Dear all -
We’are selecting the target shape for the next lab among player designs shapes!
Go to Player Puzzles page and look for the puzzles with “[Lab candidate]” in their titles.
Choose a puzzle which you think will be truly challenging to both players and bots (algorithms), that will expose the weakness of current RNA energy model we use in the game! Write down your choice of puzzles as a comment in this thread, and we’ll pick the next lab challenges from one of most voted puzzles
We are looking forward to synthesizing exciting RNA shapes from you!
I think Multiple loops tail by JerryP70 might be good for a first foray into player-designed lab shapes. We currently know more about multiloops than we do about simple internal loops and bulges, and this is a relatively straightforward design with which to learn about the latter.
I’ll throw in a vote for tommyd’s Big Loop Balancing Act. He raises a number of interesting questions that we could attempt to begin to answer. Thanks.
My first choice is Eli Fisker’s “Tripple triloops” because I think we need to learn more about how stacks just off open loops work, and I’d like to play with triloops instead of our usual tetraloops as well.
My second choice would be Joshua Weitzman’s “Bends and Ends Sampler” because those bends and ends are just so tasty
But I also think either of the above-mentioned shapes (Multiple loops tail and Big Loop Balancing Act) would be good. My only problem with Multiple loops tail is that I’m worried the stacks are too short, particularly the one just between the open loop and the single-nucleotide bulge. I’d really like a chance to test single-nucleotide bulges, but I don’t think we’re going to get as much good data as I’d like so close to the beginning/end of the sequence.
Joshua Weitzman’s “Bends and Ends Sampler”
I’ll second “Bends and Ends Sampler” by Joshua Weitzman.
Of course, Big Loop Balancing Act would be my first choice, but if that were not in the cards, then…
My second choice would be Joshua Weitzman’s “Bends and Ends Sampler”, it would be quite the challenge.
And for third, maybe either Brourd’s “Almost a Parallelogram”, or Marsman’s “Bent Key”.
we are looking for a puzzle that is truly challenging to both players and bots (algorithms) and that will expose the weakness of the current RNA energy model. My answer to that was Hard Y and a bit more. 2nd A tilted picture of running man by marsman1331
First I would like to thank those that voted for my design or commented on my design. I would like to vote for “Bends and Ends Sampler”.
Hmmm. I haven’t had a chance to look at all of the designs. Although I like “Hard Y and a bit more” for the challenge factor, I think it is a little too hard for a first player lab. My vote goes to “Fractile”… I think it will be easier to formulate and test hypotheses for it.
The lab design needs to be a puzzle with many solutions, so that we can generate more than a few candidates. I haven’t tried all the puzzles yet, so I am not yet in a position to vote.
(1)—Reversed asymetric multiloop (Eli Fisker)
(3)—Hard Y and a bit more (Joshua Weitzman)
- Broken Propeller
- Bends and Ends Sampler
- Multiple Loops Tail
I like the ones with various sized bulges and/or loops to test.
I’m going for Broken Propeller, since it is not too hard, and allows quite a bit of variation; followed by my own Fractile, but only because others have voted for it.
When are we going to take the training wheels off and really find the limitations of computation vs. reality? “Hard Y and a bit more” really pushes the envelope in this regard and is fun, too. “Bends and ends sampler” is much more conservative and familiar and doesn’t rock the boat, but is still quite interesting. We can’t be timid sheep forever. Eventually I hope we’ll synthesize something a little daring. (Baaa)
I would like to suggest:
- Broken popeller
I think Starryjess’ lab design is really interesting. A neck with a bulged we have tried. A broken neck with a bulge. That one is new.
- Reversed asymmetric multiloop (My own reversed version of former asymmetric lab puzzle)
As I think something special is going on with direction of GC-pairs, when having different numbers of nucleotides between the multiloop arm.