2013.12.04 Dev Chat
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On Spam & Issue Tracking
jeehyung: Hello all [3:05 PM]
jeehyung: welcome to bi-weekly Eterna dev chat [3:05 PM]
Eli Fisker: hi Jee :) [3:06 PM]
jeehyung: Sorry I'm late! [3:05 PM]
Eli Fisker: Glad you are here [3:06 PM]
jandersonlee: hello Jee - we don't mind waiting [3:06 PM]
jeehyung: Hi Eli, janderson : ] [3:06 PM]
jeehyung: Just a quick reminder before we start [3:06 PM]
jeehyung: The monthly Eterna meeting with Das lab will start this Friday. We'll use live streaming service which you can view on the Youtube. The meeting content will be left on the Youtube so those who can't attend will be able to view it later [3:07 PM]
machinelves: yay! thank you! :D [3:07 PM]
jandersonlee: have you got the 100 subscribers yet? [3:07 PM]
jeehyung: @janderson it turns out we don't need 100 subscribers. We deleted that news : ] [3:08 PM]
jandersonlee: ah great! [3:08 PM]
Eli Fisker: Good :) [3:08 PM]
jeehyung: Also, those who signed up for the Eterna development - we have your dev package ready. We just need some documentation - we'll probably send the instruction tomorrow. [3:08 PM]
hoglahoo: that is good news [3:09 PM]
machinelves: awesome! [3:10 PM]
jeehyung: Done with the new from our end. Please throw in any question or suggestion as usual! [3:10 PM]
machinelves: I would like to express a serious concern about trolls who may be harassing children. players have requested an urgent priority to increase the # of chat moderators, scouting volunteers from veteran regulars so that someone is always available to boot ne'er-do-wells [3:10 PM]
machinelves: and you should be aware there has been a year long campaign to infiltrate & gather intel, judging from account & wiki records [3:10 PM]
jandersonlee: if so, we need some guidelines too [3:11 PM]
machinelves: agreed [3:11 PM]
Eli Fisker: I agree very much with Machine [3:11 PM]
jeehyung: @machinelves thanks for biringing that up. Ever since our chat server had to be reprogrammed, our ban feature seems to have a problem. We'll gather more chat moderators once we get ban system settled [3:11 PM]
machinelves: i recommend a clear post of chat guidelines, with an emergency number to a children welfare hotline [3:11 PM]
machinelves: thank you. [3:11 PM]
jandersonlee: @jee any work on switch return timing? [3:12 PM]
jandersonlee: *word* [3:12 PM]
jeehyung: We'll discuss what we can do with the chat moderation in general with out budget in the team meeting this week. [3:12 PM]
machinelves: awesome, thank you [3:12 PM]
Eli Fisker: I will also like to point to a suggestion from Mat on the same note as what Machinelves is saying: [3:12 PM]
Eli Fisker: https://getsatisfaction.com/eternagame/topics/chat_trolls#reply_13395891 [3:13 PM]
jeehyung: @janderson Not yet..unfortunately we need to test puzzles in which you can add/delete bases in certain region first. So we are putting our efforts on that type right now [3:13 PM]
machinelves: Eli I agree, I would like a running record of offending handles & IPs [3:13 PM]
Eli Fisker: And Jee I'm very pleased to hear that you are taking up chat moderators on a coming meeting [3:13 PM]
jeehyung: @Eli Thanks for the pointer. [3:13 PM]
Eli Fisker: np [3:14 PM]
hellooooo: http://eterna.cmu.edu/web/news/3602467/ [3:14 PM]
machinelves: also, assume trolls are monitoring all public communication... this chat for instance :-P [3:15 PM]
hellooooo: Do the bot peeps talk [3:15 PM]
machinelves: http://prntscr.com/28rjqc [3:16 PM]
hellooooo: come on Machine i quit all the bad ones just pleasssssse [3:17 PM]
hellooooo: stop [3:17 PM]
machinelves: regarding priorities of issues, mat suggested a central roadmap to track global status & priority of active issues [3:17 PM]
machinelves: i think this is a good idea, i was wondering are the milestones or issues in github in order of priority? or is there another priority function in github? [3:18 PM]
