2014.01.29 Dev Chat

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On Shiftable Puzzles & Thanks to Diana


jeehyung: Hello all  [3:00 PM]

firedrake969: Hi Jee  [3:00 PM]

firedrake969: Oh, dev chat! :D  [3:00 PM]

jeehyung: Welcome to bi-weekly eterna dev chat . This is a session where devs (me) and players discuss eterna features & bugs. [3:00 PM]

firedrake969: Jee, I sent you a PM; did you get it? [3:00 PM]

machinelves: hey! congrats to the team on PNAS, and the upcoming press :) [3:00 PM]

jeehyung: Please throw in questions or suggstions! [3:00 PM]

jeehyung: Hi Eli, fire,achineleves [3:00 PM]

Eli Fisker: Yes, big congrats, Jee [3:01 PM]

Eli Fisker: et al [3:01 PM]

jeehyung: Thank you : ]  [3:01 PM]

MusicalSamurai: :D [3:00 PM]

firedrake969: :D [3:01 PM]

jeehyung: @firedrake checking now [3:01 PM]

machinelves: general update on Dev Chat transcript archive: now tracked through wiki, also accessible from wiki home page, here is the link: http://eternawiki.org/wiki/index.php5/Dev_Chat [3:01 PM]

Brourd: ey Jee [3:01 PM]

jeehyung: oh, yes I got it and I did put you in the list. Thanks for applying. [3:01 PM]

jeehyung: Hi Brourd [3:02 PM]

Brourd: How are you doing? [3:02 PM]

firedrake969: Ok, thanks for the response [3:02 PM]

tsunaminaut: Can I write off the hours im spending here on my taxes as a charitable donation? ; [3:02 PM]

machinelves: and Eli made a page to track the Stanford meetings as well, also accessible through wiki home page, here is the direct link: http://eternawiki.org/wiki/index.php5/Monthly_Eterna_Meeting [3:02 PM]

tsunaminaut: =) [3:02 PM]

jeehyung: @Brourd good as always. Thanks : ] [3:02 PM]

Eli Fisker: lol, Tsunaminaut [3:03 PM]

brandonjr009: Haha tsunami [3:02 PM]

firedrake969: xD tsunami [3:03 PM]

firedrake969: Jee, what are the shiftable plzyer puzzles for? [3:03 PM]

jeehyung: @machine, Eli that is so useful - thanks [3:03 PM]

firedrake969: player* [3:03 PM]

Brourd: Jee, did you receive my PM about the lack of a mutation constraint for two of the current labs? [3:03 PM]

Eli Fisker: http://prntscr.com/2ns003 [3:03 PM]

Eli Fisker: Tax deductible, yes [3:04 PM]

Eli Fisker: @Jee, np [3:04 PM]

machinelves: @jee happy to help :) [3:03 PM]

jeehyung: To all new players, Eterna holds monthly video meeting with the Das lab at Stanford. You can check the videos in the link above, or a youtube channel http://www.youtube .com/channel/UCt811OXJqe35TDhe9hPYzJg?feature=watch [3:04 PM]

Brourd: As described in this forum post as well https://getsatisfaction.com/eternagame/topics/mutations_limits_in_labs [3:04 PM]

jeehyung: @Brourd oh...I must have missed this. Let me look into this.. [3:05 PM]

hoglahoo: I don't remember if I mentioned this at a dev meeting before: it looks like players whose usernames begin with a non alphabet character are unable to connect to chat [2:05 PM]

machinelves: @jee i also simplified the Issues tracking portal on the wiki, and the last step is the Issue Roadmap / Tracking software, pending whatever devs prefer to use: http://eternawiki.org/wiki/index.php5/Issues [3:05 PM]

firedrake969: @jee--shiftable puzzles' use? [3:05 PM]

jeehyung: @firedrake - sorry, those puzzles are currently under testing. There are certain lab projects that require sequences with varying loop lengths [3:05 PM]

jeehyung: The shiftable puzzles will be use dfor that [3:06 PM]

firedrake969: Ah ok [3:06 PM]

jeehyung: @hoglahoo that is a big problem - thanks for pointing it out [3:06 PM]

