- Model script: Calculates the results of the script (mandatory)
- Parameters script: Used in some models to initialize parameters in the model (currently optional)
- Visualization script: Generates some form of visualization for the results of the model (optional)
- Model meta data encoded using the OpenFSMR template.
- Set of libraries used.
Type SId
Some properties are taking 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*
Examples of valid SId: escherichia_coli10, _eColi.
Examples of invalid SId: 0escherichia_coli, , 0.
Structure of the metadata spreadsheet
Properties with multiple values
Properties taking multiple values are encoded using the two characters || as splitter. For example two variable units grams and liters would be encoded as gram || liter. If a variable has no unit then a whitespace is used instead, e.g. gram || .
Related properties like the independent variables have the same number of values across the properties. Therefore, the independent variable names, units, minimum and maximum values must have the same number of values to describe N variables. If a value is missing like a variable without unit then a whitespace must be used instead.
| Property | Cell | Data type |
|---|---|---|
| Name | F2 | String |
| Identifier | F3 | SId |
| Organism(s)+Species | F4 | SId |
| Organism(s)+Species-Details | F5 | String |
| Environment+Compartment(s) | F6 | SId |
| Environment+Compartment(s)_Details | F7 | String |
| Creator | F8 | String |
| Reference description | F9 | String |
| Created | F10 | Date |
| Modified | F11 | Date |
| Rights-Accessibility | F12 | String |
| PMF-General-Notes | F13 | String |
| PMF-Type | F14 | String |
| PMF-Subject | F15 | String |
| PMF-Software | F16 | String |
| PMF-Link-URL | F17 | URL |
| PMF curation status | F18 | String |
| PMF goodness of fit | F19 | String |
| PMF stochastic modeling? | F20 | String |
| PMF prediction conditions | F21 | String |
| PMF dependent variable | F22 | SId |
| PMF dependent variable unit | F23 | SId |
| PMF dependent variable min | F24 | Number |
| PMF dependent variable max | F25 | Number |
| PMF independent variables | F26 | SId (multiple values) |
| PMF independent variable units | F27 | SId (multiple values) |
| PMF independent variable minimum value | F28 | Number (multiple values) |
| PMF independent variable maximum value | F29 | Number (multiple values) |
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