Main window

The user interface is made up of several screens. The screens are accessed by tabs in the upper region.

Selecting project

In the bottom of the screen there is a drop-down menu which allows a user to switch between projects (if the user has been given access to more than one project). To the right is a symbol showing the role for the user in the selected project.

Searching

Several screens feature a tool for searching the database for instances. This is true of the values window, where the user searches for instances to edit. In the export window the user searches for instances to export to Excel.

The search tool consists of a list for search results and a panel with search controls. By clicking on the more-button in the bottom right corner, the panel is expanded to show additional controls.

As search criteria are entered, the box above will list all matching instances. the figure below shows an example of a search result:

Comments, references and attachments

In theory, comments, references and attachments can be assigned to any type of data in the database. Currently, the user interface only allows these to be assigned to parameter instances and parameter entries.

When editing an entry or instance, the bottom section of the window is named “Additional information”. There are three tabs, one for comments, one for references and one for attachments.

Comments

The comment section is made up of two boxes. The upper box allows a new comment to be entered. The lower box displays all previously entered comments. When entering a comment the B, I, and U buttons can be used to change the text style. Click the link button to insert a hyperlink to a webpage. To assign the comment, click the Send button.

References

References are often re-used; for instance when several parameter values are taken from the same report. The database will store all references that have been created. You can select a previously entered reference from the drop down list and then click apply.

To enter a new reference, click the New button. You can choose either to use the built-in template or to enter free text by selecting the corresponding tab in the window that appears.

Note that you still need to click Apply to add the reference to the instance/entry.

Attachments

Any type of file can be attached to a parameter or instance. For instance, a report could be attached or a document which describes the methods used to derive the parameter values. It is recommended to only attach small files (

To attach a file, click the … button and select the file. Enter a description (optional) and finally click the Apply button.

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Opening the software

Before the parameter database interface appears, you must enter the login credentials given to you by the database administrator.

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About the parameter database

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Quality control

The quality control screen is used for quality assurance. Here an administrator or operator can request review of parameters and assign them to a reviewer. A reviewer can view the parameters assigned to him, write a review comment and either “Recommend” or “Not recommend” instances. When an instance returns from review, an administrator can change the usability status to either “accepted” or back to “draft”.

This window is in appearance much like the Values window, with the exception that values cannot be edited. The tool on the right hand side can be used to search for instances. Selecting an instance will display its values in the table to the right. As this screen is used differently depending on the users role, the function for each role is discussed.

Operator /administrator: Request review of draft parameters

Quality control (operator)

Search for instances in the search tool. To find instances with the usability status of “draft”, expand the search tool by clicking on the more button and then select draft from the Usability drop down menu.

To assign a reviewer to one or more instances, select the instances in the search window. You can select more than one instance by keeping either the SHIFT or CTRL key pressed on your keyboard while clicking in the list. Click the Request review button located in the toolbar above the search results.

A window will appear which prompts you to select a reviewer. Click OK to finish.

You should now see the usability status change from “draft” to “under revision”.

Reviewer: Reviewing data

Quality control (Reviewer)

When an operator search for instances (by using the search tool), only instances that are under review and that are assigned to him/her appear. To search for all instances, search for an empty string in the Name field.

Select an instance in the search results to display its values.

Review comments

When an instance is selected, click the Add comment button to write or change the review of the instance. A symbol will appear in the lower right corner of the instance (in the search window). Moving the mouse pointer over this symbol will display the comment.

Recommed/don’t recommend

Select instances in the search window, and click either Recommend or Don’t recommend. A thumbs up/down icon will be displayed for the instance.

Finalize review

To return an instance from review, select it in the search window and click Mark as reviewed. The usability status of the instance will change from “under revision” to “returned from revision”.

Accept or reject: Administrator

Quality control (Administrator)

The final step in the quality control process is taken when the administrator either accepts or rejects parameters that have been reviewed.

To quickly find parameters to reject/accept, expand the search control panel by clicking more and select returned from revision in the Usability drop-down menu.

To accept/reject an instance, select it in the list and click either Mark as rejected or Mark as accepted.

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Importing data from excel

In short, importing data is done through the following steps.

1. In the right section of the screen, the user selects the file which contains the data to be imported.
2. The file is analysed by the database. For each sheet in the Excel file, a tab is created in the left section. All instances found for in each sheet are then listed in the leftmost column (Excel) of a table under the corresponding tab.
3. Each instance found in the Excel file must now either be matched to an instance already in the database (which will be overwritten) or to a new instance. The database column offers drop down menus where all database instances with the same name as the Excel instance are presented. To create a new instance rather than overwriting an existing instance, click the Create button. If there is an error associated with the import of a given instance, this error is listed in the rightmost column. For an explanation of common errors, see below.
4. If either a Excel or a database instance are selected, the bottom table will display their values.
5. When new or existing instances have been assigned to each Excel instance, click the Import button.

