SyNDI (Synchronous Network Data Integration framework) [1] is a framework for synchronous network visualization and network analysis.
It comprises two main tools:
* a Cytoscape app called SyncVis (Synchronous Visualizer) for synchronous visualization of multiple networks
* A set of network analysis tools. Galaxy [2-4] is used as a central platform for these tools, but they can be also run on separate applications such as the Cytoscape app BINGO ([http://apps.cytoscape.org/apps/bingo]).
References:
[1] Lindfors, Erno & C. J. van Dam, Jesse & Ming Chi Lam, Carolyn & Zondervan, Niels & Martins dos Santos, Vitor & Suarez-Diez, María. (2018). SyNDI: Synchronous network data integration framework. BMC Bioinformatics. 19. 10.1186/s12859-018-2426-5.
[2] Goecks J, Nekrutenko A, Taylor J, Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86.
[3] Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 2010;Chapter 19:Unit 19.10.1-21.
[4] Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451–5.
