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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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They are also far more successful at avoiding vulnerabilities in practice. Still, there are occasional memory corruption bugs. It doesn't make sense to blame on them rather than the tooling. I would certainly rather open an untrusted SQLite database than an MP4 file with FFmpeg.
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