2015.10.09 Johan's Intro to Switches! - Chat Transcript

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Note: the youtube links are blocked by the wiki spam filter, so they have spaces insterted. Also the links here are links to live stream and may not work anyway. the archived video will be posted to the Monthly Eterna Meeting page.



johana: Here is the link to the Das lab eterna presentation  [9:28 AM]

johana: http://youtu .be/MZDfhqsskas [9:28 AM]

RedSpah: hi all  [9:29 AM]

Elves: yay! thank you :D [9:30 AM]

Omei: Live [9:33 AM]

Omei: Lost the sound [9:53 AM]

Omei: It's back [9:53 AM]

Xnessax: hi [9:53 AM]

Xnessax: WHAT [9:53 AM]

Xnessax: How do you color your nick  [9:54 AM]

Xnessax: O.O [9:54 AM]

Elves: hi Xnessax! check out the live presentation from the Das Lab! http://youtu .be/MZDfhqsskas [9:54 AM]

Xnessax: Hmmm, i'll take that look. [9:54 AM]

Xnessax: Is it stream? [9:55 AM]

Xnessax: :O [9:55 AM]

Elves: yep exactly :) [9:55 AM]

Xnessax: how do i steam in youtube, i never had used it, i used Livestream [9:55 AM]

Xnessax: XD [9:55 AM]

Xnessax: i wonder [9:55 AM]

Elves: just click the link [9:55 AM]

Elves: it will autolay hopefully [9:55 AM]

Elves: autoplay [9:56 AM]

Xnessax: When is it to "create" a video, so it can be auto-record online, right? [9:56 AM]

Elves: we will post a record of the video in the eterna wiki after [9:57 AM]

Xnessax: I saw youtube updated new stuff ,that can be similar to LiveStream and Twitch [9:57 AM]

Xnessax: Oh. [9:57 AM]

Elves: and i think also the youtube account of course [9:57 AM]

Elves: yay reproducability!!!! :D [9:58 AM]

Xnessax: Right! I have youtube account, i subscribed Eterna [9:58 AM]

Xnessax: :DDDDD [9:58 AM]

Elves: nice! thanks Xnessax :) :) :) [9:58 AM]

Xnessax: I'm watching at start of video autolive [9:58 AM]

Xnessax: No problem [9:58 AM]

Elves: awesome, Johan gives a great intro to switches [9:58 AM]

Xnessax: Cool [9:58 AM]

Elves: that's phenomenal improvement! as for experimenting, yes players sometimes purposefully design for a low score [10:02 AM]

Elves: that's how we tested that GU loosens up binding during single state labs - GUs used to give low scores, but knowing how to make the molecule loosen up was useful for switches [10:03 AM]

Xnessax: oh [10:04 AM]

Xnessax: Is Gu the important pair for puzzles? As like every changeller ,using a mission ,to have many of GU on. Isn't it really? [10:05 AM]

Elves: each pair, and each nucleotide has its own unique usefulness [10:05 AM]

Elves: and it also depends on the goal of the puzzle [10:05 AM]

Xnessax: Oh ,right! [10:05 AM]

Xnessax: many different pairs and making it united.  [10:05 AM]

Elves: so GU is the weakest pair, therefore use it where you want the RNA to be able to move, or where it doesn't need really strong binding [10:06 AM]

Xnessax: ohh [10:06 AM]

Elves: many puzzles ask for a lot of GU as a challenge, because it is easy to use GC because it is strongest, but RNA doesn't like to be all GC [10:07 AM]

Elves: so we want to mix it up a little :D [10:07 AM]

Xnessax: Nice quote! [10:07 AM]

Elves: hehe thx :) [10:07 AM]

Xnessax: Many puzzles as level a little high, i did solve with  almost no GC. [10:07 AM]

Xnessax: No problem. [10:07 AM]

Xnessax: It was good helpness from documents ,that teachs about boost loop and block loop [10:08 AM]

Xnessax: Like Eli Fisker's documents, Brond's documents [10:08 AM]

Elves: awesome! there are a lot of great guides by players, i'm happy it helped [10:08 AM]