jeehyung: @machinelves thanks this is really helpful [3:17 PM]
jandersonlee: @Jee what is the priority of scripting and bit competitions? [3:18 PM]
jandersonlee: *bot competitions* [3:18 PM]
machinelves: for example, here is a very simple implementation i made in the wiki using mat's example: http://eternawiki.org/wiki/index.php5/Issue_Roadmap [3:18 PM]
hellooooo: http://eterna.cmu.edu/web/news/3602467/ [3:19 PM]
jeehyung: @janderson Right now the bot competition people are working on integration with NOVA. I think the bot competition will happen after the integration is done [3:20 PM]
hellooooo: Im sorry machine [3:20 PM]
jeehyung: @machineleves noted. I like the way tasks are organized by priorities [3:20 PM]
machinelves: this serves 2 primary functions: 1) priorities 2) status [3:21 PM]
jandersonlee: @jee NOVA - is that for teaching in the classrooms? [3:21 PM]
machinelves: thanks hellooooo, i appreciate your fellow concern for our community [3:21 PM]
jeehyung: @janderson yes. Eterna will be part of an online education that NOVA offers. [3:21 PM]
hellooooo: I will be a good boy [3:22 PM]
machinelves: re: NOVA super cool!!! [3:23 PM]
Eli Fisker: :) [3:23 PM]
Eli Fisker: Agree, Machine [3:23 PM]
hellooooo: You can call me mike [3:24 PM]
Eli Fisker: They have made my all time favorite teaching video on RNA [3:24 PM]
jandersonlee: @Jee and the citizen-science paper idea that was to be tied to cloud labs? seems liek most labs don't have followups (mine included) [3:25 PM]
jeehyung: @janderson in fact, there is one about to be submitted from Das lab. I believe there is one another about the Influenza sequences. [3:26 PM]
jandersonlee: cool [3:26 PM]
jeehyung: They are still in preparation - usually papers take 1 or more years to get published : [ [3:26 PM]
hoglahoo: hellooooo: nice to meet you Mike [3:26 PM]
Eli Fisker: And here is that NOVA RNA video, should there be anyone here who have not seen it yet: [3:27 PM]
Eli Fisker: http:// www.you tube.com/watch?v=uiObPBeof5s [3:27 PM]
Eli Fisker: and wants to [3:27 PM]
jeehyung: Thanks for the link Eli. [3:27 PM]
jandersonlee: Eli Mat and I are working on data-mining - still in beta test but some info on the wiki [3:27 PM]
Eli Fisker: Jee, yep. We have learned :) and always happy to help [3:28 PM]
machinelves: @jee also, noticed that there is an account Nando, potentially posing as our ElNando888, I confirmed with him that this is not his account, has 0 points. since ElNando888 appears in chat as Nando, everyone should be aware of potential social engineering to gather PMs intended for ElNando888 http://eterna.cmu.edu/web/player/124111/ [3:27 PM]
machinelves: Eli, thanks! [3:28 PM]
Eli Fisker: @Jee, Jandersons tool is cool. I can now dig up data from all over our labs [3:28 PM]
machinelves: @janderson really cool what you're working on, i only got a peek before i got pulled into wiki, but very exciting, thanks for all your work! [3:28 PM]
Eli Fisker: Which is why I have been complaining less recently about not being able to watch our data the way we usually can. We can only when labs are up for voting. [3:29 PM]
jeehyung: @machine noted [3:28 PM]
jeehyung: @janderson that's really cool. Can you send us a link too so we can take a peek? [3:29 PM]
hoglahoo: machinelves: I created that Nando account [3:29 PM]
Eli Fisker: So now we can compare loops and barcodes across many labs [3:29 PM]
machinelves: thanks hogla, i was hoping it was a joke [3:29 PM]
hoglahoo: partly to prevent what you just noted :) [3:29 PM]
machinelves: good good, thanks for coming forward, puts my mind at ease :D [3:30 PM]
hoglahoo: well, I noted that someone could use the account to chat as him without being him and thought to grab it [3:30 PM]
jandersonlee: http://eternawiki.org/wiki/index.php5/LabDataMiner includes a link to the latest stable version [3:30 PM]
Eli Fisker: Nice of you, Hogla. [3:30 PM]
Eli Fisker: Apprechiated [3:30 PM]
