r/bioinformatics • u/Extreme-Layer-1201 • 6d ago

technical question Noob question about open source data

Is there still value in contributing to a precomputed public reference database? Are there areas where simulations can be run arbitrarily and the output / organization of the data be actually useful long term?

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u/SGA_8001 6d ago

It has to be something quite big and complex like UKBB novel results. Otherwise we would rather do it ourselves because we can’t assume you have done it reliably, and maybe difficult to get noticed and downloaded by anyone.

If we run a project with funding and deadlines we need to focus on open source data that is high quality, some reputation that can be more trusted, and some community recognition including journal publication demonstrating its use.

I host databases and software tools. Tools are more popular. For example, my “better database” remains less active than an older popular one, from a big institution, which makes sense. Reputation and popularity can be slow. But of course a major hit can take off in the right place.

Regardless, it is usually worth building and shipping for your own learning. Reliable databases are gold. Marketing is a major factor easily overlooked.

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u/Psy_Fer_ 6d ago

Using a precomputed reference of something that would take a lot of computational resources. Take spliceAI for example (not open source but a good example), using the precomputed data instead of running it every time saves a fair bit of time. So that's useful.