2014.05.21 Dev Chat
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On Welcoming Jnicol!
jnicol: Hi everyone, welcome to dev chat! [3:00 PM]
machinelves: hello! yay! huge congrats jnicol, we are so lucky to have your help! :D Jee, we will miss you. thank you so much for organizing a smooth handoff. and Eli says hello, he cannot make it to this dev chat, but wanted to express big congratulations and gratitude :) [3:00 PM]
jnicol: Jee will probably arrive, but if anyone has any questions for me? [3:01 PM]
rhiju: hi jnicol and everyone! full agreement with machine [3:01 PM]
LFP6: I second that motion. :D [3:01 PM]
jnicol: thx all :) [3:02 PM]
machinelves: hi rhiju! yay, it's a party :D [3:02 PM]
LFP6: So, welcome in to Jnicol, and glad to see Rhiju with us. [3:02 PM]
rhiju: we're happy to take questions [3:02 PM]
rhiju: or we can ask em [3:02 PM]
LFP6: Well, if you care to see the random bug I found (a contradiction in typo, if you will): https://getsatisfaction.com/eternagame/topics/a_requires_optional_field [3:02 PM]
TomoeUzumaki: hey rhiju!! [3:02 PM]
TomoeUzumaki: there goes my homework. [3:03 PM]
LFP6: :) [3:03 PM]
TomoeUzumaki: =D [3:03 PM]
hoglahoo: When can we start pestering John like we do jee? [3:03 PM]
TomoeUzumaki: hahah hog [3:03 PM]
machinelves: jnicol the chief question I've been getting is about issue intake player side. my understanding is that this will be addressed once you've received full handoff of the project, and have chosen your preferred issue tracker / workflow. if you could please confirm or correct, that will put some players at ease on the schedule of this [3:03 PM]
jnicol: today :) [3:03 PM]
jnicol: That is correct, I am still officially in training [3:04 PM]
LFP6: I also heard (from Rhiju or Jee, I think) that there was an iea of a new tracker to use, do you know about that? [3:04 PM]
machinelves: awesome, thanks! [3:04 PM]
Brourd: Unofficially? [3:04 PM]
wbt: Congrats on the new position. [3:03 PM]
TomoeUzumaki: what are the trackers? [3:04 PM]
jnicol: Since we have Rhiju now, we should probably ask some questions for him now, then you can hit me later [3:05 PM]
wbt: If you're taking questions, I do have the same one as earlier regarding how existing players can carry-over the points from PBS/NOVA [3:04 PM]
LFP6: Can't yet [3:05 PM]
LFP6: In progress [3:05 PM]
Brourd: So Rhiju, how are you today? [3:05 PM]
wbt: LFP6, that's in response to me? [3:04 PM]
jnicol: Its planned to carry over the points [3:05 PM]
TomoeUzumaki: yess [3:05 PM]
LFP6: Yep Wbt, as John confirmed [3:05 PM]
rhiju: @brourd, doing great! how are you? was last week pretty hectic with paper lab submissions? [3:06 PM]
machinelves: Rhiju, Jee mentioned possibly moving to openGL for 3D dev during chat with jnicol - is this a confirmed decision, or still in the brainstorming / investigative phase? [3:06 PM]
rhiju: @machine, not sure. i know there is discussion of at least allowing jsmol embedding of 3D in project descriptions [3:06 PM]
LFP6: And @Machine, it might be interesting to do Unity. I have a bit of knowledge, our mobile app is made with it, plus they're adding OpenGL support [3:06 PM]
jnicol: brainstormin stage right now machine [3:07 PM]
wbt: Also I don't know if you've found this with others, but eteRNA sometimes freezes my whole browser window - e.g. right now, I have one window with a game and the bubbles are rising, and the chat is scrolling by in another, but the browser (FF) is completely nonresponsive - I'm entering this on Chrome. [3:06 PM]
Brourd: Yes, 200 plus sequences were submitted by me. I plan on figuring out a way to spread the slots over more targets in the next round :) [3:07 PM]
machinelves: kk thanks for the context, interesting note on the description embed [3:07 PM]
