2014.09.24 Dev Chat

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On R88 Results, RMDB, & Spam


jnicol: Hi everyone, welcome to dev chat! [3:00 PM]

stevetclark: looking forward to the dev chat [3:00 PM]

machinelves: hello! :D [3:00 PM]

stevetclark: hi jnicol [3:00 PM]

Eli Fisker: hi John :) [3:00 PM]

hoglahoo: Hi John [3:00 PM]

jnicol: hi all :) [3:00 PM]

jnicol: I just uploaded the lab results to the game [3:00 PM]

jnicol: for R88 and R89 [3:00 PM]

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

Eli Fisker: Big thx! [3:01 PM]

civilized: Who is that? [3:00 PM]

jnicol: unfortunately the scoring to apply points to users is not working  [3:01 PM]

hoglahoo: Aww, that's too bad [3:01 PM]

hoglahoo: muahaha [3:01 PM]

Eli Fisker: As long as I can see the scores in the lab list, I don't care about points [3:01 PM]

jnicol: did you throw in a bad design on purpose? [3:02 PM]

hoglahoo: I missed half of them [3:02 PM]

jnicol: Let me know Eli, it should all be there [3:02 PM]

Eli Fisker: John, thx :) [3:02 PM]

civilized: Is this guy the owner of the website? [3:02 PM]

jnicol: We have also been busy fighting spam, thanks everyone for your help on this [3:02 PM]

Omei: Hi, All.  I think this may be my third dev chat ever. [3:03 PM]

civilized: Hey, jnicol! I had a problem yesterday. [3:03 PM]

jnicol: hi civilized, I'm a dev working for Eterna [3:03 PM]

machinelves: many thanks for your efforts John! [3:03 PM]

Eli Fisker: John, big thx for the job you pulled [3:03 PM]

hoglahoo: Cool, spam is the devil [3:03 PM]

civilized: I wanted to upload a puzzle  [3:03 PM]

stevetclark: that sucks that spam has been an issue [3:03 PM]

civilized: but it gave me a message. [3:03 PM]

civilized: Please fill in the number of (...............) I couldn't read it. [3:03 PM]

jnicol: does anyone else have a problem submitting puzzles? [3:04 PM]

hoglahoo: For new players, jnicol is EteRNA's newest game developer [3:04 PM]

machinelves: and thanks also for changing the badge to be awarded after 1 comment, I think that will help a lot too [3:04 PM]

Eli Fisker: Yay, John, all the scores are there. I'm happy [3:04 PM]

macclark52: Congratulations, J.  [3:04 PM]

jnicol: yes, hopefully much less filler comments [3:04 PM]

hoglahoo: John, it's an issue with overlapping white text on white background. It still happens with the GU pairs, and there's still the shiftable bases bug thing where the game asks you to enter the number of shiftables [3:04 PM]

jnicol: yes, its on the list for when I get into the flash code, havent started on that yet :( [3:05 PM]

hoglahoo: ^ [3:05 PM]

machinelves: one thing at a time. we're just grateful you've been patiently working through everything. A big thanks to you! :D [3:06 PM]

Omei: John, are there currently any active developers in addiition to you? [3:06 PM]

jnicol: Jee and Adrien are advising, I'm the only one in the code for now [3:07 PM]

Omei: Tx.  Good to know.  [3:07 PM]

Omei: I'm very pleased to see all the little improvements. [3:08 PM]

Eli Fisker: Me too [3:08 PM]

jnicol: trying, sorry it takes so long [3:08 PM]

machinelves: we'll be getting an issue tracker, which will help prioritize and track everything, so that things don't fall in the cracks [3:08 PM]

Eli Fisker: John, you are doing well.  [3:08 PM]

jnicol: that will help, yes! [3:08 PM]

Omei: You're doing great. [3:08 PM]

jnicol: looking at coding the capcha's for registrations now [3:09 PM]

hoglahoo: excellent [3:09 PM]

Eli Fisker: Sounds great :) [3:09 PM]

macclark52: I've been away from Eterna for a little while and I'm impressed by how well it is working.  [3:09 PM]

machinelves: thanks very much [3:09 PM]

jnicol: I already coded a lot to 'hide' spammers when their account gets blocked [3:09 PM]

machinelves: hi macclark, welcome back! [3:10 PM]

