SODAR: enabling, modeling, and managing multi-omics integration studies

Abstract

Scientists employing omics in life science studies face challenges such as the modeling of multi assay studies, recording of all relevant parameters, and managing many samples with their metadata. Further, they must manage many large files that are the results of the assays or subsequent computation.

Scientists from diverse backgrounds also have different demands for interfacing with the data, ranging from computational users that need programmatic or command line access whereas non-computational users need graphical interfaces.

We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses the points above by providing a web-based graphical user interface for managing multi assay studies and describing them using the open ISA (Investigation Study Assay) data model and ISA-Tab file format. Data storage is handled using the iRODS data management system which effortlessly handles many files and large amounts of data. SODAR also provides programmable APIs and command line access for metadata and to file storage.

SODAR supports multi-omics integration studies and can be easily installed. The software is written in Python 3 and freely available at https://github.com/bihealth/sodar-server under a permissive opensource license.