Eli Fisker: So if we think it will help solve the lab, we can add or delete a few bases [3:06 PM]

jeehyung: @Eli yes exactly [3:06 PM]

firedrake969: Will there be any new challenges added in the next few months? [3:07 PM]

MusicalSamurai: I swear I just solved a puzzle by accident... [3:08 PM]

jeehyung: @firedrake hopefully the shiftable RNAs and the switch puzzles [3:08 PM]

Eli Fisker: Lol, MusicalSamurai. Trust me, it won't be the last time [3:08 PM]

Eli Fisker: Happened to me too [3:09 PM]

Hyphema: Hello, only have a minute,  is it possible to organize our list of synthesized puzzles on our own profile page by lab?   [3:09 PM]

firedrake969: @Musical Switches are often like that :P [3:09 PM]

MusicalSamurai: Okay it's too hard now - giving up [3:08 PM]

MusicalSamurai: lol [3:08 PM]

Eli Fisker: hi Hyph [3:09 PM]

MusicalSamurai: #RageQuit [3:08 PM]

firedrake969: @jee Sweet :D [3:09 PM]

Brourd: So Jee, any news on the Semi-Open source EteRNA front? [3:09 PM]

firedrake969: @Musical you can post pics of your sequences while in the game [3:09 PM]

firedrake969: click the camera icon in the top-right corner of the chatbox [3:09 PM]

MusicalSamurai: I don't want helps :D [3:09 PM]

MusicalSamurai: NeVaRh [3:09 PM]

firedrake969: Seeking and giving advice helps all of us learn more [3:10 PM]

firedrake969: Croudsourcing ftw :P [3:10 PM]

MusicalSamurai: Level 0 puzzle failure ftw :D [3:10 PM]

firedrake969: Need help on that? [3:11 PM]

MusicalSamurai: Nope [3:11 PM]

firedrake969: Huh, hard to believe that last week and this week's dev chat I both stumbled into by accident xD [3:11 PM]

MusicalSamurai: It's a bit late for RNA sequencing  [3:11 PM]

Eli Fisker: Fire, good timing [3:12 PM]

MusicalSamurai: FUnny that I stumbled upon this entire site and you lovely lot [3:11 PM]

firedrake969: Yeah. [3:12 PM]

Eli Fisker: :) [3:12 PM]

firedrake969: @Musical how did you/ [3:12 PM]

firedrake969: I've noticed a bunch of new users over the past day or two [3:12 PM]

jeehyung: @Brourd for the mutation stuff, seems like it was an accidient .  I just manually recovered the constraints. [3:12 PM]

Eli Fisker: Hehe, a few [3:12 PM]

firedrake969: There's 122 players online right now [3:12 PM]

MusicalSamurai: Looking up Protein Folding and Neurochemistry [3:12 PM]

Brourd: Thank you jee! [3:13 PM]

MusicalSamurai: 2 fields that I like the look of but never likely to have time for :D [3:13 PM]

firedrake969: I like quantum physics :P [3:13 PM]

firedrake969: And calculus. [3:13 PM]

Hyphema: hi Eli,  i just read what i typed and not sure if that makes sense.  i said synthesized puzzles and not synthesized RNAs.  currently they are listed by score which is nice but i would like to see them categorized by lab [3:13 PM]

Eli Fisker: Hyph, I agree that it will be nice [3:14 PM]

Eli Fisker: having both options.  [3:14 PM]

Eli Fisker: like what we got and by lab [3:14 PM]

MusicalSamurai: QM is one of my research fields [3:14 PM]

Eli Fisker: And in order of the labs [3:14 PM]

Eli Fisker: Would be a lot easier than message box [3:14 PM]

MusicalSamurai: Dispite all labs and libraries - my best friend (and foe) is Google [3:14 PM]

jeehyung: @Hyphema that's a great suggestion. That shouldn't be too hard to do...will add this to the dev todo queue [3:15 PM]

jnicol: @Jee, I second Brourd's question, any further development with open source? [3:15 PM]

machinelves: @jee PM with question [3:15 PM]

firedrake969: @Musical I'm reading a book by Brian Greene [3:15 PM]

firedrake969: Green* [3:15 PM]

MusicalSamurai: What's a "book" lol [3:15 PM]

MusicalSamurai: lol [3:15 PM]

firedrake969: or Greene. Not too sure which spelling [3:15 PM]

