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

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 under a permissive opensource license. ### Competing Interest Statement The authors have declared no competing interest. * ### 6. Abbreviations API : Application Programmable Interface CUBI : Core Unit Bioinformatics ELN : Electronic Laboratory Notebook GUI : Graphical User Interface HPO : Human Phenotype Ontology HTTP : Hyper Text Transfer Protocol IGV : Integrated Genomics Viewer IRODS : Integrated Rules-Oriented Data System ISA : Investigation Study Assay LDAP : Lightweight Directory Access Protocol LIMS : Laboratory Information Management System MIT : Massachusetts Institute of Technology (also commonly used with “MIT license”) NCBI : National Center for Biotechnology Information OBO : Open Biological and Biomedical Ontologies OpenBIS : Open Biology Information System OWL : Web Ontology Language PAM : Pluggable Authentication Mechanism PEP : Portable Encapsulated Projects SODAR : System for Omics Access and Retrieval TB : Tuberculosis TSV : Tabular Separated Values UCSC : University of California Santa Cruz WebDAV : Web-based Distributed Authoring and Versioning)