2015.10.16 Community Chat

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On Fun Games, Lab Background Design, 2nd Weekly Meeting Time, Barcodes vs. Johan's Full Sequence IDs, Tuberculosis A/B Oligo Ratio Explanation, & AndrewKae's 3D RNA Guide

Astromon: hi bob  [2:55 PM]

Astromon: ELVes...heloooo  [2:55 PM]

Elves: helloooooo :D  [2:56 PM]

Leila204: Hello!  [2:56 PM]

Astromon: :D  [2:56 PM]

Leila204: Never met you before :D  [2:56 PM]

RedSpah: hi elves  [2:56 PM]

Elves: and welcome to the community chat of ultimate silliness.... i mean science... :D  [2:56 PM]

Astromon: hi red  [2:56 PM]

Elves: hi Red!!  [2:56 PM]

VirgieP3: Hi... love the colors  [2:56 PM]

Leila204: Hi RedSpah :D  [2:56 PM]

Elves: Hi Astro, Virgie, & Leila  [2:56 PM]

Elves: thanks :) :) :)  [2:56 PM]

VirgieP3: i vote for either oand both  [2:57 PM]

Elves: hahaha excellent, we shall have both  [2:57 PM]

AndrewKae: Hi Elves, Red, Virgie, Leila, and Astromon [2:57 PM]

Astromon: she triped into a magical rainbow [2:57 PM]

RedSpah: Just played the new UT [2:57 PM]

Elves: does anyone have anything they would like to present, teach or talk about today? [2:57 PM]

Elves: Hi Andrew, welcome! :) [2:58 PM]

RedSpah: sooo many memories [2:57 PM]

Elves: haha that i did, that i did [2:58 PM]

Elves: it's cool to see how games evolve over time [2:58 PM]

VirgieP3: none for me i await to be filled [2:58 PM]

VirgieP3: hi red [2:58 PM]

VirgieP3: and andrew and many more [2:59 PM]

RedSpah: UT99, Diablo 2 and NFS: MW were the most memorable games of my childhood [2:59 PM]

RedSpah: sooooo many hours lost in these [2:59 PM]

RedSpah: and then I discovered internet [2:59 PM]

Elves: hahah let's see i played monkey island and minesweeper [2:59 PM]

RedSpah: and consoles [2:59 PM]

RedSpah: I got my PS2 when I was in 2nd grade [3:00 PM]

AndrewKae: hours may not be a complete loss [3:00 PM]

Astromon: i likes space invaders [3:00 PM]

Elves: cool, i never had a console before except i guess if the Wii counts [3:00 PM]

RedSpah: and a pack of few pirated games with them [3:00 PM]

Astromon: and missle command< [3:00 PM]

Astromon: atari lol [3:00 PM]

Elves: ohhh yeah, atari [3:00 PM]

Astromon: the wi certainly counts [3:01 PM]

Elves: but only had the meteors game and one where you catch eggs in a basket lol [3:01 PM]

RedSpah: Ratchet and Clank 3, Jak 3, Burnout Revenge, some Asterix and Obelix game, something else [3:01 PM]

Astromon: hmm i dont rem that one<> [3:01 PM]

Astromon: oh astroyds? [3:01 PM]

Elves: ohhh yes asteroids, thanks :D [3:01 PM]

Astromon: asteriods [3:01 PM]

Astromon: haha [3:01 PM]

RedSpah: I remember getting stuck in multiple places in Jak 3 for a long time because of one simple reason [3:01 PM]

Astromon: that game was Awesome<> [3:02 PM]

RedSpah: I didn't know enough english to decipher what game wanted me to do [3:02 PM]

Elves: hehe i was so bad at it. timed missions are not my strong suit [3:02 PM]

Astromon: did anyone see the movie pizles? [3:02 PM]

Astromon: it was way good [3:02 PM]

Astromon: its about old arcade games and the aliens use them to fight us haha [3:02 PM]

RedSpah: I especially remember spending 3+ hours and eventually passing by random button mashing a certain task [3:02 PM]

RedSpah: I had to drive to a certain spot [3:03 PM]

Elves: no but that does sound funny [3:03 PM]

RedSpah: jump and then turn mid air [3:03 PM]

Astromon: i played supermario for months [3:03 PM]

Elves: what do you like most in a game? what keeps you playing it and entertained? [3:03 PM]

RedSpah: of course, translating individual words did nothing, and google translate wasn't around [3:03 PM]

