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Geertjan's Blog

  • April 5, 2013

Systems Biology Network Visualization on the NetBeans Platform

Geertjan Wielenga
Product Manager

Mongkie is an integrated network visualization platform which enables the interactive analysis of interconnected biological data:

Though a lot of applications on the NetBeans Platform have already been identified in the bioinformatics domain, what's especially interesting is that quite a few of them explicitly position themselves as platforms, rather than applications. In particular, take a look at BioBeans, by Gene Infinity, which consists of multiple platforms on top of each other, each adding new layers of increasingly specific biology systems development tools.

However, the Mongkie system is completely new to me, only came across it yesterday, and it seems to be a pretty new development, from last year sometime. It provides a network import/export feature, expression overlays, network clustering/grouping, pathway integration/visualization, and pipeline analysis. I think there's some interesting overlaps of functionality with Gephi, the open source graph visualization platform.

There's a lot of documentation on the site, I downloaded the software, and tried it out. I'm not a systems biologist, so didn't really understand what I saw, but there's really a of of cool built-in diagrammy stuff there, with animations, and special effects.

Watch the 20 minute silent YouTube movie below, and see how it all works, e.g., the native GraphML support looks pretty sweet:

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