2015.10.02 Community Chat

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On RMDB & Lab Data, Flag Buttons, UI Updates, Fixing 'Puzzles Left to Solve' Script, & Intro to Tuberculosis miRNA Lab Terms & Constraints


Countdown to Dev Chat: 0:00:05:23 

DevChat T-05m 

LFP6: Someone's a bit early  [2:50 PM]

Jennifer Pearl: hehe  [2:50 PM]

DevChat T-01m

DevChat T-30s

DevChat T-10s





Nando: I need to update that bot... [2:55 PM]

Nando: hi guys [2:55 PM]

Elves: lol, hi Nando! Hi Jen & LFP6 [2:55 PM]

Elves: naturally bots can live in the future that makes total sense :D [2:56 PM]

Jennifer Pearl: the futur is where i WANT TO BE [2:56 PM]

Jennifer Pearl: that was a convienence case of accidental cap locks [2:56 PM]

Elves: hehe then the future is in fact where you exist! :) [2:56 PM]

Jennifer Pearl: if the futur is present and present is past what is teh past presenttly [2:57 PM]

Elves: though if neuroscience has anything to say about it i guess technically we live in the near near past [2:57 PM]

Elves: now? [2:57 PM]

Jennifer Pearl: ok [2:58 PM]

LFP6: Yes [2:58 PM]

Elves: yestermorrow? [2:59 PM]

LFP6: Sure [2:59 PM]

RedSpah: the future is now [2:59 PM]

LFP6: Don't let your dreams be dreams! [2:59 PM]

Elves: lol [2:59 PM]


Jennifer Pearl: lol [2:59 PM]

LFP6: lol [2:59 PM]

Jennifer Pearl: So what should we talk about today? [3:00 PM]

RedSpah: LOOK  AT MY NEW LAMBORGHINI, MAKE YOUR MEMES COME TRUE https ://www.youtube.com/watch?v=0GIwTG8V-Ko [3:00 PM]

LFP6: Hm [3:00 PM]

LFP6: I'm wondering, does anyone know where the raw data comes from? [3:00 PM]

LFP6: Not the EteRNA data, but the stuff in the spreadsheets [3:00 PM]

Elves: which spreadsheets? [3:01 PM]

LFP6: Because the files in the RMDB seem to be the same as in EteRNA [3:01 PM]

LFP6: Hold on, let me find one for you [3:01 PM]

Jennifer Pearl: you mean like the R96 spreadsheets in teh results page? [3:01 PM]

LFP6: Um, maybe? [3:02 PM]

LFP6: Probably, I actually forgot about those [3:02 PM]

LFP6: I was just thinking about your tool jen [3:03 PM]

LFP6: Because a lot of the info that we don't have in EteRNA is in the spreadsheets [3:03 PM]

LFP6: And I looked at the RMDB< as they supposedly have an API [3:03 PM]

LFP6: But the data in there doesn't seem to be any better than in the EteRNA API, [3:03 PM]

Jennifer Pearl: I looked at teh RMDB before and there are no scores for teh switch data [3:04 PM]

LFP6: And the ISATAB download option doesn't work, so I don't even know what that is [3:04 PM]

LFP6: Looking forwards to when we can see that in EteRNA [3:04 PM]

Jennifer Pearl: isnt John getting more stuff accessable by the API/ [3:04 PM]

LFP6: Hoping we will be, it's a pretty big oversight otherwise [3:04 PM]

LFP6: Well, he was creating a couple queries for existing data for me [3:05 PM]

LFP6: Allowing me to speed things up [3:05 PM]

LFP6: No new data to my knowledge though [3:05 PM]

Jennifer Pearl: https://getsatisfaction.com/eternagame/topics/what-is-represented-by-the-switch-subscore-baseline-subscore-and-folding-subscore-for-ms2-labs-and-how-can-i-get [3:06 PM]

Jennifer Pearl: Look at Omei''s first comment [3:06 PM]

Jennifer Pearl: LFP6 [3:06 PM]

Jennifer Pearl: Looks like Johan makes it [3:06 PM]

LFP6: Yeah [3:07 PM]

jnicol: Hi all, yes the lab apis are on the top of my list [3:06 PM]

