UI View Boxes

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https://drive.google.com/open?id=1_4OY-hS3b8GROBgnrxTZgEsqETLx4rJr4s7kNXuCL5U

 UI View Boxes
 
We have been highlighting lab design list for analysis in our little group and I thought it would be useful in game for others too.

I have been brainstorming some view oligo inputs views options for the lab list with input from Eli. Using the energy modeling to show oligo inputs placement in the sequence.

I have asked other long term players for feedback/options to refine the view/ideas, like I have in the past for other ideas.

Any feedback would be great. I'm happy with any reply of what you think of those if any were Good, Bad and What was I thinking.

Mathew
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mat747

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Posted 3 years ago

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Brourd

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I imagine the difficult part here is that MFE structure predictions are not saved (*disclaimer: this could have been changed recently, but I wouldn't know).

Would the goal be to have every submitted sequence be parsed and compared to the sequence of the oligo to find the best matching sequence?
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Omei Turnbull, Player Developer

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It's true that the MFE predictions aren't currently being stored, and I doubt they ever will be for the legacy browser.  But I think it is a an important feature for the new browser, because filtering on predicted substructures will be very powerful.  So they will get there.  

Unfortunately, I can't promise it quickly. :-(
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Brourd

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Can you promise it slowly? And how long would it be before implementation?
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Omei Turnbull, Player Developer

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I'm glad you asked that, Brourd.

One of the advantages of the new browser is that there are no hard-coded assumptions about what columns can be put into the database.  In fact, its database already has fields defined for four 2D structure strings.  So the issue is not code to support the structures, but in getting the structure data into the database.

This was an issue for the (pre-browser) FMN lab fusion tables as well.  In that case, Meechl volunteered to do the legwork of manually running a script on Nando's dev server multiple times and, along with other data, created a spreadsheets of "extra" results.  I then merged that data into the fusion table that Eli or I had previously created and made it public.

The situation is basically the same for the new browser database, but the details differ.  Nando's script that Meechl used doesn't handle RNA inputs or outputs, so we have to develop a new procedure.  Part of that involves Javascript coding, i.e. creating a utility that loads the Flash app, queries the Eterna server for the set of puzzle designs, submits each design to the Flash app for folding, gets back the results, and enters them into a spreadsheet.  But that's a one-time effort.  The on-going effort is actually to go through that process of running the app and verfiying the results for each puzzle, both for new labs as the data is released and old ones as they get added to the database.

The time I have available right now is split among a number of different tasks:
  • Addressubf current browser issues, from outright bugs to cosmetic improvements,
  • Adding features that long-time players feel are necessary for the new browser to be "good enough" to make the switch from the legacy one.
  • Adding URL-directed invocation capabilities.  By this, I mean making it so that a properly constructed URL can load the browser with specific set of designs, columns and capabilities.  The tutorials have a couple of simple examples already, but Rhiju is eager for a lot more generality, so that links to specific data can be an integrated part of the game UI.
  • Add entirely new browser capabilities (which wasn't really feasible with the flash code.)
  • Get more data into the new browser's database. This covers both new projects and filling in "holes" (like the 2D structures) in the data for the projects that are there.
It is because of all these different things that I really can't give a timeline for anything until it gets to the top of the priority stack (which is always changing.)

Having said that, though, if a player were to say that they would take on the routine process of extracting the structure data for each lab, I would be very motivated to put the coding of the needed utility very high on my list. (Say by the end of next week.)
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Omei Turnbull, Player Developer

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@Mat, I think there is real potential here.  I added a comment to the doc saying I would be interested in seeing what it would look like to combine the traditional coloring of bases with outlines showing structure.  I decided to spend a little time experimenting myself:

This is just a rough cut; the details aren't consistent.  

It would certainly take some time for a player to look at something like this and grok the full meaning. But even without that, I suspect that a just a glance will say something about how promising a design is, because good designs are more likely to look "tidy", while ones that look "messy" are likely not to switch well.
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Eli Fisker

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This reminds me - the other day I had a case where I really wished I had a sequence highlight, while I was using the sequence search option in a lab analysis.

