2014.07.23 Dev Chat

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On 3D Jigsaw, NOVA Link, & Spreadsheet Data

jnicol: Hi and welcome to dev chat [3:00 PM]

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

Brourd: Welcome to the dev chat, jnicol. [3:00 PM]

machinelves: Hi! thank you for having dev chat!  [3:00 PM]

jnicol: Hi Eli, Brourd :) [3:00 PM]

jnicol: hi elves [3:00 PM]

jnicol: I've been busy with the sequencing scripts lately [3:01 PM]

machinelves: ooo do tell! [3:01 PM]

Brourd: Nice [3:01 PM]

jnicol: Johans lab has some special requirements :) [3:01 PM]

jnicol: the backend scripts need to be rewritten slightly to make accommodations [3:01 PM]

Brourd: Here is a question. Why have the pilot projects not been moving forward to synthesis the last few rounds? [3:02 PM]

Benjamaster1: I see you deleted the spam group I showed you, good job :) [2:49 PM]

jnicol: They did not have a script to add in the sequencing properly, so just last round, the pilot labs were taken [3:03 PM]

Brourd: ah [3:03 PM]

machinelves: The main thing on my list today is checking in on getting a NOVA link in the main menu, either directly under puzzles, or on the tutorials page itself [3:03 PM]

jnicol: yes, benjamaster, thanks for pointing them out, there are many spam groups which I am looking into requiring players to have 10k points beore being allowed to create a group [3:03 PM]

Eli Fisker: John, sounds good [3:04 PM]

machinelves: that's a good idea [3:04 PM]

jnicol: ok elves, that is on my list of high priorities now :) [3:04 PM]

Eli Fisker: Sweet :) [3:04 PM]

Benjamaster1: yeah, that's a really good idea [2:49 PM]

machinelves: yay!!! the new players will be happy [3:04 PM]

Eli Fisker: We still have many new not finding the tutorials [3:04 PM]

jnicol: I have a bug/feature tracker for ready testing within a day or 2 [3:05 PM]

Benjamaster1: perhaps you could also require solving at least a few puzzles before being able to set a user page description to help stop that spam too? [2:49 PM]

Brourd: Very nice [3:05 PM]

jnicol: *ready for [3:05 PM]

Eli Fisker: John, bug and feature tracker. Thats a lot of good news [3:05 PM]

machinelves: wow, great news! [3:05 PM]

jnicol: stopping spam in the forum is a little harder [3:05 PM]

Benjamaster1: not forum pages, I meant eterna profiles that your name in chat links to [2:49 PM]

jnicol: the user pages are easy to set the flag to block, however when I tested some 'features' everything is not blocked properly [3:06 PM]

jnicol: I really dont want to delete user pages, just set them to inactive [3:07 PM]

jnicol: so I need to get that working better [3:07 PM]

machinelves: thanks for making an effort, it is a complex issue to tackle [3:07 PM]

Brourd: Should we try to come up with ideas to make it more complex? [3:08 PM]

jnicol: sorry I havent been active with the players on that lately, but I had other fires to work on :) [3:08 PM]

machinelves: yes that sounds constructive, lol [3:08 PM]

jnicol: more complex for the spammers, yes [3:08 PM]

machinelves: jnicol i think you've been doing great prioritizing, and making progress. thank you! [3:08 PM]

Benjamaster1: I'm curious, is there a way to see a list of all user groups? [2:49 PM]

Eli Fisker: I agree with Elf [3:08 PM]

Benjamaster1: Maybe implementing a captcha would help with the spam if it's automated? [2:49 PM]

Eli Fisker: Benjamaster1, under Groups in the menu Community [3:09 PM]

jnicol: groups can be returned in the json html response [3:09 PM]

jnicol: *all groups [3:10 PM]

Benjamaster1: I'm making a pastebin of all spam user group links I can find. I'll link to it in a few minutes when I'm done [2:49 PM]

jnicol: there should be an easy way to see them all on the groups page also, but offhand I dont know [3:10 PM]

Brourd: I believe hoglahoo mentioned something about checking against known blacklisted IP's for creating accounts. [3:10 PM]

Eli Fisker: Benjamaster, thx for doing so [3:10 PM]

jnicol: actually, I wrote a script to inactivate all groups with certain characteristics [3:11 PM]

Eli Fisker: Interesting - don't tell too much :) [3:11 PM]

jnicol: 1 member, creator has 0 points [3:11 PM]

machinelves: that reminds me someone suggested the idea of making a player profile for reporting spam issues to. pro: any moderator could log into it, and more private than wiki page to / forum aggregate complaints. con: PM system easy to lose messages as they get buried. [3:11 PM]

machinelves: yes thanks benjamaster, that is helpful! [3:12 PM]

