2016.05.06 Dev Chat

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On OpenTB Challenge Release!!!, NUPACK & Snowflake Freeze Button, DPAT & SARA Presentation in 2 Weeks, News Releases, EternaCon, Meta Dot Plot Summer, & Thanks to All! 


[11:59] macclark52 Dev Chat!

[11:59] Jennifer Pearl yay

[11:59] LFP6 Indeed!

[11:59] machinelves huzzah!

[12:00] LFP6 So how's everyone today?

[12:00] whbob Great!

[12:00] macclark52 Out of class for a change.  What a treat!

[12:01] machinelves good LFP6, how are you?

[12:01] Jennifer Pearl huzzah! indeed!!!!!!

[12:01] LFP6 Good, good

[12:01] machinelves hi mac, congrats

[12:01] Jennifer Pearl im doing good. just got back from Boston

[12:01] machinelves hi Jen, lol

[12:01] macclark52 Meeting, Jen?

[12:01] machinelves super cool!!

[12:01] LFP6 Finishing up some code so you all can see the structures in the Data Broser

[12:01] Jennifer Pearl 12 hours of lectures on machine vision and anational cert test

[12:01] Jennifer Pearl national

[12:01] machinelves that sounds awesomeeeeeeeeee

[12:01] Jennifer Pearl right!!!

[12:02] jnicol I don't think having consecutive uids is an issue, you need the login info connected with the uid to be able to see the personal info of a user.

[12:02] jnicol just answering a previous concern posted

[12:02] Jennifer Pearl hung out at Fenway Park afterhours for a big party

[12:02] machinelves there is a hack announced in a documentary and various news outltes about incrementing a URL to get user ids ( and sending the person to jail )

[12:03] macclark52 Well, that sounds fun.  

[12:03] LFP6 @Elves: Link?

[12:03] machinelves sorry LFP that's off the top of my head but google may help let me see

[12:03] rhiju hi everyone, thanks for coming to dev chat!

[12:03] macclark52 Fenway, not jail. 

[12:03] BrosefStalin hi

[12:03] LFP6 Btw Jnicol, thanks for writing that my unsolved puzzles script, I am now diving into JS because of that ^.^

[12:04] LFP6 @Elves Thanks

[12:04] machinelves hi Rhiju!

[12:04] Jennifer Pearl hi Rhiju

[12:04] whbob Hi rhilu

[12:04] BrosefStalin I just joined to try and solve this puzzle i've been stuck on lol

[12:04] whbob *rhiju

[12:05] BrosefStalin also hi rhilu

[12:05] LFP6 And  hi Rhiju!

[12:05] rhiju congrats to everyone (including devs) in releasing the openTB challenge!

[12:05] machinelves Huge congrats!!! Yay!!!

[12:05] Jennifer Pearl its super cool

[12:06] whbob Quite a challenge

[12:06] BrosefStalin Lol I tried that when I first started. It is very complicated it feels like.

[12:06] machinelves now we can work towards solving problems for a specific disease which is a lot easier to explain than saying theoretical physics of how RNA folds lol

[12:06] Jennifer Pearl going to get DPAT working with NUPACK and cant wait for the first round of data to come back to run it through DPAT

[12:07] BrosefStalin I like this website

[12:07] LFP6 Happy to hear!

[12:07] machinelves awesome Jen!

[12:08] BrosefStalin I wish I had found about it earlier than I did. I like figuring out the way to get the rna to fold correctly.

[12:09] MasterStormer ?hello!

[12:09] Jennifer Pearl @bro it is fun

[12:09] rhiju @jennifer were you planning on doing a hangout describing SARA?

[12:09] BrosefStalin @Master Hi

[12:09] rhiju I know you've got some interesting results with the last round(s?) of experimental data

[12:09] Jennifer Pearl I did not hear back from you so I did not schedule it until next week

[12:09] Jennifer Pearl im at work today

[12:09] jnicol Hey Jen, was all the data uploaded correctly for Sara's submissions?

[12:09] Jennifer Pearl i looked over it again and it looks ok now

[12:10] MasterStormer @Any dev: I talked ?a bit earlier in the chat about security earlier; ?basically I heard that if the id of users increaments my one ?for each user then the site is less secure. Are you aware of that?

[12:10] Jennifer Pearl just the names werer missing

[12:10] BrosefStalin @Jen The thing most interesting for me is how the Guanine "boosts" other bases.

