2016.01.22 Community Chat

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On DPAT Server Crunching, DPAT FMN Analysis & Paper, DPAT Loop Analysis, New A OR NOT B Logic Gate Lab, Eterna Medicine Tutorial Puzzle Progression Rolling Out & Call to QA!!!, #Issues Tagging, & NUPACK Freeze Bug

Elves: hi folks! [12:01 AM]

jandersonlee: @Jen Amazon has some "free" small instances that might be cheap - will still need to pay for I/O and storage [12:01 AM]

Astromon: Hi Elves!!! [12:01 AM]

Kozilek: your name is colorful! [12:01 AM]

Elves: hey Astro!!! [12:01 AM]

Elves: lol thanks Kozilek, i accidentally fell thru a rainbow [12:02 AM]

jandersonlee: noting accidental I'm sure [12:02 AM]

jandersonlee: you jumped in! [12:02 AM]

Astromon: er gracefully danced through one [12:03 AM]

Kozilek: sounds like an exciting trip [12:02 AM]

Jennifer Pearl: @JR i need over 1 GB of ram currently so I need at a minimum their small instance for Sara but if I crunch the data for all the labs with DPAT i meed up to 17-25BG [12:03 AM]

Jennifer Pearl: GB of ram [12:03 AM]

Elves: oki janderson is right it was entirely intentional [12:03 AM]

Jennifer Pearl: lots of dancing through rainbows [12:03 AM]

Jennifer Pearl: yay [12:03 AM]

jandersonlee: @JP 52GB is some serious stuff. - OK [12:03 AM]

Jennifer Pearl: 25GB [12:03 AM]

jandersonlee: s/52/25/ [12:03 AM]

Jennifer Pearl: oh [12:04 AM]

RedSpah: Hi all [12:03 AM]

Elves: @Jen I got offered an interesting option for crunchingness recently [12:04 AM]

Jennifer Pearl: its handling ove 300 designs will over 300 points for each design at some points [12:04 AM]

Jennifer Pearl: sorry 3000 designs with over 3000 points each [12:04 AM]

Jennifer Pearl: @Elves do tell [12:05 AM]

Astromon: hi Red [12:05 AM]

Jennifer Pearl: it goes up to 25GB in debug mode but usually runing th ecompiled code uses about 17GB consistently [12:05 AM]

Elves: i was hoping eterna could utilize, if not i'm going to throw a hackathon to break these things. ok not break them but they want to push them to their limits with a cool project then write a whitepaper about it... [12:05 AM]

...in exchange for 4 weeks free crunch time & hosting

jandersonlee: NuPACK seems to be running under 500MB for me [12:05 AM]

Jennifer Pearl: It is when I start holding everythig about a design in memory. I hold everything and I mean everything [12:06 AM]

Elves: http://supermicro.com/products/nfo/Xeon_MP.cfm [12:06 AM]

Jennifer Pearl: i need to do some tweaking and have most if it write to disk and make a library [12:07 AM]

Elves: actually i have two options also this unreleased one [12:07 AM]

Elves: http://www.anandtech.com/show/9436/quick-note-intel-knights-landing-xeon-phi-omnipath-100-isc-2015 [12:07 AM]

Jennifer Pearl: I want to use that nice server @Elves [12:07 AM]

Elves: k so we would have to write a whitepaper generally explaining how the server helped us reach our goals, not necessarily publishing the specifics of DPAT [12:08 AM]

Astromon: hmmM great idea [12:09 AM]

Jennifer Pearl: ok [12:09 AM]

Elves: my 3D project may be interested also. so let me know if for sure that is compatible [12:09 AM]

Jennifer Pearl: um [12:09 AM]

Elves: like can the program utilize parallel / gpu / etc [12:10 AM]

Jennifer Pearl: it does not use the GPU [12:10 AM]

Jennifer Pearl: but it uses alot of ram and can use around 30%-50% of a highend CPU [12:11 AM]

Kozilek: what is DPAT?  I'm not familiar with it. [12:11 AM]

Jennifer Pearl: it is a program I worte ot analyze RNA [12:11 AM]

jandersonlee: Dot Plot Analysis Tool? [12:11 AM]

Jennifer Pearl: yes [12:12 AM]

Elves: k cool [12:12 AM]

Jennifer Pearl: @JR you are correct [12:12 AM]

jandersonlee: @JL or @JA @JP [12:12 AM]