Omei: It shows.  Tx. [3:10 PM]

Eli Fisker: Yep, nice to see you back, Mac [3:10 PM]

macclark52: My kiddies were in this afternoon.  I hope they weren't excessively bratty.  [3:11 PM]

jnicol: a whole family of clarks on eterna! [3:11 PM]

machinelves: hehe i missed it! [3:11 PM]

Eli Fisker: :) [3:11 PM]

macclark52: They went through Eli's lab tutorials.  [3:11 PM]

macclark52: Are those going to be THE lab tutorials?   [3:12 PM]

machinelves: those are awesome, thanks Eli for all your hard work [3:12 PM]

Eli Fisker: Elf, np [3:12 PM]

Eli Fisker: For my part I [3:12 PM]

Omei: John, in the forums we discussed getting all the syntheses in RMDB into the Eterma UI.  I'm curious whether that is likely to be a short term thing, or just on the list to do sometime. [3:12 PM]

macclark52: Yes, they were very nicely thought out.  What happens with too much this, too much that.  [3:12 PM]

Eli Fisker: only try make some material to help get the transfer from puzzles to lab easier [3:12 PM]

jnicol: It paid off, lots of high scores in Eli's labs [3:13 PM]

Eli Fisker: Yes, I was very pleased to see that, John. Counldn't help take a peak [3:13 PM]

machinelves: Eli's been making puzzle tutorials as well for training lab design methods. I hope to see these integrated into the tutorials section at some point, so it's easier than sorting through all the existing player puzzles [3:13 PM]

jnicol: @Omei, its been discussed with Jee and Rhiju, but its not on the short term list [3:13 PM]

macclark52: EteRNA's been advertising lab tutorials for a year or so, so I thought maybe This were the tutorials that would be used.   [3:13 PM]

Omei: Tx. [3:14 PM]

machinelves: hehe we're working on updating those portals exactly [3:14 PM]

macclark52: Yay.   [3:15 PM]

machinelves: the lab tutorials as advertised have not been built as far as I know. But I think between Eli's work and NOVA we can plug in something more useful there [3:15 PM]

stevetclark: sounds good [3:16 PM]

macclark52: We're happy to beta test.  :-) [3:16 PM]

Eli Fisker: :) [3:16 PM]

machinelves: hehe yay! [3:16 PM]

machinelves: silly question: is RMDB only eterna synths or incorporating library of global RNA synth data? [3:17 PM]

Eli Fisker: RMDB is the full dataset  [3:17 PM]

jnicol: Stanford biiochem synths [3:17 PM]

Eli Fisker: We only see part of the results in the eterna interface [3:17 PM]

Eli Fisker: Ah, yes, they have a lot of extra non-eterna data too [3:18 PM]

machinelves: thanks! is it only of what eterna produced? of what stanford produced? of what scientists around the world produce? [3:18 PM]

machinelves: got it. I like Omei's idea to broaden our access to data [3:18 PM]

machinelves: very much :D [3:18 PM]

jnicol: http://rmdb.stanford.edu/repository/browse [3:18 PM]

Eli Fisker: Short intro to RMDB [3:18 PM]

Eli Fisker: http://eternawiki.org/wiki/index.php5/RMDB [3:18 PM]

machinelves: thank you! [3:18 PM]

Omei: @machineelves - My question to jnicol wasn't about the non-Eterna syntheses.  But for most cloud lab rounds, there is twicw as much data in ithe RMDB files as we see in the game UI. [3:19 PM]

jnicol: In the rna repository you can see Eterna labs in the middle of the list [3:19 PM]

machinelves: oh interesting! thank you for the clarification Omei [3:19 PM]

Eli Fisker: Also here is a link to the discussion Omei was referring toon Rhiju mentioning getting the whole data set in eterna:  [3:19 PM]

Eli Fisker: https://getsatisfaction.com/eternagame/topics/what-does-the-lab-data-say-about-the-various-causes-of-high-error-rates#reply_14802647 [3:19 PM]

jnicol: yes, elves, there are 2 hairpins sythed for every design, your own and a computer generated one [3:20 PM]

machinelves: thanks Eli! [3:20 PM]

macclark52: Thanks for the link, Eli.   [3:20 PM]

