2015.01.07 Dev Chat

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On Welcoming Nando as Dev & Johan's Labs


jnicol: Hi everyone welcome to dev chat! [3:00 PM]

machinelves: yay! :D [3:00 PM]

Eli Fisker: hi John :) [3:00 PM]

jnicol: hi elves, eli [3:00 PM]

jnicol: There has been a lot of exciting developments since the last dev chat [3:00 PM]

Mayanne: hi everyone [3:00 PM]

janelle: hello [3:00 PM]

jnicol: hey Mayanne [3:00 PM]

Eli Fisker: Thats for sure :) [3:01 PM]

Eli Fisker: hi Mayanne [3:01 PM]

machinelves: hi everybody :) very excited on all the fun things happening [3:01 PM]

jnicol: First, A big welcome to the newest member of the dev team, Nando [3:01 PM]

machinelves: congratulations Nando!!! :D :D :D [3:01 PM]

Eli Fisker: :) [3:01 PM]

janelle: clap, clap [3:01 PM]

jnicol: he's online so I'm sure he will check in soon :) [3:01 PM]

jnicol: The last round of MS2 results have been published and there has been some analysis to try to understand how these switches behave [3:01 PM]

jnicol: thanks Eli and everyone for the analysis! [3:02 PM]

Eli Fisker: np [3:02 PM]

jnicol: Hopefully everyone has seen the MS2 round 2 lab that has been made active [3:02 PM]

Nando: hi everyone, and thanks :) [3:02 PM]

Eli Fisker: Hi Nando :) [3:02 PM]

jnicol: and there is also a beta lab on the development site that is testing a new flash applet feature on dimerization (implemented by Nando :) [3:02 PM]

jnicol: Hey Nando [3:02 PM]

jnicol: Please see the news item for details: http://eterna.cmu.edu/web/news/5452147/ [3:03 PM]

jnicol: Rhiju and Johan will be joining us tonight to help field any question there might be on these new developments [3:03 PM]

Eli Fisker: And for those who wishes to see and join the analysis on the MS2 lab, check out this forum post:  [3:03 PM]

Eli Fisker: https://getsatisfaction.com/eternagame/topics/switch-scores-for-eterna-switch-puzzles [3:03 PM]

jnicol: thx Eli, the more eyes (and brains) looking over this, the better [3:04 PM]

Eli Fisker: np [3:04 PM]

machinelves: thanks for the links! and very exciting [3:04 PM]

wateronthemoon: thx for that Eli [3:04 PM]

Eli Fisker: And for those who still wonders why switches are important, check out this intro:  [3:05 PM]

jandersonlee: more exciting new developments than I have time for :) [3:05 PM]

machinelves: hehe [3:05 PM]

wateronthemoon: :) [3:05 PM]

Eli Fisker: http://eterna.cmu.edu/web/blog/4551015/ [3:05 PM]

jnicol: any questions on the beta site features? [3:06 PM]

machinelves: will that bond selection tool in Nando's blog post be available for creating single state puzzles as well? [3:06 PM]

machinelves: that is really cool :D [3:06 PM]

Eli Fisker: Oh, will it be available for switch puzzle creation? [3:07 PM]

jnicol: just for solving now, [3:07 PM]

Nando: it's on my todo list, Eli [3:07 PM]

Nando: will take some time though [3:07 PM]

jnicol: but I know Nando is thinking about the puzzle maker :) [3:07 PM]

Mayanne:  the nightclub black light color gets my vote [3:07 PM]

Eli Fisker: Sweet news, Nando [3:07 PM]

machinelves: hehe [3:07 PM]

Eli Fisker: I will be thankful whenever it arrives [3:08 PM]

machinelves: i see thanks for the clarification! for solves, not design... yet :D [3:08 PM]

machinelves: like magic glue [3:08 PM]

machinelves: [ and unglue ] [3:08 PM]

Eli Fisker: Hehe, Magic glue indeed [3:08 PM]

jnicol: Does everyone know about the 'glue' feature? [3:08 PM]

wateronthemoon: magic glue--:) [3:08 PM]

Eli Fisker: Nando invented it for RNA [3:08 PM]

machinelves: nando's video in his awesome blog post http://eterna.cmu.edu/web/blog/5452094/ [3:08 PM]

jandersonlee: haven't heard of teh glue until now [3:09 PM]

Eli Fisker: Check it out, its a very interesting blog post [3:09 PM]

jnicol: I really like the dimer feature, seems a lot more creative solutions are available! [3:09 PM]

wateronthemoon: wow, Nando, that's beautiful [3:10 PM]

Eli Fisker: One more fine adventure of Nando's into the RNA world [3:10 PM]

machinelves: and the pics on what a dimer is, help explain beautifully [3:10 PM]

jnicol: Want to make sure everyone knows about the lab available on the develment server [3:10 PM]

