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== Simulation==
== Simulation==
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Click on <u>Simulation</u> in the menu bar to perform the analyses implemented in GEMsME including<br>
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Click on <u>Simulation</u> in the menu bar to perform the analyses implemented in GEMSiRV including<br>
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*<font size=3>Dead-end metabolite identification</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step1.html Step-by-step])
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*<font size=3>Dead-end metabolite identification</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step1.html Step-by-step])
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Select a metabolic model and a map (if you have), GEMsME can identify dead-end metabolites and tag them with crosses in the map.
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Select a metabolic model and a map (if you have), GEMSiRV can identify dead-end metabolites and tag them with crosses in the map.
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*<font size=3>Objective optimization</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step2.html Step-by-step])
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*<font size=3>Objective optimization</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step2.html Step-by-step])
Select a metabolic model and a map (if you have) for objective optimization, the flux result can be visulized in the map.
Select a metabolic model and a map (if you have) for objective optimization, the flux result can be visulized in the map.
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*<font size=3>Flux variability analysis</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step3.html Step-by-step])
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*<font size=3>Flux variability analysis</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step3.html Step-by-step])
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.
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.
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*<font size=3>Robustness analysis</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step4.html Step-by-step])
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*<font size=3>Robustness analysis</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step4.html Step-by-step])
Select the reactions of interest in a model to see how sensitive the objective is to the particular reactions.
Select the reactions of interest in a model to see how sensitive the objective is to the particular reactions.
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*<font size=3>Essentiality analysis</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step5.html Step-by-step])
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*<font size=3>Essentiality analysis</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step5.html Step-by-step])
Select a metabolic model for essentiality analysis, the computational essential genes or reactions can be identified.
Select a metabolic model for essentiality analysis, the computational essential genes or reactions can be identified.
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*<font size=3>Gene deletion analysis</font> ([http://sb.nhri.org.tw/GEMsME/Simulation%20step6.html Step-by-step])
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*<font size=3>Gene deletion analysis</font> ([http://sb.nhri.org.tw/GEMSiRV/Simulation%20step6.html Step-by-step])
Select a metabolic model for gene deletion analysis, the gene-deletion model can be saved and imported for further evaluation.
Select a metabolic model for gene deletion analysis, the gene-deletion model can be saved and imported for further evaluation.