LFP6: (If we're actually doing 3D game, which I believe was thrown around at some point) [3:07 PM]
jnicol: It will take some development time to go to 3D, so be patient [3:08 PM]
rhiju: 3D game is a good possibility, and necessary for us to make progress on more RNA biology and engineering [3:08 PM]
jnicol: Rhiju, any more news on Johans upcoming lab? [3:09 PM]
rhiju: we will be doing some prototyping this year, but not yet clear if we can make compelling puzzles [3:09 PM]
TomoeUzumaki: rhiju, are you saying that eterna would transition into a 3D game? [3:09 PM]
LFP6: I would suggest keeping both [3:09 PM]
rhiju: @jnicol, i saw johan this morning and he mentioned chatting with nando about some clever designs. i'm assuming that is going to be voted into a new paper lab this week -- do you know anymore? i know there were some possible tehcnical hurdles. [3:10 PM]
machinelves: yes, this is a good time to also let players know the context of development bandwidth: patience is a virtue while Jee hands off the project to jnicol, so please have patience for new feature development, as everything takes time to produce [3:10 PM]
rhiju: @tomoe, i think 3d would be part of the gameplay. but 2d is still important -- many rna's function at the level of switching between 2d states. [3:10 PM]
TomoeUzumaki: aah [3:10 PM]
LFP6: @Rhiju: Nice... Would you consider Unity? If so, I would like to *attempt* to volunteer some manpower to that. I'm still new to it, but I'm hoping to work on getting some experience, and this would be a cool project to shoot for [3:10 PM]
jnicol: yes, like are we able to remove the head, tails and barcode for his lab [3:10 PM]
machinelves: re: LFP6 yes, keeping both, I mentioned possibility of toggle between 2D 3D. at first I thought no more 2D, but then realized simplicity of interface is good for new players [3:11 PM]
machinelves: and multiple perspectives on same data always helps [3:11 PM]
LFP6: Yes [3:11 PM]
Nando: hi everyone [3:11 PM]
Brourd: Other than that, I am doing fine, Rhiju. By the way, in regards to the competition construct, I believe its use as a cross check of the Eternabrain derived parameters is probably a good idea. [3:11 PM]
TomoeUzumaki: hi Nando [3:11 PM]
TomoeUzumaki: what is eternabrain? [3:11 PM]
LFP6: Completely agree... Or even go somewhere along the lines of EyeWire's interface? [3:11 PM]
machinelves: nando! :D [3:11 PM]
LFP6: Hey Nando [3:11 PM]
TomoeUzumaki: oh yeah [3:11 PM]
rhiju: @LPF6, for 3D we would most definitely use unity. we have some experience with it when we worked on eterna mobile (which works, by the way, but would take a lot of work to properly deploy!). [3:12 PM]
LFP6: I PMed Mike about working on Mobile, and Jee said a while back that he would talk to him (about me helping out). Still haven't gotten anything back [3:12 PM]
rhiju: the major challenge with 3D, btw, is the computation time in figuring out how to connect one helix to another through available RNA 3D motifs -- its a problem we've recently solved by precomputation, but it requires database lookups [3:13 PM]
LFP6: But, I would really love to try and help. [3:13 PM]
rhiju: something like a 2-4 Tb databse, actually. should be possible to host a database at a server and answer queries quickly, but that's going to be a major optimization effort. [3:13 PM]
LFP6: Could there be any use in looking at some of the interface that Fldit has in that regard? [3:13 PM]
Nando: @rhiju: with regard to general gameplay, there seems to be a gap currently in EteRNA, new players are entering the lab area and facing very difficult puzzles, this may discourage many... would there be a way to reserve some slots for simple targets for lab newcomers? or is there a better/different way to make new players... [3:14 PM]
...slowly comfortable with labs?
