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How do you define a bio-core? #11

wilzbach opened this Issue Aug 1, 2014 · 4 comments


3 participants

wilzbach commented Aug 1, 2014

Seb: Why do you have the sequence class as core?
Seb: Something that I am imagining that should go inside this core could be a "GenericParser" which all parsers can inherit. After all they receive text and output an object. On the other side that might change too: arrays of binary data could be needed or with the upcoming ES6 Harmony browsers might finally support more structures.

Bruno: I think bio core should have helpers or util functions that are reused by most of the other bio modules.
The Sequence methods fit that description, although the reason why I have them in core is more historical than anything else. The first bionode module started as a way to provide those functions client side to the Afra project, while also being available for server side usage.
They should probably be moved to a specific bionode-sequence module, but then the bionode module would be empty since I don't have helper functions for now. In that case, the bionode module could become instead of the "core" module the "meta" module that links the other modules together in some kind of framework.

@wilzbach wilzbach changed the title from How do you define a bio-core? For me code that should go inside is something like a "GenericParser" which all components can inherit. Why do you have the sequence class as core? to How do you define a bio-core? Aug 3, 2014


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alanrice commented Aug 5, 2014

Is a bio-core even necessary? What would bio-core look like without parser and sequence methods?


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wilzbach commented Aug 6, 2014

Well it was more because what I was seeing at the Bionode core wasn't that important for every component.
With all of the discussion at #9 in mind it would be great if we don't have any dependencies.

Btw here 's the example of how an optional, generic reader one could extend could look like.
The generic read command takes an URL and calls the specific parse which takes the string.


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wilzbach commented Sep 11, 2014

During the BioJS 2.0 hackathon we created biojs-model. Currently it is somewhat empty and there isn't a widespread use. So maybe we don't need to specify schemes in a JS package that one needs to install.

However in my humbled opinion agreeing on a common format for the same data is something worthwhile to achieve.
Have you already created data schemes that you would consider fit for a global model definition?


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bmpvieira commented Apr 4, 2015

I think we should let models/schemas evolve naturally and only worry about that when it becomes a real issue for collaboration/integration among modules. Right now, this hasn't been a problem for bionode, and biojs-model also seems still empty. I agree that standards are good, but I'm always afraid we might overthink this and end up with something like Chado. The real standard we should worry about are JSON and Protobuf. Object's schemas are easy to transform in a JavaScript pipeline. Also, Bionode tries to be more functional than object oriented, which kind of solves the issue.

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