LFP6: Neato! [3:07 PM]

LFP6: And adding the data to the data viewer, maybe? :) [3:07 PM]

Jennifer Pearl: cool [3:07 PM]

jnicol: working with omei also [3:07 PM]

LFP6: Good, good [3:07 PM]

LFP6: Btw, I did figure out why all the uncleared puzzles are in the API call [3:08 PM]

LFP6: From what I can see, that's how it's determined whether any of the puzzles presented are solved (where it adds a little green check) [3:08 PM]

legohobbit2002: You should add a flag button to player puzzles [3:09 PM]

LFP6: That check might want to be flattened to with all the graphics updates... just a thought [3:09 PM]

LFP6: What kind of flag button? [3:09 PM]

legohobbit2002: when you're scrolling, you could make it so when you hover over a picture, then it would show a flag button for inappropriate puzzles [3:10 PM]

Jennifer Pearl: I wanted to ask last week if we are going to have more MS2 NG rounds? [3:10 PM]

Elves: good point on flattening the green checkmark LFP6 [3:10 PM]

Jennifer Pearl: not to change the subject [3:10 PM]

hoglahoo: there should be flag buttons for pretty much everything, imo [3:10 PM]

legohobbit2002: true [3:10 PM]

Elves: lfp6 can you please create forum post for flattening green check? [3:10 PM]

Elves: and legohobbit have you used the forums before? [3:11 PM]

legohobbit2002: not yet [3:10 PM]

legohobbit2002: i started 2 days ago [3:11 PM]

hoglahoo: ooo rainbow Elves [3:11 PM]

Elves: your suggestion for a flag button is a good idea, and there may be a post like it. but if not, it would be great to add the suggestion to the forum [3:11 PM]

Elves: hehehe hi hogla [3:11 PM]

Elves: welcome to eterna then! [3:11 PM]

Elves: here i will get you a forum link [3:11 PM]

LFP6: Will do Elves [3:11 PM]

LFP6: I need to actually head out. Will check in later! [3:12 PM]

Elves: forums: https://getsatisfaction.com/eternagame [3:12 PM]

Elves: thanks lfp6! have a great day :) [3:12 PM]

Jennifer Pearl: afk for a minute [3:12 PM]

Elves: you can also access forums and wiki etc. from the top menu called Community in eterna [3:12 PM]

macclark52: Love the multicolor nametag, Elves. [3:13 PM]

Elves: hehe thanks macclark & glad you came [3:13 PM]

Elves: so whenever you wonder if there is a feature request or issue already in progress, you can go to forums, and type a few keywords in the search field [3:13 PM]

hoglahoo: how do I link directly to the second comment in this topic https://getsatisfaction.com/eternagame/topics/tattletale_report_new_spam_group [3:13 PM]

Elves: ooo good question, i am not sure but i'll look [3:14 PM]

hoglahoo: LFP6 knows how, he linked to it from here http://eternawiki.org/wiki/index.php5/New_Issues [3:14 PM]

legohobbit2002: it won't let me log in on the forum [3:14 PM]

hoglahoo: so it’s already a suggested enhancement. So now I guess the question is what is the best way to bring more attention to it :P [3:15 PM]

Jennifer Pearl: back [3:15 PM]

Elves: @lego you click through with your eterna login [3:15 PM]

legohobbit2002: when you click the link it goes back to the forum [3:15 PM]

legohobbit2002: i did [3:15 PM]

Elves: hogla i think i see #reply_ something, checking [3:16 PM]

hoglahoo: I saw the url, too [3:16 PM]

Jennifer Pearl: @loego sometimes I have had to log into the forum via explorer [3:16 PM]

Elves: lego are you able to comment ow in the forum? ideally it should have just logged you in automatically [3:16 PM]

jnicol: Is that an old spam? [3:16 PM]

Elves: hey jnicol do you know how to link to a specific comment in forums, i don't see how? [3:18 PM]

jnicol: you mean like this? https://getsatisfaction.com/eternagame/topics/tattletale_report_new_spam_group#reply_13960045 [3:18 PM]

Elves: yes exactly [3:19 PM]

jnicol: inspect element to find the reply # [3:19 PM]

