SODAR

SODAR provides

• FAIR data management for Omics studies,
• a web interface for biomedical scientists,
• command line interface and API for bioinformaticians.

For an introduction to SODAR, view the following video by Mikko Nieminen:

Features

• Scalable data storage for
  • NGS raw data & metadata
  • Processing Results
  • Extendable metadata model, based on the ISA Tools Standard
• IGV and UCSC Integration
• Data Privacy
  • Charité & MDC user authentification
  • Project based authorization with different access levels
  • Full audit trails
• Web-based graphical user interface for biomedical scientists
• REST API for data/systems integration
• Command line interfaces for bioinformaticians
• Data storage built on iRODS
• Metadata editor
• In use for 300+ projects with 350TB+ of stored data

Related resources and documentation

• Description of the local SODAR resource
• SODAR demo site
• SODAR manual
• BIH/MDC/Charite instance is reachable from internal networks

Technology

• Slides from the talk of Mikko Nieminen on SODAR during the 2022 iRods user group meeting
• Talk on the technology and use cases at the 2019 iRODS User Group Meeting, 30 minutes on youtube

Licence and Availability

• Availability
  • Published on GitHub under the MIT license
  • SODAR Server repository
  • SODAR Docker Compose network for evaluation, development and deployment
• Contact: Mikko Nieminen

Related Publications

Nieminen M, Stolpe O, Kuhring M, Weiner J, Pett P, Beule D, Holtgrewe M (2023). “SODAR: managing multiomics study data and metadata.” Gigascience, 12, giad052. doi:10.1093/gigascience/giad052 ☞ Link

Nieminen M, Stolpe O, Kuhring M, Weiner J, Pett P, Beule D, Holtgrewe M. SODAR: enabling, modeling, and managing multi-omics integration studies. bioRxiv. 2022 Aug 22.

M. Nieminen, O. Stolpe, F. Schumann, M. Holtgrewe, D. Beule. SODAR Core: a Django-based framework for scientific data management and analysis web apps, doi:10.21105/joss.01584

Last modified: Jul 27, 2023