2013.11.13 Dev Chat

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On Lab UI Issues

2013.11.13 Dev Chat Issues

 

jeehyung: Hi all [3:02 PM]

jeehyung: Welcome to Eterna dev chat [3:02 PM]

Eli Fisker: Hi Jee :) [3:03 PM]

machinelves: yay! [3:02 PM]

Zanna: hi jee! [3:02 PM]

Nando: hi Jee [3:03 PM]

Brourd: Hi Jee [3:03 PM]

jeehyung: hi all : ] Please throw in questions & suggestions for Eterna [3:02 PM]

Zanna: https://getsatisfaction.com/eternagame/topics/a_problem_in_the_current_lab can this be fixed? [3:04 PM]

Brourd: machinelves put together a nice list of issues to look through as well. http://eternawiki.org/wiki/index.php5/Dev_Chat [3:04 PM]

fluffy3: dev chat already?  can I combine my points from both accounts? [3:04 PM]

fluffy3: fluffy9and fluffy3 [3:04 PM]

machinelves: I think that is issue 4) in the list [3:04 PM]

Zanna: you talking to me, elves? [3:05 PM]

machinelves: @zanna yes [3:05 PM]

Zanna: ok, didn't realize it was on the list [3:06 PM]

machinelves: this is our first experiment in consoidating issues for dev chat [3:06 PM]

Eli Fisker: Machine did a fine job collecting a lot of the issues mentioned in the forum [3:06 PM]

machinelves: *consolidating [3:06 PM]

jeehyung: Hi Zanna - I think those first 3 solutions were submitted before the lab went active (not sure how). We'll have to manually fix them so that they don't have GGAAA in the beginning. Let me look into it [3:05 PM]

rhiju: hi all -- thanks for devchat and also for the consolidated wiki page [3:06 PM]

machinelves: so that there is a reference for both devs and players to draw consensus on [3:06 PM]

Eli Fisker: hi Rhiju :) [3:06 PM]

Zanna: ok thanks Jee [3:06 PM]

jeehyung: As for the new lab browser interface [3:06 PM]

jeehyung: we'll soon kick in an update as a quick fix [3:06 PM]

jeehyung: where we divide "expert' viewer interface and old "Voter" interface [3:06 PM]

Brourd: Hi Rhiju [3:07 PM]

rhiju: one thing I wanted to discuss, related to the list of issues compiled by machinelves [3:07 PM]

Brourd: Sounds good Jee [3:07 PM]

jeehyung: we'll use the new HTML browser for the expert viewer interface.. and allow players to browse/vote through the usual flash interface [3:07 PM]

jeehyung: Oh hi Rhiju [3:07 PM]

rhiju: hey jee [3:08 PM]

rhiju: to players: some of these issues (and many on github) are pretty small [3:08 PM]

rhiju: but there are a lot of them. [3:08 PM]

rhiju: what if we made a 'branch' of the eterna code available for code-savvy players to update? [3:08 PM]

rhiju: for example, via github [3:09 PM]

machinelves: ooo [3:09 PM]

rhiju: and then one of us devs could review changes and incorporate into the main branch? [3:09 PM]

Zanna: ah, nice [3:09 PM]

machinelves: :D i would like this! [3:09 PM]

rhiju: in other words, if we made eterna a bit more 'open-source'? [3:09 PM]

Nando: aw man, more work for me [3:09 PM]

Nando: :P [3:09 PM]

Zanna: LOL [3:09 PM]

machinelves: so we don't have to pester you with the small stuff [3:09 PM]

rhiju: right machinelves [3:10 PM]

Nando: yay! great :) [3:10 PM]

machinelves: that would be amazing :D [3:10 PM]

rhiju: you'd pester whoever had some extra cycles and coding skills [3:10 PM]

Nando: lol :D [3:10 PM]

Brourd: lol [3:10 PM]

rhiju: and then we'd have a formal review provess, perhaps weekly [3:10 PM]

Zanna: :D [3:10 PM]

Brourd: I like it. :) [3:10 PM]

Zanna: great idea [3:10 PM]

Nando: I need to find a new identity, and a few other players too :P [3:10 PM]

Zanna: lol [3:10 PM]

hoglahoo: We will track you down [2:10 PM]

Nando: :D [3:11 PM]

Brourd: I already pester Nando, may as well make it formal pestering. [3:11 PM]

rhiju: i know that nando & omei could help, but are there others? [3:11 PM]

Nando: JL for sure [3:11 PM]

Brourd: There are a few. [3:11 PM]

rhiju: oh yea [3:11 PM]

Omei: Hi all, I just got here. [3:11 PM]

Nando: he may lack time, but he's definitely able [3:11 PM]

Zanna: jnicol, maybe? [3:11 PM]

Nando: hi Omei [3:11 PM]

Eli Fisker: Hi Omei :) [3:11 PM]

Brourd: Hi Omei. [3:11 PM]

rhiju: ok, will discuss with devs on friday [3:11 PM]

Nando: yep [3:11 PM]

machinelves: on that note, trying to iron out issue intake process: 1) Should ( non-coding ) players post issues directly to github, or filter through other channels first? Currently exploring the Forum -> Wiki flow as a pre-Dev Chat filter. [3:11 PM]

rhiju: hi omei -- your name already came up [3:11 PM]

machinelves: and 2) Do devs depend on forum comments and/or still reference the bug spreadsheet? What would be the most helpful central hub for detailing issues raised during Dev Chat? [3:12 PM]

rhiju: @machinelves, (1) I don't know what's best. perhaps jee could comment [3:12 PM]