Eli Fisker: Hmm, I can't link directly [3:20 PM]

Eli Fisker: Moment [3:20 PM]

machinelves: i saw that comment about having two data sets, with same main design but different barcodes, which is really useful [3:20 PM]

Omei: That's a really interesting forum discussion for anyone who really cares about the data. [3:20 PM]

machinelves: for investigating the barcode [3:20 PM]

Eli Fisker: https://getsatisfaction.com/eternagame/topics/what-does-the-lab-data-say-about-the-various-causes-of-high-error-rates#reply_14801846 [3:20 PM]

Eli Fisker: Look for the comment by Rhiju further down in this discussion [3:20 PM]

jnicol: Only the players design results are currently uploaded back into eterna [3:20 PM]

machinelves: i have been wanting to help with that for the last month, but not had a chance. sorry for being late to the party  [3:21 PM]

Eli Fisker: Elf, don't feel bad, you have been busy elsewhere [3:21 PM]

machinelves: thanks Eli [3:21 PM]

Omei: ... but the same design with a different barcode is also synthesized.  That's the most interesting thing the game is missing. [3:21 PM]

Eli Fisker: Yes, that on autogenerated barcodes [3:22 PM]

machinelves: yes, before we were trying to think of a way to do this on purpose, so this is actually a huge help [3:22 PM]

machinelves: so we can compare the shape of the two identical designs with different hairpins, that's great! [3:23 PM]

Eli Fisker:  That would be very interesting  [3:23 PM]

machinelves: how far going back is this process? [3:23 PM]

machinelves: in rounds [3:23 PM]

Eli Fisker: Right now we have to sift through the data to find the precious few that has been made this way on purpose [3:24 PM]

Omei: Meechl is putting all the data into spreadseets now.  That's not as useful as an Eterna-specific browser, but a lot more accesiible than the RMDB files. [3:24 PM]

machinelves: wow, many thanks to Meechl!!! [3:24 PM]

Eli Fisker: Yes, far easier to watch in spreadsheets [3:24 PM]

Eli Fisker: And Omei has made a fusion table of all the data [3:24 PM]

stevetclark: Hopefully the spreadsheets will make it easier to find data that players are looking for [3:24 PM]

Eli Fisker: which is a very easy way to get data for a full lab in a much faster way [3:24 PM]

jnicol: big thanks to everyone helping with analyzing the data [3:24 PM]

machinelves: thanks to Omei & Eli too, and good luck. if I can be of any use I will try to help [3:25 PM]

Omei: The more the merrier! [3:25 PM]

Eli Fisker: Yes, I think this will simply speed up greatly what we are capable of doing for science with Eterna [3:25 PM]

Eli Fisker: As Omei says :) [3:25 PM]

machinelves: hehe :) [3:25 PM]

Eli Fisker: Thx, John and Elf [3:25 PM]

Omei: What Eli says :-) [3:26 PM]

Eli Fisker: hehe :) [3:26 PM]

Omei: We're really the same player. [3:26 PM]

machinelves: lol [3:26 PM]

Eli Fisker: Hehe, no protest [3:26 PM]

machinelves: then that is sure a lot of work you do! [3:26 PM]

jnicol: OK, I'm going to leave soon, any more questions for me? [3:27 PM]

Omei: It helps to be on two differnt continents, so part of us is always awake. [3:27 PM]

Eli Fisker: For those who want a look at the spreadsheets and fusion table: http://eternawiki.org/wiki/index.php5/Lab#Lab_Data_Resources [3:27 PM]

machinelves: John no, same priorities as before. thanks for all your efforts! [3:27 PM]

Eli Fisker: Omei, good one :)( [3:27 PM]

Eli Fisker: Oops on the last paragraph [3:27 PM]

Omei: Keep up the good work, John! [3:27 PM]

machinelves: lol omei [3:28 PM]

jnicol: Thank you everyone! Talk to you later :) [3:28 PM]

machinelves: thanks! take care :D [3:28 PM]

Eli Fisker: Bye John [3:28 PM]

macclark52: Bye [3:28 PM]

Omei: Bye [3:28 PM]

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