2014.12.10 Dev Chat

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On Paper Labs Conclusions

jnicol: Welcome to dev chat everyone! [3:00 PM]

Eli Fisker: Thx :) [3:00 PM]

LFP6: And intros are out of the way too. :) [3:00 PM]

randomguy: O.O [3:01 PM]

hoglahoo: yay! [3:01 PM]

jnicol: Lab results for R92 just came in [3:01 PM]

machinelves: thanks John. thanks for fixing the PM spam, it's all gone! *high five* [3:01 PM]

jnicol: np [3:01 PM]

jnicol: trying to keep low key on that front :) [3:01 PM]

Eli Fisker: And the signal to noise ratio is beautiful [3:01 PM]

machinelves: hi Mayanne, glad you could make it :) [3:01 PM]

jnicol: hopefully players have seen a difference [3:01 PM]

Eli Fisker: Hi Mayanne and Hogla [3:01 PM]

machinelves: John i noticed comment numbers are gone from recent news/blogs list [3:02 PM]

LFP6: Ditto [3:02 PM]

Eli Fisker: Link to the new data: [3:02 PM]

Eli Fisker: http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R92_0000/ETERNA_R92_0000.rdat [3:02 PM]

Eli Fisker: and a small intro of how to view it:  [3:03 PM]

jnicol: YEs, comment numbers were removed by Rhiju's requesr [3:03 PM]

Eli Fisker: https://docs.google.com/document/d/1V8aRNCCgS9GMz-76wxFQD8wOHjFbI2MjsKuS_EKxyok/edit [3:03 PM]

jnicol: I would like to start this dev chat offby talking about lab conclusions and publications [3:03 PM]

machinelves: cool Eli, thanks! & interesting john, what's the news? [3:04 PM]

jnicol: Rhiju has asked me to start prodding the lab admins to submit conclusions [3:04 PM]

Eli Fisker: John, working on it [3:04 PM]

jnicol: EteRNA would like to gather these conclusions into rna 'proceedings' [3:04 PM]

Eli Fisker: I have a question.  [3:05 PM]

LFP6: Have a sort of EteRNA "symposium"? [3:05 PM]

jnicol: They would not be submitted to peer review publications, unless the admin wishes to take that step [3:05 PM]

Dat Coffee: hey lfp [3:05 PM]

macclark52: How can we help with labs that we are not the admin for? [3:06 PM]

macclark52: Or should we just keep paws off? [3:06 PM]

LFP6: @Mac: Other than submitting designs, you'd have to contact the admin on a case-by-case basis [3:06 PM]

jnicol: Rhiju felt that the paper lab concept to submit to journals may be intimidating for players [3:06 PM]

jnicol: mac, any player with 10000 points can admin a lab [3:06 PM]

Eli Fisker: Mac, you can still post your observations either as comments for the lab or in the forum [3:06 PM]

LFP6: @John: Having the option to have the support to do so would be good to have though, IMO [3:06 PM]

macclark52: Yah, pretty intimidating/  :-) [3:07 PM]

macclark52: Ah, comments,   [3:07 PM]

Eli Fisker: Mac, please, add your thoughts [3:07 PM]

macclark52: I'm thinking particularly of labs that my students have sent in designs for.  [3:08 PM]

jnicol: So we would like to relax the lab requirement for publication and hopefully get more players involved in creating labs [3:08 PM]

macclark52: One that they particpated in recently got synthesis data, so that was exciting.  [3:08 PM]

jnicol: And Rhiju will definitely any author with their conclusion and/or publication [3:08 PM]

jnicol: Eli, you had a question? [3:09 PM]

Eli Fisker: Sorry lost connection [3:10 PM]

macclark52: Is there a "help" between "definitely" and "any"?   [3:11 PM]

macclark52: Sorry, Eli, didn't mean to interrupt.  [3:11 PM]

Eli Fisker: Ok, I was thinking about all the fine posts in the forum that also holds valuable observations. Some of which are by players who left [3:11 PM]

Eli Fisker: Mac, my connection, nothing of your fault [3:11 PM]

Eli Fisker: What about these posts? [3:12 PM]

jnicol: Eli, the plan is to put all that information together in the proceedings [3:12 PM]

Eli Fisker: Ok, good [3:12 PM]

Eli Fisker: Just wanted to stress, what I didn't get put up before as it didn't went through [3:12 PM]

Eli Fisker: Lab analysis is for everybody [3:12 PM]