Omei: Have you made a specific proposal about how players could develop UI improvements? [3:12 PM]

machinelves: re: 2) https://spreadsheets.google.com/pub?key=0AsYSzvoGogJGdHNGOGlLQVJ2TEE3VTFvXzZMTnpJVGc&hl=en&single=true&gid=1&output=html [3:12 PM]

Brourd: I don't believe they use that as an issue tracker anymore. [3:13 PM]

machinelves: good to know, i am still coming up to speed on the process, thanks! [3:13 PM]

rhiju: yes, that issue tracker seems pretty old. github is active. [3:13 PM]

machinelves: so github is not dev only intake? [3:14 PM]

rhiju: @machinelves, i'll let jee answer... [3:14 PM]

machinelves: kk thanks! [3:14 PM]

Brourd: On a side note, Jee - is there any way to make the project proposal constraints mandatory? And is there any way we can make the barcode hairpin stem expempt from these constraints? [3:15 PM]

rhiju: @jee, perhaps we should take that old issue tracker offline and put  a link to github. I like how the item 'put on iphone' is labeled "can't fix"! we now are piloting an ios app. [3:16 PM]

rhiju: @brourd, what are 'project proposal constraints'? [3:16 PM]

machinelves: *drool* tabletRNA yay! [3:17 PM]

Eli Fisker: lol, Machine [3:17 PM]

Brourd: As an example Rhiju http://eterna.cmu.edu/game/puzzle/3546146/ [3:17 PM]

Eli Fisker: RNA without medical application [3:17 PM]

Brourd: In the top left, there is a constraint that states you can only mutate up to 5 bases. [3:18 PM]

machinelves: FYI bugs 2) - 5) in the wiki list reflect nucleotide correlation issues [3:18 PM]

rhiju: @brourd, oh yea. why would we make that mandatory though? i can imagine cases where the project lead wants a shape but does not have a starting sequence in mind. [3:19 PM]

machinelves: and 6) - 7) are button bugs & usability issues [3:19 PM]

Brourd: http://prntscr.com/23zdcj [3:20 PM]

NiallStyles1213: hi? [3:20 PM]

Eli Fisker: Hi Ni [3:20 PM]

NiallStyles1213: im new around here [3:20 PM]

Eli Fisker: Welcome in here.  [3:20 PM]

NiallStyles1213: thx [3:20 PM]

Eli Fisker: We are having dev chat [3:20 PM]

Brourd: Well, it would only be mandatory when the project lead wants that particular constraint to be mandatory. [3:20 PM]

Eli Fisker: (chat with developers) [3:21 PM]

NiallStyles1213: cool [3:21 PM]

rhiju: @brourd. oh you're totally right, we don't want to count the barcode sequence against the number of possible mutations... [3:21 PM]

Brourd: In the case of this particular project. [3:21 PM]

rhiju: i was about to update some of my projects to include mutation puzzles, and i definitely don't want any constraints on the barcode part [3:21 PM]

rhiju: [p.s. not sure where jee is. i went looking for him -- he's not in the lab.] [3:22 PM]

NiallStyles1213: i finished the tutorials but now it's takeing me back [3:22 PM]

machinelves: and the biggest feature request / UI ideas are 15) - 18) - make the lab popup bigger, to include plots, bigger Javascript image, and a very cool Lightbox navigation idea from mat [3:22 PM]

NiallStyles1213: gtg bye [3:22 PM]

Eli Fisker: Bye Ni [3:23 PM]

Brourd: @ Rhiju - so, in this particular case http://prntscr.com/23zdy6 [3:22 PM]

NiallStyles1213: a tuete a l'heure everyone [3:23 PM]

NiallStyles1213: bye eli [3:23 PM]

NiallStyles1213: french class [3:23 PM]

Eli Fisker: Nice you grouped the isues after type, Machine [3:23 PM]

Brourd: The goal would be to have a base structure and sequence, where the number of mutations allowed ultimately requires the presence of one mismatch to fulfill that particular constraint. [3:23 PM]

machinelves: chunking = learning [3:24 PM]

Eli Fisker: @Machine, perhaps these headlines could be added to the template [3:25 PM]

machinelves: good idea! [3:25 PM]

Brourd: However, I'm not entirely sure if the constraint is enforced at all. [3:25 PM]

Eli Fisker: I mean so people will find it easier to add things  [3:25 PM]

Eli Fisker: thx [3:25 PM]

rhiju: for the wiki-compiled issues by machine, i'll bring up the open source idea with devs on friday. one idae might be a fork/pull model on github in which a player development branch has its own tracker [3:25 PM]

rhiju: i had another quick idea to pitch to you [3:25 PM]

Nando: braces for impact [3:26 PM]

Brourd: More work for Nando? [3:26 PM]

Omei: I'll through in a question here: On the issue of player-led development, would it be possible for the devs to set up an an alternate URL for any script-writing  player to use to develop and demonstrate improvements to the UI?  If other players could access any of them, we could actually develope alternatives/fixes and let players give us feedback.  The Eterna devs could then in [3:26 PM]

rhiju: no, not more work for nando [3:26 PM]