Benjamaster1: Most of those spam groups are in another language [2:49 PM]

jnicol: I would like to give certain players rights to 'inactivate' spam: profiles, comments, etc easily with 1 click [3:12 PM]

Brourd: Yeah. The hard way takes too much energy, I agree. [3:13 PM]

Brourd: I can agree with 1 click. [3:13 PM]

jnicol: Yes, I started on that route and quickly thought there must be a better way :) [3:13 PM]

machinelves: i think that would help, as players want to spend time helping others, and manage shenanigans more quickly & easily [3:13 PM]

Brourd: Yep! [3:13 PM]

jnicol: @Vineet, are you here? [3:14 PM]

Brourd: Well, not too sure if I agree with part 1, but managing quick and easy sounds like a code to live by. [3:14 PM]

machinelves: maybe some form of moderator consensus for more permanent decisions  [3:14 PM]

Eli Fisker: I agree with Elf [3:15 PM]

jnicol: well, I would have the spam inactive with a log by who and when [3:15 PM]

Eli Fisker: One click is a danger as someone can abuse power to block unrightfull [3:15 PM]

jnicol: If disputed I can go back and check [3:15 PM]

machinelves: +1 for log :D [3:15 PM]

Brourd: Well, I think jnicol said "certain players" [3:16 PM]

jnicol: Eli, I would only give a handful of people access rights to Inactivate spam [3:16 PM]

machinelves: right, within that group of moderators, action is not unlocked until x # moderators activate option [3:16 PM]

Eli Fisker: John, good. I just want to make certain that it can not be abused [3:16 PM]

jnicol: and to have a way to revert back if necessary [3:17 PM]

machinelves: yes, agree with revert [3:17 PM]

Eli Fisker: Yes [3:17 PM]

Brourd: Oh, when does the Das lab feel they will have R87 results in? [3:17 PM]

Brourd: The revert is a bit difficult with the current system, yes. [3:17 PM]

jnicol: thats my fault brourd, tokk me awhile to get the sequences together [3:17 PM]

Brourd: ah [3:17 PM]

Brourd: No need to do it one at a time :) [3:18 PM]

jnicol: trial by fire :) [3:18 PM]

machinelves: haha brave sir john! you can do it! [3:18 PM]

Brourd: Indeed. So, another 4 weeks then? [3:18 PM]

jnicol: every I thought I was ready, I found some other anomolies [3:18 PM]

Benjamaster1: this is exhausting, almost every new group is spam :p [2:49 PM]

jnicol: *every time [3:19 PM]

Eli Fisker: Benjamaster, you are in for a big task [3:19 PM]

Eli Fisker: :) [3:19 PM]

jnicol: Benjamaster, I will take care of them [3:19 PM]

Brourd: So jnicol, are you going to try to expand group functionality? [3:20 PM]

jnicol: I saw them when you pointed out the one [3:20 PM]

machinelves: benja, if it helps you prioritize, there will be many spam groups that never go anywhere or cause trouble just get bored and leave. so i would start with profiles that actively spam other groups or comment threads [3:20 PM]

Benjamaster1: okay, i'll stop then. here's all the ones i've found: http://pastebin.com/43rCCi6z [2:49 PM]

jnicol: I was not Brourd, are you suggesting something? or just talking about the stopping spam propogation? [3:20 PM]

Brourd: I have no ideas. I'm more of a solo gamer. However, I am sure these fine individuals here can come up with unrealistic goals for you to work towards. [3:21 PM]

vineetkosaraju: @John yes I'm here, sorry for the delay [3:22 PM]

Eli Fisker: hi Vineet [3:22 PM]

jnicol: Hi Vineet! [3:22 PM]

Brourd: Hey vineet. [3:22 PM]

Eli Fisker: Bot master [3:22 PM]

machinelves: hahaha benja those look like advertisements?! wow, yes when i need to book a hotel i will be sure to find the appropriate eterna group lol [3:22 PM]

vineetkosaraju: Hi Eli, John, Brourd, elves, others :) [3:22 PM]

Eli Fisker: :) [3:22 PM]

machinelves: hi vineet! :D [3:22 PM]

Eli Fisker: lol, Elf [3:23 PM]

jnicol: Vineet has made some great progress with the 3D 'jigsaw' puzzle interface [3:23 PM]

Eli Fisker: Oh, cool. Please do tell... [3:23 PM]

machinelves: ooo that sounds exciting! [3:23 PM]

Brourd: What shall it be called? [3:23 PM]

vineetkosaraju: Yes, I'm currently working on adding some features, and I hope to post an alpha version on the dev server with a blog post by Friday [3:24 PM]

