Tools

platform - catalogue - registry - vip - armadillo - hpc

platform

EMX2 platform is the backend for many of MOLGENIS applications. It provides ability to create a custom data schema. Using this model, you get tools to capture, query and manage your data. Quickly upload data files using templates generated from your model. Or enter data via user friendly forms.

Source code: github.com/molgenis/molgenis-emx2

Getting started:

1. install molgenis platform
2. create new database and select no template
3. use the schema editor to create your model or upload a schema template

Examples:

• Prospectively study of 1000 IBD patients from the Northern provinces of the Netherlands
• Human Functional Genomics Project
• WormQTL - Public archive and analysis web portal for natural variation data in Caenorhabditis spp

catalogue

MOLGENIS Catalogue enables creation of FAIR data catalogues, including support for FDP and DCAT. In addition we provide MOLGENIS catalogue as a service a range of health research consortia and organisations to increase discoverability and accelerate reuse of data and samples.

Source code: github.com/molgenis/molgenis-emx2

Getting started:

1. install molgenis platform
2. create new database and select the ‘catalogue’ template
3. read more in catalogue docs

Public instances:

• European health data and sample network catalogue
• European directory of biobank collections (BBMRI-ERIC)
• LifeLines request portal of data and materials
• Dutch catalogue of human data and sample collections (BBMRI-NL)
• Catalogue of rare disease samples (RD-Connect)
• Dutch catalogue of pathology samples (PALGA)

News:

• publication: Bergeron et al (2024) Stress and anxiety during pregnancy and length of gestation: a federated study using data from five Canadian and European birth cohorts. Eur J Epidemiol.
• publication: Cadman et al (2024) Social inequalities in child mental health trajectories: a longitudinal study using birth cohort data 12 countries. BMC Public Health
• publication: Cadman et al (2024) Urban environment in pregnancy and postpartum depression: An individual participant data meta-analysis of 12 European birth cohorts. Environment International

registry

Best practice emx templates for patient, mutation and disease knowledge to understand relations between genetics, environment and disease.

Source code: github.com/molgenis/molgenis-emx2

Getting started:

1. install molgenis platform
2. create new database and select the ‘registry’ template
3. customize disease details

Examples:

• Deb-central: patient registry for Epidermolosis Bullosa
• International registry of Microvillus Inclusion Disease (MVID) patients and associated MYO5B, STX3 and STXBP2 mutations
• Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (ARVD/C) Genetic Variants Database
• Open-access database on CHD7 mutations

vip

MOLGENIS VIP is a flexible human Variant Interpretation Pipeline for rare disease using state-of-the-art pathogenicity prediction (CAPICE) and template-based interactive reporting to facilitate decision support. More info: https://molgenis.github.io/vip/

Source code: github.com/molgenis/vip

Getting started:

1. install VIP
2. create a sample sheet describing your data
3. start running

armadillo

MOLGENIS Armadillo is a data portal that allows data stewards to share datasets on a server, and researchers to analyse these data and those shared on other servers using the DataSHIELD analysis tools. MOLGENIS is active partner in the DataSHIELD organisation. More info: https://molgenis.github.io/molgenis-service-armadillo/

Source code: github.com/molgenis/molgenis-service-armadillo

Getting started:

1. Download and install armadillo
2. Upload data into Armadillo
3. Install DataSHIELD analysis packages and grant access

News:

• publication: Bergeron et al (2024) Stress and anxiety during pregnancy and length of gestation: a federated study using data from five Canadian and European birth cohorts. Eur J Epidemiol.
• publication: Cadman et al (2024) Social inequalities in child mental health trajectories: a longitudinal study using birth cohort data 12 countries. BMC Public Health
• publication: Cadman et al (2024) Urban environment in pregnancy and postpartum depression: An individual participant data meta-analysis of 12 European birth cohorts. Environment International

hpc

MOLGENIS provides high performance computing (HPC) clusters for large-scale genomic analysis and data processing. The clusters run on OpenStack with Rocky Linux and use Slurm for workload management. Multiple clusters are available for different research groups, including Hyperchicken and Nibbler (UMCG Research IT).

The HPC environment supports a wide range of bioinformatics tools via EasyBuild modules, Conda/Bioconda, containers (Apptainer/Singularity), Nextflow pipelines, Jupyter notebooks, and RStudio.

Source code: github.com/rug-cit-hpc/league-of-robots

Getting started:

1. Request access
2. Learn how to use the HPC
3. Generate an SSH key pair and connect via jumphost

News:

• publication: Johansson et al (2024) An interconnected data infrastructure to support large-scale rare disease research. GigaScience.