Importing an algorithm

When data is exported from the parameter database a column named Export Info is appended for each row. The Export Info fields contain the search tags of the instance from where the value is taken. Also, the GUID (global unified ID) of the instance is added to the cell as a comment.

This way the database can find which rows belong to which instance when the data is re-imported into the database. A typical scenario would be when a lot of data needs to be inserted into the database. A user can then (1) create empty instances for the data, (2) export these instances to an Excel file, (3) fill in the data in the Excel file and (4) re-import it to the database.

When the user has selected a file to import, the database will analyse the file and display its contents, before the data is imported. It will attempt to identify to which database instance each value belongs and suggest these as targets for the import.

1. First the database will look in the Export Info column. If the column contains a comment with a GUID, and there is an instance in the database with the same GUID, this instance will be selected as the target.
2. If there is no GUID, the database will see if there are tags written in the Export Info column. If there are instances in the database with the same name and the same set of tags, the database will suggest the first of these as the target.
3. If there is no instance in the database with matching name and tag, the database will not suggest anything. The user has to manually either choose an instance or create a new one.

Errors and requirements

The database require that the parameters are defined in the database before values can be imported. For example, if an Excel file contains a parameter named Kd which depends on Element and there are values for Lead, Plutonium and Iodine the database must have a definition for a parameter with this name and with the same dependency. The dependency must contain indices for Lead, Plutonium and Iodine (but can of course contain many others).

Some typical errors would be:

1. There is no definition for the parameter X. This means that there is no definition (for the selected project) with the name X. Note that the database names are case-sensitive.
2. The dependencies are invalid for parameter X. This message appears when the names of (and/or number of) dependencies do not match.
3. There is no index Y in the database. An index for a specific dependency is missing.

Exporting data

The parameter database interface supports export/import from Excel. This way parameter data can be entered in Excel and then quickly imported into the database.

In order to avoid misprinted names and indices in the database, there are some requirements.

1. The database must contain parameter definitions for all the data in the Excel file before the file can be imported.
2. The database must contain dependencies and indices necessary for the data before the file can be imported.
3. The data in the Excel file must be arranged in a fashion so that it can be read by the database.

The best way to import data is therefore to first make sure that the database contains definitions for the parameters and then export a template (blank) file. Data can then be entered into this file and then imported back into the database.

The export screen features the search tool (left) and a workbook-styled panel (right). The user searches for parameters using the search tool and then adds them to sheets in the workbook.

How to export to Excel

Initially the workbook contains only one sheet, named Sheet 0. The sheet can be renamed by clicking on the tab. To add more sheets, click the button.

When the workbook is ready, search the database for instances to add. Select one or more instances from the search result and click the > > button to add them to the current sheet.

Select a file by clicking the … button in the toolbar above the workbook. Both xls (Office -97) and xlsx (Office 2003-2010) formats are accepted.

If you wish, you may change the export options:

• Export empty rows: Add rows for all indices, even when no data is present. This option should be checked when creating “template” files.

• Create column filters: Add Excel filters for columns.

• Open file after export: Ask Excel to open the file after it has been written. Note that this feature does not work for some setups. Also, naturally Excel must be installed on the computer.

• Optimize column widths: Adjust the width of the columns to fit the data. Note that for large files this can take a long time and is better (quicker) to do inside Excel.

Finally, click the Export button to write the data to file.

• About

• Installing the Parameter Database?
• Glossary?
• Naming conventions?
• Numerical conventions?
• Units (Parameter Database)?

• Database design?
• Reference

• Starting the Parameter database
• **Windows**
• Main window
• **Selecting project**
• **Searching**
• **Comments, references and attachments**
• History window?

• Starting the parameter database user interface?
• Menu bar

• Exporting data
• Importing data

• Quality assuring your data

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1) What is the parameter database?

2) Installing and operating

3) Database design

4) Basics

5) Building your database

6) Exporting and importing data

7) Quality assurance

Select Simulation | Simulation Settings, click the Simulation Settings tool bar button or press F6 to open this window.

The simulation settings window contains four pages:

General

Here you specify the start and the end times for the simulation and output options.