Brourd: Are you going to be supporting the project for the indefinite future? [3:24 PM]

jnicol: we will be asking players to help out with the testing also [3:24 PM]

vineetkosaraju: Hmm I'm not really the best person to come up with a creative name...  [3:24 PM]

machinelves: thank you! it will be so cool to see how it is going [3:25 PM]

Brourd: No creative name! [3:24 PM]

Brourd: Vineet's RNA Jigsaw [3:25 PM]

vineetkosaraju: Nope :( not yet atleast  [3:25 PM]

TomoeUzumaki: heey Vineet [3:25 PM]

machinelves: RNA 3D Toybox [3:25 PM]

TomoeUzumaki: elves, that works [3:25 PM]

Eli Fisker: hehe [3:25 PM]

machinelves: hi tomoe! :D [3:25 PM]

Eli Fisker: Like it [3:25 PM]

jnicol: Hi Tomoe [3:26 PM]

Brourd: Hey tomoe [3:26 PM]

machinelves: maybe some kind of lego pun? [3:26 PM]

vineetkosaraju: Hey Tomoe, I'll be uploading the blog post and interface on Friday [3:26 PM]

jnicol: Thanks Vineet [3:26 PM]

Brourd: @ vineet - so, developer support? For how long will you be able to do sa? [3:26 PM]

TomoeUzumaki: sounds like a plan! [3:26 PM]

vineetkosaraju: I'm working with her (Tomoe) on analyzing the data and stuff that'll come from it [3:26 PM]

Brourd: Awesome [3:26 PM]

machinelves: wow! thanks for your help tomoe! :D [3:27 PM]

Eli Fisker: Looking forward to see it, Vineet and Tomoe [3:27 PM]

vineetkosaraju: I'll be definetly active providing support throughout August, and probably Septemeber as well [3:27 PM]

TomoeUzumaki: hehe [3:27 PM]

Brourd: oh, two months. lol [3:27 PM]

vineetkosaraju: Afterwards, I'll be on less often but the project will probably still continue, just with less of my input  [3:27 PM]

vineetkosaraju: If there are any issues/enhancements I'll just take them from the getsat or github and fix them in my free time [3:28 PM]

Brourd: Jnicol shall be handling that as well then? [3:28 PM]

jnicol: lets see how things go [3:28 PM]

TomoeUzumaki: so just to clarify, this will be on the the dev server? [3:28 PM]

vineetkosaraju: yep, we'll be piloting on the dev server [3:29 PM]

vineetkosaraju: points will still be awarded to accounts on the main server I think, through the paper lab system? [3:29 PM]

vineetkosaraju: i'm not really sure about that aspect, john and I need to flesh out the details of that [3:29 PM]

Brourd: So, what exactly will players be doing? [3:29 PM]

jnicol: on reminds me about the conclusions for paper labs [3:30 PM]

machinelves: how's that going? :D [3:30 PM]

vineetkosaraju: players will be using the interface to create solutions/sequences to the 3d puzzles, we will be adding those to a paper lab and then synthesizing, players will get back the results and points [3:30 PM]

jnicol: rhiju would like admins to post a conclusions for a project viewable at the bottom of the descriptions for a lab [3:30 PM]

Brourd: Ah. So, you have 3D puzzles in mind for that then. [3:31 PM]

jnicol: and co-admins [3:31 PM]

Brourd: So, each admin needs to post a conclusion? [3:31 PM]

vineetkosaraju: yes, for example in one puzzle you are given part of an FMN structure found here: http://www.rcsb.org/pdb/explore.do?structureId=1FMN [3:31 PM]

machinelves: are conclusions getting published verbatim for paper labs? or further processing after initial lab post? [3:31 PM]

Brourd: Nice [3:31 PM]

jnicol: only if you want some extra points and to help players reading your lab :) [3:32 PM]

vineetkosaraju: and you should use predefined junctions/hairpins/helices/tertiary contacts to finish the 3D structure [3:32 PM]

Brourd: Right [3:32 PM]

Brourd: So, will we know the significance of these 3D puzzles? [3:33 PM]

machinelves: vineet i like the combo process of solve puzzle -> direct funnel into lab synth! [3:33 PM]

Benjamaster1: gtg for now, bye eterna! [3:33 PM]

Eli Fisker: So will we get an intro to search in the PDB database? [3:34 PM]

machinelves: bye beja thanks for your help! [3:34 PM]

Eli Fisker: bye Benjamaster [3:34 PM]