LFP6: *Foldit [3:13 PM]
LFP6: Oh, I made a forum post on that Nando, per your request I think [3:14 PM]
LFP6: https://getsatisfaction.com/eternagame/topics/levels_of_difficulties_in_labs [3:14 PM]
Nando: thanks LFP6 [3:14 PM]
LFP6: I added acouple extra thoughts [3:14 PM]
LFP6: (Namely using the puzzles as a grourd for getting shape data and such) [3:14 PM]
LFP6: *Ground [3:15 PM]
LFP6: Yikes, having difficulty typing [3:15 PM]
machinelves: @nando you probably already saw this, but in case not, Eli just posted a simple walkthrough lab for new players, selecting simple past labs to explore. would be great to also as you say have slots for active new labs that are simpler to understand [3:15 PM]
Brourd: My long lost cousin, Grourd. [3:15 PM]
machinelves: lol [3:15 PM]
LFP6: Heh [3:15 PM]
rhiju: @nando, have you looked at eli's lab? its more 'entry level'. [3:15 PM]
TomoeUzumaki: lol [3:15 PM]
LFP6: Hmmm... Rhiju, would it be beneficial for me to contact someone (in looking to help with Unity stuff)? [3:16 PM]
Nando: I have to admit, I haven't checked Eli's lab, was too busy modeling in 3D I guess... [3:16 PM]
machinelves: nando, it just went up, so it is brand new [3:16 PM]
TomoeUzumaki: rhiju, Eli's lab definitely is more entry level. [3:16 PM]
LFP6: Or would that just be an as-things-go basis and things get worked out as they actually come up? [3:16 PM]
Nando: so, it will stay at player's discretion whether a simple lab is accessible or not... [3:16 PM]
LFP6: *As the opertunities come up [3:16 PM]
jnicol: LFP6, you can PM me, we can work something out [3:17 PM]
machinelves: @jnicol / rhiju / jee i think there is player consensus that there needs to be a simple labs option for new players, to gradate the difficulty [3:17 PM]
LFP6: All right, will do. I'll shoot you one now, as I'm going to have to be leaving in a short bit [3:17 PM]
rhiju: @lpf6 -- for unity, we wouldn't be ready for help until later in the summer. once we have a prototype, we might ask you to preview it, and perhaps donate time to development. [3:18 PM]
Nando: it should possibly be actually limited to new players [3:18 PM]
machinelves: ohhh nando interesting idea! [3:18 PM]
LFP6: I concur with Machine. And keep them useful though. I mean, even if it's just to get more data, that's always helpful I'd think [3:18 PM]
wbt: teaching loop boosting earleir would be good too, as is done in NOVA [3:18 PM]
Nando: not my idea, Brourd's ;) [3:18 PM]
machinelves: yay brourd! :D [3:18 PM]
LFP6: @Rhiju: Thanks. Will PM John per his request, and have things worked out as they will happen [3:19 PM]
TomoeUzumaki: nando, which lab? [3:19 PM]
rhiju: regarding keeping entry-level labs for new players, I like the idea, but you'll have to bring it up with eli! he could filter or select for players with fewer points. [3:19 PM]
LFP6: I don't have tons of knowledge, so I would have to see some things already in place anyhow [3:19 PM]
jnicol: A point value to be able submit a design, for simple labs [3:19 PM]
Nando: alright rhiju, thanks [3:19 PM]
machinelves: ohh i didn't know you could filter player access to labs already! [3:19 PM]
jnicol: can't yet [3:19 PM]
LFP6: @Rhiju: I think the thought is to have such things continuously [3:19 PM]
jnicol: sorry, Eli as the admin can pick designs, is what rhiju is talking about [3:20 PM]
machinelves: maybe labs could all be assigned a difficulty level, in pretty colors, to let players easily know what they are getting into? and quickly browse lab list & choose appropriate difficulty? [3:21 PM]
Brourd: A lot of work, picking designs can be. [3:21 PM]