Elves: lol i was afraid it would come to that [3:20 PM]

Jennifer Pearl: ouch [3:21 PM]

Elves: lego were you able to get into the forum? [3:21 PM]

Jennifer Pearl: afk - putting out fires at work [3:23 PM]

Elves: np jen [3:23 PM]

Elves: legohobbit i went ahead and added your suggestion to this forum thread that hoglahoo found [3:24 PM]

Elves: https://getsatisfaction.com/eternagame/topics/tattletale_report_new_spam_group#reply_13960045 [3:24 PM]

Elves: you have to be logged into eterna to log into the forums, so make sure you are using the same browser  [3:25 PM]

Elves: and when you do get logged in, you can search for topics related to your question, and see if there is an existing topic. If so, you can add to that thread. If not, you can start a new one [3:26 PM]

hoglahoo: jnicol: the ‘what puzzles do I have left to solve?’ script no longer works. Do you have an opinion on an update for that? Do you think it’s something a fledgline scripter might be able to solve? [3:27 PM]

hoglahoo: fledgling [3:27 PM]

jnicol: I'm sure you can, I can give some pointers [3:28 PM]

jnicol: I found that the url was using an old cmu.edu which caused the problem [3:28 PM]

jnicol: perhaps this one can be easily solved also [3:28 PM]

hoglahoo: oh, that seems pretty simple [3:29 PM]

jnicol: want to take a shot at it? [3:29 PM]

hoglahoo: yeah I might this weekend [3:29 PM]

hoglahoo: I might right now actually [3:29 PM]

Elves: awesome thanks hogla! [3:30 PM]

hoglahoo: don’t thank me yet [3:30 PM]

hoglahoo: the pressure will cause me to make mistakes [3:30 PM]

jnicol: do you have the script url? [3:30 PM]

Elves: well... thanks for trying. and good luck :D [3:30 PM]

hoglahoo: :) [3:30 PM]

hoglahoo: yeah it’s on my profile page [3:30 PM]

jnicol: yes its using the cmu.edu url, should be an easy fix :) [3:31 PM]

jnicol: drop me a line if its more [3:31 PM]

hoglahoo: it didn’t fix it [3:32 PM]

hoglahoo: oh, maybe I need the www. [3:32 PM]

hoglahoo: it works now, thanks [3:33 PM]

Jennifer Pearl: im back...for now. I wanted to throw in a comment for Lego [3:33 PM]

Elves: yay! [3:33 PM]

hoglahoo: I guess this will be Rev E [3:33 PM]

Jennifer Pearl: @lego if you still cant log into the forum later even after you have logged on send  IM to one of the Devs [3:34 PM]


hoglahoo: oh yeah that’s what I should have named it [3:34 PM]

hoglahoo: hey there’s an edit button next to the title [3:34 PM]

Jennifer Pearl: @jnicol CAn lego send you a message if they still have issues? [3:34 PM]

Elves: i'm curious, would anyone here be able to give a quick walkthrough of the active lab? pretty please with a guanine on top? [3:35 PM]

macclark52: What do you mean, E [3:36 PM]

jnicol: what issue is it? [3:36 PM]

macclark52: lves? [3:36 PM]

Elves: jnicol, they were having difficulty logging into forum [3:37 PM]

Elves: mac, when you get enough points to participate in labs, they are accessible from the top menu Cloud Lab under Active Labs. [3:37 PM]

Elves: this is the current lab http://www.eternagame.org/web/lab/6171041/ [3:37 PM]

jnicol: through faebook connect or direct? [3:37 PM]

Elves: and i am curious about nando's UI updates, and also switches in general. so i would love to try the lab, and was wondering if anyone here with more experience than me would like to help guide us [3:38 PM]

Elves: or i can try it out anyway, but i can't guarantee i'll solve it in the next 20 minutes :D :D :D [3:38 PM]

macclark52: What I found confusing about this particular lab, was figuring out what it wanted.   [3:38 PM]

Elves: i noticed that the deadline for this lab got extended to Monday http://www.eternagame.org/web/news/6225710/ [3:38 PM]

macclark52: The usual method of putting up a "target" shape couldn't be used, I finally figured out, because there were a number of possible solutions, with different shapes.   [3:39 PM]

