2. Network visualisation has become an important tool in the armoury
of the data wrangler. An increasing volume of research and
journalism is using network analysis and visualisation to gain insight
into the real world social, political and cultural networks that influence
our lives. Take for instance GFK’s analysis of the European political
Twittersphere or Gild Lotan’s piece on personalising propoganda in
the Israel-Gaza war.
3. Instagram co-tag graph produced using Gephi, highlighting three distinct topical communities: 1) pro-Israeli (Orange),
2) pro-Palestinian (Yellow), and 3) Muslim (Pink). Source: http://globalvoicesonline.org/2014/08/04/israel-gaza-war-
data-the-art-of-personalizing-propaganda/
4. VIS: Visual Investigative Scenarios
http://vis.occrp.org/
A tool for producing simple but stylish network maps using a stock of
icons for entities that often come up in investigations e.g. people,
companies and cases. It also gives you the option to share and embed
your networks online, you can also export it for print. It’s in Beta stage
at the moment, so play nice and be sure to report any bugs!
5. Network of diagram mapping the assets of Azeri Officials in Czech Republic, taken from the VIS public
gallery: http://vis.occrp.org/
6. Google Fusion Tables
https://sites.google.com/site/fusiontablestalks/
Google Fusion Tables now offers a basic network mapping tool. It
has some useful filter functionality and although it lacks the deep
customisation options and analysis functionality of Gephi (see
below) it can produce insightful visualisations.
7. OpenOil’s attempt to map BP and its subsidiaries using Google
Fusion Tables. More information [here]
(http://openoil.net/corporate-networks/bp-corporate-network/)
8. GenMAPP (Gene Map Annotator and Pathway Profiler)
is a free, open-source bioinformatics software tool designed to
visualize and analyze genomic data in the context of pathways
(metabolic, signaling), connecting gene-level datasets to biological
processes and disease.
9. History
GenMAPP was first created in 2000 as a prototype software tool in the
laboratory of Bruce Conklin at the J. David Gladstone Institutes in San
Francisco
GenMAPP 2.1 was released in 2006 with new visualization
features and support for a total of eleven species.
10. GenMAPP was developed by biologists and is focused on
pathway visualization for bench biologists. Unlike many other
computational systems biology tools, GenMAPP is not designed for
cell/systems modeling; it focuses on the immediate needs of bench
biologists by enabling them to rapidly interpret genomic data with an
intuitive, easy-to-use interface.
Focus
11. GenMAPP is implemented in Visual Basic 6.0 and is available as a
stand-alone application for Microsoft Windows operating systems,
including Boot Camp or Parallels Workstationon a Mac. The program
is freely available for download and includes an automatic update
feature that allows rapid and reliable distribution of updates to the
program and documentation.
Development
12. Features
GenMAPP builds and maintains gene databases for a variety of
key model organisms:
human - Homo sapiens
mouse - Mus musculus
rat - Rattus norvegicus
yeast - Saccharomyces cerevisiae
13. GenMAPP provides tools to create, edit and annotate biological pathway maps.
GenMAPP allows users to visualize and analyze their data in the context of pathway
collections and the Gene Ontology.
Pathways and associated data can be exported for the web as HTML.
14. Cytoscape is an open source bioinformatics software
platform for visualizing molecular interaction networks and
integrating with gene expression profiles and other state data.
Additional features are available as plugins.
16. Development
The Cytoscape core developer team continues to work on this
project and released Cytoscape 3.0 in 2013.
This represented a major change in the Cytoscape architecture;
it is a more modularized, expandable and maintainable version of
the software
17. Usage
While Cytoscape is most commonly used for biological
research applications, it is agnostic in terms of usage.
Cytoscape can be used to visualize and analyze network
graphs of any kind involving nodes and edges (e.g., social
networks).