Jennifer Pearl: @Kozilek It is specificly a program to analysze the dot plots you see in-game offline [12:13 AM]

Elves: is there a specific data / lab batch you are crunching now? [12:13 AM]

Jennifer Pearl: or JA [12:13 AM]

Jennifer Pearl: sorry  [12:13 AM]

Jennifer Pearl: wait [12:13 AM]

Jennifer Pearl: im so confussed so many J's [12:13 AM]

Astromon: haha [12:14 AM]

Jennifer Pearl: @elves not until this next round of labs is out. But i want to start looking at single oligo mRNA labs  [12:14 AM]

jandersonlee: there is an @JR - not me [12:14 AM]

Jennifer Pearl: I meant you@JL [12:14 AM]

jandersonlee: I guessed so [12:14 AM]

Astromon: I love the Mrna labs<< [12:15 AM]

Elves: ok. did we also ever look into whether we can predict / decipher shape of loops in addition to stacks? [12:16 AM]

Jennifer Pearl: not yet [12:16 AM]

Elves: k that was cool just remembered about it [12:16 AM]

Jennifer Pearl: been so focused other stuff but that is something I want to work on [12:16 AM]

Jennifer Pearl: definitly on my list [12:16 AM]

Elves: if we can use this to get enough data to have a conclusion for an eterna paper that would be a great stepping stone [12:16 AM]

Jennifer Pearl: So about a paper..... [12:17 AM]

Elves: ? [12:17 AM]

Jennifer Pearl: I am working on one right now. Using DPAT i figured out ideal FMN binding site stack lenghts for the EXl and Same stat labs [12:18 AM]

Astromon: Me and jen was able to make quite a few designs using the direction of her programs for the last round<> [12:18 AM]

Elves: excellent!!! [12:18 AM]

Astromon: im exited to see the results! [12:18 AM]

Jennifer Pearl: I forgot to CC you on the email about that [12:18 AM]

Elves: nice team work! [12:18 AM]

Jennifer Pearl: It was fun working with Astro [12:18 AM]

Astromon: Thanks its very fun  [12:19 AM]

Elves: that is great news [12:19 AM]

Jennifer Pearl: @elves check your emnail [12:19 AM]

Jennifer Pearl: email [12:19 AM]

Jennifer Pearl: also doing a GetSat [12:20 AM]

Elves: cool thanks! [12:20 AM]

Jennifer Pearl: @elves when you have time lets get together and hash out some of the stugff for figuringout loops from dot plots [12:20 AM]

Elves: I'm really happy to hear this, that is great progress, big high five :) [12:20 AM]

Jennifer Pearl: key phrase "When you have time" [12:21 AM]

Elves: ahahahaha [12:21 AM]

Jennifer Pearl: thanks [12:21 AM]

Elves: hahahah [12:21 AM]

Elves: ahah [12:21 AM]

Elves: ha [12:21 AM]

Elves: aha [12:21 AM]

Elves: :D [12:21 AM]

hoglahoo: machinelves.exe has crashed [12:21 AM]

Elves: lol [12:21 AM]

Jennifer Pearl: needs  rebot [12:21 AM]

Jennifer Pearl: reboot [12:22 AM]

Astromon: We need to get one of those magic remotes for Elves [12:22 AM]

Elves: thanks, you are true friends to shell in and bring me back to life [12:22 AM]

Astromon: this loop anylasis sounds interesting id like to learn about it also sometime [12:24 AM]

jandersonlee: does anyone have any ideas on the new logic sublabs (e.g XNOR (TFFT) or A AND NOT B (FTFF)) [12:24 AM]

Astromon: great question [12:24 AM]

Astromon: im working on the first sublab still [12:25 AM]

Astromon: havnt had much time to yet though maybe 3 hours [12:25 AM]

Elves: agreed great question janderson [12:25 AM]

Astromon: it freezes on me [12:25 AM]

Astromon: but i have found a solution to that [12:26 AM]

jandersonlee: Is there a getsat page with suggested arrangements? [12:25 AM]

Astromon: i save whenever i like where i am in a puzzle [12:26 AM]

Astromon: then when it freezes i just go back to that piont [12:26 AM]

jandersonlee: (what Eli would call geometries I think) [12:26 AM]

Astromon: And adminastrater here [12:26 AM]

Astromon: any? [12:27 AM]

LFP6: Hey all, sorry I'm late! [12:26 AM]

Astromon: next week i guess will be dev led meeting [12:27 AM]