Usually in the lab data, the oligo position is clustering a lot for the high scoring designs, making it a bit easier to pull the data out. But when deliberate experiments have been carried out and position varies a lot, it can be a lot harder to see the wanted sequence.

Without search sequence highlighted
https//lh3googleusercontentcom/Z5cBs6bWPql8kRjTX48xubyPiZbEtZ6wfklzYp23CG45XxXvbU0WoBn70vOEC5VbIAqq8aq1T5v-IAv-2wdAe0SBBsDkU2m7uPM6dEb_Now50OHMMlDC6JRHTOdlCkJ6Xh-kc2c

With search sequence highlighted
Sequence highlightpng
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mat747

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Added some Modified versions of UI 1 and 8 in the Goggle Doc.
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Omei Turnbull, Player Developer

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@Eli, I agree that highlighting (in some way) the searched-for sequence could be very helpful.

I spent some time looking into how this might be implemented, and it turns out that with the datatable library I'm using, it is not at all clear how to achieve outlining of subsequences.  In the past, I have done this by defining and coloring borders around wash base letter.  But the datatable code is managing that aspect itself, and is overriding my attempt to achieve outlining.  At this point, I don't know whether or not it will be feasible.

However, I prototyped some other other possibilities, and here's the one I thought worked best:



What are your thoughts on that?
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Omei Turnbull, Player Developer

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@Mat, my above comments about being unsure of the prospects for incorporating subsequence outlining into the main table isn't meant to discourage the UI View Box discussion.  Assuming this view box is implemented as part of some kind of separate view (as opposed to be being a mode for viewing the complete table), there would not be any compelling need to use the datatables library for that.
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Eli Fisker

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@Omei, this is sweet news! I really like what you have been up to. This looks good. I would definitely wish for that option.

Only additional wish is a slight change of colors for the background of the highlighted changes, so the sequence gets a little less weak in the colors, for easier reading.

Thx for taking time looking into this. :)
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Omei Turnbull, Player Developer

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@Eli, I tried various shades of white to light gray, and this looked the best to my eye. Anything whiter and there isn't enough contrast in the luminance to read one or another of the nucleotide letters easily.  (Edge detection in humans seems to depend mostly on changes in luminance, ignoring hue.)

We all see color a little differently.  Does this look better or worse to you?

Of course, anyone else is welcome to express an opinion.

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mat747

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I agree with Eli "this is sweet news! I really like what you have been up to. This looks good. I would definitely wish for that option."
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mat747

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I agree with Eli "this is sweet news! I really like what you have been up to. This looks good. I would definitely wish for that option."
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mat747

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@Omei

I don't see your comments in anyway discouraging the UI View Box discussion, you are only outlining. How feasible it would be to incorporating sub-sequence into the main table.

I like the feedback and good to know how feasible our suggestions are, plus you having given possible work around options and examples.

Keep up the good work.
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Omei Turnbull, Player Developer

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Thanks, Mat.
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LFP6, Player Developer

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@Omei I think what would help is lowering the opacity/alpha of the overlay, not a hue change.
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Eli Fisker

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@Omei, thx for your testing. I like your newest greyish version better.
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Omei Turnbull, Player Developer

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@LFP6, the sense that there is a semi-transparent overlay is an optical illusion.  Only the background color is changing.

But your comment does evoke another thought -- there is no reason we can't tweak the text luminosity as well as the background's, if the end result is better subjectively.
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Omei Turnbull, Player Developer

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If one of you are interested in making the selected text display better, perhaps you could experiment with a Google Doc (or any other text editor that allows full control over foreground and background text color) and post an example of what you think works best.
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LFP6, Player Developer

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@Omei: If you reduce the opacity, it should let more of the blue "through", having the same effect I think.
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mat747

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@Omei
I made some examples using similar blues to the current background #023e91
The lighter blue blends in with the current colour scheme, But can be still scene by players.


Example using colour #011e46 (Top highlight) , (Mid) #0354c3 and (Lowest)  #046af5 to highlight the background.
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Omei Turnbull, Player Developer

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@LFP6: I'm afraid I'm not understanding what you are proposing.  But here is the code that I am using to try things out.

$("tbody tr .sequence").each( function() {
    var n = $(this).text().indexOf( "ACAUGAGGAUCACCCAUGU" ); 
    $(this).find("span").each( function (index){
        if (index >= n && index <= n+18) { 
            $(this).css( "background-color", "#9999ff" );
        }
    })
})

You should be able to paste that into the debugger console window and it will change the background color of all the instances of the MS2 hairpin sequence.  Tweak whatever css attributes you want and if you find something you like better, post it here.
(Edited)
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Omei Turnbull, Player Developer

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@Mat, looking at your screenshot, I liked the #046af5 best.  But when the highlighting showed up in every line, like this

it seemed overwhelming.

This one, with #0354c3 seems better to me.


I agree that #023e91 shows up:

... but the border between what is highlighted and the rest of the sequence is hard to pick out.  So of the three, I like the middle one best.
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@Omei  - Cool that was fast.

similar colour scheme
http://www.colorhexa.com/035edc

Monochromatic Color
http://prntscr.com/atm0di
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Eli Fisker

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@Mat, I really like what you have been up to. This looks very good to me.

@Omei, I agree with you that the middle blue shade #0354c3 is great. I really like it. Its my favorite so far.

 #023e91 is nice too, but too weak. I would like to perhaps see one more test with one shade in the middle between them. Just to rule out that there is a compromise between them that would be better.

@LFP, thx for that blue shade idea
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Omei Turnbull, Player Developer

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I decided to follow up on the idea of changing both background and letter colors.  I think that will allow us to find something easier on the eyes.  Here's a possibility:

n
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Omei Turnbull, Player Developer

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... or maybe it is better to use font changes more than color changes.  Here's an example where the font changes take center stage, subtly reinforced by a black background.

It doesn't jump out from the page as most of the others, which I suspect is good.  But when expanded to a zoom level I would actually use in practice, the selected segments stand out well.
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LFP6, Player Developer

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Hey Omei. I tried using that code, and I don't see any background colors change. Anything in there I need to adjust before plugging it into the console window?
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LFP6, Player Developer

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Oh, I got it, nvm.
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mat747

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@Omei. I like the Black background, But I found the green "C" font is a bit strong with the black background.
Could you try a slightly dark green font please ?

I think the current C nucleotide font colour is #3f3 which is equal to #33ff33
(Edited)
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LFP6, Player Developer

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This is a reallydelayed reply, but here's what I'm talking about when I say change the alpha instead of the hue, using the code you provided (same color, just a different alpha):

$("tbody tr .sequence").each( function() {
    var n = $(this).text().indexOf( "CAGUACUGA" ); 
    $(this).find("span").each( function (index){
        if (index >= n && index <= n+18) { 
        this.style.backgroundColor =  "rgba(153,153,255,0.25)";
        }
    })
})

Of course, this approach doesn't work on legacy browsers (pre-IE 9), though Eterna currently uses the trans-panel/trans-panel-bg classes with an extra div to achieve the same effect throughout the rest of the site.
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LFP6, Player Developer

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This is a really delayed reply, but here's what I'm talking about when I say change the alpha instead of the hue, using the code you provided (same color, just a different alpha):

$("tbody tr .sequence").each( function() {
    var n = $(this).text().indexOf( "CAGUACUGA" ); 
    $(this).find("span").each( function (index){
        if (index >= n && index <= n+18) { 
        this.style.backgroundColor =  "rgba(153,153,255,0.25)";
        }
    })
})

Of course, this approach doesn't work on legacy browsers (pre-IE 9), though Eterna currently uses the trans-panel/trans-panel-bg classes with an extra div to achieve the same effect throughout the rest of the site.
(Edited)
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Eli Fisker

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Mat wished to make a comment here but is having trouble logging on the forum, so I'm posting it for him.

He told me that he started to take a look at Whbob_B/C-dec_V1`s designs in the lab and was getting it to a form in how he would like to review the results. He has made up a document with introduction to his idea for it. So here it comes:

Permutations of Combined Fragments/Sections
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Eli Fisker

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Mat wished to make a comment here but is having trouble logging on the forum, so I'm posting it for him.

He told me that he started to take a look at Whbob_B/C-dec_V1`s designs in the lab and was getting it to a form in how he would like to review the results. He has made up a document with introduction to his idea for it. So here it comes:

Permutations of Combined Fragments/Sections
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whbob

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I was wondering what was interesting about my B/C-dec_V1's since the new browser shows 30%'s for those submissions.  I see that R104 rev.3 spread sheets have been recalculated, improving those scores.  Players who use the new browser should also review the latest spreadsheets for changes.

I like ( but have not yet completely understood) how to use Mat's paper.  Looking forward to more info.  Thanks :)    
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Omei Turnbull, Player Developer

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@all: I've been thinking about the possible advantages of basing something like this off a graphical, rather than textual, representation.  Consider the circle diagram in this image. 



Here, the bases are arranged in order around the perimeter of a circle, and arcs are drawn between bases that are paired.  I've seen this representation before, but never saw any advantage over the 2D structure graphs we're accustomed to for viewing a single folding.  

But I'm thinking this representation may be useful for visualizing switches, where we want to compare the foldings among multiple states.  In the simplest case, we could simply draw the pairings for all states in one circle, using a different color for each state.  Overlaying four states at once might be too cluttered, but last night I ran across a visualization technique that uses an additional hierarchical relationship (which an RNA foldings has) to bundle lines, like this.

Any thoughts?
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With this circular diagram, having the ability to step from blank to state 1, 1+ 2,1+ 2+ 3,1+2 + 3 + 4 ? I think I like it :)  Then, add the ability to step through several player designs viewing the same state in each?  I'd like it evermore :) 
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Omei Turnbull, Player Developer

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Those would certainly be possible.  At this point, I was mostly thinking about whether this is a visualization that would facilitate comparison of structures.

As an example, looking at the visualization below, how long does it take you "line up" the two foldings in order to understand what is moving, and how?  Depending on whether or not I got lucky in starting with the right feature, it would probably take me somewhere between one and 5 seconds.  But with the circle diagram, the alignment between the two would be immediately obvious, because all the bases are in the identical positions in both states.

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Agreed with whbob

Being ability to step through several player designs to get over view and comparison on what maybe happening, is also needed.
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Omei Turnbull, Player Developer

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Do you think seeing them sequentially is more valuable than seeing them simultaneously? (The latter being the approach I have been taking with the right panel reflecting whatever designs the player selects.)
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mat747

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Doing able to view the Main list and 2D Structure or Switch graph simultaneously is more valuable for a number of reasons. One being a very big time saving and you don't have to go and out of multi windows saving a lot of clicking.
http://prntscr.com/axcfgz

Well it would be if the 2d structure was displayed.
http://prntscr.com/axcgog
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mat747

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Talking of simultaneously vs sequentially here is a very quick rough one.
Could we have the option of being able the view the lab descriptions in the center section of the screen, when selecting labs from the Puzzle selection list ?

For the example I used the Home button where the 2D Structure would be displayed to navigate back to the Previous Lab Projects.
http://prntscr.com/axchzo

In addition to the current display.
http://prntscr.com/axciyw
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Omei Turnbull, Player Developer

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@mat: Re the Puzzle and column selection, let me start by saying that I consider the current implementation to be only a stopgap measure.  In particular, the puzzle selection will quickly become untenable as more lab data is added. 

For the initial release, I had hoped to implement puzzle selection with one (or perhaps more) selection boxes like this:

I put this on hold because I couldn't get the library code for this control to play well with the code for the layout manager.  But I don't think it is an insurmountable problem, and that remains a possible path forward.

But this alone still would not be the ultimate solution for the bigger question of "How do I quickly find the data I am interested in"?  I interpret your request as another approach to that issue.  (Am I right?)

I do have some concern about having the open source (HTML5) browser code relying on the legacy (closed source, PHP+CoffeeScript+Flash) code any more than necessary. Certainly, while we have both, smooth integration is an asset.  But I think there is a general consensus  among the dev team that on the whole, the legacy code represents the past, not the future, of Eterna.