machinelves: very smart thinking ahead :) [3:31 PM]
jeehyung: @janderson - thanks! [3:31 PM]
jandersonlee: @jee np - suggestions welcome (though Mat and Eli usually have plenty of those) [3:32 PM]
Eli Fisker: hehe [3:32 PM]
Eli Fisker: guilty [3:32 PM]
Eli Fisker: :) [3:33 PM]
Eli Fisker: I have been using it lately when designing for lab [3:34 PM]
Eli Fisker: to dig out good elements [3:34 PM]
Eli Fisker: from past labs [3:34 PM]
jandersonlee: likewise [3:34 PM]
jandersonlee: will be intersting to see if the results are repetable [3:34 PM]
jandersonlee: *repeatable* [3:34 PM]
Eli Fisker: Yep [3:35 PM]
hellooooo: Hey Machine and Eli i just sent you both invites to my group and before u say no look at the description [3:35 PM]
machinelves: FYI i've made an initial attempt to outline the Issue tracking protocol. it could be simplified into strictly the tracking portion, but i thought it might be good to familiarize players with the research & communication stages of issue development, to prevent unresearched issues from being entered directly into the system. this whole dealio is still under development, but anyone can take a peek if they want: http://eternawiki.org/wiki/index.php5/Issues [3:35 PM]
hellooooo: http://eterna.cmu.edu/web/group/3551976/ [3:35 PM]
hellooooo: cool [3:36 PM]
Eli Fisker: Machine, I think the last part of your sentence got cut off [3:37 PM]
machinelves: last word? [3:37 PM]
hellooooo: Yeah it ends with "but anyone" [3:37 PM]
machinelves: but anyone can take a peek if they want: http://eternawiki.org/wiki/index.php5/Issues [ [3:37 PM]
machinelves: thanks [3:37 PM]
Eli Fisker: np [3:37 PM]
jeehyung: @machine thanks will definitely take a look [3:38 PM]
machinelves: @janderson sage point on repeatability [3:38 PM]
jandersonlee: have to be carefult though - if we always repeat we cease to learn as much [3:39 PM]
machinelves: @jee thanks! and no rush on this, some other things have higher priority [3:39 PM]
Eli Fisker: Good point JL [3:39 PM]
machinelves: hehe true. it is a science bugaboo though that ability to reproduce results declines over time in general, so i like to keep an eye on this stat [3:40 PM]
Eli Fisker: I don't reuse all elements but only some and experiment where I wish to see what works best. [3:41 PM]
Eli Fisker: Element reuse can sort of be used to be sure to make part of a design stable so one can better experiment elsewhere [3:41 PM]
jandersonlee: Like a stable core to test hairpin designs [3:41 PM]
Eli Fisker: Good point, JL [3:42 PM]
jandersonlee: where have I seen that idea... hmmm. [3:41 PM]
hellooooo: does anyone wanna join my group called SWAGTASTIC its for swagalicious people who love eterna [3:42 PM]
Eli Fisker: ;) [3:42 PM]
Brourd: I'm not entirely sure if seeing the SHAPE signal for various random loop sequences can tell you much. [3:42 PM]
Eli Fisker: hi Brourd [3:43 PM]
hellooooo: Hi Brourd [3:43 PM]
jandersonlee: @Jee any news on partcular RNA structure being tested by the labs? [3:43 PM]
jeehyung: Hi Brourd [3:43 PM]
jeehyung: @janderson you mean by the labs other than Das lab? [3:43 PM]
jandersonlee: @Broud - by itself, possibly not [3:44 PM]
Brourd: Hey Eli, hellooooo, Jee, janderson! How are you today? [3:44 PM]
hellooooo: Not Bad. My leg hurts a bit [3:44 PM]
jandersonlee: @Jee Das and partner projects - you started opening up projects to other labs... [3:44 PM]
Eli Fisker: Fine here [3:45 PM]
jandersonlee: @Broud fine thanks [3:45 PM]
hellooooo: @Broud How are you [3:45 PM]
jandersonlee: @Brourd - repeat typos... [3:45 PM]
machinelves: hey brourd, glad to see you [3:45 PM]
Brourd: @ janderson - now, using a system similar to the competing hairpins project by matthew seetin, yes, you can learn a little bit from comparing hairpin sequences. [3:45 PM]
jeehyung: @janderson You'll start hearing some updates from Das lab & associates in the monthly Eterna meeting. [It'll be available as youtube item) [3:45 PM]