LFP6: [Interjection]They need to be mined for feedback/bugs too.[End] [3:12 PM]

jnicol: would like outside scientists, etc to be able to search and read these proceedings in one place [3:12 PM]

Eli Fisker: You don't have to have a lab, to start analysing data [3:12 PM]

Eli Fisker: The data belongs to all of us [3:12 PM]

LFP6: Can I add a thought? [3:12 PM]

Eli Fisker: Smart point, John [3:13 PM]

Eli Fisker: So everybody, please put your thought at observing lab results. We never know how may be the next stubling on an interesting piece that can further the project and our aim at finding more RNA folding rules  [3:13 PM]

machinelves: I agree wholeheartedly, every contribution helps [3:13 PM]

jnicol: and we are familiar with how to search for all this information, but those doing research may have a hard time  [3:13 PM]

Eli Fisker: Very good point, John [3:14 PM]

macclark52: So is the comments the best place for that? [3:14 PM]

LFP6: Can we just mine out forums of everything, and then ditch them for a more organized approach of reports/analysis/discussion/etc? [3:14 PM]

macclark52: Or the forum? [3:15 PM]

jnicol: mac, yes put your comments in, the lab admin will filter the information into the article for the proceedings [3:14 PM]

Dat Coffee: Hi LFP [3:15 PM]

LFP6: Hi DC. If you want to chat, PM works best as we're in a dev chat. :] [3:15 PM]

jnicol: I think lab comments is best place for a specific lab [3:15 PM]

codygeary: john, are there past examples of these types of proceedings to refer to? [3:15 PM]

codygeary: and hi [3:15 PM]

machinelves: perhaps when the issue tracker is ready, at the same time as combing through forums for issues, we can pull observations into one central place as well. where are you thinking is the best hub for that jnicol? [3:15 PM]

Dat Coffee: Whats a dev chat [3:15 PM]

macclark52: OK, good.  Thanks.  [3:16 PM]

jnicol: forum is good if we are discussing general issues, observations that span multiple labs [3:15 PM]

LFP6: @DC: Developers (or in this case developer, Jnicol) come in to talk to us. [3:16 PM]

Nando: ah, if we only had a wiki... [3:16 PM]

Nando: wait [3:16 PM]

LFP6: lolz [3:16 PM]

LFP6: "Wait, we had a Wiki?" [3:16 PM]

jnicol: dat coffee, dev chat = developers chat, where we discuss eterna technical issues [3:16 PM]

machinelves: hi cody & DC, and welcome [3:16 PM]

machinelves: hehe nando sees where i'm headed with this... [3:16 PM]

LFP6: Heh [3:16 PM]

jnicol: Funny you should volunte.. err say that Nando :) [3:17 PM]

LFP6: So, John, thoughts on my approach specifically? :P [3:17 PM]

LFP6: (As in, destroy forums when we're done with Machine's approach) [3:17 PM]

macclark52: Forum might be good for general observations.   [3:18 PM]

machinelves: forums function as a place for discussion, we will still need that after filing [3:18 PM]

jnicol: Cody, we do not have proceedings, but Rhiju mentioned a few examples [3:18 PM]

macclark52: Cross labs.   [3:18 PM]

jnicol: I will have to ask him again and I'll post in the news item comments [3:18 PM]

LFP6: @Machine: But I'm saying re-build with everything in its place [3:18 PM]

codygeary: It's an awesome idea btw.  Especially using the forum posts for some of the content of the proceedings. [3:18 PM]

machinelves: forums are broad in scope, for any topic, whether issues, feature requests, or lab conclusion discussion [3:19 PM]

machinelves: and when particular elements are confirmed of interest and refined enough to be entered into the correlating database, we can pull from forums specifically [3:19 PM]

LFP6: afk dinner [3:19 PM]

machinelves: there are multiple hubs forum data will feed into, one for issue tracking, and then wherever we're collecting lab conclusions [3:20 PM]

LFP6: (Machine, just see that as a bear to handle!) [3:20 PM]

jnicol: I will also post a report on the conclusions, to show what players and labs still need conclusions [3:20 PM]

machinelves: happy dinner! [3:20 PM]

macclark52: That would be helpful, J.  It's in the archive, but one at a time.  [3:21 PM]

machinelves: jnicol is there a walkthrough of how to participate in conclusions? [3:21 PM]

machinelves: links, examples, etc. [3:21 PM]

jnicol: no walkthru that I know of [3:21 PM]

jnicol: but brourd has entered several conclusions [3:21 PM]