machinelves: or even have dedicated categories, depending on quantity of labs in future [3:21 PM]
Brourd: Especially 450 + sequences, if he gets that many. [3:21 PM]
machinelves: ahhh you mean filter player input after the fact [3:22 PM]
machinelves: not gate it before [3:22 PM]
Nando: I'll script him something ;) [3:22 PM]
machinelves: yes that sounds like a lot of work, lol [3:22 PM]
rhiju: @machinelves, I don't think you can do the filtering now, but the admin has the ability to choose which designs get picked (as brourd said). it should be possible to write a filter in eternascript -- eli may need some help from nando... [3:22 PM]
machinelves: good idea nando! [3:22 PM]
Brourd: Excellent [3:22 PM]
rhiju: @nando, awesome. [3:22 PM]
Nando: :D [3:22 PM]
firedrake969: Hi everyone [3:22 PM]
machinelves: hi fire! [3:22 PM]
firedrake969: Oh [3:23 PM]
firedrake969: Dev chat. [3:23 PM]
firedrake969: >_< [3:23 PM]
jnicol: good timing [3:23 PM]
rhiju: everyone, i've got to run in about 7 mins [3:23 PM]
Brourd: So Rhiju, any interesting news on your end? [3:23 PM]
machinelves: welcome :) jnicol's premiere dev chat as new lead dev! *applause* [3:23 PM]
jnicol: lol [3:23 PM]
firedrake969: @jnicol I always seem to join by chance. [3:23 PM]
TomoeUzumaki: *clap* [3:24 PM]
machinelves: rhiju thanks for coming! i have no more questions, just to say thank you so much for everyone's hospitality, it was so inspiring, and i'm really grateful you all care so deeply about the project. thanks! :) [3:24 PM]
LFP6: Hi FIre. :) [3:24 PM]
jnicol: Rhiju, I believe we still need to keep the consecutive C's and G's to 4 or less, correct? [3:24 PM]
wbt: Is there any way to update the regex used for access to the forums and/or bug tracker? I always get the message "You must have a valid email address to access EteRNA forum. Please modify your email to a valid address and access the forum again." [3:24 PM]
LFP6: I believe you would have to contact GetSatisfaction about that [3:25 PM]
wbt: and I'd like to be able to contribute bug reports in a more approriate setting than dev chat [3:24 PM]
rhiju: @jnicol, yes we are keeping the 4C/4G rule for now. [3:25 PM]
TomoeUzumaki: rhiju, before you leave, PM [3:25 PM]
LFP6: (The people who host it) [3:25 PM]
machinelves: wbt you sign into eterna, forums validate that login credential [3:25 PM]
machinelves: ( if that is what you mean ) [3:25 PM]
LFP6: Machine, he cant because of a character in his E-Mail [3:25 PM]
wbt: right...except they use a different e-mail address validator, and a bad one [3:25 PM]
LFP6: An ampersand or something similar [3:26 PM]
TomoeUzumaki: or nvm [3:26 PM]
wbt: probably a plus sign [3:25 PM]
LFP6: So, Wbt, contact GetSat, that's their problem [3:26 PM]
LFP6: Yes, that was it [3:26 PM]
machinelves: wbt, issue intake / bug reports from players workflow is currently discuss in forums, track in wiki, and raise priority in dev chat [3:26 PM]
wbt: they don't listen to people who aren't their direct customers, at least in my experience [3:26 PM]
wbt: if you're able to contact them, it'd help [3:26 PM]
machinelves: wbt simplest solution is use different email [3:27 PM]
LFP6: Heh, so, we need a dev to go and say hi. :) [3:27 PM]
wbt: yeah [3:26 PM]
machinelves: issue intake process http://eternawiki.org/wiki/index.php5/Issues [3:28 PM]
LFP6: Just realized something... Is the strategy market now completely depricated? [3:27 PM]
machinelves: will get more robust solution after handoff to jnicol, thank you for your patience! [3:28 PM]
LFP6: Oh, and Wbt, if all else fails, write your issue into a row in the New Issues table [3:28 PM]
