Player Driven Development & Tools for EteRNA (beyond scripting).

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  • Updated 6 years ago
From: Rhiju Das
To: Chris Couteau
Cc: Jeehyung Lee
Sent: Tuesday, April 23, 2013 12:42 PM
Subject: Re: EteRNA_thoughts

Hi Chris:

Thanks for contacting me, and sorry for the late response -- I've been out of town.

I've been reading your posts with much interest -- I'm amazed that you're finding the same articles that our 'expert' group also keeps track of. For example, regarding the SHAPE 'soft constraints' paper of Washietl et al, my group has checked out that code -- its not accurate in all cases of known structure, but neither is the current approach in eterna.

The validation and inclusion of known tertiary motifs is also fascinating, but we will probably wait until building a 3D version of eterna to incorporate those ideas. They are obviously critical, however, if we want eterna to be an all-purpose RNA design platform.

So what can we do? Our dev team is swamped.

What API could we create in eterna for players so that *you* could implement the ideas you've suggested and any new ones?

We've got a test scripting language, and are working on a 'library' to promote sharing of papers and writing of new ones.

What if you had read-access to the eterna database -- could you (with other players) create novel applications to highlight tertiary motifs, or implement alternative SHAPE-guided modeling algorithms.

I also wonder if the same kind of API would permit 'experts' (like Washietl) to make their own tools available as on-line apps that directly interface with eterna.

Let's stay in touch about this. Also, if you have a chance, it would be worth starting a forum thread that links many of your ideas, and also asks players to brainstorm about what the eterna team could do to make the ideas happen. Again, the constraint here is that we have limited resources -- the best thing would be to create mechanism for players themselves to develop and share new tools.

As part of that thread, please feel free to post the above reply from me.

Best,
Rhiju
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So, the question is, what can we do with this potential opportunity? I think it important enough, and have agreed to canvas the community for interest and skills and projects. What is missing that you might be able to implement? What tools do you need that we just don't have? Can you turn it into an application that works directly in EteRNA? Are you writing code for scoring functions, motif selection or something else?

The dreams will require organizational planning and implementation---you have any relevant skills that you could participate with?

The floor is open for discussion.
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eternacac

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Posted 6 years ago

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eternacac

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We may get some help on a VARNA port to js from the good folks at www.compbio.dundee.ac.uk they have done some of the work for their JalviewLite http://www.jalview.org/examples/formC....

And the people at jsmol have done this work http://chemapps.stolaf.edu/jmol/jsmol... so it seems it can be done (Java to js ports).
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eternacac

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And kudos to ElNando for the progress he has made with the Vienna port using emscripten/clang/LLVM

http://ec2-54-242-172-93.compute-1.am...
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eternacac

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The second major use of Emscripten. Great work!

From kws4679:

This is converted version of RNASSD by using emscripten. Since RNASSD and Nupack uses a lot of external resources, it nearly impossible to convert those algorithms directly into javascript. Emscripten can automatically port C/C++ projects into javascript without glitches.

http://eterna.cmu.edu/web/script/3242...
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eternacac

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Encog neural networks available in Javascript here:

https://github.com/encog/encog-javasc...

Also in C/C++ and Java.
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eternacac

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and Encog's javascript examples

http://www.heatonresearch.com/fun