Eli Fisker: Rhiju have written one a while back:  [3:21 PM]

Eli Fisker: https://docs.google.com/document/d/1y2ziNCAr2y453AfDmRVlj2zfddcikKmdqY-KkrcWD5s/edit [3:21 PM]

machinelves: i am feeling like i wouldn't know where to begin in contributing, so it may help to point players to it [3:21 PM]

machinelves: aha! thanks Eli :D [3:22 PM]

Eli Fisker: But we need something a bit shorter [3:22 PM]

jnicol: you can check out some of his labs as examples [3:22 PM]

Eli Fisker: Also I find Cody's way writing conclusions interesting:  [3:22 PM]

jnicol: elves, mostly up to the admin of a lab [3:22 PM]

machinelves: i mean as simple as where in the lab interface is the input box :D [3:22 PM]

jnicol: Yes, Cody has done some great work with conclusions! [3:23 PM]

codygeary: Sometimes individual players have written comments into their lab submissions, it would be nice to try to make it easy to follow up on any ideas that were pasted there [3:23 PM]

machinelves: so conclusions are being entered as comments per lab? [3:23 PM]

machinelves: @Eli if you shared a link it didn't come through [3:23 PM]

jnicol: no conclusions are added as part of the description in a lab [3:24 PM]

codygeary: well, I noticed on the new lab some players tried to make series of things like GU wobbles and etc. and they made notes in the comments of each sequence [3:24 PM]

jnicol: Cody, would it help if I put all comments together in an excel or doc? [3:24 PM]

codygeary: yes, I think it would [3:25 PM]

codygeary: and it would be also great if the players could post a follow-up comment after the results come in [3:25 PM]

Eli Fisker: Example by cody:  [3:26 PM]

Eli Fisker: https://docs.google.com/document/d/1Wh9uvieSFl8e96vCmLSUTtGLDWHBUN1iKJYEbO-hmOQ/edit [3:26 PM]

jnicol: they can update their comments in the sequence/design they have entered [3:26 PM]

machinelves: so in this context are conclusions only posted by lab admins in description, and theories from players are called something else and posted in comments? [3:26 PM]

machinelves: thanks Eli worked now [3:26 PM]

jnicol: elves, correct [3:27 PM]

Eli Fisker: np, Elf [3:27 PM]

Eli Fisker: and thx for saying [3:27 PM]

machinelves: np :) [3:27 PM]

machinelves: thanks John [3:27 PM]

machinelves: thanks cody for the writeup [3:27 PM]

jnicol: but we would like to gather this together for someone to easily look through [3:28 PM]

machinelves: what are we calling contributions from non-admin players on this? [3:28 PM]

machinelves: so i don't get confused explaining [3:28 PM]

jnicol: comments in the lab [3:28 PM]

machinelves: thanks [3:28 PM]

jnicol: also, as Cody suggested, players should update their specific design comments if they see something interesting on a specific design [3:29 PM]

Nando: @elves: I'd equate it to peer review, just non-anonymous [3:29 PM]

machinelves: so that 'something interesting' is akin to a hypothesis? vs. conclusion made from collection of hypothesis comments? [3:29 PM]

machinelves: ahh i like that Nando :D [3:29 PM]

macclark52: Yes, that is a good example.  [3:30 PM]

Eli Fisker: John, I think we will need an easier way to comment, I mean instead of clicking in and out of all the designs [3:30 PM]

Brourd: http://eterna.cmu.edu/web/lab/3376172/ Here is an example of a conclusion, machinelves. [3:30 PM]

jnicol: Eli, I'm open to suggestions [3:30 PM]

machinelves: so the original lab hypothesis leads to a conclusion, and the players for that lab can comment on related observations [3:30 PM]

macclark52: Someplace on the lab page itself.  [3:31 PM]

Nando: @B: I was supposed to ban you upon sighting... should I still? [3:30 PM]

macclark52: Not just on individual designs.  [3:31 PM]

Brourd: Another example http://eterna.cmu.edu/web/lab/3376118/ [3:31 PM]

machinelves: thanks brourd, checking [3:31 PM]

Brourd: Let me shower all of this data upon them, then you can do the deed [3:31 PM]

jnicol: Thanks Brourd [3:31 PM]

Nando: ok :D [3:31 PM]

macclark52: ...madly gookmarking... [3:32 PM]

macclark52: bookmarking.   [3:32 PM]

macclark52: ;-) [3:32 PM]

hoglahoo: freudian slip? [3:32 PM]

