Quickstart guide

Using our demo server

The first thing you can do is to get some hands-on experience by trying out our demo server. This server contains several data sets including biobank data and genetic data. If you want to try importing some example files, then the only thing needed from your end is that you create an account. An email will be sent containing your login in credentials. But perhaps you want to see how your own data looks like, but not upload it for other people to see, not yet anyway. So let's jump right into that.

Getting your first data in

So you have a MOLGENIS application up and running, and your dataset is sitting nice and cozy on your computer somewhere, now what? We upload the data of course! As mentioned before, MOLGENIS uses an extensible model format allowing you to model your data however you want. This is done via the EMX format. Now I know a custom format sounds scary, but if you keep reading for a bit, you will find out it's not scary at all.

We wanted researchers to be able to describe their data in a flexible 'meta model'. This sounds really interesting, but what it boils down to, is that you have one separate xlsx sheet that describes your column names, or attributes as we call them. Thats it. Thats all the EMX format is. Keep reading to find a detailed example.

Creating an EMX file

If you want to skip this theory lesson and download an excel file right away to use as a template, you can find several of them on Github. Be advised that these are files for testing purposes, and do not have real data in them, so they might not fully represent the complexity of your own data.

Now for the example. Say that you have an existing excel sheet with a couple of thousand rows of data and several columns. This data can look something like this:

Data sheet:

Identifier Gene Protein measured Protein count
A12345_Z BRCA2 P51587 321
B12345_Y BRCA2 Q86YC2 123
C12345_X BRCA2 Q9P287 213
D12345_W BRCA2 P46736 231
E12345_V BRCA2 Q8MKI9 312

Now to make this into a full fledged EMX file, all you have to do is create a new sheet within the same file and call it attributes. To give an idea on what the purpose of this sheet is, it will describe the columns that you have set for your data. This description allows MOLGENIS to properly store and display it. An attribute sheet will look something like this:

Attribute sheet

name entity dataType description refEntity idAttribute nillable
Identifier example_data_table string The identifier for this table TRUE FALSE
Gene example_data_table string The HGNC Gene identifier FALSE TRUE
Protein measured example_data_table string The protein that was measured FALSE TRUE
Protein count example_data_table int Number of proteins measured FALSE TRUE

This little bit is all you need. You specify the name, which is the name you gave to the column already. The entity is the name the table will get when it is stored in the database. The dataType is, as you might have guessed, the type of data that is present in each column. The description column allows you to describe your attribute. If you want to have a value point to another table, you can use the refEntity column. Complex data structures do not always consist of a single table, we support multiple table models through this system of reference entities. The idAttribute parameter will tell MOLGENIS that this is the primary key. It has to be unique, and it is not allowed to be null or missing. With the nillable parameter you can enforce whether an attribute is allowed to be missing or not.

This is a minimal example of how you can use one extra sheet and a few columns to properly define your meta data. MOLGENIS is now capable of importing your data, storing it, displaying it, and making the data query-able.

Importing your EMX file

So you have a MOLGENIS application running locally or on the server, and working with the example in the previous paragraph you have now converted your dataset into the EMX format. So I guess it is time to upload!

Browse to wherever your application is running, and login as admin user. Go to the Upload menu. You now should see something like this:

Importer first screen

To keep it simple, all you need to do is click the 'select a file' button, select your newly made EMX file, and press the next button until it starts importing. Don't worry about all the options you are skipping, we will handle those in the upload guide. After your import is done, you can view your data in the data explorer. Go there by clicking the 'Data Explorer' link in the menu.

Congratulations! You have now deployed MOLGENIS either locally or on a server, and you have made the first steps on getting your data into the MOLGENIS database. Play around a bit with the different data explorer filters to get a feel on how MOLGENIS works.

Of course, simply uploading and showing data is not the only thing you can do with the MOLGENIS software. In the following MOLGENIS step-by-step section, we will take you from being a simple user, and teach you on how to be an expert.

Running your own MOLGENIS

You can run MOLGENIS on you local machine or on your own linux server.

Either you run it in Maven cargo, in a local Tomcat webserver, or you clone the code from GitHub and compile it to start developing

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