Polar Mapper Overview

Polar Mapper is an open source graphical software tool suited for exposing the architecture of protein interaction networks. It further allows the superposition of mRNA expression data on the networks. In general, display of any type of binary interaction data is possible with this package.

Polar Mapper is implemented in Java for multi-platform compatibility and integrates the Polar Map algorithm (Valente, 2006) to generate visual representations of protein interaction networks. Protein nodes are displayed in a circular structured graph according to their radial and angular coordinates, whose values rely on the calculation of a betweeness centrality measure (Freeman, 1977) and the assessment of the modular structure of the network (Clauset, 2004), respectively.

The article introducing the Polar Mapper software is:

Joana P. Gonçalves, Mário Grãos and André X. C. N. Valente
Polar Mapper: computational tool for integrated visualization of protein interaction networks and mRNA expression data
Journal of the Royal Society Interface, 6(39):881-896, October 2009
[abstract] [full text] [pdf] [supp. material] [bibTeX] doi:10.1098/rsif.2008.0407

News and Updates

2008/11/28 - The article describing the Polar Mapper software was published online ahead of print ([abstract] [full text] [pdf] [supp. material] [bibTeX] doi:10.1098/rsif.2008.0407).
2008/11/04 - The article entitled "Polar Mapper: computational tool for integrated visualization of protein interaction networks and mRNA expression data" was accepted for publication in the Journal of the Royal Society Interface.
2008/08/28 - Polar Mapper poster @ ICSB 2008 (The 9th International Conference on Systems Biology), Gothenburg, Sweden, August 22-28, 2008 [abstract book]
2008/07/10 - Polar Mapper poster @ FPBC 2008 (First Portuguese Forum in Computational Biology), Oeiras, Portugal, July 10-12, 2008 [abstract] [pdf] [png]
2008/05/14 - Polar Mapper is made available online here.

Polar Mapper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. Polar Mapper is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. A copy of the GNU General Public License is included with Polar Mapper. For detailed information about the license, see GNU licenses.

Download Polar Mapper binaries.

Multi-platform
    Polar Mapper version 1.0 [jar]

Windows installer
    Polar Mapper version 1.0 [exe]

 

Download Polar Mapper source code.

Source code
    Polar Mapper version 1.0 [zip] [tar.gz]

Third-party libraries
    Libraries [zip] [tar.gz]

 

Download sample files.

    Interactions, expression and sizes [zip] [tar.gz]

Known problems or issues.

Polar Mapper Documentation.

Tutorial
    Polar Mapper Quick Guide version 1.0 [pdf]

Javadoc
   Polar Mapper Javadoc version 1.0 [html] [zip] [tar.gz]

Credits

 

Joana P. Gonçalves [website]

Researcher, Knowledge Discovery and Bioinformatics group (KDBIO), Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa (INESC-ID), Lisbon, Portugal.
PhD student, Instituto Superior Técnico (IST), Technical University of Lisbon, Lisbon, Portugal.

Joana P. Gonçalves developed Polar Mapper while she was an intern at the Systems Biology R&D Unit at Biocant, Cantanhede, Portugal.

 

André X. C. N. Valente [website]

Scientific Director, Systems Biology Unit, Biocant, Cantanhede, Portugal.
PI, Center for Neuroscience and Cell Biology (CNC), University of Coimbra (UC), Coimbra, Portugal.

André X. C. N. Valente coordinated and supervised the development of Polar Mapper software.

 

Mário Grãos [website]

Researcher, Cell Biology Unit, Biocant, Cantanhede, Portugal

Contacts

polarmapper [at] gmail [dot] com

(replace [at] by @ and [dot] by .)