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Major competitors include MIME (yes, MIME), which aimed to be emailed across various vendors (from Matrix, for MASCOT). Another competitor included plain text files, and open-source XML files. However, the plain text files were gigabytes and painfully slow. So, SQLite or HDF5.
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For the explicit use-cases I'm listing though, that is an expectation. People post proteomics files online for public use, so randomly uploading and downloading files for people to run on a local application is an expected use, much like it is with Word documents.
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Sharing image editing documents / word processing documents, etc. is irresponsible? What about media files? It's certainly a design objective of SQLite to handle untrusted files properly and they put far more effort into that than most alternative file format implementations.
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