Elves: taking a look at the lab, sounds like it's a new flavor of logic gate to tackle [12:27 AM]

Elves: hey lfp6! :) [12:27 AM]

Jennifer Pearl: ni idea right now [12:27 AM]

Astromon: yeaH Elvews [12:27 AM]

Kozilek: @ jandersonlee - Astro and I were talking about a bug on the A And Not B puzzle [12:27 AM]

Kozilek: when you paste in sequences [12:27 AM]

Astromon: i had success in the first round of these logics [12:28 AM]

Astromon: Hi Lfp6 [12:28 AM]

Jennifer Pearl: I could lok at the states with a singel oligo and take a loot at those maybe [12:28 AM]

Elves: here's the truth table for A OR NOT B https://en.wikipedia.org/wiki/Converse_implication [12:28 AM]

Elves: from the lab description [12:28 AM]

LFP6: Hey, have you all checked out the new EteRNA Medicine puzzle progression? If not, you should and give your feedback :) [12:28 AM]

Jennifer Pearl: brb [12:29 AM]

Astromon: give jl that sequence Koz [12:28 AM]

LFP6: https://getsatisfaction.com/eternagame/topics/new-puzzle-progression?topic-reply-list%5Bsettings%5D%5Bfilter_by%5D=all&topic-reply-list%5Bsettings%5D%5Breply_id%5D=16521725#reply_16521725 [12:29 AM]

LFP6: I keep forgetting I need to shortlink these things >.< [12:29 AM]

Xnessax: Hiii [12:29 AM]

jandersonlee: I think I know the "logic" of it but I'm fuzzy on design options [12:29 AM]

Elves: thanks LFP6! [12:29 AM]


Elves: hi Xnessax [12:29 AM]

Xnessax: Hi Elves!! [12:29 AM]

LFP6: Oh [12:29 AM]

Xnessax: I miss you. Internet was broken. [12:30 AM]

LFP6: THere's a news article [12:29 AM]

LFP6: http://www.eternagame.org/web/blog/6468765/ [12:30 AM]

Astromon: Hi nessa! [12:30 AM]

LFP6: Thats a shorter link lol [12:30 AM]

Elves: @janderson yes it would be great to have a landing strip areas matched / defined visually like Eli did, if that's what you mean [12:30 AM]

Xnessax: Hi I finished my manga. [12:30 AM]

Astromon: oH i was wondering where ud been<> [12:30 AM]

Xnessax: @astrmon [12:30 AM]

Xnessax: well it s in all portuguese, i will show up it to my friends and up to studio or something [12:30 AM]

Xnessax: Its almost like with matching a theme in contest "Friendship and Communication Tools" [12:31 AM]

Astromon: oH Thats great news [12:31 AM]

Xnessax: I went to my capital around to get in my psiciology and learning with her and talking in voice and sign languages. [12:31 AM]

Xnessax: Yes thanks. [12:31 AM]

Xnessax: Today's a Dev [12:32 AM]

jandersonlee: Today is Player's Chat - next week is Dev Chat [12:32 AM]

Astromon: yup its Dev meeting time YAY that means its friday [12:33 AM]

Xnessax: Thousand Words Of Love. Friendship, known hearts and feelings. [12:32 AM]

Elves: LFP6 many thanks, yep Ben & team have made great progress on new style of eterna tutorial intro, so playing with that will help us find last minute bugs and improvements [12:32 AM]

Elves: @Xnessax that sounds beautiful! :) [12:33 AM]

Jennifer Pearl: im back [12:33 AM]

LFP6: I have a  lot of feedback... It's such a mess though I haven't submitted it yet [12:33 AM]

LFP6: Like, 5 pages in A GDoc of random half-coherent notes [12:33 AM]

Elves: cool LFP6 thanks very much for your efforts! [12:33 AM]

RedSpah: How can I playtest the new tuts? [12:33 AM]

Elves: lol [12:33 AM]

LFP6: Link Red [12:33 AM]

LFP6: http://www.eternagame.org/web/blog/6468765/ [12:33 AM]

Elves: just number each thought and you'll sort it out [12:33 AM]

Astromon: they are way fun tuts for sure and challenging [12:34 AM]

Jennifer Pearl: im going to be back and forth. I have a guest over [12:34 AM]

LFP6: I'm trying to categorize everything [12:34 AM]

LFP6: But I'm running into some issues where I'm getting into some stuff that might not be appropriate for this (ie out of the scope of just the tuts) [12:34 AM]