Nando: @JAL: just a way to define a structure in a puzzle with structural freedom [3:10 PM]

machinelves: @jnicol do you mean there is an active lab only on dev server? or testing lab features? [3:11 PM]

jandersonlee: (I'll check it out later - when I have time.) [3:11 PM]

jnicol: the submissions made for the dimer lab on the dev server will be synthesized along with the MS2 lab designs [3:11 PM]

machinelves: ahh cool, i didn't get that before, thanks for the heads up! [3:12 PM]

machinelves: is there a link to it from labs here? [3:12 PM]

Eli Fisker: So we don't get SHAPE data back for the dimer labs? [3:13 PM]

jnicol: I posted a big Red notice if anyone has difficulty logging into dev [3:13 PM]

machinelves: hehe saw the notice, missed the lab lol [3:13 PM]

jnicol: It will be the same process used for the MS2 lab [3:13 PM]

jnicol: (well similar anyways) [3:13 PM]

Eli Fisker: Ok, thx [3:13 PM]

wateronthemoon: Red notice? [3:14 PM]

machinelves: http://eterna.cmu.edu/web/news/5452147/ [3:14 PM]

janelle: machine, middle of notice looks for Johan's Sensor Lab and click on that. Above the red paragraph [3:14 PM]

machinelves: thanks! i saw the red part and missed the rest haha typical elf [3:14 PM]

jnicol: Guess the notice is too overpowering :) [3:14 PM]

wateronthemoon: oh i see. Thanks [3:14 PM]

machinelves: lol no it's good, i just read slow hehe [3:15 PM]

jandersonlee: (Suggestion: make the lab link red too.) [3:15 PM]

Eli Fisker: Good idea [3:15 PM]

jnicol: thx JL, will do [3:15 PM]

machinelves: awesome! [3:15 PM]

wateronthemoon: thanks [3:15 PM]

janelle: Maybe a news notice for when it closes since not listed (or I couldn't find it) [3:16 PM]

machinelves: also excited on the note about how miRNAs can make medicine [3:16 PM]

machinelves: new players often ask about that [3:16 PM]

machinelves: so we are a step closer :D [3:16 PM]

wateronthemoon: yes, very pertinent.  [3:16 PM]

Eli Fisker: :) [3:17 PM]

jnicol: It closes with the main lab on January 19th [3:17 PM]

machinelves: I saw Janelle made a good point earlier for people who wish to help but aren't sure where to start: that making mods of other designs is a way to participate, if you don't know where to begin from scratch ( like me! ) [3:18 PM]

Eli Fisker: Thx Elf and Janelle [3:18 PM]

machinelves: and Eli made a great analysis, did you already link? [3:18 PM]

jnicol: I just updated the news item [3:19 PM]

machinelves: hehe perfect, unmissable now [3:19 PM]

Eli Fisker: Link directly to analysis:  [3:19 PM]

Eli Fisker: https://docs.google.com/document/d/15f5RyFFQQxvE8duLVDkUm_hUydGCK_fEXZdyE5ANLCI/edit [3:19 PM]

machinelves: :D [3:19 PM]

machinelves: thanks Eli! [3:19 PM]

Eli Fisker: np :) [3:19 PM]

johana: Yes, fantastic analysis by Eli [3:19 PM]

Eli Fisker: Thx, Johan :) [3:20 PM]

machinelves: and actually not sure now if it was you or Janelle or both who suggested mods. but either way, that's helpful place for beginners to start [3:20 PM]

johana: Salish99 also posted a great summary of the Same State 1 puzzle [3:19 PM]

machinelves: hi Johan! thanks for all your work on this! :D [3:20 PM]

Eli Fisker: Link to Salish's analysis:  [3:20 PM]

Eli Fisker: https://getsatisfaction.com/eternagame/topics/switch-scores-for-eterna-switch-puzzles#reply_15202695 [3:20 PM]

janelle: thanks Eli [3:21 PM]

johana: For the new switch puzzles, beginners should feel free to experiment. We're hoping to get 6000 submissions, so there's room for everyone [3:20 PM]

jnicol: Hey Johan! [3:21 PM]

machinelves: that's awesome! and reassuring. i know players care about not "wasting" slots, so it's good to know we have plenty of room to experiment [3:21 PM]

Eli Fisker: The more eyes we get on the lab data and on designing, the better chances we have at making a difference to science [3:21 PM]

Eli Fisker: np Janelle [3:22 PM]

jandersonlee: so does that mean we can submit more than 3 per design? [3:22 PM]

machinelves: and that means there's room to make mistakes on purpose too... to make designs that might break to test the limits [3:22 PM]

machinelves: so there's no bad data :D [3:22 PM]

johana: @Eli, that's the idea. I'm already very encouraged by what I have seen. [3:22 PM]