[12:10] Jennifer Pearl controlled missmatching

[12:10] jnicol @Master, I answered that above, the uid needs to connected with login credentials, so there should not be a security issue

[12:11] MasterStormer @jnicol didnt think you would see my previous message to answer it; ?good to know

[12:11] machinelves https://www.techdirt.com/articles/20130929/15371724695/dojs-insane-argument-against-weev-hes-felon-because-he-broke-rules-we-made-up.shtml

[12:12] Jennifer Pearl @rhiju I sent you an email with my presentation. FYI

[12:12] jnicol @jennifer, the names are missing? Is it anything I am able to fix?

[12:12] Jennifer Pearl they were missing but it got fixed it looks like

[12:12] LFP6 @Elves Thanks

[12:12] machinelves np

[12:12] macclark52 New TB tutorials are running really slow for me.  Is that just due to a lot of user activity?

[12:14] Jennifer Pearl @rhiju concerning the interesting data. According to Eli in one of his forum posted Sara got the abolut highest score in one of the sublabs if you factor in fold change

[12:14] jnicol @macclark, I believe the NuPACK algorhithm is slow for everyone

[12:14] machinelves whoa!!

[12:14] Jennifer Pearl She got alot of 100's

[12:14] Jennifer Pearl first tim ein use

[12:14] macclark52 Ah, OK.  Thanks. 

[12:14] Jennifer Pearl yay!!!!!

[12:14] LFP6 Nice!

[12:15] BrosefStalin @AnyMod So if eterna was something that could be downloaded then could the Tb  thing run faster? Or is that just how long it takes the program to calculate the things?

[12:15] jnicol @macclark and all lab users, there is a tutorial on using the freeze button to be able to controll when the calculations run

[12:16] MasterStormer ?@mods For me (in any pc) the in-game-chat sometimes disapear, so I have to turn it off and on. Do you know how to fix it?

[12:16] Jennifer Pearl also was able to predict good and bad designs using a few differnt methods

[12:16] Jennifer Pearl I think my new methodology isshowing much promise

[12:17] jnicol that should help some when changing bases and waiting for the calculations

[12:17] macclark52 I just noticed that.  It helps!  Thanks, Jnicol.

[12:17] machinelves Congrats Jennifer, that's wonderful news!

[12:17] joy45 The actual TB challenge puzzles don't really drag until you get to the last two (with four inputs).

[12:18] jnicol yes, te more oligos used in a puzzle, the slower the design process gets

[12:18] BrosefStalin You all are talking about the TB challenge which is more advanced than this tutorial puzzle I'm on

[12:18] BrosefStalin http://www.eternagame.org/sites/default/files/chat_screens/231586_1462562326.png

[12:18] BrosefStalin lol

[12:19] macclark52 The freeze tutorial has 4-5.

[12:19] BrosefStalin 4-5 what?

[12:19] macclark52 4-5 oligos that need to bind to the main RNA strand. 

[12:20] BrosefStalin ok

[12:20] BrosefStalin Well I'll solve this eventually

[12:20] LFP6 Btw my dad just pointed out that we were featured in the WSJ. Got an article and a video!

[12:20] LFP6 http://www.wsj.com/articles/videogamers-are-recruited-to-fight-tuberculosis-and-other-ills-1462290212

[12:21] LFP6 http://www.wsj.com/video/gaming-in-the-name-of-science/D357E351-A235-400E-BC93-E75933F69A39.html

[12:21] BrosefStalin oh that's great

[12:21] jnicol Thanks LFP6

[12:21] machinelves sweet!

[12:21] LFP6 On an unrelated note, my dad tried to reset his password and it refused to send the email... Could a dev look into taht?

[12:21] machinelves *runs into paywall*

[12:21] LFP6 Yeah...

[12:22] macclark52 Wow, that is terrific.  Good for Rhiju. 

[12:22] jnicol @LFP6, send me the details (username)

[12:22] Jennifer Pearl I have a plug for Eternacon real quick

[12:22] LFP6 @jnicol: K

[12:22] BrosefStalin What is structure notation?

[12:23] LFP6 Looks kinda like this: ...(((....)))....

[12:23] LFP6 THe dots are unpaired bases, the parenthesis are paired

[12:23] MasterStormer It is how the desighn should look at the end

[12:23] BrosefStalin Oh I see

[12:24] machinelves heh the video is cool, this is great for promotion of citizen science

[12:24] BrosefStalin Bbl

[12:24] LFP6 @John PM

[12:24] jnicol thx

[12:24] Jennifer Pearl We are trying to rais emoney for Eternacon and I would like to ask everyone to please share this link on social media to helpo us raise money for player travel funding for Eternacon

[12:24] LFP6 Thanks for looking into it

[12:24] Jennifer Pearl https://www.gofundme.com/fgv2qu6c

[12:25] Jennifer Pearl you can find out more about eternacon here. http://eternawiki.org/wiki/index.php5/Eternacon

[12:25] hoglahoo Is anyone else having trouble working in a playthrough puzzle after having just solved it? ie after having clicked the X in the upper right. Seems like the page always freezes after mutations

[12:25] machinelves thanks Jen!