MusicalSamurai: dear me... [3:15 PM]

firedrake969: a book is paper with text on it. [3:15 PM]

firedrake969: paper and ink. [3:15 PM]

MusicalSamurai: Wow paper? [3:15 PM]

MusicalSamurai: Poor trees :D [3:15 PM]

firedrake969: Paper is mushed-up trees. [3:15 PM]

MusicalSamurai: trees is mushed up atoms [3:15 PM]

MusicalSamurai: atoms is mushed up quarks :D [3:16 PM]

MusicalSamurai: Tada - soup :D [3:16 PM]

firedrake969: Yup [3:16 PM]

Eli Fisker: with tree DNA [3:16 PM]

Eli Fisker: :) [3:16 PM]

firedrake969: trees are mushed up molecules [3:16 PM]

firedrake969: molecules are mushed up atoms [3:16 PM]

MusicalSamurai: Ah yes [3:16 PM]

firedrake969: atoms are mushed up protons/neutrons/electrons [3:17 PM]

MusicalSamurai: I missed a few steps [3:16 PM]

firedrake969: those are mushed up quarks [3:17 PM]

Eli Fisker: @Jee, a problem that has been a lot up today, is that the tutorial points do not get registered, when many of the new players sign up.  [3:17 PM]

firedrake969: and squarks are mushed up strings [3:17 PM]

MusicalSamurai: I didn't want to get into spinons and whatnot... [3:17 PM]

firedrake969: and those are mushed up energy loops :P [3:17 PM]

MusicalSamurai: but hey :D [3:17 PM]

jeehyung: @jnicol, Brourd sorry I missed the question. There was a bit of mix up at the dev front as one of our dev had to leave. We are trying to re-organize dev front. [3:17 PM]

MusicalSamurai: Strings? [3:17 PM]

MusicalSamurai: lol drop that one bro [3:17 PM]

firedrake969: ? [3:17 PM]

jeehyung: @Eli thanks for the note. I'll have to take a look into that too. [3:18 PM]

firedrake969: What do you mean? [3:18 PM]

MusicalSamurai: We use the papers of string theory to wipe up coffee spills :D [3:17 PM]

Eli Fisker: @Jee, thx [3:18 PM]

MusicalSamurai: That's all I mean [3:18 PM]

starryjess: lol [2:18 PM]

firedrake969: Hh [3:18 PM]

firedrake969: huh* [3:18 PM]

MusicalSamurai: and as I said earlier - if you believe in 11 dimensions - you may as well believe in God... [3:18 PM]

starryjess: what do you do with them if nobody spills coffee? [2:19 PM]

firedrake969: Have you read the book Flatland? [3:19 PM]

MusicalSamurai: You're lucky we can talk about 3 of them... but even then it's an illusion :) [3:18 PM]

MusicalSamurai: blow ma nose on em :D [3:19 PM]

firedrake969: What about 4? [3:19 PM]

firedrake969: and the spacetime "loaf" [3:19 PM]

MusicalSamurai: 4? [3:19 PM]

firedrake969: time [3:19 PM]

MusicalSamurai: Ahah [3:19 PM]

firedrake969: or you could say time's an illusion [3:19 PM]

Eli Fisker: Coffee stains can end up as science:  [3:19 PM]

firedrake969: which it somewhat is. [3:19 PM]

firedrake969: @ELi true. [3:19 PM]

MusicalSamurai: Illusion still . but you can perceive it as this in our realm [3:19 PM]

Eli Fisker: http://www.abc.net.au/science/articles/2011/08/18/3296486.htm [3:20 PM]

Hyphema: btw. read thearticle in the PNAS. great stuff.   [3:20 PM]

firedrake969: @Hyph I did [3:20 PM]

MusicalSamurai: In the quantum realm there is no time  or direction - things don't "obey" what you think they should... [3:20 PM]

starryjess: cool Eli [2:20 PM]

MusicalSamurai: Shit gets freaky at planck length [3:20 PM]

jnicol: @Jee, not sure if this was brought up yet, but shiftable puzzles has a problem when you delete bases. [3:20 PM]

