User interface

Main Window

The main window has a set of six buttons down the left hand side. Each button is used to access different ISIS-Fish modules.

The buttons display sub-windows to access :

  • Region (fishery) definition
  • Simulation control
  • Sensitivity analysis control
  • Presentation of results
  • Editor for scripts, rules, exports, simulation plan
  • Simulation queue

Each of these sub-windows can also be opened in a new window using the Window menu.

File menu

The top menu item Server synchronization is used to synchronize local copies of scripts with the scripts on the server.

The second menu item Close closes ISIS_Fish.

Window menu

The six menu items correspond to the six buttons (but not necessarily in the same order). Each opens the corresponding sub-window in a new window.

Configuration menu

The Configuration menu items are used to set the configuration for various ISIS-Fish features.

  • Configuration to set general user preferences.
  • VCS configuration to set the version control system parameters
  • Carparmor configuration to set up the local version of ISIS-Fish to use the Carparmor supercomputer.
  • R configuration to test if R is correctly configured

Help menu

The Help menu provides

  • ISIS-Fish Website link to this website
  • API to access the various application programming interfaces
  • About with version and license information

Status bar

The status bar at the bottom of the window shows

  • the progress bar for the current operation on the left
  • a message area in the middle
  • a screenshot button, the current ISIS-Fish memory use / memory allocated and the time of day on the right

Simulation window

This window is used to set up and execute simulations.

This window has a number of tabs

  • Parameters – for setting the basic simulation parameters (name, description, region, strategies, initial populations, rules, number of months to simulate) as well as for launching the simulation process.
  • Pre simulation script – for defining a pre-simulation script which will be executed to modify the database before any simulations are run. This tab is activated when Use pre simulation script is checked in the parameters window.
  • Simulation plan – for defining a simulation plan to carry out multiple simulations. This tab is activated when Use simulation plan is checked in the parameters window.
  • Optimization – for defining the objective function, the optimization method, exported values and observations. This tab is activated when Use optimization method is checked in the parameters window.
  • Results export – for selecting scripts for exporting results.
  • Result choice – for selecting results to be kept for viewing in the Results window.
  • Advanced parameters – for setting parameters such as the simulator to be used, cache control, trace levels and Free parameters than can be used in rules, the simulator, etc.

If a rule or export script requires a result that is not selected, then the result required is added automatically to the list results selected.

When a simulation is run, the local timestamp, yyyy-mm-dd-hh-mm, is added to the simulation name.

Results window

This window displays the results of a simulation in graphical, cartographical or tabular formats

Click Open to display the results of the most recent simulation or, to display the results from a previous simulation, select the simulation results required from the dropdown list at the top of the window and click Open to open the results in a new sub-window.

Region window

This window is used to display and modify regions.

Select the region required from the dropdown list at the top of the window.

Scripts window

This window is used to edit any type of script

  • scripts
  • simulators
  • exports
  • rules
  • simulation plans
  • model formulae
  • sensitivity analyses

All scripts are stored as text files in the filing system. Any text or source file editor can, therefore, be used to edit them.

Sensitivity analysis window

This tab is used to parameterize and run a sensitivity analysis as well as display the results.

This tab is itself comprised of a number of tabs

  • Parameters – to set the basic parameters: identifier, description, region, strategies, populations, rules, number of years to simulate
  • Sensitivity analysis – to set the factors to be studied
  • Sensitivity method – to set select and parameterize the method used
  • Results export – this tab is used to select the export scripts and directory
  • Result choice – this tab is used to select the results to be kept for visualization using the Analyze results tab
  • Advanced parameters – this tab is used to select the simulator to be used, control the cache, control the statistics, filter the log and set free parameters for use by rules or the simulator, etc
  • Analyze results – this tab is used to display the results of a sensitivity analysis

If a rule or export script requires a result that is not selected, then the result required is added automatically to the list results selected.

When a simulation is run, the local timestamp, yyyy-mm-dd-hh-mm, is added to the analysis name. For each simulation the name followed by an underscore followed by the sequence number of the simulation within the sensitivity analysis.