[12:25] Jennifer Pearl This is very important. Please share teh GoFundMe link!!

[12:25] LFP6 @Hog: Yes, I noticed that

[12:25] joy45 *hoglahoo I have run into that consistently.

[12:26] LFP6 Every puzzle

[12:26] LFP6 I think

[12:26] LFP6 Definitely the tutorials

[12:26] hoglahoo thank nando for beam to puzzlemaker!

[12:27] machinelves thank you Nando!

[12:28] Jennifer Pearl @rhiju Just a quick check. Am I going to be giving my presentation next week for sure?

[12:28] Jennifer Pearl I am ready

[12:30] machinelves next week I think is Community Chat so the slot should be available

[12:32] Jennifer Pearl cool

[12:32] worseize http://prnt.sc/b132lu Check thisHello  everyone ! 

[12:32] machinelves I'm excited, thanks for preparing something to explain to us Jennifer!

[12:33] Jennifer Pearl There will be 2 presentations online and one at Eterancon

[12:33] BrosefStalin me

[12:33] machinelves hello! welcome to eterna, we're having dev chat. any bugs or issues with the new Open TB release, please let us know!

[12:33] Jennifer Pearl tyhe first one will be on DPAT, Remmy and Sara and what they are and how they work

[12:33] BrosefStalin @hoglahoo can you help me with this

[12:34] BrosefStalin http://www.eternagame.org/sites/default/files/chat_screens/231586_1462563244.png

[12:34] Jennifer Pearl then then next one will be on the data from the last FMN lab and how sara performed

[12:34] Jennifer Pearl then both will be combined for a big presentation at Eternacon and maybe a demo

[12:34] BrosefStalin I just can't seem to make it want to fold

[12:34] BrosefStalin at least not in the right places

[12:34] Jennifer Pearl use tape

[12:34] BrosefStalin lol

[12:34] Jennifer Pearl sorry

[12:35] BrosefStalin no dont be that was funny

[12:35] Jennifer Pearl lol

[12:36] BrosefStalin is hogla afk?

[12:36] hoglahoo yeah

[12:36] BrosefStalin ok

[12:36] Jennifer Pearl its hogs ghost

[12:36] BrosefStalin he is having an out of body experience

[12:37] Jennifer Pearl @hog dod you get my last email

[12:37] machinelves yay! it's so cool to see your research evolve and I'm really grateful you've kept working on it, since that is the kind of thing that will push our predictive ability forward

[12:37] machinelves hoglaBOO!

[12:37] BrosefStalin #spooked

[12:37] Jennifer Pearl @elves kinda burnt myself out a little bit adn have taken alot of time off. I think I am finally getting recharged

[12:38] whbob @ Bro: you need a boost in the loop.

[12:38] hoglahoo @Jennifer-Pearl, yes! I thought I replied, but apparently I did not. I will email you directly henceforth

[12:38] BrosefStalin ok

[12:38] BrosefStalin @whbob I'll try that

[12:38] Jennifer Pearl thanks. can you send it to my personal email

[12:39] machinelves @Jennifer that's cool that you caught a second wind. I stand amazed at how much you have done, so don't worry about the time

[12:39] hoglahoo will do

[12:39] Jennifer Pearl i really did get alot done in 8 months

[12:40] Jennifer Pearl developed 3 prgrams to analyze, design, and predict RNA

[12:40] Jennifer Pearl 10,000 lines of code in total so far

[12:40] BrosefStalin I wonder how much it costs to synthesize all the rna people design on here?

[12:40] machinelves yeah and it wasn't easy peasy pudding pie, it was hardcore data analysis and coding. you deserve a medal! okay maybe it will be made of electrons and not metal, but nonetheless...

[12:40] Jennifer Pearl I still have sooo mcuh to code  up though

[12:41] LFP6 One line at a time

[12:41] machinelves hehehe

[12:41] Jennifer Pearl NUPACK is next

[12:41] Jennifer Pearl I have a question for everyone then

[12:41] BrosefStalin Coding should be taught as a second language at schools

[12:41] Jennifer Pearl what do you want more

[12:42] LFP6 Yes?

[12:42] BrosefStalin More what?

