2013.05.29 Dev Chat

From Eterna Wiki

( Link back to Dev Chat archive )


On Lab Interface Improvements


jeehyung : Hi all ; ]

lroppy : hi

jandersonlee : any news first Jee?

lroppy : on for 15

Matt-Indykiewicz : Hello L

Zanna : hi jee

hoglahoo : Hi jee! summer's almost here!

jeehyung : @janderson ok news first : ]

jeehyung : the late scoring results are on their way, we just have to fix a final error. Hopefully by the end of the week.

jandersonlee : nice. tanks

jeehyung : There will be also small updates to the cloud labs, adding searching feature, etc.

Eli-Fisker : Sounds nice

jandersonlee : a delete button?

Eli-Fisker : Great, saved me some questions

JR : can we propose a switch by putting "Switch" in the title and state 2 in the comments?

Matt-Indykiewicz : Nice

jeehyung : Also a powerful addition to scripting interface is coming - it's now equipped with 2 versions of ViennaRNA which will allow you very deep analysis of RNA....and there also will be an RNA rendering tool + on-site sequence scoring / puzzle solving button as well

jeehyung : @janderson - yes the delete button will be there

jandersonlee : wow!

jandersonlee : @jee: thanks

TomoeUzumaki : a delete button for what?

Eli-Fisker : Jee, so we will be able to search for a particular lab?

jeehyung : @JR unfortunately switches won't yet be supportd for this version

JR : np

jeehyung : @Eli yes- you'll be able to run a script by specifying a puzzle id

TomoeUzumaki : ok

jeehyung : it'll try to score all designs submitted to the lab and return them

TomoeUzumaki : gotta go

TomoeUzumaki : byee

jeehyung : So you'll be able to run any scoring script you like before you vote, etc

jeehyung : @Tomoe bye : ]

Eli-Fisker : bye Tomoe

Eli-Fisker : That is real cool, Jee

Eli-Fisker : Then I got a question anyway.

jandersonlee : @Jee: so what is the scoring script API?

jeehyung : @Eli sure what is it?

Eli-Fisker : I will like to have a search field on the past lab page. I will love to be able to search for a particular lab, so I don’t have to look through lots of pages to find it.

jeehyung : @janderson it can be any script that takes in sequence/structure and output scores in 0~100 range

jandersonlee : seqeunce + strucrre as two parameters?

jeehyung : @Eli - that search is coming. For past labs, active labs and proposed labs page

Eli-Fisker : Great

Eli-Fisker : :)

jeehyung : @janderson yes two separate parameters

jandersonlee : OK thanks for the clarification

jeehyung : Also, we are almost ready to launch the web version of voting interface, which will allow much faster browsing/voting process

jandersonlee : nice!

Zanna : yea!

Eli-Fisker : Yay. Looking forward to that

lroppy : can we please separate design phase from voting phase

jeehyung : it now renders the rna / experimental results on the fly, so you don't have to go into the game every time to inspect the design

lroppy : first

Matt-Indykiewicz : Yay....Delayed Recation

Eli-Fisker : @Jee, I have another big wish for the lab interface

jeehyung : @lroppy that is on the way too. The web version was started before the phase idea came out so we'll probably releast the web voting browser first, then move onto phase idea

jeehyung : @Eli what is it?

Eli-Fisker : Could we get to view the labs like this so we can see the structures. That will help us pick out the shapes we are searching for. We will be able to see much more labs at once and locate the right one fast.

lroppy : thx

Eli-Fisker : https://d37wxxhohlp07s.cloudfront.net/s3_images/791094/c59447d6-fa89-43b6-97d5-386b984b15de.jpg?1347544196

Eli-Fisker : Here is an example by Mat

jeehyung : @Eli - I'll add that to the task list. Probably we can just add an "alternate view" mode

Eli-Fisker : Which reminds me, that I miss very much seing the structure of the design on the entrance page of the player projects

Eli-Fisker : The picture tells me if I want to look at the design, when I'm in a search for a structure

Eli-Fisker : Big thx

Eli-Fisker : I will like an all work dedicated interface free of hall of fame, for when solely doing lab work

lroppy : Jee - do we have a central location to report bugs? or keep sending them to you?

hoglahoo : huh, I've been using the "Report a problem" tab on the eterna forum

jeehyung : @lroppy if you report bugs to the forum they are periodically collected to our internal issue tracker.

jandersonlee : @Jee: is there an AjaxManager query that returns all lab ids? it would help to mine the lab data

lroppy : k thx

hoglahoo : glad to know it's being watched :)

jeehyung : @janderson there isn't yet. You can query Justin for that - he can add the function easily for you.

jandersonlee : @Jee: also there are still scoring problems with bad secstruct data. the script can solve it but does not get credit

jeehyung : @janderson by bad struct do you mean those with characters other than "(.)"?

jandersonlee : yes

jeehyung : I see - I'll query Justin about that. Sorry about the trouble.