LFP6: But I'm working through it [12:34 AM]

RedSpah: thanks (anonymous) http://prntscr.com/9til33 [12:35 AM]

LFP6: lol [12:35 AM]

Xnessax: Thanks @Elves [12:35 AM]

Xnessax: What's about Dev?  [12:35 AM]

Elves: lol Red [12:36 AM]

RedSpah: 2nd tut gives no points [12:36 AM]

LFP6: Can someone help me straighten out my mind? I'm starting to see papers of mental thought flying around everywhere [12:37 AM]

Elves: Xnessax there is a new eterna puzzle series to intro new players, that we can test out before it gets released [12:37 AM]

RedSpah: and "Locked bases" could use some discription [12:37 AM]

Astromon: we have talked about ideas for server time , jen -pearls D3-PaT and other programs, and lffp6 showed the new trutotials  @Xness [12:38 AM]

jandersonlee: Perhaps by the time you finish all the (new) tutorials you should get you lab badge regardless of points? [12:37 AM]

LFP6: Probably [12:37 AM]

RedSpah: like "Bases with a keylock on them are locked, and can't be modified." [12:38 AM]

Xnessax: @Elves it looks like fun!! [12:38 AM]

jandersonlee: Assuming that you should have the rquired knowlede [12:38 AM]

Elves: lfp6 keep each suggestion to 1-2 sentences max and anything more complex make as a note for tangential improvement [12:38 AM]

LFP6: Very good idea, thanks [12:38 AM]

Elves: janderson good idea [12:38 AM]

Astromon: oH its not released way cool [12:39 AM]

LFP6: @Astro: What do you mean by "ideas for server time"? [12:38 AM]

Elves: i think that labs evolve so quickly we'll never have all the training needed [12:38 AM]

Elves: so the main thing is to learn the basics first [12:39 AM]

Elves: i'm not sure, i thought it was a test server [12:39 AM]

Elves: @Red good point [12:39 AM]

LFP6: The most important thing I noticed with the new puzzles is a lack of explanation. The concepts are there, but I think it's still a problem of players not understanding concepts [12:40 AM]

Astromon: getting internet connection free for players that are developing important tools for Eterna [12:41 AM]

LFP6: Still not completely sure what that means... I'll look at the logs I guess [12:40 AM]

Elves: some states have free internet programs for low income  [12:41 AM]

Astromon: Thats what i usuallt do :P [12:41 AM]

LFP6: Ah [12:41 AM]

LFP6: Doesn't everyone have itnernet here though...? [12:41 AM]

Astromon: nope<> [12:42 AM]

RedSpah: Brourd uses an owl to send packets [12:42 AM]

Elves: LOL [12:42 AM]

LFP6: lolz [12:42 AM]

Astromon: haha [12:42 AM]

Kozilek: IP over Avian Carriers? [12:43 AM]

Elves: good point of ensuring concepts come across. the tuts are visual demos which helps but knowing why x goes to y is important especially for complex labs [12:43 AM]

LFP6: Exactly [12:43 AM]

Elves: is it an african or european owl? [12:43 AM]

LFP6: heh [12:43 AM]

RedSpah: IP/AC, this is the future [12:43 AM]

Astromon: its a hOOt owel [12:43 AM]

Elves: can it carry coconut sized packets!!! [12:43 AM]

LFP6: I think the tutorials still leave a lot unspecified, and could still lead to some random guessing, as opposed to educated decisions [12:43 AM]

Nando: a famous RFC, that Avian Carrier one :D [12:43 AM]

RedSpah: Hi Nando [12:43 AM]

Elves: hey Nando :) [12:44 AM]

Nando: hi guys [12:44 AM]

LFP6: Ey Nando [12:43 AM]

Astromon: Hey Nando! [12:44 AM]

Kozilek: Homing pigeons with micro SD cards.  Not bad if you don't mind the bird droppings. [12:44 AM]

LFP6: Off of my thoughts about the tuts & concepts, personally I think that we can no longer use the existing gamification structure. As I understand it, at this point it isn't really that useful to just "solve puzzles" using the game interface/energy model. This is only a tool [12:44 AM]

Jennifer Pearl: im back for a bit [12:44 AM]

Elves: hey wb Jen! [12:44 AM]

LFP6: And we need to teach players to use as many tools as possible to make designs that work [12:44 AM]

RedSpah: or Dropped Packets due to Wildlife [12:44 AM]

LFP6: Analyse, design, etc [12:44 AM]

