virtualcell simulations host [version 2.6.0.255]

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

Commands


Help for command ‘Experiment.Whole_Genome_Mutation’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 WholeGenomeMutation(System.String, Double, System.String)

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Information:  shell parameter is the shoal shell application program file location.
Usage: G:\GCModeller\manual\bin\vcsm.exe
Example: vcsm Experiment.Whole_Genome_Mutation
Help for command ‘Experiment.Whole_Genome_Mutation2’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 WholeGenomeMutationFromGCML(System.String, Double, System.String)

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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
Help for command ‘load.model.csv_tabular’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::SMRUCC.genomics.GCModeller.ModellingEngine.EngineSystem.Engine.GCModeller LoadCsv(System.String, Microsoft.VisualBasic.Logging.LogFile, Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘registry’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 RegistryModule(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\vcsm.exe registry <assembly_file>
Example: vcsm registry resistry /home/xieguigang/gcmodeller/models/plas.dll
Help for command ‘run’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 Run(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    -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 ""

Accepted Types

-i
-url
-t
-metabolism
-expression
-interval
-f
-suppress_warn
-suppress_error
-suppress_periodic_message
Help for command ‘unregistry’:

Prototype: LANS.SystemsBiology.GCModeller.CommandLines::Int32 UnRegistry(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\vcsm.exe unregistry <assembly_file>
Example: vcsm unregistry unregistry ~/gcmodeller/models/plas.dll