Eterna 4: What are your BIG ideas? (Dev chat followup)

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Following up on conversation in today's dev chat:

Eterna is at a really exciting moment - we have the potential to gain the resources and opportunity to completely rebuild Eterna - providing more robust infrastructure, more platforms, better global availability, and the prospect of making significant changes to the user interface, new features, and so on. The dev team wants to know the biggest dreams community members have as preparations are made for such groundbreaking changes. What have you always wanted to see from the Eterna website and game? What would make Eterna more fun? What would allow you to be more effective? What could help facilitate puzzle solving, scripting, testing hypothesis, or collaboration? What did I not even mention? Anything's fair game!

List your best, biggest, visionary ideas for the next generation of Eterna here!
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LFP6, Player Developer

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Posted 2 years ago

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rhiju, Researcher

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There's a cool discussion thread started over at on pattern languages.

as has been pointed out, one possibility for the future of eterna is to change its interface to involve manipulation of colored beads that represent these differnt domains. There could be an arbitrary number of colors, not just 4 nucleotides, to cover A, B, C, D, E,  ... R, ... and some kind of change in symbol to represent A' [or rc(A) in jandersonlee's notation]

 I'd like to point out that we could even provide an approximate folding engine that simulates the structure of such a pattern given some coarse-grained "energies" for the bead attractions (which might even be tunable by the player). And could even simulate what happens when a small molecule binds, given an appropriate energetic rule set.   And then designs of those patterns could be compiled into actual RNA sequences by eternascript.

I suspect that such a bead interface would even let us design 8-bit adders... its always been a dream of ours to solve that 'feynman challenge', and i recently did a back-of-the-envelope calculation suggesting that we could make such a device with ~2000 nucleotides, and there might even be experimental ways to synthesize lots of such designs for testing. 
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Eli Fisker

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Display alternative MS2's as stable ingame

We are doing round 2 of Single-input switches, revisited

The design scoring best in the first round (max fold change error 1.25) is a design using an alternative MS2.

The MS2 is showing up as not present and not turned off (red boxes) as the game is only made to recognize the original MS2, while the puzzle is conforming to structural constraints (green boxes). 

I would like to see the alternative MS2's showing up as satisfied too. 

I think this will greatly improve our amount of winners, because more players will start using the alternative MS2. Some of the new aptamers will work better with an alternative MS2. 

Further benefit would be that we could use the mutation booster to brew up more variations. If the puzzle is recognized in game as stable, it will allow us to do a prune and be left with the stable mutants.