Eli Fisker: for jigsaw pieces [3:34 PM]

jnicol: bye benjamaster [3:34 PM]

vineetkosaraju: I'm sure there's a scientific significance to the puzzles (I'll have to ask Dr. Yesselman at the Das lab for the details), but so far I've just been creating a puzzle that doesn't require to many modifications [3:34 PM]

machinelves: are 3D puzzles categorized under puzzles or labs or a new category? [3:34 PM]

Brourd: ah, this is a part of that. Nice [3:35 PM]

jnicol: @elves, for now labs [3:35 PM]

machinelves: thanks! [3:35 PM]

vineetkosaraju: thanks elves :) the actual game will be seperate on the dev server, but it will be part of the labs [3:35 PM]

TomoeUzumaki: yep yep [3:35 PM]

machinelves: cool! really exciting! thank you all for working so hard to make progress  [3:36 PM]

vineetkosaraju: @eli we haven't integrated the PDB database yet, I think this is a subset of the motif atlas though [3:36 PM]

TomoeUzumaki: hang on, we're integrating the PDB dataset [3:36 PM]

TomoeUzumaki: whoa [3:36 PM]

machinelves: ohhhh motif atlas? i.e. database of structures? :D :D :D [3:36 PM]

TomoeUzumaki: :D [3:36 PM]

Brourd: http://rna.bgsu.edu/rna3dhub/motifs [3:37 PM]

jnicol: we can write a description for the lab summarizing how the motifs have to be used [3:37 PM]

Brourd: there you go machinelves. [3:37 PM]

machinelves: thank you brourd! [3:37 PM]

Eli Fisker: John, sounds good [3:37 PM]

Eli Fisker: thx, Brourd [3:38 PM]

vineetkosaraju: i'm not sure if its the exact same one, but I know is that there are over a 1000 of these motif structures that you use as jigsaw puzzles [3:38 PM]

Brourd: So, back to the paper projects. Dr. Das wants descriptions to be written at the bottom? [3:38 PM]

TomoeUzumaki: descriptions for the 3D interface or mimics? [3:38 PM]

Brourd: Yes, I belive that was the one Dr. Joe pulled all of his motifs from. [3:38 PM]

jnicol: @b, correct [3:38 PM]

Brourd: How long does he want the conclusions to be? [3:38 PM]

machinelves: i didn't realize the 3D effort was connected to the motif effort. *happy dance* [3:39 PM]

jnicol: Dr Das volunteered to write the first couple of conclusions, to be sued as examples [3:39 PM]

jnicol: *used [3:39 PM]

jnicol: around 150 words [3:39 PM]

Brourd: Ah. I was goign to say, my lawyer is not here right now. [3:39 PM]

jnicol: there will be a cutoff around that length [3:39 PM]

Brourd: So, any images or anything like that? [3:40 PM]

Brourd: Or strictly text [3:40 PM]

jnicol: I'm we can have images :) [3:40 PM]

jnicol: *sure [3:40 PM]

machinelves: Thanks to Rhiju for making some examples, that is a good idea. i am still wondering - will these conclusions be published verbatim, or get further revision before going to publication? [3:40 PM]

jnicol: typing is off today?? [3:40 PM]

Brourd: Fabulous [3:40 PM]

machinelves: cool idea to include images. graphs / stats [3:41 PM]

jnicol: I'm sure the submissions to the journals will be modifications from the conclusion [3:42 PM]

Brourd: Expanded and modified. Yes. [3:42 PM]

machinelves: cool thanks, i was wondering how much processing the paper labs get between eterna & journal [3:42 PM]

jnicol: he just wants to give a player reading the lab some feedback as to the outcome, and perhaps spark some further interest [3:43 PM]

machinelves: that reminds me, the other thing I wanted to voice support for is to get lab data in a spreadsheet format through download button, to help with making graphs for paper lab conclusions [3:43 PM]

machinelves: but i understand that one will take more time! so if you're busy this week, i'll keep it on the list for next time. [3:43 PM]

Brourd: ah [3:43 PM]

Eli Fisker: This would very much help with analysis [3:43 PM]

jnicol: yes, I saw your and Eli's request [3:43 PM]

Eli Fisker: and graph making [3:44 PM]

machinelves: i think conclusions will help people understand why they are doing labs in the first place, why they are different from puzzles [3:44 PM]

jnicol: analysis is something I am very interested in [3:44 PM]

machinelves: me too! [3:44 PM]

jnicol: AEli, do you remember the original spreadsheets that I made from the early labs? [3:45 PM]

Eli Fisker: Yes [3:45 PM]

Eli Fisker: I liked them [3:45 PM]

Brourd: Being paid would be a nice change of pace as well :) [3:45 PM]

jnicol: Are you asking for something like that? [3:45 PM]