Brourd: http://eterna.cmu.edu/web/lab/4231143/ [3:32 PM]

Brourd: this lab as well. [3:32 PM]

macclark52: Freudain half-slip.  :-) [3:33 PM]

jnicol: this will be ahigh priority for das labs in the first quarter [3:33 PM]

Brourd: I have some other half baked conclusions that are delayed (You can tel Rhiju that it is a high priority to actually finish those the latter ahlf of December) [3:34 PM]

Brourd: ish [3:34 PM]

jnicol: np bro :) [3:34 PM]

jnicol: I just wanted to get players in the lab conclusion mode [3:34 PM]

Brourd: Okay, Nando. I'm looking at the flowers now. [3:34 PM]

Nando: well, since you're here, I thought you could just ban yourself, I'm feeling lazy suddenly :D [3:35 PM]

Brourd: It's not easy from my current location. :P [3:35 PM]

Brourd: I have to find the admin code, and who knows what else. [3:36 PM]

Jieux: You can ban me, I've lost my Jieuxness anyway. [3:36 PM]

jnicol: any other questions or concerns on other topics? [3:36 PM]

Brourd: btw, generating images in Varna. Difficult, but far more useful imo. [3:36 PM]

macclark52: Ah, la jeunesse... :-) [3:37 PM]

hoglahoo: I have a question and a concern [3:36 PM]

Nando: @john: I think I actually wrote a few half-baked conclusions for my pilot labs about pseudoknots and ribozymes [3:37 PM]

hoglahoo: will the recent influx of difficult fmnsanity switches make it more difficult for the lab admin to sort through [3:37 PM]

Nando: I just was lazy to copy-paste them in the new interface, but I'll try to work on that soon [3:37 PM]

Brourd: No [3:37 PM]

hoglahoo: thanks for the prompt reply [3:37 PM]

hoglahoo: I shall now commence with my 8-state fmnsanity switches [3:37 PM]

Brourd: Turns out, as the competition is going on, the puzzles are becoming less and less sane. [3:37 PM]

jnicol: nice Nando, I gave a report to Rhiju, but didnt remember seeing your pseudoknot ones [3:37 PM]

Eli Fisker: Lol, Hogla [3:37 PM]

machinelves: was thinking, that section below on wiki updates never changes. and with sticky posts I was wondering what you all would think of splitting news and blogs updates into two sections, and doing away with wiki updates section since it seems nonfunctional. or alternately, making the wiki updates section reflect actual wiki updates [3:38 PM]

Nando: @john: they must be too old then, great! :D [3:38 PM]

machinelves: *below news/blog updates [3:38 PM]

Brourd: @ Nando - prelim results on TEP. Nowhere near the amount of protection. [3:38 PM]

Nando: @B: which is weird [3:38 PM]

Jieux: Something petty: I would like to be able to scroll through pages from the top of a page instead of having to scroll to the bottom each time. [3:39 PM]

Nando: now, please disappear B, or I'll really use the ban-stick [3:39 PM]

Brourd: *poof* [3:39 PM]

hoglahoo: Nando: I believe Brourd is evading a ban at this moment already [3:39 PM]

macclark52: OH, is there a problem with the script on the lab review page.   [3:40 PM]

macclark52: I keep getting "script error" and a choice to stop the sciprt from running.   [3:40 PM]

macclark52: Is it just my browser or something else? [3:40 PM]

jnicol: Jieux, lab scrolling? [3:40 PM]

LFP6: back [3:40 PM]

Jieux: scrolling in general. [3:41 PM]

jnicol: noted [3:41 PM]

Eli Fisker: I agree with Elf. That would make the wiki section more useful. Similar for a split blog section [3:41 PM]

Jieux: the first-last page click thingy is on the bottom... would be great to have it up top. [3:41 PM]

Eli Fisker: Very much agree with Jieux [3:42 PM]

LFP6: Or maybe featured Wiki if that makes any sense for anyone? [3:42 PM]

Jieux: I feel I've made my contribution to a rare dev. meeting that I could briefly attend. Dinner calls. Later friends! [3:43 PM]

Nando: later Jx [3:43 PM]

Eli Fisker: Bye Jieux [3:43 PM]

machinelves: bye jieux good to see you! [3:43 PM]

macclark52: Bye, J.  [3:44 PM]

jnicol: I like LFP6 suggestion, would be good to link new wiki info [3:44 PM]

hoglahoo: what new wiki info [3:44 PM]