Eli Fisker: Both switches and microRNA has direct implications for making medicine [3:22 PM]

janelle: Janders 600 [3:22 PM]

janelle: 100 each sublab [3:22 PM]

Nando: 100 per design per player [3:22 PM]

jandersonlee: sweet [3:22 PM]

machinelves: whoa! [3:22 PM]

machinelves: :D [3:22 PM]

Eli Fisker: Johan, I'm very glad to hear [3:22 PM]

Eli Fisker: So there is slots for everyone. Grab the chance :) [3:23 PM]

jandersonlee: (sound like time for a 'bot contest) [3:23 PM]

Eli Fisker: hehe, good point, JL [3:23 PM]

JR: can we have more than 3 on the dimer lab? [3:23 PM]

machinelves: haha janderson  [3:23 PM]

jnicol: That is a question for Rhiju and Johan [3:23 PM]

johana: Yes, plenty of slots. @machinelves: yes, breaking things on purpose is a good idea. You could, for example make a 'good' solution and modify it to see where it breaks  [3:23 PM]

jnicol: It was planned for 40 slots for each sublab for the beta version [3:24 PM]

machinelves: I saw Eli mentioned he would test this specifically, I think it's a good idea too [3:24 PM]

jnicol: Do you want me to up that Johan? [3:24 PM]

johana: I'd have to check with Rhiju to see how many sequences we're synthesizing in total on the chip. If people are excited I'm all for increasing the numbers if possible. [3:25 PM]

janelle: oh my goodness [3:26 PM]

jnicol: Ok, we can post an update if the number for the dimer lab changes [3:26 PM]

MasterHouse: Does just doing the challenges help in anyway? [3:26 PM]

machinelves: @master yes, it helps you learn how to do labs [3:26 PM]

janelle: Master yes  [3:27 PM]

jnicol: Johan I have a question about the graphs [3:27 PM]

jnicol: The control shows a max AU of 1, but several graphs go alot higher than this. [3:27 PM]

MasterHouse: Does the data go anywhere usful? or is there a different place to solve actual problems [3:27 PM]

machinelves: the data from challenges is just for your learning benefit [3:27 PM]

Eli Fisker: I have a question too. What do AU stands for - assuming it is not our known and loved basepair [3:28 PM]

machinelves: and the labs is where problem solving happens :D [3:28 PM]

jnicol: MasterHouse, the challenge and player puzzles are not used for analysis [3:28 PM]

KidGenius300: AU=gold [3:28 PM]

janelle: Master, your actually in a dev. chat right now discussing the "actual Labs" that you can join in with your points [3:28 PM]

machinelves: @Eli where are you looking? [3:28 PM]

Eli Fisker: Masterhouse, the lab dtata gets uploaded in a database at the stanford lab [3:28 PM]

jandersonlee: you need to earn 10000 pointe to do the labs [3:28 PM]

johana: @jnicol: Correct. The intensity in the graphs is normalized to the MS2 control. For some reason, some designs have a much higher signal. It could because more RNA is transcribed. [3:28 PM]

johana: We don't know yet what exact cause is yet. [3:29 PM]

Eli Fisker: Elf, John was asking the following: jnicol: The control shows a max AU of 1, but several graphs go alot higher than this. [0:27 AM] [3:29 PM]

machinelves: oh thanks! missed the sentence [3:29 PM]

Eli Fisker: np [3:29 PM]

janelle: Eli, can you post what you were just talking ? [3:29 PM]

janelle: about? [3:29 PM]

Eli Fisker: Just did above [3:30 PM]

johana: @Eli: AU=arbitrary units [3:29 PM]

Eli Fisker: Thx, Johan :) [3:30 PM]

darosmajorana97: someone expert in loops? :D [3:34 PM]

jandersonlee: XP [3:30 PM]

rhiju: hi all, sorry I 'm late -- just caught up with the discussion so far [3:30 PM]

jnicol: Hi Rhiju! [3:30 PM]

MasterHouse: so i need 10,000 points to do labs? [3:30 PM]

machinelves: hi Rhiju! :D so exciting all the good news! [3:30 PM]

Eli Fisker: hi Rhiju :) [3:30 PM]

johana: It's a normalized fluorescence signal, so it depends on the signal for the MS2 control. [3:30 PM]

rhiju: i like JR's proposal to have more slots per user in the test dimer lab.  [3:30 PM]