Eli Fisker: They were a help to me [3:45 PM]

Eli Fisker: Something like that [3:45 PM]

Eli Fisker: Yes [3:46 PM]

jnicol: If you and elves come up with a sample format (dont go crazy) it would help me [3:46 PM]

machinelves: yes, basically output each value into a cell in the spreadsheet, rather than single text string [3:46 PM]

jnicol: unless you want something very similar [3:46 PM]

Eli Fisker: Basically the data which is in the lab [3:46 PM]

Eli Fisker: I can copy the info out from the new UI, but I can't dump it in a spreadsheet [3:47 PM]

machinelves: kk - good idea. will do. to start, i was thinking of using the values in the existing lab table, since we can sort and modify columns in the existing interface [3:47 PM]

jnicol: A cell per base shape value [3:47 PM]

Eli Fisker: I basically want it in a spreadsheet for further processing [3:47 PM]

jnicol: ? [3:47 PM]

machinelves: so output would be whatever is currently displayed in table [3:47 PM]

Eli Fisker: John, yes [3:48 PM]

machinelves: breaking up categories into rows / columns. yes one cell per base shape value [3:48 PM]

Eli Fisker: As is everything I copy out from the lab interface ends in one cell [3:48 PM]

machinelves: i twith nt position correlated in preceding row [3:48 PM]

machinelves: * with nt position [3:48 PM]

Eli Fisker: I don't know which spreadsheets are good for graph making and further analysis [3:49 PM]

jnicol: Here is an example I made from an old lab: [3:48 PM]

jnicol: https://docs.google.com/spreadsheet/ccc?key=0Apw3bnrsZxDbdG9hck42dTJIelJwcmZiSU1kZmd5bEE&usp=drive_web#gid=0 [3:49 PM]

Eli Fisker: So is this a spreadsheet we can make graphs based upon? [3:49 PM]

Eli Fisker: Meechl is making cool graphs from lab data and so is Omei [3:49 PM]

Eli Fisker: I don't know which is best for what will be easy to work in [3:49 PM]

jnicol: Can you send me a link for an example of theirs? [3:50 PM]

Eli Fisker: Yes, moment [3:50 PM]

Eli Fisker: https://docs.google.com/presentation/d/1dpigCJrTNwGCqtLjW2XChL4k3aqHJOpm6Z01-UV8go4/edit [3:50 PM]

machinelves: awesome thanks! john this spreadsheet you linked is a good example. i would move the sequence column last column position, split each nt base letter into separate cell / column, make each design have 3 rows,  [3:52 PM]

machinelves: null values for title columns in extra rows, populate one row with nt # position 12345, second row with AGCTG etc..., third row with shape value ( color coded if possible ) [3:52 PM]

jnicol: Looks like she used an overall summary, not a base by base analysis [3:52 PM]

machinelves: eli, thanks for the link haven't seen that [3:53 PM]

Eli Fisker: And Omei's graphs [3:53 PM]

Eli Fisker: https://getsatisfaction.com/eternagame/topics/discovery_that_padding_strategy_seems_to_affect_reactivity_error [3:53 PM]

Eli Fisker: Elf, np [3:54 PM]

machinelves: cool! i didn't know this one either [3:54 PM]

RedSpah: Hi All [3:54 PM]

Eli Fisker: Hi Red [3:55 PM]

machinelves: actually maybe nt # position only needed once, in a meta header row, per project, since all designs have same # nts in one lab, right? or not? [3:55 PM]

machinelves: hi red! [3:55 PM]

RedSpah: Hi Eli, Elves [3:55 PM]

jnicol: I think I can come up with some samples for you to look at Eli, thanks for the examples [3:55 PM]

jnicol: Hi RedSpah [3:55 PM]

Eli Fisker: Thx, John :) [3:55 PM]

Eli Fisker: and np [3:56 PM]

TomoeUzumaki: hey Red! [3:55 PM]

RedSpah: Hi John, Tomoe [3:56 PM]

jnicol: I am leaving in a few minutes, any last questions? [3:56 PM]

machinelves: would you like dev chat wiki posted as link in dev chat comments, PM you, or how to deliver? [3:57 PM]

machinelves: transcript i mean [3:57 PM]

jnicol: link in news items is fine, thankyou! [3:57 PM]

Eli Fisker: Bye John [3:57 PM]

machinelves: you got it! thanks for all your hard work! hope you have a good week [3:57 PM]

jnicol: Thanks everyone for a great talk! [3:57 PM]

Eli Fisker: :) [3:58 PM]

machinelves: likewise! :D [3:58 PM]

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