2015.08.07 Community Chat

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On EteRNA Medicine, Switches, & NuPACK XOR MS2 Challenge


Elves: hi folks! how goes it? [3:01 PM]

Brourd: Hello, machinelves. Everything is fine here. How are you today? [3:02 PM]

Elves: hi brourd! :D [3:02 PM]

Elves: glad to hear it. [3:02 PM]

Elves: i'm having a small adventure in having hurt my finger, which makes typing... interesting. :D so be prepared for a typo avalanche.  [3:03 PM]

Brourd: Are you here for the player led chat? [3:03 PM]

Elves: yep, i am here to review the forum discussions from dev chat and say hi to everybody [3:04 PM]

Nando: http://eterna.cmu.edu/web/news/6096508/ [3:05 PM]

Nando: oops, sorry, didn't mean to send that [3:05 PM]

Nando: hi guys [3:05 PM]

Elves: i'd like to invite the scientists to come hang out actually, i would not mind them intruding as it were. it would be cool to be able to ask questions about eterna medicine. but maybe i can figure it out from... [3:06 PM]

...the posts

Elves: hi nando! [3:06 PM]

Elves: it's okay, that post has the forum links so it's helpful :D [3:06 PM]

Brourd: What is it that you would like to know about Eterna medicine? [3:07 PM]

Elves: where do we start? [3:07 PM]

Brourd: I'm half here, so start at the beginning :) [3:08 PM]

Elves: lol [3:08 PM]

Elves: well for example, are there active labs to just immediately dive into?  [3:09 PM]

Elves: was that an on the horizon initiative, or is there something specific we can already do to help? [3:09 PM]

Nando: not yet, but coming very soon [3:09 PM]

Elves: cool, thanks Nando! [3:09 PM]

Elves: so general learning about switches and labs is the most constructive thing to do for now? [3:10 PM]

Nando: you could try to hone your skills on the challenge with the highest reward, this may be a frustrating experience, but it will prepare you to the thinking I believe [3:10 PM]

Brourd: I believe one player has solved it so far, Nando. We're making progress. [3:12 PM]

Elves: the challenge with the highest reward... oh! hahaha thanks Nando! I stopped looking at the Challenges link a long time ago because I had completed all of them, but I see a dozen new ones since I last looked [3:12 PM]

Elves: I had no idea! :D :D :D [3:12 PM]

Nando: @Brourd: it would seem I was too pessimistic, yes ;) [3:12 PM]

Elves: okay i clicked the play button. i'm guessing that was the easiest part of what is about to ensue... :D [3:13 PM]

Brourd: There is lag associated for the type of puzzle as well. [3:13 PM]

Elves: thanks for the heads up brourd! [3:14 PM]

Brourd: There has been some discussion on ways to alleviate this, but Nando is busy, and any choice will probably require some time and work. [3:15 PM]

Elves: lol. Nando, how is that cloning experiment coming along? [3:15 PM]

Nando: no progress on that front so far ;) [3:16 PM]

Elves: so this NuPACK XOR challenge begins in state 2, with a hairpin. Is that MS2? or ...? [3:16 PM]

Elves: here's the puzzle for anyone who wants to see what it looks like http://eterna.cmu.edu/game/puzzle/6096060/ [3:16 PM]

Nando: yes, the signal is again MS2 [3:17 PM]

Nando: which you want to have in states 2 and 3, not in 1 and 4 [3:17 PM]

Elves: ahh okay. so at the top left there are two conditions per state 1 & 4, http://prntscr.com/822z2s and the condition on the left is the shape that *is* wanted, while the condition on the right is a shape that is... [3:18 PM]

...*not* wanted

Nando: correct [3:19 PM]

Elves: and right now it shows a red hairpin in the image thumbnail because my shape is folding into MS2 in state 1, but it in fact should not be. [3:19 PM]

Nando: exactly [3:19 PM]

Elves: therefore, I have not met that condition yet, for the NO box for state 1 [3:19 PM]

jnicol: Hi Nando, Elves, Brourd [3:20 PM]

Nando: hey John [3:20 PM]

Elves: hi jnicol!!! :) [3:20 PM]

Elves: i'm getting a crash course in nupack :D [3:20 PM]

Nando: @Meechl: well done on the XOR challenge :) [3:20 PM]

Meechl: Thanks :) [3:20 PM]

Elves: highfive to Meechl! :) and hi [3:20 PM]

Meechl: Unfortunately, I still can't solve any of the old gate challenges :P [3:21 PM]

Meechl: Hi elves, nando, jnicol, brourd [3:21 PM]

jnicol: Hi Meechl [3:20 PM]

Elves: i find myself wishing that clicking on the condition boxes triggered a state change, but maybe that's crazy talk [3:22 PM]

Brourd: Hello John, Meechl. [3:22 PM]

jnicol: Only 2500 points? [3:23 PM]

Nando: Meechl found it easier than the old gate puzzles... [3:24 PM]

Meechl: The old ones have too many locked bases! [3:24 PM]

Nando: also, inflation in games is easy to cause and way harder to remedy, so I refrained to go fast there [3:25 PM]

hoglahoo: oo 2500 points [3:25 PM]

Elves: so i am guessing it will help to switch to Natural mode to see where state 1 is folding into the MS2 hairpin that we don't want for that state? [3:26 PM]

hoglahoo: must carve out some time for that one [3:26 PM]

vineetkosaraju: Hello all [3:26 PM]

jnicol: oh, we only did 1000, 1000, 2000 pts last time, I thought it was more [3:25 PM]

