2014.08.06 Dev Chat

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On 3D & Chat Help Button

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

machinelves: woohoo! hello :) [3:00 PM]

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

vineetkosaraju: hello john :) [3:00 PM]

jnicol: hey vineet! [3:00 PM]

vineetkosaraju: thanks for adding the news post! [3:00 PM]

Brourd: Hey there jnicol. [3:00 PM]

jnicol: lots of excitement over the 3D interface [3:00 PM]

jnicol: hi Brourd [3:01 PM]

machinelves: yeah a huge congrats! thank you! [3:01 PM]

jandersonlee: my brain is still spinning (in 3D) [3:01 PM]

jnicol: any questions, suggestions? [3:01 PM]

jnicol: yes, 3D will take some getting use to [3:02 PM]

jnicol: Vineet, theer are comments under the news item and your blog [3:02 PM]

vineetkosaraju: we know that 3d is hard to use right now, but we are working on adding some features to make using the extensive motif library easier [3:02 PM]

machinelves: i haven't had a chance to play with the 3D release yet, but i am really looking forward to it! right now just taking a quick work break to ask about the possibility of getting a help button embedded in the chat window, for new players [3:02 PM]

machinelves: for the kids before school starts up [3:03 PM]

jandersonlee: is there some way to view the motifs so we can get a better idea of what they are and where they might fit or be useful? [3:03 PM]

Brourd: It seems Dr. Yesselman and Vineet are working on a feature for viewing all possible combinations at one time, correct vineet? [3:03 PM]

machinelves: here's a page in the wiki it can link to, with top 10 best places to start for new players http://eternawiki.org/wiki/index.php5/HELP [3:03 PM]

jnicol: I think one of the suggestions to be able to filter which motif can be used next is a good idea [3:03 PM]

vineetkosaraju: yes @Brourd, @jandersonlee we are currently adding a feature that will show where the ending point of all of the motifs are so you can just pick based on where you want to go  [3:04 PM]

jandersonlee: nice idea eleves +1 [3:04 PM]

vineetkosaraju: @jnicol I'm adding them slowly but surely to a github page :) [3:04 PM]

jandersonlee: @vineekosaraju that mihgt help thanks [3:04 PM]

jnicol: thanks for all the good work you are doing! [3:04 PM]

machinelves: thanks! Eli helped me get it together, and pulled all the best content. so that players don't have to search for it, we can just link, or maybe hoglahoo can add a handy .intro to linkbot :D [3:04 PM]

machinelves: @vineet, i really love the idea of this 3D motif toolbox for designing, i am looking forward to playing with it. thank you so much for all your hard work! [3:06 PM]

vineetkosaraju: thanks machinelves, I really hope you enjoy using it :] [3:06 PM]

jandersonlee: do the motis have 2D equivalente? that mihgt help us bridge the knowledge gap [3:07 PM]

jandersonlee: the names are Greek to me [3:07 PM]

Brourd: Some may, like a NgN/NgN 1x1 2-junction. [3:08 PM]

machinelves: hehe thanks! i know i will. yes, i agree with janderson, being able to see both 2D & 3D versions would be cool ( i haven't examined the interface, so i don't know if there is a feature for this already ) [3:08 PM]

stlnegril9: Hi @JN, Vineet and thx for 3D. Will the "feature that will show where the ending point of all of the motifs", show... [3:10 PM]

jnicol: its a great start, and we can give feedback, we can look back and say I remember when eterna first experimented with 3D :) [3:11 PM]

Brourd: Vineet, any ideas on whether or not the RNA can ever be longer than 90 nucleotides in length? [3:11 PM]

jnicol: hi stlnegril9 [3:11 PM]

stlnegril9: show which motif is able to be picked, e.g. hilight a possible endpoint and the motif name highlights/shows? [3:11 PM]

machinelves: before actually i was thinking a slider or button between 2D / 3D, but now I wonder if maybe a popup window of 2D like we can get for the dot plots, so we can see both at the same time, and wrap our heads around the structure? [3:11 PM]

jandersonlee: It's also unclear to me how to design a multiloop, loop, or hairpin with the 3D mode [3:12 PM]

vineetkosaraju: @Brourd, yes feel free to work with longer than 90 nucleotides [3:12 PM]

Brourd: There are none (right now) jandersonlee [3:12 PM]

Brourd: Currently, you are just connecting two points in space. [3:13 PM]

vineetkosaraju: @stlnegril9, we were thinking that it shows the ending points, and you can just click on the ending point and it will automatically load the motif, but it can also show the motif name [3:13 PM]

Brourd: a 2-junction is an internal loop. [3:13 PM]

jandersonlee: I was guessing that [3:13 PM]

machinelves: it's probably just because the first time i am visiting the 3D site, and also need to restart my browser, but i'm getting a hang on loading motifs http://prntscr.com/4a9pnd [3:13 PM]

Brourd: There are other motifs that will be included eventually [3:13 PM]

Brourd: including hairpin loops, 3+ way junctions, and tertiary contacts. [3:14 PM]

jnicol: @V, How many motifs are there? [3:14 PM]

vineetkosaraju: I think 460 including the helix [3:14 PM]

vineetkosaraju: 459 two ways and 1 helix [3:14 PM]

jandersonlee: so right now, all motifs effectively are compatable to join with helixes [3:15 PM]

