- Module-Administration
- System Settings
- User Administration
- Review Data
- Types
- Formats
- Sources
- Set up Catalogue
- Concepts
- Concept Implementations
- Concept Usages
- Parameters
- Parameter Roles
- Parameter Types
- Parameter Type Aliases
- System Reports
- Define Project Types
- Define Assay Stages
Module-Administration¶
The administration module provides a set of functionality to adapt BioRails to integrated into your current IT infrastructure minimising the need to code integration modules. The sub module are presented in the order in which the system needs to be set up. These steps are (assuming you have successfully installed the application):
System Settings¶
The system settings are used to set the theme, messaging and a number of other system configuration settings. These can be extended by appending to the config/systemsettings.yml file.
User Administration¶
After bootstrapping login to BioRails using admin/admin, then register each of your users with a default role. By default the users are added to the all-users team. There are roles loaded with the bootstrapped data. These can be modified.
Teams can be added however for smaller systems everyone may as well be in the same team.
Review Data¶
There are a number of data entities that should be reviewed when setting the system up.
Types¶
These are the types of data managed in the system and you are very unlikely to ever need to change these, in fact our advice is DO NOT CHANGE DATA TYPES.
Formats¶
Data formats provide data validation and display functionality, mainly for dates and text values.
Sources¶
External databases can be integrated as data sources in BioRails which allows concept implementations or look-ups to defined against them in the catalogue
Set up Catalogue¶
With the data sources in place the catalogue can now be extended. Concepts can be [[Glossary-ConceptImplementation|implemented] providing lookups that can be exposed as dictionary-based parameter types by adding a usage.
Concepts¶
Concepts represent a class of dictionaries and can be arranged in a hierarchy of specialisations. The structure of this names space should reflect the requirements of the implementation. Along with parameter-types this step is a key consideration as a well organised catalogue will help assure consistency and simplify the query and reporting processes.
Concept Implementations¶
Multiple lookups can be defined for a concept. These can be of three types and point to any data source. These are- Lists - added as comma separated strings eg
text1, text2, text3 - Model - added as the model name (usually singular of the table name)
- SQL - added as a select statement
SELECT id, name FROM table WHERE clause;
Concept Usages¶
To implement a dictionary based parameter type an implemented concept must exist. The name and description are then used for the new parameter type.
Parameters¶
parameter types are either based on data types or on concept implementations.
Parameter Roles¶
By default, four parameter roles are provided. These can be changed but their usage can be summarised as follows
| Role | Description | Example |
|---|---|---|
| subject | The subject of the experiment | Patient, Animal, Compound, Plate |
| input | a measurement or observation | CPM, body weight |
| variable | a condition of the assay | Receptor, Species, Dose, Control |
| result | an output of the process, key or summary data | Activity, IC50, body-weight reduction |
Parameter Types¶
Parameter types form the key dimensions against which structured data are captured. By design parameter types are high level which are then specialised as assay parameters where they may be renamed but will inherit the behaviour of their parent parameter type. An example may be a parameter type of Response which is implemented as Inhibition or Activity in assay definitions.
Parameter Type Aliases¶
A parameter type can have an extra level of control placed over its usage by declaring an Alias. If an alias is defined the alias(es) become a selection when the parameter type is added as an assay parameter. This functionality is available from the show of parameter types.
System Reports¶
Review System reports can be modified in the same way as project reports, changing the content, column order, adding filters etc.
Define Project Types¶
Any number of project types can be defined. When it is registered, the layout of the project dashboard is selected from the sub folders in app/views/project/projects
Define Assay Stages¶
Assay stages can be renamed or extended