Nando: lol [3:26 PM]

machinelves: great! i am not attached to the forum, wiki, github etc... just want to know how devs prefer us to track issues so they don't fall thru the cracks [3:26 PM]

rhiju: @omei, yes, that's what i was hoping too, but we'll have to hear from jee if thats feasible. [3:27 PM]

rhiju: ok, here's the other idea [3:27 PM]

rhiju: i want to have tighter connections of devs to players and to folks in my lab (who also happen to be players) [3:27 PM]

hoglahoo: sandy beach convention? [2:28 PM]

rhiju: and i want a 'live forum' -- @hog we actually were thinking about eternacon [3:28 PM]

hoglahoo: sweet [2:28 PM]

rhiju: but here's a cheaper alternative [3:28 PM]

rhiju: and i think more ffective [3:28 PM]

rhiju: my stanford group meets every friday [3:28 PM]

rhiju: what if we made this meeting open online to anyone for the first friday of every month? [3:29 PM]

Nando: awesome [3:29 PM]

Eli Fisker: nice [3:29 PM]

Omei: Sounds good to me. [3:29 PM]

Zanna: me too [3:29 PM]

rhiju: each of us presents 'flash slides' in our meetings -- for this one, we would present a slide on what we've been doing on eterna in collaboration with players [3:29 PM]

machinelves: that would be great! [3:29 PM]

rhiju: and we'd have one lab member present a more detailed 40min talk, again on something happening in eterna [3:29 PM]

rhiju: in some cases, we'd have you players present your work instead. [3:30 PM]

rhiju: (but that would be totally voluntary) [3:30 PM]

rhiju: i think google hangout should make this pretty feasible [3:30 PM]

Nando: I was thinking of asking for a simple monthly lab-oriented chat here, with you or Ann [3:30 PM]

Nando: this goes way beyond any of my hopes [3:30 PM]

Zanna: :D [3:31 PM]

hoglahoo: sounds like a neat idea rhiju, are the dev-players on board already? [2:31 PM]

rhiju: well, get this nando, the first presenter will probably be pablo (tsuname on eterna) and he was going to bug you for help in talking about pseudoknots [3:31 PM]

rhiju: so you're not totally out of trouble [3:31 PM]

Nando: oh boy [3:31 PM]

Nando: :D [3:31 PM]

Eli Fisker: :) [3:31 PM]

Nando: great :) [3:31 PM]

Zanna: lol [3:31 PM]

Omei: Are you thinking of a one-way brodcast, or something like a Google hangout? [3:31 PM]

rhiju: @hog, yes the people in my group are on board -- i discussed with them last night [3:31 PM]

Brourd: See, told you more work for Nando ;) [3:31 PM]

Nando: lol :D [3:31 PM]

rhiju: the first one would be dec. 6, 11:30am-1:30pm PST [3:32 PM]

rhiju: which is probably horrible for most players, but well, this is hard to schedule. [3:32 PM]

rhiju: we can also try to make a recording available for streaming [3:32 PM]

Omei: For the first one, there will be more players want in than a hangout can support. :-) [3:32 PM]

hoglahoo: cool [2:33 PM]

rhiju: this summer, on a dev chat, we discussed a 'school' for helpnig to write papers that i would lead, and i realized that it wouldn't scale. but i think this will work since about 8 people in my group will be involved. [3:33 PM]

rhiju: @omei, doyou know the limits of hangout? is there something better that is free? [3:33 PM]

Zanna: IRC [3:34 PM]

Omei: 10, unless they've upped it. [3:34 PM]

Omei: And no, I don't know of anything better. [3:34 PM]

Zanna: IRC has no chat room limit [3:34 PM]

rhiju: does IRC allow a screen share? [3:34 PM]

Zanna: you can post  links, that's all [3:34 PM]

hoglahoo: talking about video here right [2:34 PM]

Zanna: teamviewer, maybe? [3:35 PM]

rhiju: @hog, yea video [3:35 PM]

hoglahoo: google hangout is the best popular free thing I know of [2:35 PM]

rhiju: teamviewer requires download, but i see that its free [3:35 PM]

Zanna: yes [3:35 PM]

Zanna: not sure if there is a limit to people though [3:36 PM]

Zanna: hog might know? [3:36 PM]

rhiju: @hog, yea google hangout looks good. i think there's a way to at least broadcast widely if not accept chat [3:36 PM]

rhiju: right -- i see it now. 'hangouts on air' [3:36 PM]

hoglahoo: Zanna, the practical limit for me is determined by my crappy laptop :) teamviewer sucks the resources [2:36 PM]

Omei: That's right, I forgot about that. [3:36 PM]

Zanna: ah, ok [3:37 PM]

hoglahoo: yes google hangout accepts chat as well [2:37 PM]

rhiju: and 10 folks can take part in interactive video [3:37 PM]

Omei: So you could at least let everyone watch who wanted to  [3:37 PM]

hoglahoo: as far as I know the number of chat participants is unlimited [2:37 PM]

rhiju: so one option is to have 9 players get nominated as representatives, and everyone else can watch [3:37 PM]

rhiju:  and we could use eterna chat as an interactive chat [3:37 PM]

hoglahoo: watchers could have the option to ask questions, etc [2:37 PM]

Brourd: I like that watching idea. [3:37 PM]

