Manage your metabolic models with the help of this tool
CytoSEED was built as a Cytoscape plugin that can help you view, manipulate and analyze metabolic models created using the Model SEED.
The CytoSEED plugin was designed in order to enable users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest.
Users may load any model for which they have access in the Model SEED. The CytoSEED plugin downloads the model data, reactions and compounds from the Model SEED, and organizes the reactions into networks based on their corresponding KEGG pathway maps.
After the initial load (which may take several minutes), the model data is stored on the user's desktop in a specified folder for quick loading in subsequent sessions.
The CytoSEED plugin was designed in order to enable users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest.
Users may load any model for which they have access in the Model SEED. The CytoSEED plugin downloads the model data, reactions and compounds from the Model SEED, and organizes the reactions into networks based on their corresponding KEGG pathway maps.
After the initial load (which may take several minutes), the model data is stored on the user's desktop in a specified folder for quick loading in subsequent sessions.
Here are some key features of "CytoSEED":
· Downloading models from the Model SEED; creation of Cytoscape sessions for viewing models; saving and reopening Cytoscape sessions
· Creation and deletion of pathway maps; moving/copying reactions between pathway maps; hiding/showing nodes within pathway maps
· Visualization of Flux Variability Analysis results in multiple media; reactions are colored based on essential/active/inactive/gap-filled categories
· Capability to open models for multiple organisms in one Cytoscape session, to enable comparative model analysis
· Visualization of Flux Balance Analysis results
· Downloading models from the Model SEED; creation of Cytoscape sessions for viewing models; saving and reopening Cytoscape sessions
· Creation and deletion of pathway maps; moving/copying reactions between pathway maps; hiding/showing nodes within pathway maps
· Visualization of Flux Variability Analysis results in multiple media; reactions are colored based on essential/active/inactive/gap-filled categories
· Capability to open models for multiple organisms in one Cytoscape session, to enable comparative model analysis
· Visualization of Flux Balance Analysis results
Requirements:
· Java
· Cytoscape 2.8.3
· Java
· Cytoscape 2.8.3
| Publisher | : | Matt DeJongh |
|---|---|---|
| License | : | Freeware |
| Size/OS: | : | 3.2 MB / Windows XP / Vista / 7 |
| Date | : | February 19th, 2013 |
Download | : | CytoSEED 1.4 |