Eli Fisker: MasterHouse, correct [3:30 PM]

rhiju: Up to 300/user seems fair to match the FMN labs [3:30 PM]

johana: The fluorescence depends on the MS2 protein, the laser power, the camera, the exposure time etc.  [3:30 PM]

janelle: HI Rhiju [3:31 PM]

jandersonlee: @MasterHouse and you get them and practice RNA folding by doing the Challenges [3:31 PM]

jnicol: so you want 1000 slots for each sublab and 100 slots for each player per lab? [3:31 PM]

rhiju: Right ... [3:31 PM]

jnicol: I put that in after chat! [3:31 PM]

jandersonlee: with voting ?! [3:31 PM]

rhiju: for some reason I thought we say each player can give up to 300 (not 100). [3:31 PM]

jnicol: *I'll [3:32 PM]

Eli Fisker: Voting kind of looses it meaning [3:32 PM]

Eli Fisker: with that many slots [3:32 PM]

Nando: 3 targets x 100 slots [3:32 PM]

Eli Fisker: There will be more than enough work with designing [3:32 PM]

jandersonlee: and gets tedious [3:32 PM]

machinelves: hehe, are votes even necessary for these? [3:32 PM]

jnicol: Its 100 per sublab, we have 6 sublabs, which makes 600 per player for the MS2 round 2 lab [3:32 PM]

rhiju: @nando, aha. OK [3:32 PM]

janelle: Oh my 900 designs [3:32 PM]

machinelves: actually, if one wanted to save time? [3:32 PM]

darosmajorana97: http://eterna.cmu.edu/sites/default/files/chat_screens/201173_1420673574.png [3:36 PM]

rhiju: @jnicol thanks for clarifying. 100 per sublab sounds good. [3:32 PM]

darosmajorana97: Help :c [3:37 PM]

janelle: daro, we are in dev. chat right now [3:33 PM]

jandersonlee: how many palyer participate in labs these days - just divide the slots with a 50% overbooking? [3:33 PM]

darosmajorana97: Sorryyyyyyy [3:37 PM]

janelle: daro, after the dev chat you can get help but not right now [3:34 PM]

rhiju: @elves, in response  to your earlier comment, it is indeed incredibly exciting in eterna now! [3:34 PM]

machinelves: @daros http://prntscr.com/5pr25i [3:34 PM]

jnicol: Rhiju, will we have a monthly eterna meeting this week? [3:34 PM]

machinelves: ( and janelle is right, dev chat now, feel free to ask on puzzles after :) ) [3:34 PM]

rhiju: @jandersonlee, I have a bet with some of the other devs (I won't name who) that players will indeed get us 6000 designs. [3:35 PM]

rhiju: Its an amazing challenge  [3:35 PM]

jnicol: me :) [3:35 PM]

machinelves: @rhiju hehe omg i'm really really happy you all brought on Nando, that is simply amazing for all of us. * high five * [3:35 PM]

janelle: thanks machine [3:35 PM]

rhiju: I wasn't going to say [3:35 PM]

machinelves: lol [3:35 PM]

jnicol: I really hope we get to 6000! [3:35 PM]

hoglahoo: rhiju: if you'll give us unlimited submission potential you can secure your bet win [3:35 PM]

machinelves: i'm booked until the 14th but i finally got a computer that's not overheating so i hope to try [3:36 PM]

rhiju: @elves, yes, that's the most thrilling thing -- nando is in the house! (officially!) [3:36 PM]

Eli Fisker: :) [3:36 PM]

Nando: I sneaked in a long time ago :P [3:36 PM]

machinelves: w00t! [3:36 PM]

machinelves: hehe [3:36 PM]

hoglahoo: how long have you been beating nando's door down to get him to sign the papers [3:36 PM]

jandersonlee: but now they gave you a key [3:36 PM]

machinelves: as you said Nando, just putting the official gold seal on the hard work you've already been doing [3:36 PM]

Nando: @JAL: right :D [3:36 PM]

machinelves: thanks for your constant dedication to science around here :D [3:36 PM]

machinelves: lol [3:36 PM]

jandersonlee: and well deserved [3:37 PM]

machinelves: agreed [3:37 PM]

Eli Fisker: Yup [3:37 PM]

rhiju: @hoglahoo. I like the enthusiasm! Given the enthusiasm players have already given to several challenges (incl. brourd's FMNsanity) I suspect that we will have enough players to make 6000 without increasing the per-player limit.  [3:37 PM]

jandersonlee: what of Brourd's labs this time around? [3:38 PM]

janelle: It's mind boggling to go from 8 to several hundred [3:38 PM]

rhiju: And if we dn't make it to 6000, nando has some tricks up his sleeve to make puzzle solving even easier in future rounds. [3:38 PM]

Omei: Hey, Nando!  I'll throw in my congratulations! [3:38 PM]

rhiju: @janelle,yea crazy! [3:38 PM]

jnicol: Brourd's lab will be made active on January 19th [3:38 PM]

