Visualization of the stoichiometric model of the hepatocyte
This is a cooperation project in the platform modeling of the HepatoSys initiative. Participating groups are the people from Berlin (Holzhuetter) and Magdeburg (Klamt).
The goal is the visualization of the stoichiometric model of the hepatocyte metabolism. This model is maintained in the Berlin group.
At the moment we have a model in SBML format comprising network structure and equilibrium constants. There are two ways of store the additional model data:
- use SBML file
- use additional tab delimited text files (see visualization of analysis results in logical models)
One idea is to separate the structure from the network data (initial concentration, equilibrium constants, reaction rate) and the visual data (layout, notation and visual properties).
This results in a model which can have multiple layouts (encoded in different graphML files) and multiple visualizations (encoded in different visual scenarios).
Todos
- Test workflow using small test model
- Import HepatoNet model into Cytoscape (import SBML), test layout facilities
- Test layout facilities of yEd using HepatoNet model
- Create models for use cases
Workflow
- Import of the model (SBML import functionality, File > Imort > Import SBML)
- Apply initial layout using the ProMoT Editor
- Open model in the ProMoT Explorer
- Export of the network model (GraphML export functionality, Model > Export > Export Layout)
- Apply layout using an external tool, see useful tools below
- Import of the new layout information (GraphML import functionality, Model > Import > Import Layout)
Use cases
- Small pathway network
- Huge complete model
- Edge routing test model
Small networks of sub models
Often sub pathways, manual layout, diverse visualization requirements
Huge networks of the complete model
Complete stoichiometric model of the metabolism, need automated layout
Edge routing test model
Some compartments, lots of links between them (terminals sufficient). How to perform a good edge routing?
Useful tools
Open Questions
- Is it possible that in same cases the ids in a SBML file can be changed when importing it into ProMoT?
- How to cope performance issues (memory, runtime)?
- What about layout information from KEGG? Is it somehow able to integrate?