Eli-Fisker : @Jee, did you find out about what caused the script interface fail on that puzzle Mat found and yet the sequence the test server put out, were a perfect solve for that puzzle it just failed?

Eli-Fisker : sent a mail about it

jandersonlee : is that the one wth the blank at the end?

jeehyung : @Eli unfortunately, not yet. I haven't had a time to look into it yet (it's the msg you sent me today right?)

Eli-Fisker : Yes, sorry, message

lroppy : low priority - but is there a reason why some names in chat lead back to userIDs that are different? can be a bit confiusing.

Eli-Fisker : It is happening regularly.

Eli-Fisker : Mat says that player names linked to the wrong profile is an old issue

hoglahoo : Is this thing still on?

jandersonlee : @Jee: Nando pointed out that proposed labs can be viewer in the lab tool by changing the url.

jandersonlee : it would be nice to have that link on the review page

jandersonlee : so we can see locked bases etc

Eli-Fisker : Agree with JL

jandersonlee : give them a test drive before signing the lease :)

Eli-Fisker : hehe

jeehyung : @lroppy, Eli - noted the bug. Will work on it!

Eli-Fisker : thx

lroppy : k thx

jeehyung : @janderson - you mean we need a way to preview the proposed lab - correct?

jeehyung : preview the lab in the game

jandersonlee : yes. it already works - just need the link

jeehyung : yes definitely. We'll allow previewing/replaying the proposed/past labs in this update

jandersonlee : viewed as game/puzzle i believe

jandersonlee : (in a forum thread)

jandersonlee : thanks!

Eli-Fisker : @Jee, in the update, are we getting a sort option in the labs?

Eli-Fisker : I wish to get the labs sorted after Static labs and Switch labs and Player projects.

lroppy : gtg thx Jee and all bye

Eli-Fisker : Just like the tags for lab that says current lab and past lab.

Eli-Fisker : bye Iroppy

starryjess : the last group of labs that just closed don't have a review botton to get into them

jeehyung : @lroppy bye!

jeehyung : @Eli no sort optins in this update - but I'll add that task

Eli-Fisker : Big thx. It will make it a lot easier

jeehyung : @starry that came up - we'll put those buttons back in our next update. Sorry about the trouble

Eli-Fisker : Jee, one more thing. When looking through the past labs pages, I have to go to the bottom of each page to get to the next

Eli-Fisker : Can't we have that option on the top too?

jandersonlee : more feedback on the labs summary page would be good: eg.g how many slots/votes left

jeehyung : @Eli putting the pager on the top?

jeehyung : @janderson noted!

Eli-Fisker : Yes, or make the pages with labs shorter, a la mat's idea with pictures of the labs

jandersonlee : also how many candidate seqeunces submitted

Eli-Fisker : instead of long hall of fame for each lab. As an option

Eli-Fisker : for faster navigation

jeehyung : @Eli ok noted. All the noted feedbacks will be added to the task tracker.

Eli-Fisker : Jee, thx :)

jandersonlee : Jee: Is there/will there be documentation on teh coming script interface library updates?

jeehyung : @janderson - Justin is preparing that. You should let him know if you have any functions/codes you want to be deployed/documented in the official interface

jandersonlee : I haven't got the local interface to work so nothing to add yet :P

jeehyung : @janderson if you are having trouble setting that up, please let me and justin know. We should fix that : ]

jandersonlee : ok tx.

Eli-Fisker : Jee, on the votes for the lab player projects, I have a comment. Can we at least have something like 60 slots pr lab as a default? Some may choose to not participate in a lab, if they don't think they have a chance to get synthesized. I mean if the lab only claims 40 slots or less.

jandersonlee : Yes a larger default please say 1/20th of the estimated run (80?)

jandersonlee : Baucause more that 20 labs is bonkers!

Eli-Fisker : Fine point JL

Eli-Fisker : Also it will make it more merry afterwards when getting the data

jeehyung : @Eli,janderson - noted. That'll be included in the next update

jandersonlee : Because more than 20 labs (at once) is bonkers!