Eli Fisker: Sounds great [3:38 PM]

darosmajorana97: doesn't do @machineselves [3:42 PM]

Nando: hi Omei, long time :) [3:38 PM]

Eli Fisker: Hi Omei :) [3:38 PM]

machinelves: a points bonus won't make a difference to the hardcore players, but to new players if there were additional incentive you might get more subs, which is partly what drove DMNsanity [3:39 PM]

jandersonlee: so 12 days left for the two new labs? [3:39 PM]

Omei: Ye, it has been quite a drought.  Hopefully that will be changing very soon. [3:39 PM]

machinelves: @daros keep trying! i only had time to fill in some of the bubbles, it's not a complete solve [3:39 PM]

jnicol: correct JL [3:39 PM]

janelle: Yes jander and submit 900 [3:39 PM]

rhiju: @jnicol as for an open group meeting, yes we'll have one definitely on 2/6, but I'd like to have a more general 'state-of-eterna' broadcast in january. [3:39 PM]

machinelves: @daros have you tried .nova ? [3:39 PM]

LinkBot: http://www.pbs.org/wgbh/nova/labs/lab/rna/ [3:39 PM]

machinelves: omei!!! :D [3:39 PM]

Omei: Hi, Eli I've been trying to keep an eye on your research. [3:40 PM]

Eli Fisker: Hehe, thx [3:40 PM]

machinelves: woohoo state of eterna i love it [3:40 PM]

machinelves: hehe [3:40 PM]

janelle: Points for all the designs? Please say Yes [3:40 PM]

jnicol: Hasnt been decidied yet janelle [3:40 PM]

jandersonlee: do we need barcodes on the new labs? can there be an auto-barcode feature? [3:40 PM]

janelle: : ) [3:41 PM]

Eli Fisker: No barcodes is needed for MS2 [3:41 PM]

jnicol: no barcodes are necessary [3:41 PM]

hoglahoo: who wants to score 6000 designs other than a bot [3:41 PM]

johana: @janelle: Points sounds like a good idea [3:40 PM]

jnicol: Ask Johan how he does that :) [3:41 PM]

jandersonlee: (Whew) [3:41 PM]

janelle: johana has become my instant BFF [3:41 PM]

hoglahoo: Johan how do you do that [3:41 PM]

machinelves: good question on barcodes [3:41 PM]

johana: @hoglahoo: Score them? [3:41 PM]

rhiju: for points, let's use the same formula as for our normal SHAPE score -- going 'point' @janelle -- @jnicol easy to do? [3:42 PM]

rhiju: *good 'point' [3:42 PM]

machinelves: lol [3:42 PM]

hoglahoo: yeah [3:42 PM]

jnicol: Rhiju, the question is on how many do we score? [3:43 PM]

hoglahoo: oh nevermind [3:43 PM]

rhiju: anyone have issues with state of eterna on jan. 23? [3:43 PM]

hoglahoo: jnicol was talking about no barcodes [3:43 PM]

jandersonlee: Gee I migh make it back in teh top 50 ;) [3:43 PM]

machinelves: i can do 23rd [3:43 PM]

janelle: You meeting on 1/23 rhiju? [3:43 PM]

janelle: You mean meeting I meant to say [3:43 PM]

Brourd: It would have been nice to have it on the 7th, but oh well. [2:44 PM]

Eli Fisker: By the way, I have a wish on the UI [3:44 PM]

jnicol: Hey Brourd! [3:44 PM]

rhiju: @jnicol (getting confused -- are we talking about the last round of johan's lab?) [3:44 PM]

janelle: Hi Brourd [3:44 PM]

Eli Fisker: I regularly need to make a copy of a sequence [3:44 PM]

rhiju: @brourd, 'the state of eterna is good' [3:44 PM]

Brourd: ha [2:44 PM]

jnicol: No, the new one with 900 entries per player [3:44 PM]

Eli Fisker: It would be a big help if I didn't have to click the okay button to make the box go away:  [3:44 PM]

Eli Fisker: http://prntscr.com/5pr6b4 [3:44 PM]

rhiju: esp. since you're here -- great to have you, and congrats on getting puzzles for FMNsanity [3:44 PM]

jnicol: players are drooling at getting all those points :) [3:44 PM]

jandersonlee: and scoring them! [3:45 PM]

rhiju: @jnicol, I know. [3:45 PM]

ethan2002324: Guess who's back? ME!  YOu probably dont rememember me XD [3:45 PM]

Brourd: Won't be a long meeting then I guess! [2:46 PM]

jnicol: FMNsanity marathon to get switch design was a resounding success! [3:45 PM]

janelle: Hi ethan, I do remember you and we're in dev. chat meeting right now, your welcome to follow along [3:46 PM]

jandersonlee: (seemed more like insanity form this side!) [3:46 PM]

jandersonlee: but glad you pulled through with it! [3:46 PM]

jnicol: 311 entries, 6 winners [3:46 PM]

