Simulation

Before simulation, make sure you have set the path of linear programming solver.

To download GNU Linear Programming Kit (GLPK).

http://sourceforge.net/projects/winglpk/ (for windows) or

http://www.gnu.org/software/glpk/ (for Linux/Mac).

After extracting the file you downloaded (e.g. winglpk-4.45.zip), please add the path of glpsol.exe to your Environment variables.

Open the Control Panel -> Click System -> Click Advanced system setting -> Open Environment variables -> Edit Path -> Add variable value ";the path where glpsol.exe locate" (e.g. ;D:\winglpk-4.45\w64)

Click on Simulation in the menu bar to choose which analysis you want to perform.

As a case study for demonstration of simulation, we import the E.coli textbook model which was exported from the BiGG into GEMSiRV and use a customized map E.coli_core.cartomap for visualization. You can find and download the model and the map from http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Models and http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Maps, respectively.

Dead-end metabolite identification

A network reconstruction is converted into a mathematical model including a stoichiometric matrix which describes the connectivity feature of the network and defined systems boundaries before simulation. GEMSiRV can examine the connectivity of all metabolites in a network for dead-end metabolite identification and tag such metabolic dead ends with crosses in the map.

You can select a model and a map (if you have) to perform the examination of network connectivity for dead-end metabolite identification.

A dead-end metabolite list is generated and those metabolites are tagged with crosses in the map.

A list for dead-end metabolites:

A visualization map with dead-end metabolites: