- Molgenis default
How to
a. Websites
b. Publications - 1000IBD
a. Websites
b. Publications - BBRMI-ERIC
a. Websites
b. Publications - VKGL
How to
a. Websites - Chromosome6 project a. Websites b. Publications
MOLGENIS: Flexible software for scientific data
Css minified in molgenis repository using: https://cssminifier.com/
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:
| Logfile | Description |
|---|---|
| logs.txt | Contains all rows with invalid data |
| breaking_rows.txt | Contains data invalid rows that are not uploaded in the new model on the target server |
Association of Clinical Lab Diagnostics (Vereniging Klinische Lab Diagnostiek)
This script generates the consensus table for the VKGL project
To run: incude a config.txt in the directory of this project. The file should look like: config_example.txt.
Make sure you have loaded tables with the metadata of the VKGL project on your molgenis server.
Now run VKGL_consensus_table_generator.py
Work in progress
http://www.vkgl.nl/nl/
http://molgenis.org/vkgl
The chromosome 6 project aims to compare alterations in chromosome 6 (the genotype) with the effect they have on the appearance features and other clinical features of individuals with chromosome 6 abberations.
The phenotypic spectrum of proximal 6q deletions based on a large cohort derived from social media and literature reports - Engwerda et al. https://www.nature.com/articles/s41431-018-0172-9