jandersonlee: @Jee ah - will try to catch taht then [3:46 PM]
Brourd: hi machinelves [3:46 PM]
mat747: hi all (no reply needed) [3:47 PM]
machinelves: re: the friday meeting, is this a watch-only for players, or is there a forum / channel for questions, or ? [3:48 PM]
Brourd: @ Jee - how goes the development of the puzzles where we can add/delete nucleotides to the structure? [3:48 PM]
jeehyung: hi mat [3:49 PM]
jeehyung: @machine you'll be able to post questions in real time as well. [3:49 PM]
mat747: Hi Jee [3:49 PM]
jeehyung: Although there is 30-40 sec delay between players and presenter [3:49 PM]
Brourd: hey mat [3:50 PM]
jeehyung: @Brourd we hope to have something up for testing next week. [3:50 PM]
machinelves: @jee thanks! through youtube? does that require the infamous G+ account lolz? [3:50 PM]
hellooooo: Hey mat [3:50 PM]
mat747: Hi Brourd, hello [3:50 PM]
Nando: hi everyone [3:51 PM]
Brourd: Good news Jee, look forward to that. [3:51 PM]
Eli Fisker: hi Mat and Nando [3:51 PM]
machinelves: hey nando, mat :) [3:51 PM]
jeehyung: hi Nando [3:51 PM]
Brourd: Hey Nando [3:51 PM]
Nando: @jee: has any work started on alternative lab scoring modes? [3:51 PM]
jeehyung: @machine you don't need account to watch. But you'll proabably need one to ask question during the meeting [3:52 PM]
mat747: Hi Eli, Machine, Nando [3:52 PM]
machinelves: @jee right right, thank you for the clarification. thanks for putting this together, very cool :) [3:52 PM]
hellooooo: @Brourd ur top player? [3:53 PM]
jeehyung: @Nando, it's sort of up there.. You can actually pick any script to score submitted designs from the lab page. But we haven't quite polished it to be used for rewards. Thanks for bringing that up though. I think it just needs a little push.. [3:53 PM]
jeehyung: All, I'll have to leave in 5 minutes - please throw in final questions & suggestions! [3:53 PM]
Brourd: I believe my top player would be Eli, followed closely by hoglahoo then Nando. [3:54 PM]
Nando: ok thx, Jee [3:54 PM]
hellooooo: I Got To Go :( [3:54 PM]
Nando: I see myself more as a top script-butcher... [3:55 PM]
machinelves: @jee PM with final question [3:55 PM]
machinelves: [ private ] [3:55 PM]
machinelves: bye hellooo thanks for making an effort [3:56 PM]
hellooooo: Bye machine,Nando,Brourd,Jee,Eli,Mat, and everyone else [3:56 PM]
Brourd: later [3:57 PM]
mat747: bye [3:57 PM]
machinelves: @jee thanks, received [3:58 PM]
Nando: if you're really bored Jee, I have a microscopic issue with switch handling... [3:58 PM]
Brourd: It's a trap! [3:58 PM]
Nando: it's "presented" in that puzzle: http://eterna.cmu.edu/web/puzzle/3510358/ [3:58 PM]
jeehyung: @Nando Oh what is it? [3:58 PM]
Nando: a matter of "logic", if you will [3:59 PM]
machinelves: lol [3:59 PM]
Nando: this 3-states puzzle should not be valid... [3:59 PM]
Nando: but as I said, it's only for those times when you feel so totally bored [4:00 PM]
Nando: really, ignore that as long as there's something better to do, like have a beer or something [4:00 PM]
jeehyung: @Nando sorry I'm not sure how this puzzle is invalid : [ [4:00 PM]
Brourd: I believe nando means In vitro [4:01 PM]
Nando: no Brourd, in silico [4:01 PM]
Brourd: wait, maybe this is another, lol [4:01 PM]
Nando: @Jee, I'll do a write-up on the wiki and I'll PM you the link [4:01 PM]
Brourd: not the one about the multiple binding sites bonus thing, I see ;P [4:02 PM]
jeehyung: @Nando that'll be great. I'll see if I can figure this one out too : ] [4:02 PM]
machinelves: @nando does wiki wiziwig support sortable tables do you know? i saw you can enter specific values but haven't had luck yet [4:02 PM]
Nando: @B: this one is a better version of the multiple binding issue [4:02 PM]
hoglahoo: which state will the FMN bind to? [4:02 PM]
jeehyung: Ahhhhhhh [4:02 PM]
hoglahoo: since it appears in more than one state in a separate loop [4:03 PM]
hoglahoo: different loop* [4:03 PM]
Nando: that's the point, yes [4:03 PM]
