Changes between Version 1 and Version 2 of VisModelHepatocyte


Ignore:
Timestamp:
Nov 4, 2008, 4:47:22 PM (17 years ago)
Author:
mirschel
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • VisModelHepatocyte

    v1 v2  
    11= Visualization of the stoichiometric model of the hepatocyte =
    22
    3 This is a cooperation project in the platform modeling of the HepatoSys initiative. Participating groups are the people from Berlin (Holzhuetter) and Magdeburg (Klamt).
     3This is a cooperation project in the platform modeling of the !HepatoSys initiative. Participating groups are the people from Berlin (Holzhuetter) and Magdeburg (Klamt). [[BR]]
    44The goal is the visualization of the stoichiometric model of the hepatocyte metabolism. This model is maintained in the Berlin group.
    55
    6 == Steps in the workflow ==
     6At 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:
     7
     8 1. use SBML file
     9 1. use additional tab delimited text files (see visualization of analysis results in logical models)
     10
     11One 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). [[BR]]
     12This results in a model which can have multiple layouts (encoded in different graphML files) and multiple visualizations (encoded in different visual scenarios). 
     13
     14
     15== Todos ==
     16
     17 * Test workflow using small test model
     18 * Import !HepatoNet model into Cytoscape (import SBML), test layout facilities
     19 * Test layout facilities of yEd using !HepatoNet model
     20 * Create models for use cases
     21
     22== Workflow ==
    723
    824 1. Import of the model (SBML import functionality, File > Imort > Import SBML)
    925 1. Apply initial layout using the ProMoT Editor
    1026 1. Open model in the ProMoT Explorer
    11  1. Export the network model (GraphML export functionality, Model > Export > Export Layout)
    12  1. Apply layout using an external tool, e.g. [http://www.yworks.com/products/yed/ yEd], [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio]
    13  1. Import new layout information (GraphML import functionality, Model > Import > Import Layout) 
     27 1. Export of the network model (GraphML export functionality, Model > Export > Export Layout)
     28 1. Apply layout using an external tool, see useful tools below
     29 1. Import of the new layout information (GraphML import functionality, Model > Import > Import Layout) 
    1430
    1531== Use cases ==
     32
     33 1. Small pathway network
     34 1. Huge complete model
     35 1. Edge routing test model
     36
     37=== Small networks of sub models ===
     38
     39Often sub pathways, manual layout, diverse visualization requirements
     40
     41=== Huge networks of the complete model ===
     42
     43Complete stoichiometric model of the metabolism, need automated layout
     44
     45=== Edge routing test model ===
     46
     47Some compartments, lots of links between them (terminals sufficient). How to perform a good edge routing?
     48
     49== Useful tools ==
     50
     51 * [http://www.yworks.com/products/yed/ yEd]
     52 * [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio]
     53 * [http://www.cytoscape.org Cytoscape]
     54 * [http://sbml.org/Facilities/Validator SBML Validator]
     55
     56== Open Questions ==
     57
     58 * Is it possible that in same cases the ids in a SBML file can be changed when importing it into ProMoT?
     59 * How to cope performance issues (memory, runtime)?
     60 * What about layout information from KEGG? Is it somehow able to integrate?
     61