AndrewKae: hope they try to use halo against us, they will get the dirt kicked out of them [3:03 PM]

Astromon: story lines i like  [3:04 PM]

Astromon: like lor or somwthing [3:04 PM]

Elves: ohh yes, story helps a lot, that's a great one [3:04 PM]

Astromon: lol andrew true that [3:04 PM]

Astromon: it must be challenging [3:04 PM]

Astromon: but not too too chalenging at first [3:05 PM]

Astromon: heh [3:05 PM]

Elves: i like comedy too, if there are jokes then i am way happy [3:05 PM]

Astromon: oH yes comedy is a must in general [3:05 PM]

Astromon: laughter is such an upper<> [3:06 PM]

Elves: yes that's a good point. i'm partly asking because Ben Keep is working on the puzzle progression, and now is our opportunity to provide feedback on how that can help new and old players [3:06 PM]

Elves: i liked the little animations in the NOVA tutorials, that kind of helped with the story aspect [3:06 PM]

Astromon: yes it did [3:07 PM]

VirgieP3: yep and I like how they have covered macs top [3:07 PM]

VirgieP3: too [3:07 PM]

Astromon: could we put a planetarium type back ground in the labs [3:07 PM]

Astromon: it might encourage players to go there more [3:08 PM]

Elves: what do you find too challenging about puzzles. like would it be helpful or annoying to have little steps in the puzzle that guide you through things like meeting puzzle restrictions? or would you prefer a separate puzzle for learning each restriction? [3:08 PM]

Astromon: i think it would be good to do that [3:08 PM]

Astromon: for the starters [3:08 PM]

Elves: haha cool suggestion on background change in labs. I don't know what the flexibility is on background specifically, since we would want to still see the data clearly. but brightening it up somehow might help, i know they were thinking of colors at one point [3:09 PM]

Astromon: maybe a supernova can happen in the background when all the constraints are met and a solution is obtained [3:10 PM]

Elves: LOL [3:10 PM]

Astromon: once we get rolling and have plenty of money to spend on such a thing <> haha [3:10 PM]

Elves: i liked also the idea they had for the pre-pre-alpha demo of little floating molecules. like if we could see the nucleotides that would be cool. but exactly, one thing at a time [3:11 PM]

Astromon: hmm neet idea [3:11 PM]

Elves: by the way, for those who missed it, monthly scientist chats are back on! [3:11 PM]

VirgieP3: cool [3:11 PM]

Astromon: when? [3:12 PM]

Elves: this is where scientists from the Das Lab present their research as it relates to what we do at eterna [3:12 PM]

Elves: generally first friday of the month, at 9am PST [3:12 PM]

Elves: http://eternawiki.org/wiki/index.php5/Monthly_Eterna_Meeting [3:12 PM]

Astromon: oh yeah cool [3:12 PM]

Astromon: i stubles upon the last one<< [3:12 PM]

Elves: and if any players would like to do a presentation for their own research or projects at that slot, or any dev chat slot, you're always welcome [3:13 PM]

Astromon: ill look forward to the next<< [3:13 PM]

Astromon: okay thanks Elves [3:13 PM]

Elves: yeah! it's super cool. And nice that they put up the videos so we can watch any time [3:13 PM]

Elves: also we talked about a second meeting time during the week, so that others could attend. [3:14 PM]

Astromon: Any time is good for me<< haha [3:15 PM]

Elves: it sounds like Tuesday 4-5pm PST is open for me, Jen Pearl, and Ben Keep to trade off and keep it going.  [3:15 PM]

Elves: I'm not sure if that is late enough for those busy during the work day, but I'll update the forum now and see what folks think [3:16 PM]

RedSpah: oh dayuuum [3:16 PM]

RedSpah: Binding of Isaac dev just posted a tweet showing working lua scripting [3:17 PM]

RedSpah: the modding is happening [3:17 PM]

Elves: okay here's the forum post for anyone who wishes to comment [3:18 PM]

Elves: https://getsatisfaction.com/eternagame/topics/hi-here-is-where-you-can-tell-the-devs-what-is-the-best-times-for-you-to-attend-a-dev?topic-reply-list%5Bsettings%5D%5Bfilter_by%5D=all&topic-reply-list%5Bsettings%5D%5B [3:18 PM]


Elves: omg [3:18 PM]

Elves: https://getsatisfaction.com/eternagame/topics/hi-here-is-where-you-can-tell-the-devs-what-is-the-best-times-for-you-to-attend-a-dev [3:19 PM]

