MOLGENIS Research

Background

The amount of biological data and biological data layers is rapidly increasing. Many medical doctors and biomedical researchers without a bio-informatics background are generating large big data so-called ’-omics’ datasets, but do not always have the skills to process, manage or publicly share these data. In this paper, we present MOLGENIS Research, an open-source web-application that allows non-bioinformaticians collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills.

Data flow

MOLGENIS Research contains a selection of apps that are of particular interest to life science investigators. These apps are grouped into the five categories that represent the typical flow of research data: (i) Collect: the gathering or entering of data into the database; (ii) Manage: the inspection and handling of data inside the database; (iii) Analyze: detect patterns and statistically significant differences in the data using algorithms and statistical tests; (iv) Visualize: creating graphs and other visualizations; and (v) Share: making data, the visualizations, and the results available to collaborators or the entire scientific community.

Therefore, the menu structure of MOLGENIS Research is as follows:

Home -	Collect Import data quick Import data advanced Import data manually or annotate Ingest files remotely Fill in questionnaire	Manage Explore data tables Explore data folders Edit metadata Manage users Manage permissions	Analyze Query and filter data Add and run scripts View execution log Use APIs for R, Python and REST Screen genome with GAVIN	Visualize Browse genome and charts Plot data in R how-to Visualization using R Customize data reports View data model	Share Setup data catalogue Setup FAIR endpoints Expose data via APIs Tag data with ontologies Integrate data with ontologie Ask a question	Admin Change menu Change theme Application log Application settings Reindex database	My account -

Installation

MOLGENIS Research can be installed first setting up a default MOLGENIS, followed by importing an EMX file with custom menu structure and minimal demo data. In a nutshell:

• Download and install MOLGENIS (v5.2.0) at: ​http://search.maven.org/remotecontent?filepath=org/molgenis/molgenis-app/5.2.0/molgenis-app-5.2.0.war
• Download and import MOLGENIS Research at: ​http://molgenis.org/downloads/molgenis-research/MOLGENIS_Research_v0.1.xlsx
• Use the Advanced Excel Importer, andselect the option to 'Add entities / update existing'.
• For detailed instructions and more installation options, please see the documentation at: ​http://molgenis.github.io/

Demo and citation

A functional MOLGENIS Research demo application is running at: ​https://molgenis83.gcc.rug.nl.

This work has been published as Van der Velde et al. MOLGENIS Research: Advanced bioinformatics software for non-bioinformaticians, PubMed? ID xxxx, DOI: xxxxx.