Manual @Mar 17, 2011 11:28:26 AM

Reconstruction

Click on Reconstruction in the menu bar to open Model databases and Reference databases.

  • Model importing and editing

Right click on Model databases to Import SBML file (.xml) or to Import spreadsheets (.xls), you can import a metabolic model in SBML/spreadsheet format as described in Metabolic Models.

You can directly edit/update the content of the imported model.

  • Reference database creation

Right click on Reference databases to Import database (.xls), you can import a reference database provided in Reference Databases to create your own reference database.

You can add the information about metabolites and reactions described in a model to the reference database by right clicking on the metabolic model to add rxn&met to the Ref. DB.

  • Draft reconstruction generation

A draft reconstruction can be generated by mapping a blank reconstruction outputed by GBKParser, containing gene information only, to a reference reconstruction. You just simply right click on the blank reconstruction to Draft a reconstruction

GEMsME will extract the reactions whose associated orthologous genes are present in the target organism and obey Boolean statements as described in the reference reconstruction.

  • Reconstruction refinement

You can right click on a model to Generate simulation tables, so that a mathematical model including a stoichiometric matrix which describes the connectivity feature of the network as well as default systems boundaries can be generated.

With the generated simulation tables, you can identify dead-end metabolites.

Then, you can right click on the model with simulation tables to Define environmental conditions, e.g. the complete medium to simulate all extracellular metabolites can enter/exit the cell freely.

Simulation

Click on Simulation in the menu bar to perform the analyses implemented in GEMsME including

  • Dead-end metabolite identification

Select a metabolic model and a map (if you have), GEMsME can identify dead-end metabolites and tag them with crosses in the map.

  • Objective optimization

Select a metabolic model and a map (if you have) for objective optimization, the flux result can be visulized in the map.

  • Robustness analysis

Select a metabolic model and

  • Flux variability analysis

Select a metabolic model and a map (if you have) for flux variability analysis, the min and max fluxes of reaction can be plotted in the map and the blocked reaction are tagged with crosses.

  • Essentiality analysis

Select a metabolic model for essentiality analysis, the computational essential genes or reactions can be identified.

  • Gene deletion analysis

Select a metabolic model for gene deletion analysis, the gene-deletion model can be saved and imported for further evaluation.

Visualization

Click on Visualization in the menu bar to open Maps wherein you can create metabolic maps.

  • Metabolic map creaction

Right click on Maps to Create new map. You can add maps, reactions, metaboltes and lines to create a map onto the main network view window.

  • KEGG map loading

Right click on Maps to Load KEGG maps by either Import KEGG map (.xml) or Retrieve KEGG map.

  • Map replacement

With two lists for metabolite and reaction mapping, you can right click on a map to Replace caption of nodes to convert the map to a customized map.

  • Information extraction

Right click on a map to Extract reaction information from a model and choose a model you want to extract information from. Then you can show the extra information of reaction on the map by right clicking a reaction to Show extra info..

  • Flux visualization

Right click on a map to Load reaction fluxes, the reaction fluxes were be superimposed on the map.

  • Gene expression visualization

Right click on a map to Load gene expressions, the gene expressions were be superimposed around the associated reactions on the map.