LFP6: I mean, if there's something useful to what's going on, good for new players, etc. [3:44 PM]

hoglahoo: oh I guess that's the point [3:44 PM]

LFP6: lol Hog [3:44 PM]

hoglahoo: to see if there's new ingo [3:44 PM]

hoglahoo: info [3:44 PM]

hoglahoo: are people contributing new content? [3:44 PM]

Eli Fisker: This is recent:  [3:45 PM]

Eli Fisker: http://eternawiki.org/wiki/index.php5/EPCR [3:45 PM]

hoglahoo: very neat [3:45 PM]

Nando: it's not exactly easy to select automatically articles to feature [3:45 PM]

jnicol: or even link into a forum topic [3:45 PM]

LFP6: That's the thing, it would have to be done manually [3:45 PM]

machinelves: i assumed it meant it was pulling from recent changes list [3:45 PM]

LFP6: True John [3:45 PM]

Eli Fisker: Nando, you have a point. However if it could be picked from what is known to be genuine wiki contributers, that could avoid the spammers [3:46 PM]

Eli Fisker: Then it could still be randomly picked [3:47 PM]

LFP6: But do we want randomly picked? [3:47 PM]

Nando: the recent changes list has a bit of many things, and contributors don't necessarily use the minor change checkbox very carefully [3:47 PM]

LFP6: Or would it be more useful to pick manually? Or would that just be a time sink? [3:47 PM]

LFP6: (Or never updated) [3:47 PM]

Nando: that's the risk LFP [3:48 PM]

Eli Fisker: If we can avoid manual pic that will be the best [3:48 PM]

Eli Fisker: as it won't take energy [3:48 PM]

jnicol: Nando I would have an admin page that I just put a link and description into [3:48 PM]

jnicol: like the news items is [3:48 PM]

jnicol: then we can chosse what we feel is relevant [3:48 PM]

Nando: if we can have a few players with access to that page (like for blogs), that would be cool [3:49 PM]

LFP6: Aye [3:49 PM]

LFP6: Perhaps have a list of "This is what stuff we want there" to make it easier? [3:49 PM]

Nando: well, we could always try manual updates, and see later if we can come up with an automatic scheme [3:49 PM]

jnicol: I would use the same same 'has blog' rights flag  [3:49 PM]

LFP6: (As in, more likely to be updated because it's easier to pick) [3:49 PM]

Nando: @john: if it's no biggie for you, let's go for that [3:50 PM]

jnicol: great chat everyone, anything else before we adjourn? [3:51 PM]

LFP6: You never responded to my though [3:51 PM]

machinelves: thanks john! [3:52 PM]

macclark52: stop script in the lab archive? [3:52 PM]

hoglahoo: could we hold the next devchat in tahiti [3:52 PM]

jnicol: sorry LFP6, please repeat the question [3:52 PM]

LFP6: If we mined everything from the forums, could we just get rid of that database of stuff, and start again with feedback in issue tracker, analasys in that place, discussion in a regular forum, etc? [3:52 PM]

LFP6: ("that place" being wherever you were talking about putting it) [3:53 PM]

LFP6: And have guides and such in the nonexistant "EternaU" [3:53 PM]

jnicol: No, I think we will stick with the forum, the issue tracker does not have the same features [3:53 PM]

LFP6: I mean, there is the difficulty, but personally Im not sure how viable re-posting everything would be [3:53 PM]

jnicol: the tracker is more like a summary spot to link to the forum [3:54 PM]

LFP6: @John: Why not do it like Foldit or such? Tooc omplicated that way? [3:54 PM]

Nando: @macclark52: scripts can't be stopped, you have to kill the tab if it's lost in an endless loop or something like that [3:54 PM]

jnicol: I'm not familiar with the way FoldIt does this [3:54 PM]

LFP6: http://fold.it/portal/feedback [3:54 PM]

LFP6: Basically forums with tracking features. :P [3:55 PM]

macclark52: Endless loop, that's it.  But I do get a message that gives me an option to stop the script.   [3:56 PM]

jnicol: yes, vey nice [3:55 PM]

mr.mola-mola: hi [3:56 PM]

LFP6: I just hate to duplicate, it makes no sense to me, especially as duplication is manual [3:56 PM]

LFP6: VERY easy to miss stuff, I've seen it in the forums [3:56 PM]

LFP6: That's why we need to mine them in the first pace! [3:56 PM]

Eli Fisker: Hi Mola [3:57 PM]

jnicol: ok, thanks everyone for the chat [3:57 PM]

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