Scientific publications and related software sourcecode
You could try to extract this information from the Related identifiers of Zenodo software records (the related identifiers that are marked as Supplement to). 

Here are two examples:


https://zenodo.org/record/345130
https://zenodo.org/record/570830


This is the search for all software records in the database:

Zenodo offers data following the crawling protocol OAI-PMH. So harvesting this information should be managable.