Xnessax: Indeed, it's great to help  [10:09 AM]

Xnessax: People love helping people and getting new ideas for them back. [10:09 AM]

Xnessax: I also gave some clubs to Astromon ,he was able to solve Oryza Sativa Level 4  [10:10 AM]

Elves: exactly! everyone has something to contribute. thanks for helping! :) [10:11 AM]

Xnessax: No problem :))) [10:11 AM]

Xnessax: What are those graphics for? (-12:14)  [10:18 AM]

Xnessax: or 12:30 [10:18 AM]

Elves: xnessax I'm not sure since i'm further along but i'll check after the broadcast [10:19 AM]

Xnessax: koay [10:19 AM]

Xnessax: Okay* [10:19 AM]

Elves: hehehe aww eternabot [10:20 AM]

Xnessax: Oh eternabot? O.O [10:21 AM]

Elves: yeah players are able to get better scores than dear eternabot so we have to teach it our best strategies in the strategy market so it improves :) [10:22 AM]

Elves: @Johan / everybody - do we have any analysis of what is the degree of variability between designs being submitted? i.e. mostly mods or unique designs? [10:23 AM]

Astromon: hi xness, Elves [10:23 AM]

Elves: hi astro! [10:23 AM]

Xnessax: Hi astromon [10:23 AM]

Xnessax: We are on dev right? On youtube Live-action [10:23 AM]

Astromon: oH [10:24 AM]

Xnessax: Or what do we call it [10:23 AM]

Jennifer Pearl: i am [10:24 AM]

Astromon: hi everyone is this a dev chat? [10:24 AM]

Xnessax: Hi Jennier. [10:24 AM]

Elves: exactly, wondering if the high score cluster has variability between submissions [10:25 AM]

Xnessax: This youtube https://www.youtube .com/watch?v=MZDfhqsskas&feature=youtu.be [10:25 AM]

Jennifer Pearl: I came late but I would like to let you know that DPAT can now pick out stacks that only accur in high scoring NG labs or any score range [10:25 AM]

Xnessax: Variability. [10:25 AM]

Elves: @johan can you explain more about the cooperative designs? [10:25 AM]

Xnessax: It remind me from my high school [10:25 AM]

Jennifer Pearl: I like the presentation [10:26 AM]

Elves: thanks for starting the monthly meetings back up!! :D [10:26 AM]

Xnessax: I also would like to know about Cooperative Designs  [10:25 AM]

Astromon: nice work jen [10:26 AM]

Xnessax: Presentation is well organizated and simple. Very nice. [10:26 AM]

Elves: @johan I also wanted to know about something I heard that we are moving towards not doing protein binding switches and instead focusing on miRNA. is this true, and is it related to what you said about... [10:27 AM]

...modularity of miRNAs?

Jennifer Pearl: nice [10:27 AM]

Elves: lol [10:27 AM]

Xnessax: [color=white]hi[/color]  [10:27 AM]

Xnessax: lol [10:27 AM]

Elves: hahaha [10:28 AM]

Jennifer Pearl: can you expand on that Rhiju? [10:28 AM]

Elves: @Jen in that case i think the stack identification in dpat should be made into motifs [10:29 AM]

Astromon: i like mirna labs< [10:29 AM]

Jennifer Pearl: motoif as in the entire shape of thge structure [10:29 AM]

Elves: motif as in a short segment of the whole molecule [10:29 AM]

Jennifer Pearl: I havnt done anything really with motifs. will look into it [10:30 AM]

Elves: ohhh so cooperativity means first binding potentiates a second binding? [10:30 AM]

Jennifer Pearl: so cooperativity is kinda like jumpstarting [10:31 AM]

Jennifer Pearl: the first one jumpstarts teh second [10:32 AM]

Jennifer Pearl: right? [10:32 AM]

Astromon: for the switch? [10:32 AM]

Elves: so are you saying multiple binding sites for same molecule means flooding with that molecule in solution will trigger an on / off state faster or 'more sharply'? [10:32 AM]

Elves: ohh interesting exactly like a mini logic inside the binding itself lol [10:32 AM]