[12:42] Jennifer Pearl the ability to find patterens in where the oligos make stacks of the abilty to look at a dot plaot and know instantly what scores have what structures

[12:42] machinelves oooooo

[12:42] Jennifer Pearl a dot plot color map with the stacks iwth colors showing how many designs have that stacks

[12:42] Jennifer Pearl or feature

[12:43] Jennifer Pearl or nuc in general

[12:43] LFP6 That would be pretty slick

[12:43] machinelves wait a meta dot plot?!?!

[12:43] Jennifer Pearl one or the other casue that will take awile to code

[12:43] Jennifer Pearl yep

[12:43] BrosefStalin probably find wher ethe oligos make stats i guess

[12:43] machinelves awwww that is genius!!

[12:44] Jennifer Pearl meta dot plot has been a goal since day one

[12:44] BrosefStalin lol it hyperlinked wwww

[12:44] worseize Could i ask a question ?  Is there ability to copy paste sequence but no all only part? 

[12:44] Jennifer Pearl i know how to do it too just need time

[12:44] Jennifer Pearl I can only focus on one unless I et more volunteers to code up stuff

[12:44] LFP6 @worseize: No, sorry

[12:44] LFP6 You can make a forum post to suggest it though!

[12:45] Astromon hi

[12:45] LFP6 There has been similar requests, I think...

[12:45] LFP6 Hey astro

[12:45] BrosefStalin I would volunteer to help code but I only know apple basic for the apple 2 computer

[12:45] Jennifer Pearl I coding in C#

[12:45] machinelves meta dot plot i think would produce most actionable results, but that is a guess

[12:45] BrosefStalin yeah

[12:45] whbob Hi Astro

[12:45] Jennifer Pearl @elves I agree

[12:45] machinelves if we can average out success then we can even through bot generated input at it

[12:45] LFP6 @Jen: Le me know when you want to look at setting stuff up on Github, we can chat about how you want to have things structured

[12:46] machinelves throw

[12:46] Jennifer Pearl players could design to the dot plot using the meta dot plot

[12:46] machinelves yes!

[12:46] machinelves exactly

[12:46] machinelves omg i love it

[12:46] Jennifer Pearl and it would give everything in the RAW DPAT files in a graphical presentation that can be digested in moments

[12:47] Jennifer Pearl DPAT cna generat 3,000 ines wiht 3,000 columns of data on agood day

[12:47] machinelves that would help with the bottleneck of mystery, if we can lean on generated initial inputs, then use the refined meta dot plot to narrow down design strategies

[12:47] BrosefStalin Can eterna be accessed on mobile?

[12:47] Jennifer Pearl so kinda hard to filet without knowing what to filetr for but meta dot plot is like BAMN here you go

[12:47] BrosefStalin oh well I got to go

[12:47] BrosefStalin Bye!

[12:48] Jennifer Pearl bye

[12:48] machinelves only with a flash enabled browser like Photon on iOS

[12:48] Jennifer Pearl filter not filet

[12:48] macclark52 Jennifer you have some special kind of brain. 

[12:48] MasterStormer Whenever I mutate something, the screen becomes dark while its calculating. ?why is it like that?

[12:48] machinelves yeah Jennifer you're right the ability to see the information instantly and rapidly is a huge help

[12:49] Jennifer Pearl ok. So I think meta dot plot after nupack

[12:49] machinelves woot!

[12:49] Jennifer Pearl that is going to be a project in itself

[12:50] Jennifer Pearl have enough time too

[12:50] Jennifer Pearl I think I can use code from DPAT2 to make it go faster

[12:50] machinelves a worthy project at least

[12:50] whbob @ master: Sounds like the freeze fold tab is not activated.

[12:50] Jennifer Pearl already have the dot plot generator coded up

[12:51] Jennifer Pearl so import DPAT2 code to DPAT3 and then tweak and I think I could have it doen in a couple months

[12:51] Jennifer Pearl maybe 3

[12:51] MasterStormer What is DPAT?

[12:51] machinelves super cool!

[12:51] Jennifer Pearl Dot Ploit Analysis Tool

[12:51] MasterStormer ooh! a new button?

[12:51] gian666 is it possible that blye glue tool (i.e. alt+mouse) does not work in linux ?

[12:51] Jennifer Pearl It is the family of analysis programs I developed

[12:52] MasterStormer @gian you must choose a SINGLE bond-line; what I mean is that it isnt really smart

[12:52] Jennifer Pearl @masterStormer I will be giving a presentation on it next Friday at the same time as todays meeting

[12:52] rhiju hey everyone any more questions for devs? if not, we do have a quick question or two for you

[12:52] MasterStormer So did you try to glue something complex?

[12:52] machinelves

[12:52] MasterStormer friday is today, right?

