Systrip

Systrip
Stable release	1.0 / 27 May 2011
Repository	tulip.labri.fr/Systrip/1.0/files/tulip_3_4_1_with_systrip_1_0.tar.gz ;
Operating system	Windows, Linux
License	LGPL, GPL
Website	tulip.labri.fr/TulipDrupal/?q=systrip

Systrip is a visual environment for the analysis of time-series data in the context of biological networks. Systrip gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process. It had been used to analyze various real biological data.^[1]

Presentation

Systrip is developed in C++ and is based on Tulip, an information visualization framework dedicated to the analysis and visualization of relational data.

The Model-View-Controller architecture of Tulip allows Systrip to support multiple and synchronized views. Any interaction on a view (e.g. selection of an element) implies the automatic update of all views displaying this data. In addition to the algorithms and views developed specifically for Systrip, the Tulip plug-ins system allows Systrip users to access all its available plug-ins (plug-ins integrated in Tulip releases but also via Tulip plug-ins server).

Features

Input

Import and export metabolic network using the SBML format
Time-series data from CSV file
Import data from CSV file
Load and save state of a session

Structure manipulation

Pathways creation and removal
Elements removal
Sub-network creation and manipulation (Help user to focus on a small part of the network)

Visualization

Multiple kind of metabolic network representations (3D, force directed, biological convention preserving, hierarchical ...)
Visualization interaction tools (drawing, bends ...)
Animation of time-series data
Visualization of time-series in the context of the metabolic network
Data analysis views (histogram, spreadsheet, scatter plot, parallel coordinates)
3D molecular visualization

Analysis

Tulip graph analysis algorithms
- Degree
- Betweenness centrality
- Eccentricity
- Strahler
Network analysis algorithms
- Choke points
- Shortest path (dedicated to metabolic networks)
- Scope selection

References

^ Copeland, WB; Bartley, BA; Chandran, D; Galdzicki, M; Kim, KH; Sleight, SC; Maranas, CD; Sauro, HM (May 2012). "Computational tools for metabolic engineering". Metabolic Engineering. 14 (3): 270–80. doi:10.1016/j.ymben.2012.03.001. PMC 3361690. PMID 22629572.

External links

Systrip overview
In context visualization of time-series data
3D molecular geometry
Biological convention preserving layout
Visualization and analysis of time-series data.

[PMC-3361690-1] Copeland, WB; Bartley, BA; Chandran, D; Galdzicki, M; Kim, KH; Sleight, SC; Maranas, CD; Sauro, HM (May 2012). "Computational tools for metabolic engineering". Metabolic Engineering. 14 (3): 270–80. doi:10.1016/j.ymben.2012.03.001. PMC 3361690. PMID 22629572.

[1]