Zanna: sounds good, rhiju [3:38 PM]

machinelves: possible to post visual resources somewhere prior to meeting? [3:38 PM]

rhiju: @machinelves, i bet we could have visuals posted 5 mins before the meeting. ;) [3:38 PM]

machinelves: yay! [3:38 PM]

Zanna: hehe [3:38 PM]

Zanna: posted where? the forum? [3:39 PM]

rhiju: ok, will bring this up for discussion with devs on fri. this seems like a go. will post something on news to announce the first date/time. [3:39 PM]

Eli Fisker: Would be good to post it somewhere folks can't easy miss it [3:39 PM]

machinelves: awesome! thank you! [3:39 PM]

rhiju: probably on the site News [3:40 PM]

Zanna: ah, good place, I think [3:40 PM]

Zanna: eterna devs ROCK! [3:40 PM]

rhiju: my guess is that the first one won't be too oversubscribed, but we'll see [3:40 PM]

Omei: Are you a betting man, Rhiju? [3:41 PM]

Zanna: haha [3:41 PM]

machinelves: players consistently express a wish to be more tightly involved in development, so i think this will be well received on this end [3:42 PM]

Zanna: I think so too [3:42 PM]

rhiju: well, i've said this many times before, we could certainly use help on development [3:42 PM]

machinelves: i think ironing out the protocol will help us know how to participate in a way that is most useful to the dev team [3:43 PM]

machinelves: vis a vis github etc [3:43 PM]

Omei: Yes, that's the key. [3:43 PM]

rhiju: if you could help us code up small things, we could spend more time exploring new experimental technologies, getting a mobile app, etc. [3:43 PM]

machinelves: :D precisely [3:43 PM]

Zanna: does the squeaky wheel get the oil around here? if so, I need to squeak... AGAIN :P [3:44 PM]

Omei: It doesn't even need to be limited to small things, if we have a way to present the results to other players as well as the devs. [3:44 PM]

Brourd: Hey rhiju, you mentioned in the dev blog post that you had to "specially resynthesize" round 78. What exactly was necessary to fix that? [3:45 PM]

Omei: But nobody is going to be able to look at code and say whether it is good or not. [3:45 PM]

rhiju: also, a little announcement -- our first scientific paper on eterna (describing player-proposed rules and their automation) has just received glowing reviews. expect publication in early 2014. it will be going to an 'open-access' but extremely prestigious journal, so you can show and  boast to your friends. [3:45 PM]

Brourd: Awesome [3:46 PM]

machinelves: Wow! congrats!! [3:46 PM]

Eli Fisker: Sweet [3:46 PM]

Omei: Superb! [3:46 PM]

hoglahoo: magnifique! [2:46 PM]

Zanna: yay! [3:46 PM]

rhiju: thanks everyone -- congrats to you too! [3:46 PM]

Nando: wow [3:46 PM]

machinelves: open access ftw [3:46 PM]

Zanna: any chance we could get the hairpin in the barcode unlocked, to open up more barcode options? and/or add a pair to the stack? (squeak if you like this idea) :P [3:47 PM]

rhiju: @brourd, we had to re-synthesize the library of >1000 sequences leaving out the 20 or so that took over the library during PCR amplification. Sigh [3:47 PM]

Brourd: ouch [3:48 PM]

rhiju: @zanna, i've been thinking about that too.  [3:48 PM]

Zanna: yay! [3:48 PM]

Eli Fisker: Zanna, would be interesting seing other barcodes.  [3:48 PM]

Eli Fisker: I mean other loops [3:48 PM]

Brourd: Had to reorder the DNA without those sequences, or you had to remove them from the pool? [3:49 PM]

rhiju: @zanna & eli: is the idea to have a different kind of barcode element? or to have a barcode inside the sequence of interest? [3:49 PM]

Omei: Eli told me you were experimenting with non-hairpin barcodes.  Any conclusions? [3:49 PM]

Brourd: Well, actually rhiju, Nando has an idea there... [3:49 PM]

Nando: a few, yes [3:49 PM]

Nando: http://eternawiki.org/wiki/index.php5/User:ElNando888/Blog/Reverse_Transcriptase [3:50 PM]

Nando: at the bottom [3:50 PM]

rhiju: @omei, i haven't come up with a generatl strategy for non-hairpin barcodes, let me read nandos page [3:50 PM]

Zanna: rhiju, the labs are getting crowed and good  barcodes are hard to find [3:50 PM]

Eli Fisker: I think Zanna meant that trying unlocking the loop types could be tested too [3:50 PM]

machinelves: @zanna squeak! i frequently run into barcode writer's block due to barcode designs already being taken + limited options that still fold [3:50 PM]

machinelves: ( if that is what you mean? ) [3:50 PM]

rhiju: @brourd, we couldn't comeup with a robust strategy to selectively remove those sequences, so we had to reorder the whole thing (at a cost of $3000) [3:50 PM]

Nando: ouch [3:50 PM]

Brourd: Indeed [3:51 PM]

Omei: I ask because I think that in many cases, antiparallel alignment of the barcode and neck result in the trailer sequence forming bonds with the main design. [3:51 PM]

Zanna: yes, elves, that is what I mean [3:51 PM]

Brourd: @ Omei - how did those designs turn out? [3:51 PM]

Eli Fisker: Interesting idea having the barcode inside an element, Rhiju. Is that possible? [3:52 PM]

hoglahoo: I have to run, thanks all for the devchat [2:52 PM]

