- 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.
Model metadata
One row table with metadata of the model read from the file. Every column describes a different property.| Column name | Data type |
|---|---|
| Model name | String |
| Model id | SId |
| Model link | String |
| Organism | SId |
| Organism details | String |
| Environment | SId |
| Environment details | String |
| Model creator | String |
| Model family name | String |
| Model contact | String |
| Model reference description | String |
| Model reference description link | String |
| Created date | Date |
| Modified date | Date |
| Rights | String |
| Notes | String |
| Curation status | String |
| Model type | String |
| Subject | String |
| Food process | String |
| Dependent variable | SId |
| Dependent variable unit | SId |
| Dependent variable type | String |
| Dependent variable min | Number |
| Dependent variable max | Number |
| Independent variables | SId (multiple values) |
| Independent variable units | SId (multiple values) |
| Independent variable types | String (multiple values) |
| Independent variable mins | Number (multiple values) |
| Independent variable maxs | Number (multiple values) |
| Independent variable values | Number (multiple values) |
| Has data? | String |
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.
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.
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