wbt: I could also contriubute directly on GitHub with access to create issues there [3:28 PM]
rhiju: @LPF6, we don't have devs who can code up strategies. Our hope is that we can recruit players to help write those scripts later this year and catch up. I thin it will be important especially if we find rules for switch design and want to automate. [3:29 PM]
LFP6: Ah [3:29 PM]
LFP6: Thanks [3:29 PM]
machinelves: wbt currently please use the stated issue workflow. github is dev side access atm. we will update you if that changes! [3:29 PM]
LFP6: I have to go. Nice talking with youall, will catch up later [3:29 PM]
machinelves: however you can reference github for issue status [3:29 PM]
jnicol: Thanks LFP6 [3:30 PM]
machinelves: bye LFP6! :) [3:30 PM]
LFP6: (Or write a new one in the table!) [3:30 PM]
rhiju: nice talking to everyone too! hope jnicol can stay for a little bit. [3:30 PM]
jnicol: thank you for your time rhiju! [3:30 PM]
jnicol: I can stay [3:30 PM]
machinelves: bye rhiju! thanks for coming! :D [3:30 PM]
Brourd: Take care Rhiju. [3:31 PM]
Brourd: So jnicol, any idea when the free cookies will show up? [3:31 PM]
jnicol: They are serving them at the Nova website [3:32 PM]
Brourd: dang [3:32 PM]
machinelves: wbt yes, as LFP6 says, there is a wiki table for current issue tracking. obviously could be better, but is what we have atm, to supplement forums & dev chat. once a more solid tracker is implemented, everyone will receive notice. until then: http://eternawiki.org/wiki/index.php5/New_Issues [3:32 PM]
jnicol: First 10 players get a free 20000 point cookie [3:32 PM]
Brourd: Not bad :) [3:33 PM]
jnicol: or was it 2000 [3:32 PM]
Brourd: Only one way to find out! [3:33 PM]
machinelves: om nom nommerkins! [3:33 PM]
jnicol: Thanks Elves for coordinating the issues, you help is appreciated [3:33 PM]
Brourd: So, how does it feel to officially be in training? [3:34 PM]
machinelves: happy to help! thank you for diving right in! [3:34 PM]
jnicol: Guess the same as picking 450 slots in 24 hours [3:34 PM]
Brourd: Well, Nando wrote a script for 150 of them :) [3:35 PM]
jnicol: That helps! [3:35 PM]
machinelves: B zomg! *faint* [3:35 PM]
Brourd: and I had picked a good 200+ before Sunday. [3:35 PM]
machinelves: everyone here deserves huge gratitude for their constant efforts and research. Thank you to everybody!!! :D [3:35 PM]
Brourd: So, I guess that still adds up to 450 sequences being picked :P [3:35 PM]
jnicol: Jee was talking about integrating scripts into the lab, but there were issues [3:36 PM]
jnicol: so I will probably look into it in 2-3 weeks [3:36 PM]
Brourd: Yes, like for custom constraints. [3:37 PM]
jnicol: yes [3:37 PM]
Brourd: Will be good to get those up and running *before* the next round ;) [3:37 PM]
jnicol: agreed [3:37 PM]
machinelves: just a random thought, i don't know the motivations or necessities behind the schedule, but it seems like everyone is always rushing to prep & finish labs. what do you all think about possibly extending length of time, to reduce rushing? [3:39 PM]
Brourd: well, they go for 4 weeks. [3:39 PM]
machinelves: not for just one lab round, but in general [3:39 PM]
Brourd: If I can submit 300 designs in 24 hours, players can handle 60 over 4 weeks. [3:39 PM]
machinelves: i don't do labs myself, so i don't know what is ideal. but i just wonder, would it help if it were 5 weeks? or not really make a difference? [3:39 PM]
jnicol: seems like most people (including me) procrastinate to complete the labs [3:39 PM]
machinelves: and how about for the prep time? [3:39 PM]
machinelves: proposals i mean [3:40 PM]
jnicol: players are starting to get use to the additional time neeed on the front end [3:40 PM]