jandersonlee: why not both? [4:03 PM]
jeehyung: Thanks or the clarification hoglahoo. Yeah, this is definitely a bi-product of binding bonus hack [4:03 PM]
Nando: if in silico, you may assume one FMN molecule, or many [4:03 PM]
hoglahoo: behold the power of Nando: jee stays past the closing hour [4:03 PM]
machinelves: @nando are you saying there are more than 3 potential forms for this molecule? [4:04 PM]
Nando: in both cases, this puzzle is a 2-states, not 3 [4:04 PM]
machinelves: hehe [4:04 PM]
machinelves: @nando so not 4 states? [4:04 PM]
Nando: nope [4:04 PM]
jeehyung: Ok really gotta go now. Thanks for pointing this out Nando. Will definitely think about this.. [4:04 PM]
machinelves: AB AC DB DC? [4:05 PM]
Eli Fisker: Bye Jee [4:05 PM]
machinelves: bye jee, thanks! [4:05 PM]
jandersonlee: unless FNM is very dilute... [4:05 PM]
Nando: bye Jee [4:05 PM]
machinelves: many thanks to the team too!!! [4:05 PM]
Brourd: hmmm, I still see this as more of an in vivo issue, since the 2nd state could use a different aptamer. Your digital molecule isn't required to bind to any specific sequence or loop. [4:06 PM]
Nando: if you assume 1 FMN and BoundA better than BoundB, then the solution is {Unbound, BoundA}, or if you assume multiple FMN, then the solution is {Unbound, BoundA&B} [4:06 PM]
Brourd: Just to any general internal loop. [4:06 PM]
jandersonlee: @Nando - concur [4:07 PM]
jandersonlee: nice catch [4:07 PM]
machinelves: @nando, thanks, interesting. i am new to the science behind the folding process [4:07 PM]
Nando: @B: yes, I'm looking at perfectly defined binding sites [4:07 PM]
Brourd: Simply put, it is just a matter of how a puzzle is presented. [4:08 PM]
Brourd: I knew it! [4:08 PM]
mat747: jee - thx for adding the chat log [4:08 PM]
Nando: which, by the way, makes me doubt about the validity of any puzzle without perfectly defined binding site... [4:08 PM]
Brourd: Yep :) [4:08 PM]
Nando: but that's another story ;) [4:08 PM]
Brourd: One way to fix this, of course [4:08 PM]
hoglahoo: remove all switch puzzles? [4:09 PM]
Nando: no, just implement them very strictly :) [4:09 PM]
jandersonlee: ok, two ways :P [4:09 PM]
Brourd: would be to apply the binding bonus to a specifc loop, and then all instances of that loop would theoretically be considered bound in the free energy landscape. [4:10 PM]
hoglahoo: is "the free energy landscape" a fancy name for the place where we usually play or is it something different [4:10 PM]
Brourd: For example, if I apply the binding bonus to loop NNN/NN, then all identical instances of said loop can also bind the digital molecule. [4:10 PM]
Nando: if I understand you correctly, then that's what I did in Vinnie, B [4:11 PM]
Nando: yes, B, and that's a terrible mess! :D [4:11 PM]
Nando: if you use N's [4:11 PM]
Brourd: So, if I had a GUAA/CAAAA loop bound with a bonus, any instances of said loop within -4.9 kcal of the MFE could potentially be more stable than my ON state. [4:12 PM]
jandersonlee: right. that's how I work it too [4:12 PM]
Brourd: Yeah, that would be a mess, for a loop without a defined sequence. [4:12 PM]
Brourd: However, upon submitting the puzzle, said loop could be defined (I guess). Although, this system would definitely lead to some rather nasty puzzles... [4:13 PM]
Nando: well, as I said before, it's a boring technicality at this point, but I know of some sneaky lab admins who could design a lab with "special properties"... :P [4:13 PM]
Brourd: Those sneaky lab admins! [4:14 PM]
Nando: :D [4:14 PM]
Brourd: With their quadruple nested FMN binding pseudoknots :P [4:14 PM]
Nando: lol [4:14 PM]
Nando: ok fellas, time for me to hit the sheets, g'night [4:16 PM]
Brourd: later nando [4:16 PM]
greensun: hello [4:17 PM]
hoglahoo: hi [4:18 PM]
machinelves: thanks everyone. got to go. hope you have a great day! :) [4:21 PM]
hoglahoo: see you [4:22 PM]
greensun: you too [4:22 PM]
Brourd: later machinelves [4:22 PM]
machinelves: bye! :) [4:23 PM]