Eli Fisker: Bye Hogla [3:52 PM]

Nando: bye hog [3:52 PM]

Zanna: bye hog [3:52 PM]

Brourd: later hoglahoo [3:52 PM]

rhiju: @nando, cool ideas -- a panel of barcode styles [3:52 PM]

machinelves: bye hog! [3:52 PM]

rhiju: another option would be to fix the barcode stem sequence, but let players design the loop -- any idea if that would be easier to work with for players? [3:52 PM]

Nando: intriguing [3:53 PM]

Zanna: we just need more options for barcode [3:53 PM]

Brourd: Hmmm [3:53 PM]

Omei: @brourd - which designs are you referring to? [3:53 PM]

Zanna: so many designers, it gets hard to find an unused one that won't misfold  [3:53 PM]

Eli Fisker: Rhiju, I think it might leave players with too few mutation options - given the loop is the same size [3:54 PM]

Eli Fisker: Only 4 bases to play with and a lot of labs [3:54 PM]

Brourd: I believe you designed a sequence regarding that theory in one of Eli's projects, in round 78. [3:54 PM]

rhiju: @nando, oh i only just got your pseudoknot barcode idea. that is awesome. if you can figure out a robust motif that sequesters the tail, we'll definitely use it. [3:54 PM]

Nando: the loop would be a heptaloop, I assume [3:54 PM]

machinelves: hmmm. question: how much does the energy of the barcode affect the rest of the molecule ( regarding the non-canonical energy interactions nando mentioned )? [3:55 PM]

rhiju: @nando, yes heptaloop or longer for the barcode hairpin [3:55 PM]

Zanna: I think, add a pair to it, AND unlock barcode :D [3:55 PM]

rhiju: @nando, i just had second thoughts about the barcode pseudoknot [3:55 PM]

machinelves: does this skew the results? treating the barcode as invisible when it actually may affect the total balance? [3:55 PM]

Eli Fisker: Good point, Machine [3:55 PM]

Eli Fisker: What I have seen till now is that the barcode do affect the main lab design [3:56 PM]

machinelves: it would only be a constant if we all used the same code... which defeats the uid [3:55 PM]

Eli Fisker: How much depend of diffrent things [3:56 PM]

rhiju: we use the tail sequence as a place to hybridize the reverse transcription primer. if its sequestered into a pseudoknot, we'll have low yields of reverse transcription... [3:56 PM]

Omei: Ah.  Yes, I have lots of examples that seem to demonstrate that.  But I haven't figured out how to predict which designs will or won't show the effect. [3:56 PM]

Eli Fisker: Like how far is the barcode from the main design - single base distance [3:56 PM]

Eli Fisker: and the length of the stems in the main design itself [3:56 PM]

Nando: the Don Quixote lab was precisely the experiment about that Rhiju [3:56 PM]

Nando: it seems to have affected yields a little, but not too much, in most cases [3:56 PM]

machinelves: so a ranking / weighting of barcode options based on energy influence may be in order? [3:57 PM]

Omei: I think the assignments to the bases between the neck and the barcode can have a substantial effect on how the two align, assuming the 3D alignment is relevant [3:58 PM]

rhiju: @nando, i see. let me review a bit. [3:58 PM]

rhiju: @nando, also perhaps this can be discussed on dec. 6. [3:58 PM]

Nando: sure, why not :) [3:58 PM]

rhiju: i've got run everyone -- thanks again for an engaging chat! [3:58 PM]

machinelves: thank you!! [3:59 PM]

Eli Fisker: Bye Rhiju [3:59 PM]

Nando: thanks rhiju, bye [3:59 PM]

Brourd: Later Rhiju, take care. [3:59 PM]

Omei: Thank you, Rhiju! [3:59 PM]

Brourd: I wonder what happened to Jee. [3:59 PM]

machinelves: solving an easy brourd [4:00 PM]

Nando: well, well, hangouts with the labcoats... [4:00 PM]

Omei: I wanted to ask Jee  what his plans were for the future. [4:00 PM]

Brourd: for the future of EteRNA? [4:01 PM]

Omei: His future role in Eterna. [4:01 PM]

Omei: He's finished up his PhD, so I would imagine he's looking to move on. [4:02 PM]

Brourd: Completely different topic ;) [4:02 PM]

machinelves: between tighter collaboration, branching the code, and github or somewhere to track issues, things are looking good! :D [4:05 PM]

Zanna: yep :D [4:05 PM]

Omei: Nando, are yu still here? [4:06 PM]

Nando: well, partly [4:06 PM]

Zanna: we need to somehow incorporate that lab script into the game..the one stlnegril9 wrote, and jnicol recently fixed [4:06 PM]

Brourd: partly not here I suppose. [3:07 PM]

Nando: feels like I got hit by something... [4:07 PM]

Omei: You made a reference to yields and I wondered how you judges that. [4:07 PM]

Brourd: Cupid's lab arrow? [3:07 PM]

Nando: RMDB [4:07 PM]

Nando: the data has a signal strength indicator [4:07 PM]

Nando: weak, medium or strong [4:08 PM]

Brourd: signal to noise? [3:08 PM]

Nando: yes [4:08 PM]

Eli Fisker: Zanna, nice idea [4:08 PM]

Brourd: I believe they were medium that round. [3:08 PM]

Eli Fisker: Would enhance the use even more [4:08 PM]

