Back in early 2014, the R@CMon team assisted SBI Australia to deploy the VISIONET (Visualizing Transcriptomic Profiles Integrated with Overlapping Transcription Factor Networks) visualisation web service on the Monash node of the NeCTAR Research Cloud. Since then, VISIONET has been further enhanced to support more complex transcription factor network topologies. To date, VISIONET has been published in two papers.
Nim, H.T., Boyd, S.E., and Rosenthal, N.A. (2014). Systems approaches in integrative cardiac biology: Illustrations from cardiac heterocellular signalling studies. Progress in Biophysics and Molecular Biology 117, 69-77.
Nim, H.T., Furtado, M.E., Costa, M.W., Rosenthal, N.A, Kitano, H., and Boyd, S.E.. (2015). VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. BMC Bioinformatics.
The R@CMon team will continue supporting SBI Australia with its plan to further develop the VISIONET web service this year.
VISIONET (Visualizing Transcriptomic Profiles Integrated with Overlapping Transcription Factor Networks) is a visualisation web service for cellular regulatory network studies. It’s been developed as a tool for creating human-readable visualisations of transcription factor networks from user’s microarray and ChiP-seq input data. VISIONET’s node-filtering feature provides a more human-readable large networks visualisation compared to CellDesigner and Cytoscape.
Gata4-Tbx20 transcription factor network.
R@CMon helped SBI Australia in porting the VISIONET web service into the NeCTAR Research Cloud, enabling rapid development and customisation. VISIONET’s .NET-based framework is now running on a Windows Server 2012 instance inside R@CMon, and it’s now using persistent storage (Volumes) for storing large generated network visualisations. VISIONET is now publicly available to biologists, and user traffic is expected to grow in the near future.
We’re currently working on deploying the Garuda/Flint K3 system in the NeCTAR Research Cloud.
The Garuda platform provides fundamental technology to link software and knowledge in systems biology in a coherent manner.
Flint K3 is an online simulation platform that receives PHML and SBML models from PhysioDesigner, CellDesigner and other applications.
More about the Systems Biology Institute can be found on their website.