Elves: yes - the constraints for the lab are defined in the boxes on top, but these are more complex than usual [3:39 PM]

Elves: or i should say, more complex than single state puzzles. [3:39 PM]

macclark52: They are indeed.   [3:39 PM]

jnicol: wow, 5.8 years to finish all the puzzles [3:40 PM]

Elves: one strategy is to copy a sequence from another player's design, and then make a modification, and say in the title that it is a mod. i am curious about how to approach solving it from scratch, but maybe that... [3:40 PM]

...is too ambitious for the time we have left... :D

macclark52: But very interesting.  I gave the two labs to my students to try.  They all elected the first one, because it looked more doable, although I don't know if that is actually the case.  Most of them were able to come up something that worked.  [3:41 PM]

Elves: lol  [3:41 PM]

Elves: nice! [3:41 PM]

boganis: Hi there<<<<<1 [3:41 PM]

Elves: hi boganis [3:41 PM]

jnicol: hey boganis! [3:41 PM]

boganis: been a while [3:42 PM]

Elves: so i have loaded the first one in the active lab: http://www.eternagame.org/game/puzzle/6171039/ [3:42 PM]

jnicol: Is it the last 2 constraints in the lab that are the question? [3:42 PM]

macclark52: I did one solution from scratch because I wanted to see if I could have one sequence bind in the middle and the other one to the two ends of the main sequence.  [3:43 PM]

Elves: it looks like there are a few kinds of constraints or rules. the first kind of constraint is to not have more than 3 Gs in a row, for example. that just means don't have long sequences of the same colour next... [3:43 PM]

...to each other. 

jnicol: The first couple of constraints have been iused in previous labs [3:43 PM]

Elves: the next one is your design must have less than 40% adenines, which just means in total the whole design should not be too yellow [3:44 PM]

macclark52: I think that is one of the difficulties of the puzzle -- that there isn't a fixed end to work toward.  But it also made it interesting.   [3:44 PM]

Elves: so yes jnicol i am guessing last 2 constraints most confusing or new [3:44 PM]

jnicol: Its really similar to the last lab, just trying to represent it a little differently [3:44 PM]

Elves: 1 - In state 1 your RNA must bind with Reporter; and 2 - In state 2 your RNA must NOT bind with Reporter, and must also bind with TB-B signature [3:45 PM]

jnicol: yes, correct [3:45 PM]

Elves: thanks! i'm approaching it as a new user essentially, since I have missed the last lab [3:46 PM]

jnicol: the mouse over should also help with the text explanation [3:46 PM]

Elves: oh weird i can't click on the title in the top left to go back to the description page? [3:46 PM]

Elves: what i typed is the mouseover [3:47 PM]

Nando: the point of the new labs is to test whether we can replace MS2 with miRNAs [3:47 PM]

macclark52: MS2? [3:47 PM]

Nando: MS2 tends to "destroy" the chip rapidly [3:47 PM]

Elves: MS2 is a protein that binds to an RNA molecule? [3:47 PM]

Elves: so is Reporter a miRNA? [3:48 PM]

Nando: the MS2 protein / hairpin combination, yes [3:48 PM]

Elves: sorry to be so basic, but I'm catching up myself so I'm starting from a total n00b perspective [3:48 PM]

Elves: thanks! [3:48 PM]

Nando: so, replacing that reporter by a fluorescently marked miRNA would be advantageous [3:48 PM]

Elves: and miRNA is microRNA or just tiny short piece of RNA that we want to stick to the larger or main RNA molecule [3:49 PM]

macclark52: So you want to replace a protein marker with an RNA marker? [3:49 PM]

Nando: we're testing that, yes mac [3:49 PM]

Elves: so in past labs called MS2 labs, we designed RNA molecules that would bind to the MS2 protein. and now we want to design molecules that will instead bind to a miRNA strand [3:49 PM]

Elves: so in that way, miRNA is taking the place of MS2 protein [3:50 PM]

Elves: is Reporter a reference to the miRNA strand? [3:50 PM]

Nando: we may still use MS2 in the future, but maybe not that frequently [3:50 PM]

