-based Modeling, Simulation, and Visualization

RuleBender 2.3

:: DESCRIPTION

RuleBender is a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry.

::DEVELOPER

RuleBender team

:: SCREENSHOTS

RuleBender

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 RuleBender

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012;13 Suppl 8:S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.
Smith AM1, Xu W, Sun Y, Faeder JR, Marai GE.