OMICtools uses code versioning to enhance tool traceability
Software tools on the Web evolve over time, with developers adding or removing features to improve their product, making code versioning an essential aspect of sustainable software development. Reliable code versioning allows developers to automatically track their work and revert to previous versions when needed.
Discover here how OMICtools can help you facilitate the traceability of your tool – and learn how to successfully upload your work in a community-controlled repository.
Benefits of version control
- Provides a mechanism to keep track of code changes
- Allows you to track the history of changes, work on the same code files, and merge code from different branches
- Shows conflicts on code merges, allowing you to resolve them quickly
Following the FAIR data principles
The FAIR system provides recommendations for scientific data management and stewardship. OMICtools applies the FAIR guidelines to bioinformatics tools, by making them easily Findable, Accessible, Interoperable and Reusable.
- Findability: Software and code versions are easy to find with the OMICtools advanced search engine. We continuously collect and update information from original articles, websites and repositories to make available the latest bioinformatics tools.
- Accessibility: OMICtools ensures ongoing access to software tools, contributing to make knowledge and support available for users. Clear and accessible relevant information as well as a direct link to the original source are provided for each tool. We also provide metadata about the tool maintenance and use (name and email of the tool developer, forum and feedbacks from the biomedical community).
- Interoperability: As far as possible, we record all tools which can be combined with other datasets by either users or computer systems. Maintainability of software is only one of the quality dimensions. Each tool on the OMICtools website also has a unique Research Resource Identifier (RRID), developed under the Resource Identification Initiative, which is transferred to the Neuroscience Information Framework (NIF) registry.
- Reusability: OMICtools keeps a complete history of code versions so that they can be easily accessed and/or downloaded. This long-term software archive allows all users easy access to a previous version.
Uploading and versioning your source code
If you want to version your source code, you can get started by finding your tool in the OMICtools repository using the search engine. Once you find it, click the upload version button and follow the instructions. All you need to do is indicate the version of the source code, the operating system and architecture, and add the publication linked to the code. It’s as quick and easy as that – and of course you can contact us with any questions.
Once your code is uploaded, the programmatic access to DataCite’s API automatically generates the corresponding DOI. This unique identifier is defined by the International DOI Foundation and assigned by OMICtools to allow precision long-term preservation of your tool. If a DOI has already been attributed for your code version, you can let us know and it will be directly imported from the software platform you used. The DOI and files can’t be modified later.
This control repository service is designed to facilitate the development, maintenance and follow-up of bioinformatic tools by the designers themselves. An overview of the variety of distribution channels of the tools
Remember that each published source code version is registered with a unique DOI which provides a permanent identification of your resource, even if material is moved or rearranged. Hence OMICtools, not only supports scientists in the analysis and understanding of biological datasets, but also improves the precision of citing bioinformatics methods used to produce and reproduce results, thereby promoting the quality of scientific publications in accordance with the FAIR guiding principles for scientific data management.