Elves: hahaha that's very clever [10:33 AM]

Astromon: what type of solution? [10:34 AM]

Astromon: like greasing a machine haha [10:34 AM]

Elves: cool, i like moving towards miRNA just making sure I understand, thanks! [10:35 AM]

Elves: @Jen will explain motifs later, was some good videos [10:35 AM]

Xnessax: at start i was wondering GU was the important ,he said it was a weakest binding, but it helps Rna moves freely. So it can change into other state. [10:35 AM]

Elves: Thank you!!! [10:36 AM]

Jennifer Pearl: thanks [10:36 AM]

Astromon: i have beehn replacing gu for gc in my labs latley for that reason ness [10:36 AM]

Elves: @astro solution i think means liquid solution literally, that is washed over the RNA, and there can be other molecules in that liquid that do or do not bind to the RNA... but someone else can answer better... [10:36 AM]

...than me on that

Astromon: i hope it tests ok< [10:36 AM]

Astromon: hmm ty interesting [10:37 AM]

Xnessax: Oh cool ,nice and random answer for astro. [10:37 AM]

Elves: @Jen short answer is motifs are like the different shaped legos that fit together to build one RNA molecule [10:37 AM]

Elves: or once you see, you'll know basically stacks and their binding loops [10:37 AM]

Xnessax: Oh wlel, astro ,did you use GC and GU [10:37 AM]

Xnessax: in lab, so it makes different pairs and a little strong binding? [10:37 AM]

Astromon: i replaced gu for gc [10:38 AM]

Xnessax: oh. [10:38 AM]

Astromon: so maybe it will switch easier [10:38 AM]

Xnessax: ah i see [10:38 AM]

Astromon: i dunno yet<< [10:38 AM]

Elves: thanks everybody for the great presentation!!! [10:38 AM]

Xnessax: i had solved one switch from malcolm i used all GCs [10:38 AM]

Astromon: thanks sry i was late [10:38 AM]

Xnessax: I thought it was kinda impossible. [10:38 AM]

Xnessax: like they need strong binding and shack or something [10:39 AM]

Elves: no worries astro i will post a link to the archive of the video as soon as it is available, usually within 24 hours [10:39 AM]

Xnessax: There are some little big loops. [10:39 AM]

Astromon: oH video too cool thanks Elves [10:39 AM]

Xnessax: And Elves, hi... I'll present myself.. I am Vanessa and deaf, with Implanted Cochlear. I still am beginner with it, I live in Brazil ,so can that video be subbed ,maybe? [10:40 AM]

Astromon: gc's are much needed sometimes its finding the balance maybe [10:40 AM]

Elves: also feel free to design however you are inspired - we never know what will work until we try. then you can discover what does work for the specific design, and that is a big help to have your creativity! [10:40 AM]

Astromon: thats a great idea xness! [10:40 AM]

Xnessax: Yes, i would like to understand what it says in video, so i can't hear as being deaf with IC ,or not known English full-english yet, as like speech voices. [10:41 AM]

Elves: hi Vanessa, I'm very happy to meet you! Brazil, that's very cool, I read about the rainforest there, I love it :) [10:42 AM]

Xnessax: My dominated language was only Portuguese, so from hearing ,I can notice sometime which sound is. [10:41 AM]

Astromon: to be honest ness i find it hard following what is being said also in alot of the eterna videos<< [10:42 AM]

Xnessax: Thanks, elves. Brazil is great place and lots of lifes there.  [10:42 AM]

Xnessax: And also good to meet you! [10:43 AM]

Elves: It's a great idea to sub the video. I know we would love to have subtitles in english or any languages possible. If anyone wants to submit the text for it just let me know and I will see if we can get it... [10:43 AM]

...integrated. you can create a forum ticket about it to make sure we keep track of the request

Xnessax: So astromon, isn't your dominated language ? If in video was that language or other europure language, i don't know? [10:43 AM]

Astromon: well sometimes i cant hear exacly what is said [10:44 AM]

Xnessax: oh i see. [10:44 AM]

