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vcsm
Module AssemblyName: file:///G:/GCModeller/manual/bin/vcsm.exe Root namespace: LANS.SystemsBiology.GCModeller.CommandLines
All of the command that available in this program has been list below:
| Function API | Info |
|---|---|
| Experiment.Whole_Genome_Mutation | shell parameter is the shoal shell application program file location. |
| Experiment.Whole_Genome_Mutation2 | shell parameter is the shoal shell application program file location. this command is required the GCML format model file. |
| load.model.csv_tabular | The csv_tabular format model file is the alternative format of the GCModeller virtual cell modle, as the GCModeller only support the GCML xml file as the modelling data source, so that you should using this command to load the csv_tabular format model file as the GCML format. |
| registry | |
| run | |
| unregistry |
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 WholeGenomeMutation(System.String, Double, System.String)
Information: shell parameter is the shoal shell application program file location.
Usage: G:\GCModeller\manual\bin\vcsm.exe
Example: vcsm Experiment.Whole_Genome_Mutation
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 WholeGenomeMutationFromGCML(System.String, Double, System.String)
Information: shell parameter is the shoal shell application program file location. this command is required the GCML format model file.
Usage: G:\GCModeller\manual\bin\vcsm.exe
Example: vcsm Experiment.Whole_Genome_Mutation2
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::SMRUCC.genomics.GCModeller.ModellingEngine.EngineSystem.Engine.GCModeller LoadCsv(System.String, Microsoft.VisualBasic.Logging.LogFile, Microsoft.VisualBasic.CommandLine.CommandLine)
Information: The csv_tabular format model file is the alternative format of the GCModeller virtual cell modle, as the GCModeller only support the GCML xml file as the modelling data source, so that you should using this command to load the csv_tabular format model file as the GCML format.
Usage: G:\GCModeller\manual\bin\vcsm.exe
Example: vcsm load.model.csv_tabular
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 RegistryModule(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\vcsm.exe registry <assembly_file>
Example: vcsm registry resistry /home/xieguigang/gcmodeller/models/plas.dll
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 Run(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\vcsm.exe run -i <model_file> -mysql <mysql_connection_string> [-f <gcml/csv_tabular> -t <time> -metabolism <assembly_path> -expression <assembly_path>]
Example: vcsm run run -i ~/gc/ecoli.xml -t 1000 -url "http://localhost:8080/client?user=username%password=password%database=database"
Parameters information:
-i
Description: This switch value specific the model file that the simulation engine will be load
Example: -i "~/gc/ecoli.xml"
-url
Description: Setup the data storage service connection url string.
Example: -url "http://localhost:8080/client?user=username%password=password%database=database"
[-t]
Description: Optional, This switch specific that the cycle number of this simulation will run, this switch value will override the time value in the loaded model file.
Example: -t "1000"
[-metabolism]
Description: N/A - The engine kernel will not load the metabolism module.
Example: -metabolism ""
[-expression]
Description: N/A - The engine kernel will not load the gene expression regulation module.
Example: -expression ""
[-interval]
Description: This switch value specific the data commit to the mysql database server time interval, if your compiled model is too large you should consider set up this switch value smaller in order to avoid the unexpected memory out of range exception.
Example: -interval ""
[-f]
Description: This parameter specific the file format of the target input model file, default value is gcml format.
Example: -f ""
[-suppress_warn]
Description: T/TRUE/F/FALSE
Example: -suppress_warn ""
[-suppress_error]
Description: T/TRUE/F/FALSE
Example: -suppress_error ""
[-suppress_periodic_message]
Description: T/TRUE/F/FALSE
Example: -suppress_periodic_message ""
Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 UnRegistry(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\vcsm.exe unregistry <assembly_file>
Example: vcsm unregistry unregistry ~/gcmodeller/models/plas.dll
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