Elves: thanks Nando, this is all really helpful!  [3:51 PM]

macclark52: I'll have to go back to the task page and look at it again.  I had to look at your example, which I'm glad you provided, because I couldn't figure out what the thing was supposed to be doing.   [3:51 PM]

Nando: that is, if miRNA-based markers prove efficient [3:51 PM]

Elves: here is the description page for the lab http://www.eternagame.org/web/lab/6171041/ [3:51 PM]

Jennifer Pearl: in that case if DPAT works out I will have to redevolp in Java to run on linux [3:53 PM]

Elves: so i see a few terms and i'm confused which are a reference to the same thing: miRNA, ligand, Reporter, TB-B signature [3:53 PM]

Elves: is it the case that state 1 and 2 are responding to two different miRNA strands [3:53 PM]

Elves: ? [3:53 PM]

Jennifer Pearl: since I cant get NUPACK to compile in windows due to an issue with roots and the cammand used [3:53 PM]

Nando: @elves, different miRNA compostions, can be different miRNAs or simply different concentrations of the same ones [3:54 PM]

Elves: is the TB-B signature a miRNA? same question for ligand and reporter [3:54 PM]

Elves: ohhh interesting about concentration, thanks Nando! [3:54 PM]

Nando: TB-B is a miRNA, yes [3:55 PM]

Elves: lol Jen & sawry :D [3:55 PM]

Elves: and the description says state 1 is a ligand - is that also a miRNA? [3:55 PM]

Nando: "reporter" is a generic term, meaning "fluorescently marked molecule" [3:55 PM]

macclark52: What is the ligand?  What does the TB-B stand for?   [3:55 PM]

Nando: Tuberculosis B [3:55 PM]

Elves: ahhh thank you very much for reporter definition [3:56 PM]

Nando: we're actually using the TB-A as a reporter here [3:56 PM]

macclark52: Ah, is that part of the "get ready to target tuberculosis"  [3:56 PM]

Elves: ok, so are both TB-A & TB-B ligands? [3:56 PM]

Elves: @mac yep you got it exactly :) [3:56 PM]

Nando: "ligand" is a generic term meaning "small molecule that interacts with others" [3:57 PM]

Elves: ok thanks Nando for helping to sort out these terms, i am starting to understand better. let's see if i get it straight heheh... [3:57 PM]

Nando: FMN is a ligand, the MS2 coat protein is a ligand, etc [3:57 PM]

macclark52: And what is that molecule in this case? [3:57 PM]

Elves: so state 1 and state 2 each feature a main RNA molecule that is the big part.  [3:58 PM]

Elves: and both state 1 and state 2 will bind to a ligand ( a small molecule that interacts ), and both states bind to a ligand that is a miRNA [3:58 PM]

Elves: a ligand could be an FMN molecule or an MS2 protein, but in this case both states use lignds that are miRNAs or microRNAs ( tiny RNA strands ) [3:59 PM]

Elves: *ligands [3:59 PM]

Nando: I've got to join a meeting, bye everyone [3:59 PM]

Elves: bye Nando! thank you!! [3:59 PM]

Jennifer Pearl: bye nando [4:00 PM]

Elves: so it sounds like the constraint 1 saying "your RNA must bind with Reporter" means that the large main RNA molecule must bind with the ligand miRNA TB-A strand [4:00 PM]

Elves: and constraint 2 saying "your RNA must NOT bind with Reporter & must bind with TB-B signature" means that the large main RNA molecule must NOT bind with the ligand miRNA TB-B strand, and must also bind with... [4:01 PM]

...the ligand miRNA TB-B strand

macclark52: So you want the fluorescent reporter molecule to tell you whether or not the ligand (TB-B?) has been bound? [4:03 PM]

Elves: i think so but someone else should confirm. it sounds like iif there is flourescence then state 1 is bound to the flourescing reporter miRNA ( the TB-A ligand ) [4:04 PM]

Nando: @mac, yes, in the absence of TB-B, the reporter binds (fluorescence detectable by Johan's apparatus), if the TB-B is present though, the reporter "flies off", no fluorescence (cluster is dark) [4:04 PM]

Nando: in the other target, it's the opposite [4:05 PM]

Elves: ohh that is interesting, it's not just about binding to either a or B, it's about B preventing binding to A? [4:05 PM]