[12:53] Jennifer Pearl yes

[12:53] Jennifer Pearl but next friday

[12:53] MasterStormer I mean ?im pretty much between friday and saturday here

[12:53] rhiju has anyone online tried the openTB starter challenges? were they doable? 

[12:53] Jennifer Pearl Here is DPAT's code. Sorry to interup Rhiju

[12:53] Jennifer Pearl https://getsatisfaction.com/eternagame/topics/dpat3-beta-2-0-released

[12:54] whbob I got through them ok.

[12:54] joy45 The starter challenges are fairly straightforward.  I thought it a good idea to structure things the way that you did.

[12:55] rhiju @joy thanks

[12:55] joy45 The actual TB challenge stuff is significantly trickier.

[12:55] Jennifer Pearl I havnt tried them. I dont really do anything other thatn y coding now and I let my programs design for me. I am lazy.

[12:55] machinelves @Rhiju you mean the tutorial within Open TB lab and not the puzzle progression?

[12:55] macclark52 I'm still working on the Freezer tutorial. 

[12:56] LFP6 @Elves: Yeah

[12:56] LFP6 There are multiple actually

[12:56] machinelves it's helpful that the tooltips explain why the calculations take so long, and how to use the snowflake freeze button

[12:56] LFP6 "starter" puzzles

[12:57] LFP6 After that one

[12:57] rhiju @joy haha yes the actual challenges are harder. neverthtless, somehow i'm guessing that they didn't take you that much time.

[12:58] machinelves are the calcs being done server side?

[12:58] rhiju @elves ok thanks. credit goes to @nando, @jnicol, @bekeep, and @calebgeniesse for the structuring & tips. they've put a lot of thought and iteration into it.

[12:58] rhiju no calcs are on your computer

[12:58] machinelves k thanks

[12:58] Jennifer Pearl thanks you guys

[12:59] rhiju @jennifer what do you think about presenting in 2 weeks? we could put up a blog post to advertise as well as in-chat reminder.

[12:59] machinelves thank you everyone, this is a very helpful way to learn with the step by step tips

[12:59] Jennifer Pearl @rhiju that sounds good. 

[12:59] rhiju it will be a good warmup to eternacon.

[13:00] Jennifer Pearl Do you want me to try to add my results into it then?

[13:00] Jennifer Pearl so that I do both DPAT and the results or do you want me to give another one 2 weeks after that one?

[13:00] rhiju great! send me a reminder, and i'll ask the dev team for help in advertising. maybe a couple weeks after that we can bug others to present stuff. 

[13:00] Jennifer Pearl on the lab results

[13:01] Jennifer Pearl ok

[13:01] rhiju @jen, how about lab results

[13:01] LFP6 On a completely unrelated note, I'm planinng on making a chocolate mold with the Eterna logo in tech

[13:01] rhiju ok everyone, i've got to run. 

[13:01] LFP6 Thanks Rhiju!

[13:01] rhiju @lfp6 -- take a picture, and post on your profile!

[13:01] rhiju bye 

[13:01] LFP6 Will do

[13:01] Jennifer Pearl I will integrate lab results into my presentation then

[13:02] Jennifer Pearl bye Rhiju

[13:02] whbob Bye rhiju.

[13:02] machinelves thanks Rhiju! Thank you Nando, Jnicol. Bekeep, Caleb, and all!!

[13:02] rhiju will talk again in 2 weeks, perhaps via hangout/broadcast as part of jennifer's presentation

[13:02] macclark52 Bye, Rhiju

[13:02] machinelves super cool!

[13:02] machinelves looking forward to it

[13:02] Jennifer Pearl already at 21 slides

[13:02] Jennifer Pearl will probablit go u to 40

[13:02] machinelves oh lol LFP6

[13:02] Jennifer Pearl oh fun

[13:03] worseize Why not all boosts work in NuPack lab ?

[13:03] machinelves see you all later, have a great weekend

see you all later, have a great weekend

[13:03] Jennifer Pearl El;ves can you post chatlog

[13:03] Jennifer Pearl i dont have a mouse

[13:03] Jennifer Pearl just a trackpad adn it is hard

[13:03] Jennifer Pearl with trackpad

[13:03] machinelves yep

[13:03] whbob Bye Elves

[13:03] Jennifer Pearl thanks

[13:03] Jennifer Pearl bye

[13:03] machinelves working on it

[13:04] machinelves bye!!

[13:04] Jennifer Pearl afk

[13:04] LFP6 @worseize Different energy models work differently

[13:04] LFP6 Some will change the energy impact of boosts, or maybe suggest no impact at all

[13:08] macclark52 Got an exam coming up.  See you all. 

[13:08] Astromon seeya mac