Brourd: a few strongs, some weak [3:08 PM]

Nando: and so it was for Don Quixote as well [4:08 PM]

Zanna: Eli, sure would  [4:08 PM]

Nando: medium [4:08 PM]

Brourd: Not bad for 2000+ sequences [3:09 PM]

Nando: indeed [4:09 PM]

Omei: II had come to the conclusion that designs that showed consistently high error rates across all bases indicated a yueld problem.  Is that essentially the same indicator you are using? [4:09 PM]

Eli Fisker: Zanna, keep it in mind and preferable put it up somewhere. Perhaps ask Machinelves [4:09 PM]

Zanna: ok [4:10 PM]

Nando: I'm not entirely sure, but I believe so Omei, yes [4:10 PM]

Nando: can't wait to be able to clarify some of these points in the lab hangouts [4:11 PM]

Brourd: Lower signal to noise probably has some correlation to higher error rates. [3:11 PM]

Omei: That's one of the indicators I am using to conclude there has been "barcode" (batter called "trailer") interference. [4:11 PM]

Nando: many factors may influence yield and errors [4:12 PM]

Omei: Right. [4:12 PM]

Brourd: Right, like the inclusion of GUUGUUGUUGUU ;P [3:12 PM]

Nando: I'm talking about one of the important issues in that last blog post of mine [4:12 PM]

machinelves: i'll work on an issue reporting protocol in the wiki, for now 1) brainstorming: chat, forums 2) reporting fully described and exampled issues: wiki ( append to Dev Chat page until further organization of process ) 3) tracker: github or whatever the devs want [4:13 PM]

Nando: :D [4:13 PM]

Omei: That's another form of trailer interference. [4:13 PM]

Nando: great job, machinelves [4:13 PM]

machinelves: thank you kindly :) [4:13 PM]

Nando: and so my conclusion: "You just don't mess with RT" :) [4:13 PM]

Brourd: Three cheers for machinelves, creating a list of things for player coders to work on. Hip hip hooray! [3:13 PM]

Zanna: hip hip hooray! [4:14 PM]

machinelves: aww *blush* [4:14 PM]

wateronthemoon: My internet went down--did i miss dev chat? [4:14 PM]

Eli Fisker: hi Moon, yes, unfortunately [4:14 PM]

Nando: I'm afraid so water [4:14 PM]

Omei: Nothing important. :-) [4:14 PM]

Brourd: Most likely. [3:14 PM]

Eli Fisker: lol, Omei [4:15 PM]

Zanna: aww, bummer water [4:15 PM]

machinelves: thanks everybody your ideas on how to make this project better are amazing and i am so glad that everyone cares so much about this community [4:15 PM]

Eli Fisker: Chat log will be up later [4:15 PM]

wateronthemoon: just all the lab stuff [4:15 PM]

Nando: but nothing happened, really... :P [4:15 PM]

Eli Fisker: Machine, thx :) [4:15 PM]

Brourd: Well, Jee is the one who usually posts the dev chat. [3:15 PM]

Eli Fisker: Yes, they are up the second after it finishes.  [4:15 PM]

wateronthemoon: oh good, nothing happened :) [4:15 PM]

wateronthemoon: as usual [4:15 PM]

Eli Fisker: But since he got lost it might take a while [4:16 PM]

Zanna: I thought a lot happened!! [4:16 PM]

wateronthemoon: i count on nothing happening--saves a lot of worry :) [4:16 PM]

Zanna: lol [4:16 PM]

Eli Fisker: hehe [4:16 PM]

wateronthemoon: all together [4:16 PM]

Brourd: Most of it will be reiterated in the future. [3:16 PM]

Omei: It was all talk. [4:17 PM]

wateronthemoon: and reiteration--that's a good thing too [4:17 PM]

Brourd: There is at least one thing that seems certain. The other is up in the air for now. [3:17 PM]

wateronthemoon: what seems certain? [4:17 PM]

Omei: But it's not clear which one is the certain one. [4:17 PM]

wateronthemoon: haha [4:18 PM]

Nando: certain? more work for Nando, that is for sure :P [4:18 PM]

Brourd: :D [3:18 PM]

Zanna: lol [4:18 PM]

machinelves: hey water! highlights: possibly branching the code for player development to fix little issues ourselves, first friday of the month meetings with rhiju's stanford group [4:18 PM]

Omei: But we ought to tell her about the hangout with the labcoats. [4:18 PM]

Zanna: poor nando [4:18 PM]

Brourd: We all knew that, now when is your analysis of the mismatch labs coming out ;) [3:18 PM]

Nando: :D [4:18 PM]

wateronthemoon: that's what got interrupted--analysis of mismatch labs [4:19 PM]

wateronthemoon: and to reiterate: poor nando )P [4:19 PM]

Zanna: :D [4:19 PM]

Brourd: For any players who want to know my analysis, they were all a success, unfortunately. [3:20 PM]

wateronthemoon: :) [4:20 PM]

Nando: lol :D [4:20 PM]

Zanna: why is it unfortunate? [4:20 PM]

Nando: ok, catching some fresh air, bbl [4:20 PM]

wateronthemoon: so mismatches don't really matter, as far as chemicals go? [4:20 PM]

machinelves: bye! [4:20 PM]

Brourd: Eh? No, they worked. A little bit too well. [3:21 PM]

Zanna: seems a good thing to me, we learned something! [4:21 PM]

