2014.04.09 Dev Chat

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On Bugs & Spam

jeehyung: Hello all [3:02 PM]
Nando: hi Jee [3:02 PM]
hoglahoo: hi jee [3:03 PM]
Jieux: ack... my brain was hacked! [3:03 PM]
Eli Fisker: hi Jee :) [3:03 PM]
machinelves: hi jee :D [3:03 PM]
jeehyung: Welcome to bi-weekly eterna dev chat [3:02 PM]
Jieux: Wow, I made one! [3:03 PM]
machinelves: @Jee Thank you! LFP6 requested that I send you new issues which are pending addition to github: http://eternawiki.org/wiki/index.php5/New_Issues [3:03 PM]
starryjess: no, I don't want to know how it works, just what it is [3:03 PM]
Jieux: now I know I've been hacked. [3:03 PM]
starryjess: but, now dev chat started, so nevermind [3:03 PM]
machinelves: Are there any issues on this list that you already have entered into GitHub, which we should now remove from New Issues? [3:03 PM]
Brourd: Hey Jee. [3:04 PM]
firedrake969: Hi jee :D [3:04 PM]
jeehyung: @machinelves - thanks for the link. I'm looking into it now [3:04 PM]
machinelves: awesome, thanks! [3:05 PM]
JR: we can't post 2 state switches? [3:05 PM]
jeehyung: @JR I didn't know the problem - let me look into it [3:05 PM]
JR: and how is search for your replacement going [3:06 PM]
JR: problem is a forum post [3:06 PM]
JR: *is in [3:06 PM]
firedrake969: Jee, I'd like to report a shiftable bug... [3:07 PM]
firedrake969: pics ina moment. [3:07 PM]
jeehyung: @JR actually we are doing good in finding a new dev lead. We narrowed down to 2 good candiates [3:06 PM]
machinelves: that's great news! [3:07 PM]
JR: great to hear [3:07 PM]
firedrake969: http://eterna.cmu.edu/web/puzzle/4200511/ [3:07 PM]
firedrake969: Adding and then removing a base gives this: http://prntscr.com/38joy7 [3:08 PM]
Brourd: Jee, as of right now, I am having issues with updating lab projects. One example being the addition of target structures in the labs.. [3:09 PM]
jeehyung: @firedrake thanks for the pointer. We'll look into this [3:09 PM]
JR: jee - another forum post describes missing structure notation from all lab projects [3:11 PM]
jeehyung: @Brourd - sorry about the trouble. Is title and description edit working? [3:10 PM]
Brourd: I can check right now [3:11 PM]
jeehyung: @JR - Eli told me about that - that will be fixed in our next update [3:11 PM]
Brourd: Title and description editing work fine. [3:12 PM]
Eli Fisker: Jee, thx, glad to hear [3:12 PM]
jeehyung: @Brourd - will look into the target structure issue then. [3:12 PM]
Brourd: Hopefully we get a fix on the addition of subprojects soon :) [3:14 PM]
jeehyung: @Brourd will do my best to fix this ASAP. Sorry about the trouble [3:16 PM]
machinelves: @everybody general announcement: chat guidelines are now available for reference as a link from the wiki home page, and also thanks to hoglahoo adding it to LinkBot, you can call it up by .conduct [3:16 PM]
LinkBot: http://eterna.cmu.edu/content/code-conduct [3:16 PM]
machinelves: @jee, FYI there is an eterna email address in this link. if there is not bandwidth to collect community feedback, you may wish to remove the email address, while leaving the guidelines. [3:16 PM]
machinelves: with thanks to hoglahoo, eli, and nando for helping to think of a constructive solution for managing spam [3:16 PM]
Eli Fisker: Thx, Machine [3:16 PM]
Brourd: btw, I was not entirely sure, but, does the script for custom constraints apply to all subprojects? [3:16 PM]
machinelves: :) [3:17 PM]
Brourd: Or, can we have a different scripted constraint for each individual sub project? [3:17 PM]
jeehyung: @machineleves - thanks for the link [3:17 PM]
machinelves: np [3:17 PM]
jeehyung: @Brourd it applies to all subprojects now. We plan to allow using different scripts for each subproject though [3:17 PM]
Brourd: Ah, very good, and thanks. [3:18 PM]
Nando: if the script gets the puzzle ID as a parameter, it's manageable [3:18 PM]
Brourd: right [3:19 PM]
JR: is the synthesis problems being smoothed out? [3:19 PM]
jeehyung: @Nando - that's actually a great idea [3:18 PM]
jeehyung: @JR yes we think so. We have uploaded latest results yesterday [3:19 PM]
JR: did you identify the problem [3:20 PM]
Eli Fisker: So was it mainly the repeat bases? [3:21 PM]
jeehyung: Yes we think we should stick to max length of 130 bases and without 4Cs and 4Gs in a row [3:21 PM]
JR: just interested [3:21 PM]
Eli Fisker: Great, thx [3:21 PM]
JR: are you going to hardcode that into the requirements [3:22 PM]
jeehyung: @JR Yes - now you can't submit anything with 4Cs and 4Gs [3:22 PM]
JR: good - too easy to skip otherwise [3:23 PM]
Nando: not everything seem to have gone smoothly, even with the recently uploaded R83 results, but shouldn't we talk about that on Friday? [3:22 PM]
Eli Fisker: I wonder if it will still be a problem if one submit a design with 3 G's + another base + 3 G. [3:23 PM]
Eli Fisker: I mean that repeat will still be possible [3:23 PM]
Brourd: Well Nando, it was only a few nucleotides short :) [3:23 PM]
Eli Fisker: I wonder if synthesis will react to this equally bad [3:24 PM]
Eli Fisker: Or there is something special about 4 repeat G's or C's on their own' [3:24 PM]
