Editing MS-howto

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

The Model-seed operations are located

to load the Model-seed plug-in

== Model-seed plug-in operations ==


*Login: operation to login in the local model-seed
* Logout: operation to logout
* Pull:
** Model: import a model from model-seed to OptFlux
** Media: import a media from model-seed to OptFlux
* Commit:
**Model: send a model from OptFlux to model-seed
**Media: send a media from OptFlux to model-seed

*Merge Biochemistry: merge two biochemistries in local model-seed.
*Import from server to local model-seed
**Biochemistry: import biochemistry 
**Mappings: import mappings 
**Genome: import annotation
*Model
**Build: build a model in local model-seed
**FBA
***Wild Type
***Reaction KOs


== Technical documentation for developers  ==

*[[Create a new plugin using the plugin builder (pdf)]]
@@ 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 />
+The Model-seed operations are located
-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.
+to load the Model-seed plug-in
 == Model-seed plug-in operations ==
-[[File:Menu-ms.png]]
-*[[ms-loginout | Login: operation to login in the local model-seed]]
-*[[ms-loginout | Logout: operation to logout]]
+*Login: operation to login in the local model-seed
-*[[ms-pull | Pull (from MSeed to OptFlux):]]
+* Logout: operation to logout
-**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]
+* Pull:
-**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]
+** Model: import a model from model-seed to OptFlux
-* [[ms-commit | Commit (from OptFlux to MSeed):]]
+** Media: import a media from model-seed to OptFlux
-**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]
+* Commit:
-**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]
+**Model: send a model from OptFlux to model-seed
-*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]
+**Media: send a media from OptFlux to model-seed
-*[[ms-import | Import from server to local model-seed:]]
-**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]
+*Merge Biochemistry: merge two biochemistries in local model-seed.
-**[[ms-import#Import_mappings | Mappings: import mappings ]]
+*Import from server to local model-seed
-**[[ms-import#Import_genome | Genome: import annotation]]
+**Biochemistry: import biochemistry
-*[[ms-model | Model]]
+**Mappings: import mappings
-**[[ms-model | Build: build a model in local model-seed]]
+**Genome: import annotation
-**[[ms-fba | FBA]]
+*Model
-***[[ms-fba#Wild-type_FBA | Wild Type]]
+**Build: build a model in local model-seed
-***[[ms-fba#Reaction_KO_FBA | Reaction KO]]
+**FBA
-***[[ms-fba#Gene_KO_FBA | Gene KO]]
+***Wild Type
+***Reaction KOs
 == Technical documentation for developers  ==
 *[[Create a new plugin using the plugin builder (pdf)]]