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.
This framework had been used to analyse various real biological data
Some key features :
- SBML file import and export.
- Multiple kind of metabolic network representations (3D, force directed, biological convention preserving, hierachical ...).
- Both graph theoritical measures and metabolic network analysis algorithms (choke points, scope, centrality...).
- Time-series data import and visualization (table view, parallel coordinates, scatter plot).
- Visualization of time-series in the context of the metabolic network.
- 3D molecular visualization.
- Database querry tools (Kegg, PublicHouse).
Presentation of the Systrip features.
You can download the data used in this video in the samples ( DFMODataset ), see the download section.
This video shows an analysis of the metabolic data generated by Metaboflux concerning flexibility of glucose metabolism network in the T. brucei parasite when the excretion of acetate increase from 1 to 99%, with a 5% increment.
This video shows how to visualize shared elements by two different networks using a SBML file containing the union of the elements of the two networks and a CSV file with the origin of each element. The approach taken is to automatically annotate the Mollicute genomes (Phytoplasma and Mycoplasma) using RAST and reconstruct their metabolic network from the annotated genome using SEED.
With the reconstructed metabolic networks, we then "merge" them using Rast2Systrip.
You can download the data used in this video in the samples, see the download section.
If you work with windows use the Windows installer.
Source code packages
If you have trouble with Systrip mail the project maintainer or use the Tulip forum.
Dubois Jonathan (project maintainer)
Romain Bourqui (project maintainer)