PathwayExplorer 3.0.2 – Construction of Biological Pathway Diagrams

PathwayExplorer 3.0.2

:: DESCRIPTION

The PathwayExplorer is an easy to use and platform independent interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them. This novel drawing tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links. Further it is possible to map expression datasets to the pathways by using gene RefSeq ids. It is also possible to use a SOAP interface to access the pathways online.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 PathwayExplorer

:: MORE INFORMATION

Citation

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z.
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Nucleic Acids Res. 33: W633-W637 (2005)

PathJam – Biological Pathway Integration Tool

PathJam

:: DESCRIPTION

PathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists. This server integrates pathway-related annotations from several public sources (Reactome, KEGG, Biocarta, etc) making easier the understanding of gene lists of interest.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

 PathJam

:: MORE INFORMATION

Citation

Daniel Glez-Peña, Miguel Reboiro-Jato, Rubén Domínguez, Gonzalo Gómez-López, David G Pisano and Florentino Fdez-Riverola.
PathJam: a new service for integrating biological pathway information.
Journal of Integrative Bioinformatics, 7(1):147, 2010.

 

Curator tool 3.1 – Annotate Biological Pathways based on the Reactome Schema

Curator tool 3.1

:: DESCRIPTION

Curator tool is meant for use by curators to annotate biological pathways based on the Reactome schema.

::DEVELOPER

Reactome Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Curator tool

:: MORE INFORMATION

Citation

iPathways 1.2.1 – Biological Pathways on the iPhone

iPathways 1.2.1

:: DESCRIPTION

iPathways explores biological pathways on your palm. In comprehending the biological complexity of living systems in disease and healthy states, molecular pathway maps form an integral part of a researcher’s arsenal.

::DEVELOPER

The Systems Biology Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • iPhone / iPad

:: DOWNLOAD

 iPathways

:: MORE INFORMATION