Elves: there you go a shorter url that makes it through :D [3:19 PM]

Astromon: nice to see everyone have a great dev chat i have to go! [3:19 PM]

Elves: thanks astro, take care! [3:19 PM]

Astromon: You too! [3:20 PM]

AndrewKae: see ya Astromon [3:20 PM]

VirgieP3: ditto [3:20 PM]

whbob: Bye Astro. [3:21 PM]

Elves: any time any of you feel like sharing a walkthrough or presenting something, please feel free to PM me and I'll help schedule you in.  [3:21 PM]

VirgieP3: thanks [3:22 PM]

Elves: i bet you all know way more tricks about solving and labs than i do :D [3:22 PM]

Elves: ( looks at no hoglahoo or starry in particular ) [3:23 PM]

VirgieP3: not me.  but I would like to work towards being more active in synthesizing [3:24 PM]

Elves: that's a great goal, Virgie, I'd like to do that as well [3:24 PM]

VirgieP3: know how to start? [3:24 PM]

Elves: a little. let's try together! [3:25 PM]

Elves: the top menu says cloud lab, and clicking Active Labs takes you to labs that are currently up [3:25 PM]

VirgieP3: ok deal... love the puzzles... but want to get in there [3:25 PM]

Elves: hehe me too. it was easier during single state puzzles, and adding in switches has made even us old timers a little intimidated, but i think we can figure it out [3:26 PM]

VirgieP3: its been a long time since I was here... did they solve on how to create unique keys yet? [3:26 PM]

Elves: i think you are asking about what became called "barcodes" to id each RNA? [3:27 PM]

VirgieP3: that's it [3:27 PM]

Elves: yes, the barcodes id each strand. in the last monthly meeting I think Johan mentioned that they are still part of the process, so I think they are still being used. but someone else would need to confirm [3:27 PM]

whbob: I haven't seen them used in the last 4 labs.  [3:28 PM]

Elves: okay part of the hurdle in labs is just understanding the description. which is easy to skip for puzzles. but for labs, it has the important info on what we are doing [3:29 PM]

Elves: whbob that's why i'm confused also, i don't think we have to manually design the barcodes anymore now that we tested how they work. I assume they are either randomized and attached as a standard operating procedure, or that they are not used because of something to do with the chip positioning? like maybe its ID is location based now? [3:30 PM] 

Elves: this would be a good question for devs or forum, as i don't know for sure [3:30 PM]

jnicol: the method johan uses in the array labs do not use barcodes anymore [3:28 PM]

Elves: yay! thank you jnicol! [3:31 PM]

jnicol: the cloud labs with the SHAPE data requires the barcodes [3:29 PM]

Elves: is it based on the location of the glowing spot in the array? [3:31 PM]

whbob: I think Johan explained it somewhere, but I'm not sure how they ID now either. [3:31 PM]

Elves: here's a link to the current lab http://www.eternagame.org/web/lab/6204762/ [3:32 PM]

jnicol: believe he sequences the whole strand to uniquely identify each one [3:30 PM]

Elves: whoa that is... awesome [3:32 PM]

Elves: okay i'm going to walkthrough the lab description, and please correct me as to my interpretation, since I'm learning along side everyone here... :D [3:34 PM]

Elves: "Many diseases can be diagnosed by the combination of several RNA molecules or other ligands." [3:34 PM]

Elves: I think this means things like Tuberculosis can potentially be detected when an RNA molecule and other small molecules come into contact with it, and change in response to the presence of the Tuberculosis [3:34 PM]

Elves: so if we can make little RNA molecules that respond to the environment, we can measure those changes and detect things like Tuberculosis [3:35 PM]

jnicol: actually the marker oligos that signal tuberculosis is present [3:33 PM]

whbob: The main page for a lab uses text and diagrams to explain the testing methods.  [3:36 PM]

Elves: thank you for the clarification. So tuberculosis is detected through deduction? where a person with tuberculosis also has marker oligos ( other tiny molecules that are present with tuberculosis ) [3:36 PM]

jnicol: many diseases have 'abnormal' concentrations of these oligo rna's which we are trying to detect [3:34 PM]

Elves: and does oligo mean small strand or ? [3:37 PM]

jnicol: trying to detect the relative difference in concentrations [3:35 PM]

jnicol: the oligos strands are the 2 separate strands in the lab puzzles [3:35 PM]

