= 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) [[span(style=color: #0000FF, '''Collect''' )]]: the gathering or entering of data into the database; (ii) [[span(style=color: #0000FF, '''Manage''' )]]: the inspection and handling of data inside the database; (iii) [[span(style=color: #0000FF, '''Analyze''' )]]: detect patterns and statistically significant differences in the data using algorithms and statistical tests; (iv) [[span(style=color: #0000FF, '''Visualize''' )]]: creating graphs and other visualizations; and (v) [[span(style=color: #0000FF, '''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:

{{{
#!html
<table border="1" cellpadding="2">
	<tr>
		<td valign="top">
			<b>Home</b>
			<br><br> -
		</td>
		<td valign="top">
			<font color="blue"><b>Collect</b></font>
			<ul>
				<li>Single-click importer</li>
				<li>Step-by-step Importer</li>
				<li>Manual data entry</li>
				<li>Remote File Ingest</li>
				<li>Questionnaire</li>
			</ul>
		</td>
		
		<td valign="top">
			<font color="blue"><b>Manage</b></font>
			<ul>
				<li>Explore data tables</li>
				<li>Navigate data folders</li>
				<li>Edit table metadata</li>
				<li>Manage users</li>
				<li>Manage permissions</li>
			</ul>
		</td>
		<td valign="top">
			<font color="blue"><b>Analyze</b></font>
			<ul>
				<li>Query and filter data</li>
				<li>Add and run scripts</li>
				<li>View execution log</li>
				<li>Use APIs for R, Python and REST</li>
				<li>Screen genome with GAVIN</li>
			</ul>
		</td>
		<td valign="top">
			<font color="blue"><b>Visualize</b></font>
			<ul>
				<li>Genome Browser</li>
				<li>Plot data in R how-to</li>
				<li>Visualization using R</li>
				<li>Customize reports</li>
				<li>View data model</li>
			</ul>
		</td>
		<td valign="top">
			<font color="blue"><b>Share</b></font>
			<ul>
				<li>Setup data catalogue</li>
				<li>Setup FAIR endpoints</li>
				<li>Expose data via APIs</li>
				<li>Tag Wizard</li>
				<li>Mapping Service</li>
				<li>Ask a question</li>
			</ul>
		</td>
		<td valign="top">
			<b>Admin</b><br>
			<ul>
				<li>Change menu</li>
				<li>Change theme</li>
				<li>Application log</li>
				<li>Application settings</li>
				<li>Reindex database</li>
			</ul>
		</td>
		<td valign="top">
			<b>My account</br>
			<br><br> -
		</td>
	<tr>
</table>
}}}

== 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 ==

{{{#!comment
A functional MOLGENIS Research demo application is running at: https://research.molgeniscloud.org/.-->
}}}
This work has been published as Van der Velde et al. ''MOLGENIS Research: Advanced bioinformatics software for non-bioinformaticians'', Bioinformatics. 2019 Mar 15;35(6):1076-1078. doi: 10.1093/bioinformatics/bty742.