1. Molgenis default
   How to
   a. Websites
   b. Publications
2. 1000IBD
   a. Websites
   b. Publications
3. BBRMI-ERIC
   a. Websites
   b. Publications
4. VKGL How to a. Websites

MOLGENIS: Flexible software for scientific data

Css minified in molgenis repository using: https://cssminifier.com/

http://molgenis.github.io/

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. - Swertz et al.
https://www.ncbi.nlm.nih.gov/pubmed/21210979
Beyond standardization: dynamic software infrastructures for systems biology. - Swertz & Jansen
https://www.ncbi.nlm.nih.gov/pubmed/17297480

The 1000IDB project describes patients and samples with inflammatory bowel disease.

A public MOLGENIS data server can be found here.
It contains an overview of data and research results.

TODO: add papers + url's

BBMRI-ERIC aims to establish, operate and develop a pan-European distributed research infrastructure of biobanks and biomolecular resources in order to facilitate the access to resources as well as facilities and to support high quality biomolecular and medical research.

A public MOLGENIS data server can be found here.
It contains the BBMRI-ERIC Directory containing biobanks and sample collection metadata form organizations all over Europe.

You can read more about the BBMRI-ERIC groups and projects at http://www.bbmri-eric.eu/

Biopreservation and Biobanking - Holub Petr, Swertz Morris, Reihs Robert, van Enckevort David, Müller Heimo, and Litton Jan-Eric
http://online.liebertpub.com/doi/10.1089/bio.2016.0088

This script downloads data from one server of BBMRI eric and uploads it to a specified target server. The datamodel is altered. This new model is specified in the data_model folder. This new model will be uploaded. The old data retrieved from the specified server will be converted to the new model. Invalid rows will be filtered out and written to logfiles. The valid data will be uploaded in the models

Add a config.txt file in the format of config_example.txt, in the same directory.
Config.txt:

url=http(s)://source-server/api/
account=username
password=password
countries=AT,BE,CZ,DE,EE,FI,FR,GR,IT,MT,NL,NO,PL,SE,UK,LV
target_server=http(s)://target-server/api/
target_account=username
target_password=password

To upload without countries, set the "countries" parameter to "FALSE" in the config file.

Run the script:

python3 Bbmri_data_mover.py

Model for countries will be created in /datamodel/countries. Model for general directory is already in /datamodel and will be zipped as: meta_data.zip

Data will be retrieved from one server, converted to new model and put in the new server. Invalid rows are filtered out.

Logs will be created in /Bbrmi_eric_quality_checker. Two logs will be written:

Association of Clinical Lab Diagnostics (Vereniging Klinische Lab Diagnostiek)

This script generates the consensus table for the VKGL project
Requirements before running:

• Incude a config.txt in the directory of this project. The file should look like: config_example.txt.
• Include omim.txt, which is a biomart export with unique rows containing the columns: Gene_stable_ID, MIM_disease_accession, HGNC_symbol
• Make sure you have loaded tables with the metadata of the VKGL project on your molgenis server.

Run:

python3 VKGL_consensus_table_generator.py

This script generates the ClinVar export per lab. Variants exported to ClinVar meet the following rules:

• Variant has consensus classification
• Only one OMIM code is selected for the variant in the consensus table

Requirements before running:

• Incude a config.txt in the directory of this project. The file should look like: config_example.txt.

python3 ConsensusTableParser.py

http://www.vkgl.nl/nl/
http://molgenis.org/vkgl