Brourd: later Nando. [3:21 PM]

wateronthemoon: bye. fresh air is excellent. They have that in Beijing? [4:21 PM]

Zanna: later nando [4:21 PM]

Zanna: haha water [4:21 PM]

Zanna: the CC mismatches did especially well [4:22 PM]

machinelves: like two peas in a pod eh? :D [4:22 PM]

Zanna: ahaha [4:23 PM]

wateronthemoon: so is nando writing an analysis of mismatch labs? [4:23 PM]

wateronthemoon: peas--haha [4:23 PM]

Brourd: He better! [3:23 PM]

Zanna: hopefully, he will tell us a story about them :D [4:23 PM]

jeehyung: Hi all - sorry I had a network problem and just got back online again. [4:23 PM]

Zanna: wb, jee [4:24 PM]

Brourd: Hey Jee [3:24 PM]

machinelves: hey! [4:24 PM]

wateronthemoon: hi jee [4:24 PM]

Brourd: So, is this the end of the devchat? [3:24 PM]

jeehyung: I'm not sure what happened after I got disconnected. Did Rhiju have the chat with you? [4:24 PM]

TomoeUzumaki: hi! [4:24 PM]

wateronthemoon: glad to get here for the end at least [4:24 PM]

steven123505: hey gues [4:24 PM]

TomoeUzumaki: hahah i made it [4:24 PM]

steven123505: guys* [4:24 PM]

steven123505: wait...i thought this started at 6... [4:25 PM]

Zanna: hi sven [4:25 PM]

wateronthemoon: too late for all of us tomoe [4:25 PM]

Brourd: Yeah, rhiju proposed a few things and we had a nice chat :) [4:25 PM]

machinelves: @jee rhiju said to ask you if it is okay for players to post issues to github directly, or if you would rather branch out a player portal, or ? [4:25 PM]

TomoeUzumaki: yep. [4:25 PM]

wateronthemoon: but not 6 your time [4:25 PM]

TomoeUzumaki: hey, jee, I have a question for Mike [4:25 PM]

TomoeUzumaki: (who is not here) [4:25 PM]

jeehyung: Let's run the meeting for 20 more minutes for me to catch up, and answer more questions [4:25 PM]

machinelves: so as to track issue details, status, etc... as opposed to wading thru forums etc... [4:26 PM]

TomoeUzumaki: alrighty [4:25 PM]

steven123505: awesome :D [4:26 PM]

jeehyung: @machinie - ok noted. I'll have to discuss it with the dev team on that one [4:25 PM]

Omei: Hi, Jee! [4:26 PM]

wateronthemoon: great :) [4:26 PM]

jandersonlee: hey I didn't miss it all! [4:26 PM]

jeehyung: @Tomoe ok what did you want to ask? [4:25 PM]

machinelves: currently using forums to brainstorm, wiki to consolidate, and holding off on github until the green light [4:26 PM]

jeehyung: Hi Omei, [4:25 PM]

Brourd: @ Jee http://prntscr.com/23zdcj [4:26 PM]

TomoeUzumaki: it's more of a glitch, but in the mobile version [4:26 PM]

wateronthemoon: we're the leftovers [4:26 PM]

Brourd: I was also wondering, are the mutation constraints enforced upon submission? [4:27 PM]

TomoeUzumaki: sometimes while i'm on it, and get a notification [4:27 PM]

machinelves: @ jee thanks! [4:27 PM]

jeehyung: @Brourd Noted. Thanks for catching it [4:26 PM]

jeehyung: @Brourd No - the only constraints enforced is the barcode uniqueness [4:26 PM]

steven123505: elves, did you ask everything on the list? [4:27 PM]

Zanna: nice solution to the problem, B [4:27 PM]

TomoeUzumaki: the swiping down of the menu kind of... haha how do I describe it? [4:27 PM]

TomoeUzumaki: it doesn't meld seamlessly? [4:27 PM]

Brourd: Ah, is there some way we can have the constraint enforced? [4:28 PM]

jeehyung: @Brourd right now no...I assume you want it for your lab project? [4:27 PM]

machinelves: @jee fyi here is currently consolidated list of bugs & feature requests re: lab UI http://eternawiki.org/wiki/index.php5/Dev_Chat [4:28 PM]

Brourd: Right :) [4:28 PM]

machinelves: ( not counting millions of additional issues in forums & chat lol ) [4:28 PM]

Omei: Jee, i've discovered that the scripting library's RNA constructor is quite buggy.  Is that a known issue?  If not, I'll submit a bunch of examples. [4:28 PM]

Brourd: Or a few lab projects, I can wait until all the other issues are fixed. [4:28 PM]

TomoeUzumaki: that's all, jee [4:28 PM]

jeehyung: @machineleves yep saw that. Thanks for the list. Will read through them [4:28 PM]

machinelves: @steven we'll see what santa brings lol [4:29 PM]

jeehyung: @Omei didn't know that - can you send us an example? It could help debugging [4:28 PM]

steven123505: haha [4:29 PM]

steven123505: what about the customizable next puzzle button? [4:29 PM]

mat747: hi [4:29 PM]

Zanna: hi mat [4:30 PM]

Brourd: hey mat. [4:30 PM]

Eli Fisker: hi Mat :) [4:30 PM]

machinelves: @jee many thanks! :) [4:30 PM]

