https://github.com/bihealth/sodar-server

SODAR: System for Omics Data Access and Retrieval

https://github.com/bihealth/sodar-server

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SODAR: System for Omics Data Access and Retrieval

README.rst

SODAR
=====

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SODAR (System for Omics Data Access and Retrieval) is a specialized system for
managing data in omics research projects. SODAR provides biomedical scientists
with a single point of access to data in their projects, along with linking out
to external resources and systems.

The main features of SODAR:

- Project based access control and data encapsulation
- Modeling study design metadata
- Large scale data storage
- Linking files to metadata
- Validation of file uploads
- Various tools for aiding in data management

See the
`SODAR Overview video on YouTube `_
for an introduction to the system and its features.

Getting Started
---------------

For instructions on using and administering the system, see the
`SODAR manual `_.

For trying out the system or deploying it in production, see the
`SODAR Docker Compose `_
repository.

**NOTE:** The v1.0 release of SODAR contains breaking changes for its deployment
environment! For instructions on how to upgrade an existing system, see the
`administrator upgrade guide `_.

Technical Information
---------------------

SODAR provides a web-based GUI and REST APIs running on the
`Django `_ web server.

Studies are modeled with the `ISA Model `_ specification.
For file storage SODAR uses the `iRODS `_ open source data
management software.

Django apps provided by SODAR:

- **Samplesheets**: Modeling of study metadata in the ISA-Tab format
- **Landingzones**: Management of file validation and uploads into iRODS
- **Irodsadmin**: iRODS data administration helpers
- **Irodsbackend**: Backend app for iRODS queries and operations
- **Irodsinfo**: Display iRODS server information and create user configurations
- **Isatemplates**: Upload and manage custom ISA-Tab templates
- **Ontologyaccess**: Parse, store and serve ontologies for local lookup
- **Taskflowbackend**: Run iRODS transactions with full rollback for project and
  file operations

The project is built on the `SODAR Core `_
framework, which provides the base functionalities for project management, user
interfaces and dynamic app content inclusion.

**Note:** The project and documentation may refer to practices, services or data
specific to research work at Berlin Institute of Health, Core Unit
Bioinformatics. You may need to adapt them if you wish to deploy your own SODAR
instance.

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