MOLGENIS How-to
With MOLGENIS you can generate a complete experiment database from one specification.
Step 1a: What do you want to have?
We want to have a web database to store our experiments in, with accompanying samples and
measurements:
Experiment
Sample Measurement
Step 1b: Describe it
MOLGENIS uses XML to define an application intuitively (see XML primer, below).
TIP: the button nicely layouts your XML. Alternatively, use your favority XML
editor.
The “entity” attribute indicates the data type we want to edit in the form. These we will detail in
step 2.
Step 2a: Add details: what exactly do you want to store?
Experiment
Name: string (unique)
Description: text
Added: date (automatic)
Can have many samples
Can have many measurements
Added date cannot be changed.
Sample Measurement
Name: string (unique) Id: number (automatic, unique)
Strain: string Data: text
Weight(mg): number …
Can have many measurements
Step 2b: Describe it in DSL
…
Step 3: Run the generator.
Complete specification blueprint.
Xml primer
Well-formed XML
XML has a simple set of rules:
1.
has to be closed with .
2.
can contain something, e.g., sometext
3.
with the slash cannot contain anyting and doesn’t have to be closed
4.
or can have attributes
Valid XML
XML is extendible, so people can add additional rules. MOLGENIS has added the following
rules (see ref[1] for complete documentation):
... [1 or more field]
...[1 or more field]
...[a form can contain 0 or more or ]
...[a menu can contain 0 or more or ]
...[0 or more menu or form]