= 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
Home

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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


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}}} == 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 (v5.1.0) 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.