Elves: so a sample from a person with an abnormal concentration of these oligos will indicate they have TB or some other disease? [3:38 PM]

jnicol: correct [3:36 PM]

Elves: the 2 separate oligo strands being the ones labelled "[A] / [B]" [3:38 PM]

jnicol: yes [3:36 PM]

Elves: awesome thanks! [3:38 PM]

whbob: The oligo's (ligands) are the micro RNA strands smaller than the main RNA molecule you need to design. [3:39 PM]

jnicol: for instance, if you have a 1:1 ratio of these oligos, it is normal [3:37 PM]

jnicol: a 4:1 ratio indicates tb [3:37 PM]

Elves: ahh very interesting [3:39 PM]

Elves: thanks whbob! [3:39 PM]

Elves: so the ratio is important to understand the next sentence about "relative concentrations" [3:40 PM]

Elves: "Sometimes they may all be present at low abundance so the relative concentrations are more predictive for the disease state." [3:40 PM]

jnicol: yes [3:38 PM]

Elves: and also this sentence explains the ratio of oligos we want to understand in this lab: "Using two input RNA molecules, oligo A and B, the expression we want to solve is the concentration of A divided by the concentration B, or [A] / [B]." [3:41 PM]

Elves: and the next sentence explains why we still have the MS2 hairpin involved in addition to binding to the A / B oligos: "As in previous puzzles, the primary output will be a fluorescently labeled MS2 protein that binds to an MS2 hairpin." [3:43 PM]

jnicol: yes, actually this lab is easy to understand compared to labs being talked about with 3 or 4 markers of different concentrations [3:41 PM]

Elves: so i take this to mean that when the main RNA molecule binds to A or B oligo ( smaller RNA strand ), then it also does or does not bind to the MS2 flourescent protein, which we need to glow on Johan's chip to tell whether A or B got bound [3:44 PM]

jnicol: correct [3:42 PM]

Elves: yes logic gets so much more complicated when you add variables :D [3:45 PM]

Elves: thanks :) [3:45 PM]

jnicol: and the point at which it glows or does not glow should be at a 4:1 ratio [3:43 PM]

VirgieP3: exciting though [3:45 PM]

VirgieP3: cool [3:45 PM]

VirgieP3: do they need lab rats? [3:47 PM]

Elves: hehe participating in solving the labs puzzles is the best way to help [3:47 PM]

Elves: do we need to understand the difference between on/off binding vs. designing a molecule to responds to subtler concentration gradients? [3:48 PM]

Elves: I see it says "We're hoping that the binding constraints associated with the R2 puzzle will make sure that designs actually react to the ratio of the input concentrations, and not to just one of them" [3:48 PM]

Elves: so i am guessing we are doing this lab to help answer that question of how to build molecules that react to different levels of concentration, not just on or off [3:49 PM]

whbob: When the MS2 hairpin is formed, it will flouresce,  When the hairpin "slides" or offsets it's nucleotides several places  or "opens" , it stops flourescing.  [3:51 PM]

Elves: wow, I'm looking again at Nando's explanation of this lab and now I understand better [ though not completely i'm sure ] why he's explained about concentrations [3:51 PM]

Elves: http://eternawiki.org/wiki/index.php5/User:ElNando888/Blog/Designing_for_the_A_B_lab [3:51 PM]

Elves: thanks whbob! [3:51 PM]

VirgieP3: there is a current round... so do we vote or do we ? [3:51 PM]

Elves: you can vote, but there are 2000 slots available and 4-500 submissions, so i don't think voting is necessary, since that just helps decide which ones to synth if there are too many [3:52 PM]

jnicol: well, the science of this lab is new, so this experiment is also for the lab personnel to get the process correct [3:50 PM]

AndrewKae: "When the scientist is away, the lab rat will play" - Eli [3:52 PM]

Elves: :) :) :) [3:53 PM]

Elves: i'm myself still trying to get over the hurdle of understanding all the information needed to design. I think this is why people do a lot of mods, so that is an option if you don't know how to design from the ground up, which is to use an existing design and change a small part of it [3:54 PM]

whbob: The main page usually has a participate button and that bring you to another similar page. [3:54 PM]

whbob: This page will show the "sub-labs". [3:55 PM]

whbob: You have a choice to design or vote. [3:55 PM]

AndrewKae: Elves, I had something to share if we have time. [3:55 PM]

whbob: Voting takes you to a "list" mode whre you can see a list of all the designs submitted so far. [3:56 PM]

