Line 6:
Click on <u>Reconstruction</u> in the menu bar to open '''Model databases''' and '''Reference databases'''.
Click on <u>Reconstruction</u> in the menu bar to open '''Model databases''' and '''Reference databases'''.
-
*<font size=3>Model importing and editing</font> ([http://sb.nhri.org.tw/GEMsME/Reconstruction%20step1.html Step-by-step])
+
*<font size=3>Model importing and editing</font> ([http://sb.nhri.org.tw/GEMSiRV/Reconstruction%20step1.html Step-by-step])
Right click on '''Model databases''' to<u> Import SBML file (.xml)</u> or to <u>Import spreadsheets (.xls)</u>, you can import a metabolic model in SBML/spreadsheet format as described in [[Metabolic Models]].
Right click on '''Model databases''' to<u> Import SBML file (.xml)</u> or to <u>Import spreadsheets (.xls)</u>, you can import a metabolic model in SBML/spreadsheet format as described in [[Metabolic Models]].
Line 12:
You can directly edit/update the content of the imported model.
You can directly edit/update the content of the imported model.
-
*<font size=3>Reference database creation</font> ([http://sb.nhri.org.tw/GEMsME/Reconstruction%20step2.html Step-by-step])
+
*<font size=3>Reference database creation</font> ([http://sb.nhri.org.tw/GEMSiRV/Reconstruction%20step2.html Step-by-step])
Right click on '''Reference databases''' to <u>Import database (.xls)</u>, you can import a reference database provided in [[Reference Databases]] to create your own reference database.
Right click on '''Reference databases''' to <u>Import database (.xls)</u>, you can import a reference database provided in [[Reference Databases]] to create your own reference database.
Line 18:
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<u> add rxn&met to the Ref. DB</u>.
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<u> add rxn&met to the Ref. DB</u>.
-
*<font size=3>Draft reconstruction generation</font> ([http://sb.nhri.org.tw/GEMsME/Reconstruction%20step3.html Step-by-step])
+
*<font size=3>Draft reconstruction generation</font> ([http://sb.nhri.org.tw/GEMSiRV/Reconstruction%20step3.html Step-by-step])
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<u> Draft a reconstruction</u>
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<u> Draft a reconstruction</u>
Line 24:
-
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.
+
GEMSiRV will extract the reactions whose associated orthologous genes are present in the target organism and obey Boolean statements as described in the reference reconstruction.
-
*<font size=3>Reconstruction refinement</font> ([http://sb.nhri.org.tw/GEMsME/Reconstruction%20step4.html Step-by-step])
+
*<font size=3>Reconstruction refinement</font> ([http://sb.nhri.org.tw/GEMSiRV/Reconstruction%20step4.html Step-by-step])
You can right click on a model to <u>Generate simulation tables</u>, 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.
You can right click on a model to <u>Generate simulation tables</u>, 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.