Eli Fisker: Starry, thx [3:21 PM]

jeehyung: @Hyphema thanks : ] [3:20 PM]

firedrake969: How was the planck length derived? [3:20 PM]

firedrake969: and what's its use? [3:21 PM]

jeehyung: @jnicol Can you tell me the details? [3:21 PM]

MusicalSamurai: Thought experiment like everything - definition of the smallest possible thing we can make sense of [3:21 PM]

hoglahoo: firedrake969, MusicalSamurai, any chance we could focus on the dev chat for the next half hour or so? it's getting tough to read through the quantum physics discussion! [2:21 PM]

firedrake969: Ok :P [3:21 PM]

MusicalSamurai: or theoretically - no one Works at this scale :D [3:21 PM]

firedrake969: sorry, I tend to get carried away. [3:21 PM]

starryjess: I believe that's where the Heisenberg uncertainty comes into effect [2:21 PM]

starryjess: *principle [2:21 PM]

firedrake969: @Jee Yup, there's a pretty nasty bug with them, elt me find the puzzle that I can demonstrate it on... [3:21 PM]

firedrake969: let* [3:21 PM]

MusicalSamurai: Uncertainty and Chaos are always in effect [3:21 PM]

jnicol: http://eterna.cmu.edu/web/puzzle/3727288/ [3:22 PM]

MusicalSamurai: but yes - Dev chat guy - I'll shut up too :) [3:21 PM]

firedrake969: http://eternagame.org/web/puzzle/3736549/ [3:22 PM]

starryjess: I just said it badly [2:22 PM]

jnicol: Jee, add a base in this puzzle, then delete it [3:22 PM]

firedrake969: *facepalm* bad liin, sorry [3:23 PM]

jeehyung: @jnicol, firedrake ohhhh....this is a very clear bug. Thanks. I'll make sure to fix this [3:23 PM]

firedrake969: link* [3:23 PM]

firedrake969: off to do homework, bye [3:24 PM]

firedrake969: may get back on since I odn't have too much. [3:24 PM]

firedrake969: don't* [3:25 PM]

jnicol: I need to leave, later all [3:25 PM]

machinelves: bye! [3:25 PM]

Eli Fisker: Bye John [3:26 PM]

firedrake969: Oh one question [3:26 PM]

firedrake969: @Jee when are lab tutorials expected to come? [3:26 PM]

Brourd: Well, I just posted all the comments for my lab project, we shall see how many redesign, if possible, to match the mutation constraint. [3:27 PM]

jeehyung: @firedrake it's been pushed back, as we are still trying to restructure cloud lab a bit. It would be best we work on the lab tutorials after the cloud lab is solid.. [3:28 PM]

Brourd: @ Jee - so, which developer did we have to say farewell to? [3:28 PM]

firedrake969: Oh, ok [3:28 PM]

jeehyung: @Brourd sorry about the trouble there. [3:29 PM]

Brourd: No problem :) [3:29 PM]

firedrake969: and what's cloud lab again?  (it's been a while sinc I've been on EteRNA, this is only my 2nd week back) [3:29 PM]

firedrake969: since* [3:29 PM]

Brourd: #def Cloud lab [3:29 PM]

DictionaryBot: Visit http://eternawiki.org/wiki/index.php5/Cloud_Lab [3:29 PM]

firedrake969: Thanks [3:29 PM]

firedrake969: Now I really should go :P [3:29 PM]

firedrake969: Bye [3:29 PM]

machinelves: welcome back & cya! [3:30 PM]

Brourd: later firedrake, take care. [3:30 PM]

jeehyung: @Brourd Diana had to leave  although she may come back in few months. We'll see. [3:30 PM]

Eli Fisker: Bye Fire [3:30 PM]

jeehyung: bye firedrake [3:30 PM]

Brourd: ah, does that cause some delays on the flash embedded design browser? [3:30 PM]

machinelves: @jee, farewell to Diana, and many thanks for all her hard work! [3:30 PM]

machinelves: also she was managing the wiki, so Nando will need a new contact whenever that is appointed [3:31 PM]

jeehyung: @Brourd unfortunately yes. It's a shame. I think ti had a really good potential (with embedded flash that is) [3:31 PM]

jeehyung: @machinelves will send your message to her. I'm sure she'll appreciate it [3:32 PM]

machinelves: yay! :) [3:32 PM]

