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bioRxiv · 10.1101/2022.08.19.504516

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

Nieminen, M.·Stolpe, O.·Kuhring, M.·Weiner, J.·Pett, P.·Beule, D.·Holtgrewe, M.
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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. They must manage many large files that are the results of the assays or subsequent computation. Users with diverse backgrounds, ranging from computational scientists to wet-lab scientists, have dissimilar needs when it comes to data access, with programmatic interfaces being favored by the former and graphical ones by the latter. We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses these challenges by providing a web-based graphical user interface for managing multi assay studies and describing them using the ISA (Investigation, Study, Assay) data model and the ISA-Tab file format. Data storage is handled using the iRODS data management system, which handles large quantities of files and substantial amounts of data. SODAR also offers programmable APIs and command line access for metadata and file storage. SODAR supports complex 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 the MIT license.

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Nieminen, M., Stolpe, O., Kuhring, M., Weiner, J., Pett, P., Beule, D., Holtgrewe, M.. 2022-08-22. SODAR: enabling, modeling, and managing multi-omics integration studies. https://doi.org/10.1101/2022.08.19.504516

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