Nando: @Eli: like, the notice should fade away after a few seconds? [3:47 PM]

jnicol: plus some  [3:47 PM]

rhiju: Back to 1/23, I was thinking of having an open gruop meeting at 9am PST and then another dev chat session laterin the day to accommodate folks who can't make the first time. [3:47 PM]

ethan2002324: I wasnt in dev,  Whatever that is.  I was just here earlier today. :/ [3:47 PM]

Eli Fisker: Nando, exactly [3:47 PM]

Eli Fisker: that would be brilliant and a huge help [3:47 PM]

rhiju: @ethan, welcome! [3:47 PM]

Nando: @Eli: noted, I'll look into it [3:47 PM]

janelle: Rhiju, fine here [3:47 PM]

ethan2002324: XD its nando! [3:47 PM]

Eli Fisker: Nando, big thx! [3:47 PM]

machinelves: @ Eli & Nando good idea! [3:47 PM]

jnicol: Another question on the MS2 graphs, The 'ideal' switch seems to be the red graph shifted to the right (based on the control graph) [3:47 PM]

Brourd: I was pleased with the turnout. Players submitted hundreds of puzzles, even those who are normally not into puzzlemaking. [2:48 PM]

jnicol: Is it better if the red graph stayed flatlined at 0, or is that impossible? [3:47 PM]

ethan2002324: Nando remember me?  The annoying one? XD [3:48 PM]

hoglahoo: it's a miracle, something pleased Brourd [3:48 PM]

rhiju: hahaha [3:48 PM]

machinelves: congrats on submitting so many switch designs everybody! and congrats brourd on scoring them! [3:48 PM]

ethan2002324: How old r u guys?  Im 13. [3:49 PM]

jnicol: players took it as a badge of honor to score under 1.0/10.0 :)  [3:49 PM]

jandersonlee: can we discuss APIs for bot submission offline? [3:49 PM]

hoglahoo: it's nice to see so many people involved in that lab [3:49 PM]

Brourd: 3pm PST dev chat on the 23rd, Rhiju? [2:50 PM]

machinelves: @Rhiju sounds smart to have a followup for those who miss the first round of the meeting [3:49 PM]

rhiju: @brourd, yes tentatively -- will try to confirm after dev meeting this friday [3:50 PM]

machinelves: 9am PST is the middle of the night in elf time zone lol, but will try to make both [3:50 PM]

hoglahoo: @jandersonlee, how so - snail mail? [3:50 PM]

Brourd: Maybe earlier, maybe later. [2:50 PM]

Brourd: I can't really predict how my own schedule will play out. [2:50 PM]

ethan2002324: What does dev mean????!?!?!?!?!?!?!?!?!??!?!?!~?!!?!?!? [3:50 PM]

jandersonlee: @hoglahoo that work [3:50 PM]

machinelves: dev = development [3:50 PM]

johana: @jnicol: For the perfect switch, the curve is moved so far to the right that it is essentially flatlined at all measured concentrations. In practice, the energy from FMN binding is not enough to result in such a large shift. [3:50 PM]

jandersonlee: or email [3:50 PM]

jnicol: thx, Johan [3:51 PM]

Eli Fisker: Johan, could you post a picture of such a perfect switch curve, so we can better recognize it? [3:51 PM]

Nando: @JAL: can you give me some specifics in PM, I might be able to help [3:51 PM]

vcarter0: why are switch puzzles so hard? [3:51 PM]

jandersonlee: @Nando -tx [3:51 PM]

rhiju: @JAL This is it -- rise of the bots... [3:51 PM]

ethan2002324: YAAAAY! I BEAT ANOTHER PUZZLE! :D [3:51 PM]

ethan2002324: Whoa i just moved up so jmuch! XD [3:51 PM]

machinelves: congrats ethan :) [3:52 PM]

janelle: ethan, it means development, were talking about the lab and general business of eterna right now [3:52 PM]

ethan2002324: Omg.  This is a giant puzzle. [3:52 PM]

Brourd: @ Johan - what you may want to do with the graphs (if possible) is to also define your ideal target in some way. [2:52 PM]

ethan2002324: http://eterna.cmu.edu/sites/default/files/chat_screens/201903_1420674738.png [3:52 PM]

Eli Fisker: vcarter, they takes some more training than normal puzzles. There are tutorials though [3:52 PM]

vcarter0: where? [3:52 PM]

Eli Fisker: moment [3:52 PM]

ethan2002324: Gigantic! :O [3:52 PM]

rhiju: @vcarter also some switch puzzles may be impossible (though we try to vet those before deploying on eterna) [3:52 PM]

johana: @broutf: like including a grey target curve? [3:53 PM]