Simulation time

• Start Time - This setting specifies the start time of the simulationMost often this value will be left at zero (default value), but there might be cases where another value is required. Default value = 0

• End Time - This setting specifies the stop time of the simulation. Default value = 100

• Time unit - Select the time unit for the simulation.

Simulation outputs

• Output option – By default, the time vector returned from a simulation contains the exact time steps the ODE-solver has chosen. For difficult numerical solutions the number of time points may be very many. Also, it might be of interest to the user to get values for specific time points. The three output options are:

  • Produce no additional output - The time vector will only contain the time steps chosen by the ODE solver. This is the default setting.
  • Produce additional output - The time vector will contain both the time steps chosen by the ODE solver and the time points given in Time Series. Use this setting when your Model contains discrete events to force the ODE solver to include those time points.
  • Produce specified output only - The time vector will contain only the time points given Time Series. This setting will greatly decrease memory consumtion and will improve simulation speed.

Note

For probabilistic, sensitivity analysis and simulation table simulations the output option should be Produce specified output only, otherwise only the start and end time is included in the result. A warning message will be presented in the Errors window. This is to limit the amount of data produced and to guarantee that the same time vector is returned from all simulations.

• Time series – This field is only available when the output option is set to either ‘Produce additional output’ or ‘Produce specified output’. To create a time series click the Add button. From the window that appears select the type of time series you want to create using the drop-down list. You can add as many time series as you want. However, the possibility to add more than one time series is typically only used when you wish to combine a linear/geometric time series with some custom time points. To remove a time series just click the time series to be deleted and click the Remove button.

  • If you select ‘Custom’, enter the time points in the Time point field separated with commas or blank space.
  • If you select ‘Linear’ or ‘Geometric’ time series enter the first and the last time in the Min and Max box respectively. Enter the number of times points in the N box. For example: Start = 5, End = 10, N = 6, Type = Linear will give a time series with the values 5,6,7,8,9 and 10.

In the case of the Linear time series the default value for the Min time is set to the Start Time and for the Max time is set to the End Time. In the case of the ‘Geometric’ time series the default values for the Min and the Max times is set to auto. * If you select ‘Linear Increment’ time series, enter the first and the last time in the Min and Max box respectively. Enter the increment in the increment box. The default value for the Min time is set to the Start Time and for the Max time is set to the End Time. For example: Start = 5, End = 10, Increment = 2.5 will return a time series with the values 5, 7.5 and 10.

• Discrete points - If there are time points that you wish to force the solver to include you can add these here. For instance, if you have conditions at specific time points it might be a good idea to include these time points here so that the solver does not “step over” an important phase of the simulation.

• Add table points - When selected, all time points from lookup tables are added as discrete time points.

Outputs

Note	By default, values for all enabled blocks and parameters for all enabled materials will be returned from the simulation. To exclude materials from the simulation you must enable/disable them in the materials window.

The output page lets you choose simulation endpoints. All blocks of the project are displayed and are organized by sub-system. By selecting/unselecting either endpoints or whole sub-system nodes, you determine which simulation outputs will be available after the simulation is finished.

By removing simulation outputs the simulation time and memory consumption decreases. Also, the list of results will be shorter which makes it easier when creating charts and tables.

As soon as a new block is added to the model, it is also added to the list of outputs.

Solver

(ODE toolbox) The solver page lets you select numerical solver and edit it’s settings.

For more information on solver settings see Solver settings.

Batches

(ODE toolbox) This page lets you set up simulation batches which can improve the simulation time drastically.

• Batch mode - Select to run simulation batches

• Independent batches - Only allow independent batches.

• Join compartments - Create one batch for each compartment (if possible). All materials of each compartment will be run together.

• Join materials - Create one batch for each material (if possible). All compartments will be run together for each material.

• Preview - Shows the batches created following the settings provided above.

Advanced

• Use cache - When set, the results of calculations for the current time point is stored. This will cause a small overhead, and might require more memory, but will in general provide faster simulation speeds.

• Use internal cache - When set, variables that used several times in the same expression will be cached locally prior to the calculation of the expression. Using an internal cache causes slighlty larger models but can give faster simulation speeds.

• Debug mode - When a simulation is run in debug mode, extra checks are added for NaN and infinite values. When the calculations for one object returns NaN or Infinity, the simulation is aborted and an error message is displayed. Also, statistics of the solver performance is displayed after a simulation completes. The debug option can also be set in the simulation preferences window and is global (not project specific).

See also

• Running simulations

The Ecolego 5 Wiki

The Ecolego 5 Player Wiki

The Eikos Standalone Wiki

Eikos help document