Astromon: for sure @Lfp6 [12:45 AM]

Astromon: wb jen [12:45 AM]

Jennifer Pearl: Ive been away for a few minutes. If you have somehitng you want to track remebr to add a hashtag in chat and I will search through the transcript leter [12:45 AM]

LFP6: Scoring model doesn't work with that, and the tutorials are still more focused on puzzle "solving" [12:45 AM]

Elves: yes, analysis and concept comprehension need to receive gamification ( pints + breakdown into concrete achievable steps ) [12:45 AM]

RedSpah: just reminded myself of something [12:45 AM]

Elves: *points [12:45 AM]

Nando: I like pints :D [12:45 AM]

Jennifer Pearl: going to be working on the issue track the next couple of weeks [12:46 AM]

Jennifer Pearl: !@elvs did you catch that? [12:46 AM]

RedSpah: does the engine still commit suicide if you try to create a 0-base loop? [12:45 AM]

Elves: lol [12:46 AM]

Elves: yeah, there are suggestions about #issues near the part about tutorials / puzzle progression earlier [12:46 AM]

LFP6: @Jennifer: How will this fit in with the forums, which are supposed to be used for official tracking (once I, you know, finish categorizing all the old stuff which has taken way too long) [12:46 AM]

Elves: good reminder, thanks Jen! [12:46 AM]

jandersonlee: https://tools.ietf.org/html/rfc2549 April 1, 1999 [12:46 AM]

Nando: haha, yep JL, that's the one :) [12:47 AM]

LFP6: Nice [12:47 AM]

Jennifer Pearl: this tracker is just for issues that come up durrin gDev chat like question adn things that would nto quite merit a GetrSat i think,. I am still trying to figure out how I really wnt to do it [12:47 AM]

RedSpah: I have a tut proposal [12:47 AM]

jandersonlee: Still it's hard to beat the bandwith of a stationwagon full of hard drives [12:47 AM]

RedSpah: you should disable dopt plot and melt curve keyboard shortcut [S] for tutorials  [12:48 AM]

LFP6: @Jennifer: Would also be good as a pre-queue for GetSat just to hold things before writing them up, possible [12:48 AM]

Jennifer Pearl: nice idea [12:48 AM]

Jennifer Pearl: ill look into that [12:48 AM]

LFP6: @Red Yeah, I ran into that a couple times [12:48 AM]

Jennifer Pearl: away again for a moment [12:49 AM]

Elves: k i'm going to wrap this chat up and get it posted then, as i must away on my fine rainbow steed or some such somethingness [12:49 AM]

Elves: thanks everyone for coming, and check out the puzzle progression! [12:50 AM]

Elves: feel free to keep chatting. alas, i have shoes to cobble [12:50 AM]

Astromon: @ nando I have been woring on the first sublab in the gate series  Nupak seems to be working faster but it frequently freezes on me [12:51 AM]

Astromon: i save sequences i wish to go back to once it frezzes now as the solutiuon [12:51 AM]

Astromon: is this just happenning to me er anyone else? [12:52 AM]

Nando: @astro: known problem I believe, I mentioned elsewhere it's very hard to pinpoint the problem, specially for me because it freezes exceedingly rarely on my machine [12:52 AM]

jandersonlee: occasionally - I thought it was my anchient laptop [12:52 AM]

Astromon: oH what machine do you have  [12:53 AM]

jandersonlee: 4G Lenovo T410 [12:52 AM]

Astromon: my styf is brand new and no other labs does this so i dunno heheh [12:53 AM]

Nando: I'm on a MacBook Pro, fairly recent [12:54 AM]

Astromon: ya think i just need more ram memory then? [12:54 AM]

Astromon: mine is just 4gb i beleive [12:54 AM]

jandersonlee: I don't know. Check the TaskManager while running [12:55 AM]

jandersonlee: or top (linux) [12:55 AM]

Astromon: but good job anyways getting it wo work faster [12:55 AM]

Astromon: that slow motion couple rounds ago was unbearable [12:55 AM]

jandersonlee: lunch is over - later folks [12:56 AM]

Elves: cheers! [12:57 AM]

jandersonlee: nich chatting [12:56 AM]

Astromon: is there a usb stick that boosts ram er do i have to open my laptop to add ram? [12:57 AM]

jandersonlee: nice* [12:56 AM]

Elves: likewise! :) [12:57 AM]

Astromon: seeya JL [12:57 AM]