Nando: yes elves [4:06 PM]

Elves: thanks Nando :) [4:06 PM]

Nando: preventing, or in the other target, helping [4:06 PM]

Elves: ahh okay thanks, i forgot I was only looking at one of two labs [4:06 PM]

macclark52: Comprehension, at last!  Thanks, Nando.   [4:07 PM]

Nando: np guys [4:07 PM]

Elves: this was really helpful in getting my head around the basic terms, thank you so much!! [4:07 PM]

Nando: meeting starting now, see ya [4:07 PM]

Elves: thx & cheers! [4:07 PM]

hoglahoo: goodbye Nando [4:07 PM]

macclark52: Can I ask what Johan's apparatus is? [4:08 PM]

Nando: microarray [4:08 PM]

macclark52: Ah, thanks.  [4:08 PM]

macclark52: Sorry to be such a dunce.  I finally figured out what the formal task was, but couldn't make sense of it in functional terms, in spite of the many clues scattered about.  [4:09 PM]

Elves: don't feel badly, i also wasn't sure how to connect the dots, and this was a huge help to me in understanding how to even approach the labs [4:10 PM]

Elves: a lot of the terms have overlap, so it can get confusing fast! [4:11 PM]

Elves: it sounds like the basic problem or puzzle we are trying to solve these days is how an RNA molecule binds to other small molecules, whether that is a protein, a miRNA, or another small molecule like FMN [4:12 PM]

Elves: and then how to make them switch or move between states where there are different small molecules, or what it sounds like is calle a "ligand" [4:13 PM]

Elves: *called [4:13 PM]

Elves: and by getting a flourescent Reporter marker to show up, we can tell which state is active, and use that to build little machines, sensors, etc. [4:14 PM]

boganis: monitoring this chat (compared to 2011 standards) makes me  feel thoroughly out of bounds, regardless of energies! Toodle-oo [4:17 PM]

macclark52: I have to say that by working on these various projects, I have developed an enormous respect for RNA.   [4:18 PM]

macclark52: Thanks for asking your question, Elves.  It gave me the hutzpah I needed to ask mine.  :-) [4:19 PM]

Elves: thanks! and happy to help. :) thank you for walking through it with me, it gave me some courage too [4:21 PM]

Elves: i was just making a screenshot to do a visual summary of the two pieces of miRNA, since i just realized the constraint boxes have a visual of the little lines in them http://prntscr.com/8n380c [4:21 PM]

Elves: that is state 1 [4:22 PM]

Elves: where miRNA A ( TB-A ) binds to the main molecule [4:22 PM]

Elves: and just a minute will make state 2 screenshot [4:22 PM]

Elves: ( i'm determined to figure out how to do labs again lol ) [4:22 PM]

Jennifer Pearl: @elves Can you post everyting that was discussed about the miRNA even the stuff that went over 1 hour [4:22 PM]

Elves: yep sure thing i'm planning to& good idea, just wanted to challenge myself to follow through with understanding these 2 constraints  [4:26 PM]

Elves: here's state 2 http://prntscr.com/8n3abc [4:28 PM]

Jennifer Pearl: cool. I wish I had time to be in this conversation today. So busy at work [4:29 PM]

macclark52: Thanks, Elves. [4:29 PM]

Jennifer Pearl: @el;ves see you laters [4:29 PM]

Elves: so you can see each little piece of RNA hanging out there has a job to either bind or not bind. and a reminder that this is for the first of 2 labs, and as Nando said ( I think ) that the second is the... [4:29 PM]

...opposite, or at least just read the constraints carefully to compare to this one for reference here's the link to the one we did http://www.eternagame.org/game/puzzle/6171039/

Elves: np mac! [4:29 PM]

Elves: bye Jen thanks for coming! [4:30 PM]

Elves: i'll post the transcript shortly [4:30 PM]

Elves: so the other constraint we didn't talk about today is the actual shape of each state http://prntscr.com/8n3bou [4:32 PM]

Elves: but that is at least a familiar goal, so hopefully this helps explain a little how to approach the labs! [4:33 PM]

Elves: thanks everyone for your participation!! [4:33 PM]

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