We created MOLGENIS to accelerate scientific discovery and improve peoples lives. MOLGENIS promotes data, tool and best practice (re)use and helps you to implement Open Science and FAIR principles. MOLGENIS provides the following features:

Structured Data Management

Model, capture, and manage your data. Quickly upload data files, or enter data via user friendly forms. Refine your data model dynamically using MOLGENIS advanced 'object-relational' data definition format and the online metadata editor.
Example: https://hfgp.bbmri.nl/

FAIR data sharing

Make your data findable, interoperable, accessible, reusable (FAIR). We believe data sharing and re-use should be easy. MOLGENIS enables you to quickly create explorers for your data sets and variables to the outside world while preventing exposure of (sensitive) data values using the fine-grained permission system.
Example: http://www.palgaopenbaredatabank.nl

secure access

Easily control group, role and individual access. MOLGENIS data is organised following scientific practice. Data can be divided in research groups, within the groups you can assign roles such as 'data manager', 'data editor' and 'data user'. Authentication can be ensured by connecting you institute account via SURFconext (NL) and BBMRI/ELIXIR AAI (Europe) or using Google two-factor authentication.

Scripting & visualisation

Bioinformaticians can take full control in MOLGENIS. Add scripts in your favorite programming languages (e.g. R, javascript, python) and connect to the data using API's to add great analysis tools and views. Or even create complete html + javascript apps to make MOLGENIS completely your own.
Example: http://molgenis.org/ase

Harmonization and integration

Make your data interoperable. Combined analysis is much more powerful than running smaller analyses on each data set separately, but data integration is hard. MOLGENIS offers you multiple 'FAIRification' tools to find related data, codify your data contents and transforms different tables into one standardized table.
Examples: http://biobankconnect.org and http://molgenis.org/sorta

Task automation

Automate data upload, tranformation and statistics. Frequently data from multiple sources must be combined for success. Therefore, data exchanges, transformations, and analyses must be repeated often. We believe in reproducible science so you can automate tasks with MOLGENIS job scheduling tools.


Get data directly from the source. Use the questionnaire tool to ask for individuals input. The tool provides chapters, subquestions, advanced validations, conditional or 'skip' questions and intermediate save (so you can fill in the rest of the survey later).

Extreme customization

Change data structure, menus, logic and layout. MOLGENIS is the only software in its class that allows complete data model freedom. In addition you can completely change menu structure, user interface and permission system. Finally, use theme styles to fit your website seamlessly, like a chameleon.

App development platform

Add your own user interfaces to the app store. MOLGENIS gives programmers the complete freedom to create HTML+JavaScript applications using MOLGENIS REST-style programmers interfaces. But it gets even better: you can upload these apps like plugins to become part of MOLGENIS itself and use them seamlessly.

High performance computing

Easily schedule large scale analysis jobs on a computer cluster. MOLGENIS does also provide a high performance computing framework. We call it simply 'compute' and it uses simple spreadsheets to define workflows, and templates to define workflow steps. It works on PBS and SLURM.