Brourd: Yeah :( Well, perhaps you guys will be able to find somebody to pick up her work if she is unable to return. Tell her good luck with whatever it is she is doing :) [3:32 PM]

Vachekuri: Hi everybody [3:32 PM]

Eli Fisker: Yes, best wishes to Diana [3:33 PM]

Eli Fisker: hi Vachekuri [3:33 PM]

Vachekuri: I heard on a French radio that I can be a geek and save the world with eterna [3:33 PM]

Vachekuri: Fun :) [3:33 PM]

Eli Fisker: Welcome in to the developers chat [3:34 PM]

Vachekuri: Thanks [3:33 PM]

Eli Fisker: hehe, yes, thats practically it [3:34 PM]

Vachekuri: Nice idea [3:34 PM]

Eli Fisker: Say thx to Jeehyung, it is his [3:34 PM]

Vachekuri: Ok thanks Jeehyung :) I hope you will be able to do good things with my "geeking" [3:35 PM]

mat747: Jee - could you add - Yes, Best wishes to Diana and thanks for listening to my ideas. [3:36 PM]

zaglas: i like it more and more i think !! [3:36 PM]

mat747: hi vachekuri [3:36 PM]

hoglahoo: sorry to lose Diana, I hope she does well wherever she is going! [2:37 PM]

jeehyung: @Vachekurl I'm sure we'll Eterna players will eventually become a big part of RNA research community : ] [3:37 PM]

machinelves: many thanks to everyone who makes this research possible! we ask for features much more than we give praise, but everyone here really appreciates that you all continue to dev on the platform and improve it [3:37 PM]

Eli Fisker: Glad to hear, Zaglas [3:37 PM]

jeehyung: @mat,hoglahoo - will do. I'm sure she'll be happy to hear it  [3:37 PM]

jeehyung: @machine and thanks always for passionate suggestions : ] [3:38 PM]

machinelves: :) [3:38 PM]

jeehyung: All, I'l have to run in 7 minutes - please throw in final questions & suggestions! [3:38 PM]

hoglahoo: let the compliment contest begin! [2:38 PM]

machinelves: @jee only pending thing for me is whether you want a 3D consult, PM, don't need an answer today, but scheduling in next month. [3:39 PM]

jeehyung: @machine checking PM... [3:39 PM]

brandonjr009: Do the heads mean how many times that puzzle has been completed? [3:40 PM]

jeehyung: @machine this is an interesting opportunity. Let me check with the PIs though. I won't be in charge of Eterna 3D so it's not my decision to call. Thanks for the opportunity! [3:41 PM]

hoglahoo: brandonjr009: yes [2:41 PM]

Eli Fisker: Brandon, yes, the number beside it.  [3:41 PM]

machinelves: kk whatever I can do I'll try to facilitate. and if you're busy no worries, you have a lot on your plate! [3:41 PM]

machinelves: thanks! [3:41 PM]

Brourd: Jee, any ideas when they will have low error results for the last few rounds of EteRNA out? [3:42 PM]

JR: for what it is worth - I thought diana was an excellent programmer with lots of potential - dealing directly with the end user is alway frustrating [3:42 PM]

jeehyung: @Brourd actaully, we ordered another repeat last week with sequences up to 130 bases only. Hopefully we'll get better results this time.. [3:43 PM]

jeehyung: @JR Agreed. She was an excellent developet with skills and ideas. A shape that she had to move on. [3:43 PM]

jeehyung: I meant shame [3:44 PM]

machinelves: I second JR's thoughts, I was very impressed with the scope of workload she managed, and that she was so nice. [3:44 PM]

jeehyung: All I have to go now. Thanks for the suggestions and feedbacks. I'll post a news item with the chat log! [3:45 PM]

machinelves: bye and many thanks! [3:45 PM]

Brourd: Okay, I hope it turns out well Jee! Take care. [3:45 PM]

Eli Fisker: Bye Jee [3:45 PM]

mat747: Bye Jee [3:46 PM]

Brourd: btw, for any players who see this proposed lab http://eterna.cmu.edu/web/lab/3766985/ I am currently taking suggestions for the third stem. Please leave a note in the comments section if there are any hairpin/internal loop sequences you would like to see synthesized. [3:47 PM]

hoglahoo: bye jee, thanks [2:48 PM]