Omei: Want just examples?  Or a Jira issue? [4:30 PM]

mat747: Hi all - carry on [4:30 PM]

machinelves: hey! :) [4:30 PM]

Omei: Hi, Mat [4:30 PM]

jeehyung: @steven we didn't have chance to look into the feature yet. But it's on our todo list [4:30 PM]

wateronthemoon: most important lab issue seems to me being able to back up to list of labs--otherwise voting, as now, is a real pain. [4:31 PM]

Eli Fisker: I agree with Moon [4:31 PM]

steven123505: thank you jee :) [4:31 PM]

jeehyung: @Omei not sure what a Jira issue is? [4:30 PM]

wateronthemoon: starting from scratch every time you look at a dot plot [4:31 PM]

wateronthemoon: thanks, Eli [4:31 PM]

machinelves: wait... are you telling me we have jira? [4:31 PM]

TomoeUzumaki: jee, can you tell mike that when I swipe down to view a notification (in mobile), it doesn't meld smooothly? [4:31 PM]

jeehyung: @Tomoe will do [4:31 PM]

Omei: Sorry,, wrong issue tracker.  I meant write up a github issue. [4:32 PM]

TomoeUzumaki: thank you [4:32 PM]

jeehyung: @Eli, water For a temporary fix, we'll move back the flash (old) browser for the voting, and have the new browser used as an expert viewer interface [4:32 PM]

jeehyung: @Omei - Please send kws4679 (script developer) a message - he'll organize the task and upload it to github himself. Thanks! [4:32 PM]

wateronthemoon: that could work, temporarily [4:33 PM]

TomoeUzumaki: ok, but jee, how do we get back to the old lab interface? [4:33 PM]

jeehyung: @water and we'll of couse try to make the voting smooth in the new interface as well [4:33 PM]

wateronthemoon: thanks, jee [4:33 PM]

TomoeUzumaki: from the button? [4:33 PM]

jeehyung: @Tomoe We'll make an update soon. When you click on vote, you'll automatically be tkaen to the old interface instead of new one [4:33 PM]

jeehyung: The new one will be accessible only by clicking on "expert view"  [4:33 PM]

Omei: OK.  During the part with Rhiju, I asked "On the issue of player-led development, would it be possible for the devs to set up an an alternate URL for any script-writing  player to use to develop and demonstrate improvements to the UI?  If other players could access any of them, we could actually develope alternatives/fixes and let players give us feedback.  The Eterna devs coul [4:34 PM]

TomoeUzumaki: aah. Thanks, jee [4:34 PM]

TomoeUzumaki: going to eat dinner, catch y'all on the flipside [4:34 PM]

Eli Fisker: Omei, a snippet of the message got cut off [4:35 PM]

Omei: ...  The Eterna devs could then incorporate the mods they thoughth were best into the "official" version." - he said he would need to discuss it with you.  I thought I would bring it up with you now in case you wanted to talk about the issues. [4:35 PM]

wateronthemoon: seeing how many votes you have left, who you voted for, and easy navigation between various data modalities [4:35 PM]

Omei: Does that fill it in? [4:35 PM]

jeehyung: @Omei - thanks that does help me a lot.  [4:35 PM]

Eli Fisker: bye Tomoe [4:36 PM]

machinelves: @jee want to voice support for steven's player puzzle next button request, both for A) randomizing and weighting towards most solves and / or B) potentially having the option to customize results based on same checkboxes in player puzzles list, i.e. most/least solves, switch, etc... [4:36 PM]

wateronthemoon: have a good dinner, tomoe [4:36 PM]

machinelves: bye tomoe! [4:38 PM]

jeehyung: @machinelves noted. Will try to stabilize the lab interface ASAP and look into the issue [4:37 PM]

machinelves: @jee thanks! [4:38 PM]

jnicol: jee, do you have a javascript front end to design puzzles as well as the flash one? [4:38 PM]

Eli Fisker: Thx, Jee [4:39 PM]

jeehyung: @jnicol For now no. The only puzzle design interface is in flash. [4:38 PM]

jnicol: ok, guess I misread your response [4:39 PM]

machinelves: @jnicol lol i was holding my breath 0.o [4:39 PM]

machinelves: would it ever be possible / likely to fully transition out of flash? [4:41 PM]

machinelves: not sure what you're doing for iOS [4:42 PM]

jeehyung: @machine Not in near future.. we don't have the manpower to recode everything [4:41 PM]

machinelves: right right, thanks just curious! [4:42 PM]

jeehyung: We do have one person develoiping iOS and Android version [4:41 PM]

jeehyung: I have to run now - thanks for all the feeback, and sorry about missing out the first part of the dev chat [4:42 PM]

machinelves: bye! thank you very much! :D [4:43 PM]

jnicol: bye jee [4:43 PM]

Zanna: thanks jee, and bye [4:43 PM]

Brourd: Bye Jee, take care. [4:43 PM]

Eli Fisker: Bye Jee [4:43 PM]

Omei: Thank you, Jee.  Take care. [4:43 PM]

steven123505: bye Jee! [4:43 PM]

steven123505: thanks for everything! [4:43 PM]

mat747: Bye Jee [4:43 PM]

Omei: Steven's been quietly lurking? [4:43 PM]

wateronthemoon: thanks, jee! :) [4:43 PM]

Zanna: lol [4:43 PM]

Eli Fisker: :) [4:44 PM]

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