Elves: thanks whbob! [3:56 PM]

Elves: yes andrew please do share [3:57 PM]

AndrewKae: For anyone interested I wrote a short guide to creating 3D-RNA structure models. [3:56 PM]

Elves: wow!! awesome :D [3:57 PM]

AndrewKae: I thought it may be useful for students that would like to share their EteRNApuzzle solutions or creations in a more recognizable manner. [3:57 PM]

AndrewKae: http://tinyurl.com/pu7aobu [3:57 PM]

AndrewKae: thats all [3:57 PM]

Elves: Andrew, here is a spot on the Wiki where you can post the guide as well http://eternawiki.org/wiki/index.php5/Player-Created_Guides [3:58 PM]

AndrewKae: thanks :) [3:58 PM]

whbob: Thanks, Andrew:) [3:58 PM]

AndrewKae: np whbob  [3:58 PM]

Elves: thanks very much, that is great :) and if you ever want to walk us through your guide, you're very welcome to ask for a time to present [3:59 PM]

VirgieP3: thanks [4:00 PM]

Elves: well we didn't quite get to do the lab did we? i think next time we'll try doing a mod together. [4:01 PM]

VirgieP3: will read it then ask questions later... be ready to be bugged... thanks again everybody...  [4:01 PM]

VirgieP3: definitely [4:02 PM]

VirgieP3: between you and me... lab rats are easier... ;) [4:02 PM]

Elves: it's good to have unique designs in labs, but with the learning curve being so steep i bet we can get a little further through learning by example [4:02 PM]

Elves: hahaha cool [4:02 PM]

Elves: thanks everybody for participating!!! [4:03 PM]

VirgieP3: thank you too and everybody [4:03 PM]

whbob: Thank you Elves:) [4:03 PM]

Elves: whbob thanks for explaining how to get into labs, i know there being several pages can be confusing, so I think that helped explain [4:04 PM]

Elves: happy to help :) [4:04 PM]

Elves: Big high five to Andrew for writing a guide on making 3D RNA, that is super cool :) :) :) [4:04 PM]

VirgieP3: high high five five... Andrew [4:04 PM]

AndrewKae: Thanks Elves, whbob, jnicol and everyone else [4:05 PM]

Elves: Andrew let me know if you need a hand with the Wiki. and hope to see you over there :)  [4:05 PM]

jnicol: welcome :) [4:03 PM]

Elves: thanks jnicol for bringing the facts to the party!! :D [4:05 PM]

AndrewKae: 2nd and 3rd that [4:06 PM]

whbob: These last few labs have been great.  Can't wait for the results:) [4:07 PM]

Elves: awesome! hey whbob, if you've gotten to the point of successfully designing and submitting, it would be amazing if you could do a walkthrough for those of us catching up! [4:08 PM]

whbob: I could try:) [4:09 PM]

Elves: i think you would do great, you were breaking down the steps earlier and it was easy to understand [4:09 PM]

Elves: that's what we really need is just to know what to click on next D [4:09 PM]

Elves: :D [4:09 PM]

VirgieP3: thanks Elves for this support... [4:10 PM]

whbob: When would you like to do a walkthrough?  Now or later? [4:10 PM]

Elves: yeah! thanks for coming! [4:10 PM]

Elves: i think later at a scheduled meeting would be perfect. [4:10 PM]

Elves: so it can either be in 2 weeks, or I can PM you this week when finalizing the 2nd weekly meeting time [4:11 PM]

VirgieP3: keep me posted... would want to read up so I can follow [4:11 PM]

Elves: we were looking at tuesdays 4-5pm PST [4:11 PM]

Elves: but not confirmed yet [4:11 PM]

whbob: OK, I don't always get to every meeting, but I'll try to be there in 2 weeks. [4:12 PM]

Elves: yeah! I'll go ahead and post this chat to the wiki now, and same with all meetings so that people can follow along even if busy at that time [4:12 PM]

Elves: cool, that would be a huge help. thanks whbob! :) [4:12 PM]

whbob: np Elves:) Good Night everyone. [4:13 PM]

VirgieP3: nite all too [4:13 PM]

Elves: good night! :) [4:13 PM]

Elves: bye Virgie & whbob, take care & see you next time [4:13 PM]

VirgieP3: yep... you all made it good to be back..  [4:13 PM]

Elves: awesome that means a lot to hear, thank you kindly :) :) :) [4:14 PM]