FSK-Lab nodes

 

FSK Creator

Creates a FSK object with the script and metadata provided by the user. The variables defined in the parameters script are ensembled in a default simulation called defaultSimulation.

Dialog Options

  • Model script. File path of the model script (mandatory).
  • Visualization script. File path of the visualization script (optional).
  • Readme. README file (optional).
  • Working directory. Directory with resource files used by the model: possible formats are .csv, .xlsx, .txt, .r, .RData, .py, .json, .sedml (optional).
  • Selected XLSX spreadsheet. File path of the XLSX spreadsheet of the Model Annotation Excel template Version 1.04 with metadata (mandatory). An error occurs if an empty spreadsheet is provided.
  • Selected sheet. Name of the selected sheet in the spreadsheet (e.g., Generic Metadata Schema, Predictive Model, etc.).

Ports

  • Inputs: data table (optional)
  • Outputs: FSK object

FSKX Writer

Creates a FSKX file with the scripts, metadata, model encoded in SBML, workspace, working directory, simulations SedML and R packages in the FSK object.

Supported images. Images generated in the model script are saved into the archive. The supported image files are: bmp, jpeg, png and tiff.

Allowed image names. The plot generated with the visualization script is named plot.png, so any other image generated in the model script with this name will be overwritten.

Dialog Options

  • Output location. Path to FSKX file. May be an absolute URL, a mount relative URL or a local path.

Ports

  • Inputs: FSK object

FSKX Reader

Creates a FSK object with the scripts, metadata, simulations, resource files and R packages in the referred FSKX file.

Dialog options

  • Input location. Selected file path. May be an absolute URL, a mount-point relative URL or local path. Examples:
    • Absolute URL: knime://LOCAL/my_resource.txt
    • Mount-point relative path: knime://knime.mountpoint/my_resource.txt
    • Local path: C:/workspace/my_resource.txt

Ports

  • Outputs: FSK object

FSK Runner

Runs the input model and updates its workspace with the model results.

Visualization scripts with interactive output such as Plotly are not supported.

Dialog Options

  • Width. Width of the plot.
  • Height. Height of the plot.
  • Resolution. Resolution of the plot in PPI.
  • Text size. Default point-size of plotted text, interpreted as big points (1/72 inch) at the given resolution.
  • Simulation. The name of the selected simulation to run. If no simulation is selected then the default simulation will be selected.
  • Save Output To JSON File. Possibility to save all parameters (input and output) with metadata and values in a JSON file. Path to the file is available in the Flow Variable generatedResources. (optional).

Ports

  • Inputs: FSK object
  • Outputs:
    • FSK object with results stored in R workspace and if selected in the file parameters.json
    • Image output. Plot generated with the provided visualization script. If the input FSK object has no visualization script then this port will hold no image (optional).

FSK Editor

Edit the scripts and the model metadata in a FSK object. In case there is no input FSK object connected then it will create a new FSK object from the user interface.

When a new FSK object is created, a default simulation called defaultSimulation will be created with the parameters defined in the metadata (the model math part).

Ports

  • Inputs: FSK object (optional)
  • Outputs: FSK object

FSK to R

Extracts the R workspace out of a FSK object. The R workspace may be used with KNIME R nodes. If the R workspace is null or non-existent (as when the model has not been run), the generated RPortObject would be null.

Ports

  • Inputs: FSK object
  • Output: RPortObject

FSK to metadata

Extracts the metadata from a FSK object into a KNIME JSON table.

Ports

  • Inputs: FSK object
  • Outputs: KNIME table with metadata

FSK Simulation Configurator JS

Creates simulations for a FSK object.

The defaultSimulation settings created by the FSK Creator and FSK Editor JS are disabled by default. The simulation selected in the view is set as simulation to run in the runner node.

Simulation names. The simulation names only take unique identifiers of type SId. The SId type follows the pattern:

  • letter ::= ’a’..’z’,’A’..’Z’
  • digit ::= ’0’..’9’
  • nameChar ::= letter | digit | ’_’
  • name ::= ( letter | ’_’ ) nameChar*

Simulation parameters. Values for all the parameters in the FSK object. Values of parameters which are classified as constant, cannot be modified.

Ports

  • Inputs: FSK object
  • Output: FSK object

FSK Joiner

Joiner of FSK objects. Joins two, three or four FSK objects and produces a combined FSK object which keeps all of the provided objects.

Ports

  • Inputs: Two to four FSK objects
  • Outputs:
    • Combined FSK object
    • Joining diagram

FSK DB View

This node visualizes FSK models as a HTML table. The source of this metadata can be read from remote repository which can be set via the “Repository URL” option in the settings window. Also this metadata can be provided as KNIME table via the input port.

Dialog Options

  • Repository location. By default refers to https://knime.bfr./landingpage/.
  • Max Selection Number. Sets the maximum number of models, can be selected.
  • Show Download Button. Set to true if you like to show the Download button in each row in the HTML table.
  • Show Details Button. Set to true if you like to show the Details button in each row in the HTML table, which opens a window to show more details about the current FSK model.
  • Show Execution Button. Set to true if you like to show the Execution button in each row in the HTML table. The model then will be executed on the remote server.
  • Show Header Button. Set to true if you like to show the Header button in each row in the HTML table.

Ports

  • Inputs: FSK metadata table (optinal)
  • Outputs: FSK metadata table