Elves: hi vineet!! [3:26 PM]

jnicol: hi Vineet [3:25 PM]

vineetkosaraju: @jnicol, banner looks great :)  [3:27 PM]

jnicol: thx to sharif :) [3:25 PM]

vineetkosaraju: so what have I missed so far? [3:27 PM]

Meechl: @elves I think I stayed in natural state most of the time I was solving [3:27 PM]

Elves: so i had no idea what to do to break up the hairpin, since all the bases in it are locked. so I just painted the loop with random nucleotides to see if it would disengage at all. it did, and now states 1 & 4... [3:27 PM]

...are happy not having the hairpin.but of course now i've lost the hairpin in states 2 & 3 http://prntscr.com/8232ho

Elves: thanks Meechl!! [3:27 PM]

Elves: hi Vineet! we are preparing for helping with eterna medicine, and Nando suggested starting with the NuPACK XOR challenge [3:28 PM]

Elves: http://eterna.cmu.edu/game/puzzle/6096060/ [3:28 PM]

jnicol: there are other 'real challenge' puzzles on Nandos dev server if you want to practice more [3:27 PM]

Elves: cool, thanks jnicol! that would be helpful to know [3:29 PM]

Nando: brb, afk [3:33 PM]

Elves: ooo i was looking for the black circles nucleotide marker, which on the mac is command+click, but i accidentally pressed alt+click on the nucleotides and got that cool blue glowing highlight. http://prntscr.com/8235 [3:33 PM]


Elves: lol [3:34 PM]

Elves: http://prntscr.com/82354f [3:34 PM]

Elves: so i recall Nando made this or something like it a while back, I thought as glue in the puzzlemaker? am I imagining things? is this the same or different feature [3:34 PM]

hoglahoo: yeah that's a feature you can use to alter the target shape [3:36 PM]

hoglahoo: for example you might use that to help you visualize a stack you want to build around a new ms2 area or whatever for stabilization help [3:36 PM]

Elves: here i see it functioning as a highlighter much like the black circles, so that when i switch between natural and target mode, i can see where the nucleotides move, but i feel like i am missing something about... [3:37 PM]

...how it functions

jnicol: You can specify the bases to pair that way when the constraint allows those bases to be paired or unpaired (signified by the purple highlight around the base) [3:37 PM]

jnicol: the bases highlighed with alt click need to balanced to be able to pair properly [3:38 PM]

hoglahoo: yeah you've got to select two separate strings, each with the same number of bases - when you select them, they'll glue together into a stack in target mode [3:38 PM]

hoglahoo: I wonder if there's a video guide out there for it [3:38 PM]

Elves: so it does act as glue, but only when it is the same number of nucleotides on each side in target mode [3:39 PM]

jnicol: correct [3:39 PM]

Elves: i think nando posted one in the intro blog post [3:39 PM]

Elves: http://eterna.cmu.edu/web/blog/5452094/ [3:40 PM]

Elves: stack painting tool video at bottom. thanks hoglahoo! [3:40 PM]

hoglahoo: you found it, thank you [3:41 PM]

Elves: so if you use this tool improperly, it could also act as a secondary highlighting tool for temporary logical deduction purposes? :D [3:41 PM]

Elves: in concert with the black circle marker [3:42 PM]

Elves: np [3:42 PM]

Elves: okay and even after it loses blue glowing highlight you can undo the glue by redrawing over it with alt+click [3:43 PM]

hoglahoo: I don't think the glowing things stick around the same way [3:44 PM]

Elves: thanks! good point. just figured that out :-P  [3:44 PM]

hoglahoo: yeah you can undo just part of it too. maybe you want to turn a long stack into two stacks with a 1-1 loop in between, you can alt click select a basepair to do that [3:45 PM]

Elves: ooo that's very clever! [3:46 PM]

Tyrannosaurus Rekt: Hi guys! [3:46 PM]

hoglahoo: hi [3:47 PM]

Tyrannosaurus Rekt: Just curious, what exactly is a switch? what does it do? [3:47 PM]

Elves: hi tyrannosaurus, and welcome! [3:48 PM]

Elves: the first RNA puzzles you do here have one shape, or "state", like the tutorials [3:49 PM]

hoglahoo: A switch is a sequence fold that changes shape when some kind of external input it added (I think) [3:49 PM]

hoglahoo: is added* [3:49 PM]

Elves: and switches have more than one possible shape [3:49 PM]

Tyrannosaurus Rekt: cool. [3:49 PM]

Tyrannosaurus Rekt: thanks! [3:49 PM]

Elves: like hoglahoo says, when you add an external stimulus to the RNA molecule, then it gets triggered to change shapes [3:49 PM]

jnicol: @T-Rekt, try this tutorial: http://nando.eternadev.org/game/puzzle/3389090/ [3:48 PM]

Tyrannosaurus Rekt: thanks man! [3:50 PM]

Elves: thanks this is awesome! [3:54 PM]

Elves: i solved the tutorial, hehehe. NuPACK on the other hand... only made a tiny amount of progress, but better than before. thanks everybody for sharing info on switches. it helps to know where to start.  [3:58 PM]

Elves: i've got to go back to work. see you all next time! [3:58 PM]

hoglahoo: see you later [4:00 PM]

Brourd: Later, machinelves. [4:01 PM]

Elves: bye hoglahoo, bye Brourd! glad to see you :) [4:01 PM]

hoglahoo: you too :) [4:03 PM]

machinelves: :) :) :) [4:03 PM]

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