Astromon: er someone may have an accent [10:44 AM]

Elves: I also find subtitles really helpful, and technically I speak english hehehe [10:44 AM]

Xnessax: Indeed! [10:44 AM]

Astromon: i would like subtitles myself is my main piont [10:44 AM]

Astromon: so literaly all someone has to do is listen to the video and type out what was aid [10:45 AM]

Astromon: said* [10:45 AM]

Astromon: i dont mind doing that [10:46 AM]

Astromon: how long is it? [10:46 AM]

Xnessax: I also knew well at English, as i studied from my highschool ,my dicionary, my favourite games as i tried to translate and learn. [10:46 AM]

Elves: It won't be the same as subtitles, but I can also ask about whether they have any notes for reading the slides, which may be faster to put up.  [10:46 AM]

Elves: but if you or anyone types out a transcription, we would be most grateful and give you credit, and post it to the wiki [10:46 AM]

Xnessax: HMm. [10:47 AM]

Elves: here's a wiki link to past Das Lab broadcasts http://eternawiki.org/wiki/index.php5/Monthly_Eterna_Meeting [10:48 AM]

Elves: this is where I will post the new video when it is available [10:48 AM]

Astromon: okay thanks [10:48 AM]

Elves: and we can also post transcripts here, or ideally get the video itself subbed. so if you come up with a transcript for this or any vid, just send me a PM and I will help make sure it gets posted!! [10:49 AM]

Astromon: is the dev CHAT STILL ON TODAY? [10:49 AM]

Xnessax: oh well ,it also happens in livestream ,when i finish recording online ,it already would be avaliable in few hours for channel. But i configurated the account, they wouldn't be avaliable for my own channel only on Live. And i get those videos exported to my pc and i could submit them to youtube. [10:49 AM]

Astromon: opps caps< [10:49 AM]

Elves: I believe so but i suppose anything could happen in 4 hours :D [10:49 AM]

Xnessax: :) [10:49 AM]

Elves: i wonder if there is any auto transcription service that actually works, hehehe [10:50 AM]

Xnessax: My liveStream hobbies were talking about how to animate and draw something [10:50 AM]

Xnessax: I love drawing and i am good at it. [10:50 AM]

Elves: @xnessax thanks, but don't worry about that - stanford will post the videos themselves soon [10:50 AM]

Astromon: yeah shes way good^^ [10:50 AM]

Xnessax: Animating is sometime really fun and sometime hard. [10:50 AM]

Xnessax: @elves No problem, yeha i would wait. As goodness <: [10:51 AM]

Elves: omg i love animation!!! :D haha that's awesome.  [10:51 AM]

Astromon: check out her profile elves [10:51 AM]

Xnessax: Yeah theres are my animations in my profile. Angelic Kitten, some practice sketch Fighting, and one my avatar ( molecule animated) [10:51 AM]

Elves: whoa!!! Xnessax!!! beautiful :) :) :) [10:52 AM]

Astromon: that romance bond drawing is just the cutest drawing ever [10:52 AM]

Xnessax: Thanks!! :) :) [10:52 AM]

Elves: omg that cartoon of RNA ... i love it [10:53 AM]

Elves: :D [10:53 AM]

Xnessax: yes i was inspirated from playing EteRNA ,then i drew that romance RNA. [10:53 AM]

Xnessax: :D [10:53 AM]

Jennifer Pearl: me too [10:53 AM]

Elves: i absolutely love it wow [10:53 AM]

Elves: thanks for sharing your art :) [10:53 AM]

Xnessax: c: [10:53 AM]

Astromon: so talented indeed [10:53 AM]

Xnessax: welcome~~ ! [10:53 AM]

Xnessax: ^_^ [10:53 AM]

Jennifer Pearl: very talented [10:54 AM]

Xnessax: Thank you so much ,Jennif [10:54 AM]

DevChat T-04h

Elves: ok posting the chat transcript now, and check back in the next day or two for the video link. and please do feel free to make a forum post about vid transcripts, and / or ping me if you make a transcript or find a transcription automatic tool that works [10:55 AM]

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