Eli Fisker: Here is a collection of switch puzzle tutorials:  [3:53 PM]

ethan2002324: I get the feeling that most of you guys are like in college or getting your masters or something.  You are sounding so mature. :/ [3:53 PM]

Eli Fisker: https://docs.google.com/document/d/18MmROVShMkrw8CCKPXvvq-Taip4Mrv4oASn462mpK_0/edit#heading=h.2871iz9iae28 [3:53 PM]

hoglahoo: *raises eyebrow*do we have new impossible switch puzzles? [3:53 PM]

janelle: ethan, most of us are really a bunch of kids at heart [3:54 PM]

machinelves: @vcarter those tutorials Eli linked will help, and here's a guide to switches https://docs.google.com/document/d/1ga8v6GoJxuHcs0LwNkljOLXX9VZWZLwsZmfWJfseYhA/edit [3:54 PM]

jandersonlee: immpossible puzzles - or labs? [3:54 PM]

jnicol: ribonucleic has one hog [3:54 PM]

rhiju: @hoglahoo, I can make some for you [3:54 PM]

hoglahoo: john, I remember. thanks [3:54 PM]

darosmajorana97: damn it [3:58 PM]

Brourd: Maybe. I can't really say what players would prefer, Johan. [2:54 PM]

hoglahoo: been awhile though :) [3:54 PM]

rhiju: but wait until we unleash the next set experimental switch puzzles [3:55 PM]

machinelves: @janelle, second the notion of being kids at heart :D [3:55 PM]

janelle: oh, oh rhiju [3:55 PM]

ethan2002324: WAIIIIIIT a second!  SO you guys work at eterna or something?  WHOA! [3:55 PM]

hoglahoo: rhiju that's fine, I have grown accustomed to waiting :D got 300 submissions to turn in soon anyway [3:55 PM]

janelle: So, people like Vinnie can be used to churn out the designs by the players? [3:55 PM]

ethan2002324: Im just a normal kid who had to play this in science class. [3:55 PM]

rhiju: :D [3:55 PM]

hoglahoo: Vinnie is good people [3:55 PM]

ethan2002324: And now i like it XD [3:56 PM]

Brourd: As you may recall, hoglahoo, some of the original challenge switches were impossible as well. (or maybe not recall) [2:56 PM]

rhiju: @ethan, did you try the nova? [3:56 PM]

jnicol: Rhiju, are the oligo starnds always a fixed sequence, are there some more valuable in research [3:56 PM]

ethan2002324: XD i love that name.  hogalahoo [3:56 PM]

hoglahoo: Brourd: maybe but I don't see them around anymore [3:56 PM]

Eli Fisker: Hoglahoo reported a lab bug in chat recently. That ones player votes did not get counted on individual main lab pages: [3:56 PM]

ethan2002324: I finished all 3 trials in the nova [3:56 PM]

hoglahoo: I thought maybe some new ones were released I didn't see yet [3:56 PM]

Eli Fisker: http://i.imgur.com/DQqXjWl.png [3:56 PM]

janelle: ethan, stick around, you'll love it [3:56 PM]

ethan2002324: So i came here [3:56 PM]

Brourd: They were removed, or renamed "Brourd's mod of switch" [2:56 PM]

rhiju: @ethan nice [3:56 PM]

rhiju: @brourd lol [3:57 PM]

machinelves: ethan, rhiju is right, try .nova in this link if you haven't yet, it's really easy and fun intro to eterna [3:57 PM]

LinkBot: http://www.pbs.org/wgbh/nova/labs/lab/rna/ [3:57 PM]

ethan2002324: I will stay but im doing Social Studies Homework.  I'm doing Anicent History: Ancient Egypt [3:57 PM]

ethan2002324: BLEGH [3:57 PM]

jnicol: Eli, I will check that [3:57 PM]

hoglahoo: ah ok. drake did one too now that I think back, if I remember right [3:57 PM]

Eli Fisker: Thx, John :) [3:57 PM]

ethan2002324: So interesting but so annoying i have to do 3 2 collumn note papers due tomorrow. [3:57 PM]

rhiju: ok everyone i've got to go -- any last qs? [3:57 PM]

machinelves: oh haha i am slow catching up to chat, congrats ethan on finishing nova :D  [3:57 PM]

Nando: cya Rhiju [3:57 PM]

ethan2002324: OH! I HAVE A QUESTION! [3:57 PM]