Brourd: Correct [3:15 PM]

jnicol: did you use all of Joe Y's library? [3:15 PM]

vineetkosaraju: @machineleves, if it still doesn't load in a couple of minutes or so let me know, otherwise it might just be taking a long time to load for the first time [3:15 PM]

jandersonlee: is there some way to reasonably cluster the 459 cases?? [3:15 PM]

machinelves: hmm, i think i just don't have opengl enabled in safari yet, it works in firefox [3:16 PM]

vineetkosaraju: not the entire library, I used his two ways, but there are still hairpins, N  way junctions, tertiary contacts, and more helices [3:16 PM]

stlnegril9: @vineet - re: endpoints. I think knowing which motif use is about to select may help. have only played w/ 3D a bit, but guess that 459 endpoints may overlap quite a bit [3:16 PM]

stlnegril9: coming filter of motifs may help that [3:16 PM]

stlnegril9: *motif user is about to [3:16 PM]

vineetkosaraju: @jandersonlee, yes there are plans to make subgroups based on motif name/ motif angle/ motif shape [3:16 PM]

Brourd: Thank goodness I was messing with the 3D game when vineet first brought his dev server instance up. I would probably still be loading it, haha. [3:17 PM]

jnicol: Can the motif library be filtered based on which puzzle is used? [3:17 PM]

jandersonlee: so for now you are always working from one space trying to bridge a gap? [3:18 PM]

machinelves: @vineet it would be cool to be able to drag & drop from the motif window [3:18 PM]

jnicol: for example, the tutorials may show less motifs to make it easier to use [3:18 PM]

machinelves: @vineet once you add a motif to the global design, can you select that motif & highlight / examine what it is? or is it totally absorbed into the main design at that point? [3:19 PM]

machinelves: i.e. can motifs retain their block properties once added to main design? [3:19 PM]

vineetkosaraju: @jandersonlee - yes that's the main idea. @jnicol - yes we could do that, that's a great suggestion [3:20 PM]

vineetkosaraju: @machinelves - on the code side they can be differentiated but in the actual interface you can't tell apart motifs atm [3:20 PM]

machinelves: @vineet definitely would be huge help to toggle simultaneous window view of 2D version of motif & even main design [3:21 PM]

machinelves: cool, hehe one step at a time of course! it is beautiful by the way! great job!  [3:21 PM]

machinelves: is there a way to examine just one motif's 3D structure at a time? [3:22 PM]

jnicol: I think we should digest the 3D version first before we think about mapping back to 2D [3:22 PM]

machinelves: sounds like a smart idea! [3:23 PM]

jandersonlee: Are the two pairs of target ends supposed to flash. I have troule making them out. [3:25 PM]

stlnegril9: @JL - I had similar issue - truning on atoms (in addition to bonds) helped me see it [3:26 PM]

machinelves: in atom mode i get a flicker too [3:27 PM]

JR: to see direction you might make the backbone of the added motifs bolder, each a different color [3:27 PM]

jandersonlee: or draw a bar between the endpoints? [3:28 PM]

jandersonlee: endpoint bar plus helix as minimal skeleton? [3:28 PM]

jandersonlee: (less clutter) [3:29 PM]

machinelves: at some point would be cool to translate the puzzle requirements into the little square icons, rather than a list, but that is way low priority compared to the other 3D related things [3:30 PM]

jnicol: or a cube [3:31 PM]

machinelves: i really like that you can view each nucleotide with its correlating color  [3:31 PM]

jnicol: that you could rotate to see all the constraints :) [3:31 PM]

machinelves: lol that is brilliant!!! [3:31 PM]

machinelves: do eeet! [3:32 PM]

jnicol: lol [3:32 PM]

jnicol: maybe I shouldn't say things like that in jest :) [3:33 PM]

machinelves: okay now i have to ask for the eterna equivalent of the foldit wiggle toggle: flipple, just push the button and let it flip pairs until the whole molecule is happy [3:33 PM]

machinelves: bonus points if you animate the flipping process [3:34 PM]

machinelves: :D [3:34 PM]

jandersonlee: afk [3:34 PM]

machinelves: yes, animated cube easier imagined than programmed lol, we will be patient [3:34 PM]

machinelves: so how about that chat window help button? :D :D :D  [3:36 PM]

machinelves: hopefully with the wiki page as the landing point, you wouldn't have to create or keep a page updated [3:36 PM]

Brourd: Hmmm, I should have wrote down this sequence of motifs that got me to a distance of 24, lol [3:36 PM]

stlnegril9: ability to interogate individual motifs (outside the clutter of a large puzzle) might help. am aware there are external programs that allow same, and coming [3:36 PM]

machinelves: ooo what about a breadcrumb linear points for 3D to show you what motifs you've placed, mouseover point and get popup of individual motif? [3:37 PM]

stlnegril9: "potential end points' may help, but currently find myself looking at individual motifs in tutorial  (b/c it is the smallest) one by one [3:37 PM]

stlnegril9: by "interrogate", just meant, besides mispelling it ;) use same interface to view a single motif [3:38 PM]

machinelves: @vineet my initial assessment is #1 priority removing endpoint flicker from atom mode, #2 priority getting individual / block motif recognition once placed in main design [3:39 PM]

machinelves: and overall, really really really cool! thank you so much!!! [3:39 PM]

stlnegril9: right now just trying to bridge from pt A to pt B but someday Brourd/Nando/et. al. will be telling me why this "bridge" is bad b/c some dangling-tetraloop-or-soemthing or other [3:40 PM]

jnicol: Thanks everyone for your input and suggestions! [3:40 PM]

machinelves: thank you! [3:40 PM]

jnicol: and thanks Vineet for your contributions! [3:40 PM]

machinelves: happy programming :D [3:41 PM]

stlnegril9: "got me to a distance of 24," - how do you know 24? [3:41 PM]

machinelves: and good luck with the 3D adventure! [3:41 PM]

Brourd: Any correct submissions for the FMN and other tetraloop receptor motif yet? [3:41 PM]

Brourd: @ stlnegril - they added it a few hours ago next to the motif box. [3:42 PM]

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