If you include research software and code in a journal article, the copyright for the article may be transferred to the publisher (in traditional journals), but this does not automatically transfer copyright for the underlying software, unless explicitly stated in the terms and conditions of the publisher. Researchers should therefore check the terms of the publishing agreement carefully.

Researchers should not transfer the copyright of your code & software to the publisher, but to publish your code & software separately (e.g., on GitHub, Zenodo) under an open-source license (e.g. MIT, GPL, Apache), and then to cite it in your paper.

For example, the Journal of Open Source Software allows authors to retain their copyright whilst any code is subjected to MIT license.  

Before publishing under an open-source license, researchers should check with NTUitive if the IP is commercially viable/feasible.   

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