Editing MS-howto

{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}

== Model-seed plug-in operations ==
*[[OptFlux3:CORE:NewProject|New project]]
**[[CORE:Readers:Drains | Drains Definition]]
**[[OptFlux Readers]]
***[[SBML Reader]]
***[[OptFlux3:MR | OptFlux Repository]]
***[[Flat Files Reader]]
***[[Table format Reader]]
***[[Cell Designer Reader]]
*[[OptFlux3:CORE:ImportProject | Import Project]]
*[[OptFlux3:SMP |Model Simplification]]

== Technical documentation for developers  ==

*[[Create a new plugin using the plugin builder]]
@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}
-The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br />
-If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
-In the log window (bottom of the OptFlux window) it is possible to see the communication between OptFlux and Model-seed and the commands that are being executed.
 == Model-seed plug-in operations ==
-[[File:Menu-ms.png]]
+*[[OptFlux3:CORE:NewProject|New project]]
-*[[ms-loginout | Login: operation to login in the local model-seed]]
+**[[CORE:Readers:Drains | Drains Definition]]
-*[[ms-loginout | Logout: operation to logout]]
+**[[OptFlux Readers]]
-*[[ms-pull | Pull (from MSeed to OptFlux):]]
+***[[SBML Reader]]
-**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]
+***[[OptFlux3:MR | OptFlux Repository]]
-**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]
+***[[Flat Files Reader]]
-* [[ms-commit | Commit (from OptFlux to MSeed):]]
+***[[Table format Reader]]
-**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]
+***[[Cell Designer Reader]]
-**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]
+*[[OptFlux3:CORE:ImportProject | Import Project]]
-*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]
+*[[OptFlux3:SMP |Model Simplification]]
-*[[ms-import | Import from server to local model-seed:]]
-**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]
-**[[ms-import#Import_mappings | Mappings: import mappings ]]
-**[[ms-import#Import_genome | Genome: import annotation]]
-*[[ms-model | Model]]
-**[[ms-model | Build: build a model in local model-seed]]
-**[[ms-fba | FBA]]
-***[[ms-fba#Wild-type_FBA | Wild Type]]
-***[[ms-fba#Reaction_KO_FBA | Reaction KO]]
-***[[ms-fba#Gene_KO_FBA | Gene KO]]
 == Technical documentation for developers  ==
-*[[Create a new plugin using the plugin builder (pdf)]]
+*[[Create a new plugin using the plugin builder]]