Eli-Fisker : it is better having 80 results in the same lab than 20 results in 4 labs

jandersonlee : tqvm

Eli-Fisker : Much better for finding what is good and why

Brourd : Seems like a waste of slots to spend 80 on a single design, especially one repeated 5 times

Brourd : I had to push that out there :)

jandersonlee : You can lower the default if you like

Brourd : Of course, but then, that brings back the "More than 20 labs is bonkers idea"

jandersonlee : Like only 10 will be chosen...

Brourd : Oh by the way, hi Jee, hope you day has been going well so far

jandersonlee : and I wil likely pass on the low slot number labs if I don't have time to do them all

jandersonlee : which is fine too

Eli-Fisker : @Jee, I have a suggestion from Mat

Brourd : Yes, it is rather difficult to determine, for one, we could just make the default for every lab 60 or 80, but then it pushes smaller labs out of the loop, and I for one do not see 80 slots for a lab like RNA strength being a good idea

jeehyung : hi Brourd : ]

jeehyung : @Eli oh what is it?

Eli-Fisker : Have the sort option for the “See results of player puzzles” list. We will like to be able to sort The “Result” columns after Pass/Fail.

Brourd : Hey Jee :)

Eli-Fisker : We will also like to be able to sort after “Time(sec)”, so it sort by length of time longest and shortest.

Eli-Fisker : In here:

Eli-Fisker : http://eterna.cmu.edu/web/script/test/2896089/

jeehyung : @Eli noted

Eli-Fisker : Thx :)

Brourd : I do hope I didn't throw too many ideas out into the cloud lab feedback Jee :)

jandersonlee : Some realy good ones though :)

jeehyung : @Brourd, janderson agreeed: Very good ones.

jeehyung : Thanks everyone for the feedbacks : ]

Brourd : Yes, I saw all the stars, I personally like the idea of the multiple targets per project idea

Eli-Fisker : :)

jandersonlee : And fully automated labs for testing combinatorial issues?

Brourd : Since all the targets like the recent Zigzag lab proposals would fall under one umbrella project

jandersonlee : E.g. exhaustive testing of loop closures

jeehyung : Everyone I'll have to leave in 5 minutes now : ] Please throw in final questions/suggestions!

Brourd : well, the thing is, I am not looking for a "one time" result with my projects, but more of an average

jandersonlee : then you need more than 12 result :)

Eli-Fisker : @Jee, Mat also had an idea for the script server: Dev could have different categories of run time based on the puzzle size. A few seconds for a larger puzzle is like trying to have an instant answer.

Brourd : Oh, Jee, the "latest played puzzle" in the player profiles seems a bit buggy

jeehyung : @Eli noted!

jeehyung : @Brourd can you tell me how it's buggy?

Eli-Fisker : thx :)

Brourd : @ janderson - actually, with that lab, you will be surprised. It is mostly to confirm my observations in Quasispecies labs

starryjess : it doesn't seem to be working

starryjess : there is nothing in it

starryjess : the "latest played puzzle"

Brourd : Yes, and on new profiles I believe it just shows {titl}

Brourd : *{title}

starryjess : once I saw one that said {title}

Zanna : I've never seen one say anything at all

hoglahoo : talking profiles, what will they think of next?

Eli-Fisker : Talking puzzles

Eli-Fisker : ;)

Zanna : haha

hoglahoo : that would be Brourd

starryjess : lol

Brourd : and, on the new filters for switch and single only

Brourd : I do not believe anything shows up, unless I am doing it wrong

Brourd : http://eterna.cmu.edu/web/playerpuzzles/?switch=fail&sort=date

starryjess : yep didn't work for me either

jeehyung : @Brourd, starrry I confirmed the problem. The bug will be added to the tracker. Thanks!

Zanna : doesn't work for me either, Brourd

Brourd : http://eterna.cmu.edu/web/playerpuzzles/?single=fail&sort=date

jeehyung : Also the switch/single problem has been noted as well

Eli-Fisker : @Jee, I was having a problem in the WIKI while trying to edit. The tool icon boxes are so small I have trouble seeing the icons.

Brourd : And I am not entirely sure it should say switch/single=fail

Eli-Fisker : I can off cause hover over them with my mouse or enlarge page in my browser setting. But everything else has a fine size.

jandersonlee : off cause == of course

Eli-Fisker : hehe, chat has spell check

jeehyung : @Eli noted!

Zanna : lol

Eli-Fisker : Great, thx, Jee

jeehyung : ok I have to run everybody. Thanks for all the feedbacks today.

starryjess : hahaha, jl, you always wanted spell check. Now you are it :P

Zanna : bye jee

jandersonlee : thanks again

starryjess : bye jee

jeehyung : Please PM me if you have any other concern