Brourd: true [3:41 PM]
machinelves: kk. i just figure, if there's no concrete deadline and giving more time would help on either proposal or submission side, that would be easy enough to change [3:41 PM]
jnicol: I think the automatic tools (scripting constraints and such) would be the biggest help right now [3:41 PM]
Brourd: 4 weeks is a long time :) [3:42 PM]
Nando: @jnicol, can you do me a small favor? please delete http://eterna.cmu.edu/web/puzzle/4609361/ I made a mistake in that one [3:42 PM]
Brourd: Is it not unsolvable? [3:42 PM]
machinelves: brourd, how much time do you have between receipt of submission, and selection / final submission of lab for synthesis? [3:42 PM]
Nando: no, just forgot to mutate a specific base ;) [3:43 PM]
machinelves: just wondering if there is a way to give you more time to choose submitted slots and not be rushed [3:43 PM]
jnicol: ok, deleted [3:43 PM]
Brourd: None :) That could potentially work, however, making the rounds shorter to give the admins time would just get complaints. [3:43 PM]
machinelves: i think we want to balance gameplay with solid scientific output, so it's good to explore the options [3:44 PM]
Nando: thanks john [3:44 PM]
jnicol: yw [3:44 PM]
machinelves: brourd, nando, you guys are at the forefront of what it takes to get lab submissions selected & finalized. so it is up to you to know whether it would help to have more time to select, i can't say myself since i don't proctor labs [3:45 PM]
Nando: I wish we would get 24 hours before deadline [3:45 PM]
Brourd: Potentially, we could create a 5 week cycle. However, that has to be the Das Lab's decision. [3:45 PM]
Nando: no more submissions, but votes allowed [3:45 PM]
Brourd: Right, close it the Saturday before the 4th Sunday. [3:46 PM]
Nando: the picking can be scripted and done in a minute [3:46 PM]
jnicol: @Nando, I thought you would have asked Rhiju some more technical questions, like what is the real aptamer sequence for Theophylline [3:46 PM]
machinelves: that's interesting... so during full lab run, close off submissions at least 24 hours - 1 week before final due date, allow votes, and extra time for lab owners to select [3:46 PM]
Nando: @john: I do have the answer to that question, I never found a different sequence than the one I showed you [3:47 PM]
Brourd: lol, "You can only submit to this paper lab after it is submitted" I guess that puzzle was deleted. [3:47 PM]
jnicol: maybe we can make a lab to find the best aptamer sequence to bind :) [3:48 PM]
Nando: why not :) [3:48 PM]
jnicol: Ok, I'm going to officially close Dev Chat, thanks to all for contributing! [3:49 PM]
jnicol: I'll post the log in a little while [3:49 PM]
machinelves: thanks jnicol! so glad to have you on board! good luck :D [3:49 PM]
Brourd: are you referring to the 3x3, 3 base pair, and 1x4 aptamer? [3:49 PM]
jnicol: correct brourd [3:49 PM]
Brourd: Would you run the lab with Johan's protocol? [3:50 PM]
jnicol: quote from Nando "As far as I know, the Theophylline aptamer is not just a 3-3 loop. In all scientific documents I've read about it, the sequence is 5' NAUACCAN and 3' NCCUUGGCAGN, with structure 5' (...(((( and 3' )...)))...) in essence, a 3-3 loop and a 0-3 bulge (or sometimes a 1-4 loop instead, because the AU pair actually does not exist in the bound form) joined by a small stack. Th [3:50 PM]
Brourd: yeah [3:51 PM]
Brourd: Would you be using Johan's protocol? :) [3:52 PM]
jnicol: what protocol? [3:52 PM]
jnicol: the MS2 aptamer? [3:53 PM]
Brourd: Right, RNA arrays. [3:53 PM]
jnicol: Yes, he is in a meeting now finding out more details, [3:53 PM]