Brourd: As Nando likes to always point out, it is all a matter of concentration. [3:25 PM]
Nando: yep [3:25 PM]
Jieux: I have a hard time concentrating sometimes. [3:25 PM]
Eli Fisker: So more like if a whole lab has locked bases with a bad sequence [3:25 PM]
Nando: for instance [3:25 PM]
Eli Fisker: That would make sense since there has been 4+ repeat C's and G's before in individual lab designs [3:26 PM]
Eli Fisker: lol, Jieux [3:26 PM]
Eli Fisker: Never when it comes to telling jokes [3:27 PM]
Brourd: So Jee, will the Das lab and associates have their own "paper labs" running alongside those ran by players? [3:28 PM]
jeehyung: @Brourd soon - but for the first round, it'll be entirely from players [3:28 PM]
Brourd: Got it. [3:29 PM]
JR: who decides on turning paper into proposal [3:29 PM]
jeehyung: @JR - you mean how the labs will be chosen? It'll first be based on votes. and then selected projects will have to gothrough review rounds by Rhiju, his lab, and possibly volunteer Eterna players [3:30 PM]
JR: it was the review i was looking for - ok [3:31 PM]
JR: there is a diff. between proposal and pilot project- correct [3:32 PM]
JR: proposal is real mccoy [3:32 PM]
JR: pilot is test [3:32 PM]
JR: ??? [3:32 PM]
Nando: paper labs have strings attached to them: a write-up possibly culminating in a publication in some journal [3:33 PM]
Nando: pilot is to test ideas [3:33 PM]
JR: and tab = proposal is a paper then [3:34 PM]
Nando: that's my understanding, yes [3:34 PM]
JR: go into lab proposals - look at tab desc [3:35 PM]
JR: ok - got it [3:35 PM]
Nando: just curious, how's the work on Novalabs going? [3:40 PM]
jeehyung: @Nando - it's going ok. I think we'll have launch around late-April [3:40 PM]
Nando: nice [3:41 PM]
Eli Fisker: Agreed [3:41 PM]
machinelves: that's great to hear, good luck! [3:41 PM]
Jieux: Does a paper have to have a lab associated with it, or can it just be a straight up paper? [3:41 PM]
Eli Fisker: We regular have new players requesting more tutorials [3:41 PM]
Hideyoshi101: hi nando it is me [4:44 PM]
Hideyoshi101: the guy from davinci [4:44 PM]
Hideyoshi101: i just kid [4:44 PM]
Nando: hi Hideyoshi [3:43 PM]
Hideyoshi101: hey [4:45 PM]
Hideyoshi101: i was in the conversation with those davinci students [4:45 PM]
Hideyoshi101: how did you know what school they went to [4:46 PM]
Hideyoshi101: i live in california [4:46 PM]
Hideyoshi101: where is davinci [4:46 PM]
Nando: we're in a meeting right now, Hideyoshi, I'd rather have this conversation later, if you don't mind [3:45 PM]
Hideyoshi101: oh that is ok sorry for bothering you [4:46 PM]
Nando: no problem [3:45 PM]
Hideyoshi101: ok bye [4:47 PM]
Nando: @Jee: we had some issues in the past couple days with turbulent kids, fyi [3:46 PM]
machinelves: i remember that, yes they are quite excitable [3:47 PM]
firedrake969: I probably wasn't here during that time [3:47 PM]
firedrake969: What happened? [3:47 PM]
jeehyung: @Jieux - the paper projects don't necessarily have to be associated with actual labs. [3:47 PM]
jeehyung: @Nando, machineleves. Thanks for the heads up. I'll be on watch when NOVA launches [3:48 PM]
Jieux: so if I wanted to write a paper on color patterns and RNA stability, I would not have to have a lab associated with it, but could just use existing lab data to blah blah blah about it? [3:48 PM]
Eli Fisker: @Jee, glad to hear [3:49 PM]
machinelves: @jee thanks, it will only increase of course ;) to followup, are there any github ticket #s we should update the new issues with? if not yet, no worries. just wanted to double check. [3:49 PM]
jeehyung: @Jieux I think I misunderstood your previous question. To write an Eterna paper, you'll have to be an admin or a co-admin of an existing eterna paper project [3:52 PM]
Jieux: and that requires a lab component yes? [3:54 PM]
jeehyung: @machinelves - we don't have github ticket nubmers yet unfortuntately. I think the task management will have to be handled by the next dev lead. [3:53 PM]
jeehyung: @Jieux - yes it has to be about experiments from eterna lab [3:54 PM]
machinelves: @jee, that's exactly what i needed to know, I'll update LFP6 - thank you! :) [3:54 PM]
jeehyung: All - I'll have to leave in 5 mintues - please throw in last questions & suggestions [3:54 PM]
Jieux: I guess I'm not being clear. [3:55 PM]
Jieux: it is about experiemnts from the lab, just won't have a new lab experiment assoicated with the paper. [3:55 PM]
Jieux: will use existing labs for basis of paper. [3:55 PM]
jeehyung: @Jieux - we actually haven't thought about that. I'll bring that up in our dev discssion. We still haven't figured out exactly how the paper writing process will work [3:56 PM]
Brourd: I suppose you could write a rough draft and submit it to Rhiju, Jieux. [3:57 PM]
Jieux: about a year ago I thought I was doing something like that when i wrote my little switch thing... [3:58 PM]
Jieux: I think that's the last dev. chat I made actually ;) [3:58 PM]
jeehyung: All I have to go now - thanks for all the suggestions. I'll post the chat log as a news item! [3:59 PM]