Brourd: btw, Rhiju, what is the theoretical throughput on this pipeline? [2:58 PM]

johana: @jcnicol [3:57 PM]

jnicol: Rhiju, are the oligo starnds always a fixed sequence, are there some more valuable in research [3:57 PM]

janelle: Have a great night rhiju, thanks for coming [3:58 PM]

machinelves: thank you Rhiju! great to see you, and looking forward to the next meeting [3:58 PM]

jnicol: Thanks Rhiju, Johan and Nando for your expertise tonight, very much appreciated! [3:58 PM]

Eli Fisker: Bye Rhiju [3:58 PM]

ethan2002324: Ugh [3:58 PM]

Brourd: including the time it takes to run the experiment, etc. [2:58 PM]

rhiju: @nando, just read your blog post explaining the switches -- very nice. [3:58 PM]

johana: The RNA sequences we use are based on microRNAs that regulate gene expression in cells [3:58 PM]

jandersonlee: 'night all - and thanks for all the good/hard work [3:58 PM]

machinelves: thanks Johan for all your work behind the scenes! [3:58 PM]

ethan2002324: I just realized that I am probably the youngest person here [3:58 PM]

rhiju: everybody, thanks for coming! [3:58 PM]

machinelves: and huge congrats to Nando, :D [3:58 PM]

johana: Now we're using one that's implicated in heart disease, but we may use others later on\ [3:58 PM]

Brourd: And another question, what is the experimental error? [2:59 PM]

jnicol: nide, johan, thx! [3:59 PM]

johana: @elves: thanks! [3:58 PM]

jnicol: *nice [3:59 PM]

Eli Fisker: Oh, Johan, thats a nice detail.  [3:59 PM]

machinelves: Johan that's very helpful to know [3:59 PM]

rhiju: @brourd, ask in the switch getsat thread and ye shall receive (maybe from johan) [3:59 PM]

ethan2002324: I have  5310 of those $ things. YAAAY XD [3:59 PM]

Eli Fisker: We love to hear when what we are working with has practical use [3:59 PM]

machinelves: if we have any example with a specific path towards medicine that we could showcase to players [3:59 PM]

janelle: @johana, were trying to develop better folding on known swithces for heart disease? [3:59 PM]

Nando: @Brourd: theoretical limit is 10 million sequences, practically, more like 100'000 [3:59 PM]

machinelves: they have difficulty grasping the abstractness of fundamental research [4:00 PM]

Brourd: And the experiment length, Nando? [3:00 PM]

rhiju: @elves, connections to medicine will be major topic of state-of-eterna [4:00 PM]

machinelves: so being able to say this RNA affects this type of medicine discovery would be great [4:00 PM]

Brourd: Weeks, days, months. [3:00 PM]

Eli Fisker: We science gamers generally love to hear the why of what we are doing [4:00 PM]

machinelves: @rhiju awesome :D :D :D  [4:00 PM]

johana: @janelle:  [4:00 PM]

machinelves: will really help connect the dots [4:00 PM]

jnicol: Thanks everyone! [4:00 PM]

rhiju: thanks everyone! [4:00 PM]

Eli Fisker: Bye John [4:01 PM]

janelle: Yes, johana? [4:01 PM]

hoglahoo: bye devs [4:01 PM]

Nando: it'll get much faster than the first round, Johan and Rhiju learned along the way [4:01 PM]

janelle: bye john [4:01 PM]

machinelves: @ Eli exactly [4:01 PM]

Hyphema: nother dev chat missed.  oh well.  will read later.  hello all [4:01 PM]

machinelves: Bye John! thank you! [4:01 PM]

Brourd: I would not mind hearing about that adventure, Nando. [3:01 PM]

johana: The miRNA is related to heart disease. The long-term goal is to develop smart RNA molecule that can shut these miRNAs down, for example [4:01 PM]

Eli Fisker: Hi Hyph :) [4:01 PM]

machinelves: bye Rhiju! [4:01 PM]

machinelves: hey hyph & welcome will post transcript shortly [4:02 PM]

Eli Fisker: Johan, super cool! [4:02 PM]

janelle: johana, question. Is that what is up were working on? [4:02 PM]

machinelves: @johan wow that is so cool! thank you so much for the explanation [4:02 PM]

johana: @brourd: weeks (hopefully), not months. [4:03 PM]


and more from Johan on heart miRNAs:


janelle: @johana, the microswitch/heart disease were trying to improve on? [4:05 PM]

johana: @janelle: There is some info on Nandos blog,  [4:07 PM]

janelle: k, thank you for responding [4:08 PM]

johana: it's called hsa-mir-208a [4:08 PM]

janelle: Let's say we find a "good switch" RNA you think works well to alleviate a particulart type of disease state in the lab.  How/what would be the next state to test in?   [4:12 PM]

johana: @janelle:  "miR-208a is one of the most important heart-enriched mirRNA playing a crucial role in the heart health and disease" [4:11 PM]