Interface Idea: next few lowest energy shapes

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  • Updated 7 years ago
It has occured to me a few times now while solving puzzles that it might be beneficial to view the next three to five lowest energy shapes of the current sequence. I'm thinking in a small side window, like the ones currently used for meltplot and dotplot in the designer. In fact, it would serve kind of like a visual representation of the dotplot showing the most likely misfolds under the current energy model. It would also be very interesting to see their energies. Sorry if this or a similar idea has been posted before, i didn't come across it yet.

Of course it should be natural mode only, and if the current puzzle/design has a red shape and the target shape is whitin the views, it should be highlighted.
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drake178

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Posted 7 years ago

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rhiju, Researcher

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I was independently thinking about this very same thing -- a kind of 'spectrum' of states. This is going to particularly important I think in upcoming weeks when we start to create 'switch' puzzles. It will also be a very interesting way to teach players (and soon collect the community's insights) about energy scales and alternative states, which are fundamental features in our description of RNA folding. I'm bringing this up with the devs now.
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drake178

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Oooh i completely forgot about switch puzzles, you likely have thought about this before. Thanks rhiju :)
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Quasispecies

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Rhiju - that will be really cool. Looking forward to it. Would it somehow be possible to incorporate the program barriers into the EteRNA game? It's slow enough that you couldn't run it on the fly every time a player made a change, but maybe you could have a "calculate" button.

Drake - Check out the server version of barriers and tell me what you think.
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drake178

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It keeps telling me "This does not make sense" to my sequences :D

Otherwise i can only see the tree, which is a much more technical oriented view of something i only half understand. It would only help with pictures or if i already knew what i'm looking at/for. I'm assuming it's meant to give me an idea about how strong alternate structures are and how much energy difference there is between various misfolding states (like, if there are two different ones very close to each other and then everything else way above). The problem is, i don't see which sequence is which fold, although that might be because i only tried really short sequences. Without that i'd find this too generic to be really useful outside very special circumstances, so i'm assuming i just messed something up and i was supposed to see the shapes not just the tree view.

So while i can clearly see how this can be useful, it seems i can't really use it without some form of picture reference. Which, if done well, can already include most of the data i'm looking for here, so i definitely wouldn't use this on the fly. But at the same time, if it can be readily incorporated, i would do it, using a "calculate" button, like Quasi suggested. There's only soo many little pictures you can fit on the side of the screen, and barriers gives an excellent energy overview of all the shapes in one picture. I really need to see which fold is which though :D
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Quasispecies

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Sorry, I should have been more specific about the program.. it's to 100 nucleotides so you have to trim off the dangling ends of the molecule. I don't think this is too big of a deal, but you might want to leave 1-nt overhangs.

To actually view the structure, you have to go down to "folding paths" and specify which a starting and ending structure.

Here's a tutorial.
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drake178

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Oh i get it now, thanks Quasi :)

I'm not sure i need all that extra information though. That is, it's nice to know, but given my current state of understanding it provides no more help than simply being able to see the next few shapes and their energies. I need to get more smart before i'll be needing barriers :D
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mrblue92

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Rhiju - Has there been any movement on this topic?

I was going to suggest basically the same thing -- that in natural mode it would be great if we could see the next most likely folding(s). Once we're on the right track, that information should make it much easier to winnow out some of the poor alternatives by just swapping a few base pairs.
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Jeehyung Lee, Alum

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Hi mrblue92

the issue is tracked at

https://github.com/EteRNAgame/EteRNA-...

It is likely that we'll consider this along with switch puzzle interface improvements. We'll post further updates later.