But as an example of a concept, I'm interested in your example.  Can you elaborate on how you would use the lab pages, and perhaps distill that down to something that could be implemented within the browser?
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Omei Turnbull, Player Developer

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@mat: Re the 2D structure that didn't completely load, I have had that happen to me once or twice also, but I haven't figured out what triggers it.  In my experience, it has just been a one-time occurrence, and isn't repeatable if you select a different puzzle and then come back to the original.  Is that what you saw?  If you observe any pattern in when it happens, please let me know so I can track it down. 
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Sorry to interrupt, but I'm in the new browser and highlighted one sequence, called up the graph on the right hand side.  Clicked on another line calling up another sequence with the graph.  Change to 2D and the structure never loads.

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Omei Turnbull, Player Developer

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Thank you, whbob.  I can reproduce that, which means I can fix it.  Stay tuned.
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@Omei - Re the Puzzle and column selection.
Ok stopgap measure for the initial release. Np

"ultimate solution for the bigger question of "How do I quickly find the data I am interested in"?"
I'll make another goggle doc or add to the Viewing Lab Archive faster page, in there could brainstorm ideas with the pro's and con's of those.

"the legacy code represents the past, not the future, of Eterna"
Agreed, The example was a possible stopgap measure only.
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Omei Turnbull, Player Developer

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@whbob, @mat - I consulted with Nando, and he offered a possible fix for the 2D- Structure not fully initializing when it isn't visible.  I tried that, but it didn't seem to work.   However, the Chrome debugger wa acting up, so I rebooted my machine, and then it worked.  So the problem has gone away for me, at this time. What I don't know is whether it is the code change or my rebooting that "fixed" it.

In any case, I have uploaded the changed code to the dev site.  If you can still reproduce the problem, try rebooting.  And let me know what you find.

Thanks.
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mat747

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@omei - 2D Structure still didn't display maybe I tried the wrong Devsite ?
 Running Windows 10 on desktop, still try laptop with Windows 7

Started Data Browser Brainstorm only one image so far.
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Omei Turnbull, Player Developer

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The dev URL is http://www.eternadev.org/lab/data-browser.html.  It works fine for me.

Did you try rebooting your machine?  Based on the fact that there are other flash app features (like the base shifting tool, and zooming with my mouse wheel) that will stop working for me, and won't start working again until I reboot my machine, I'm pretty sure that there is some resource leak in the flash app that the OS/browser combination can't detect.  This may be another case of that phenomenon.
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Omei Turnbull, Player Developer

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@mat: Started Data Browser Brainstorm needs sharing privileges.
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mat747

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@Omei - Oops - Should be able to view and comment now.
Haven't added much text into the doc yet.
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Omei Turnbull, Player Developer

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Thinking about how to efficiently compose individual kernel attractions into a complete solution, I took a design I had already submitted and tried creating a visualization that reflected how I think of it. Here's the result:


Conventions I used:
  • The design sequence (5'-3' order) is in the middle row.  I omitted the static stem.
  • C', R' and A' are the oligos, with the ' indicating they are in 3'-'5 order.
  • Kernel attractor bases, i.e. design bases that form distinct stems in multiple states, are underlined along with their oligo partners.
  • Extended attractors, i.e. the kernel attractors plus the additional bases needed to balance the energies to satisfy each state, are bolded.
  • The orange/cyan background coloring denotes purine/pyrimidine bases.
  • Design bases that don't bind in either state retain their Eterna background colors.
  • Gray arcs denote stems formed exclusively by design bases.
I can envision this not only as a way of visualizing designs, but as a way of creating them.  For example, one might select a set of kernel attractions (which is what I do now) and then interactively slide them back and forth, either specifying design base assignments and having the application evaluating them on the fly, or having the application interactively offering suggestions.

What do others think of the visualization?
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bekeep, Learning Researcher

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I am probably not the person you were hoping to hear from, but I really like this approach and would love to try designing with it.  This representation makes the important factors of a design more far more apparent.  The only feedback I have right now is on the visual importance of these factors.  Is the purine/pyrimidine distinction the most important?  It visually dominates the representation - a little trickier to see the kernel attractors.  It might also be helpful to display the unbound bases of the oligos in the same way that you display the unbound bases of the design sequence.

(Keep in mind, this is coming from someone who has more experience failing than succeeding with these designs, and little experience generally.)
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Omei Turnbull, Player Developer

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Your observations are very much appreciated, Ben.

As for using coloring that emphasizes the R/Y class instead of individual bases, I used to do the latter. But take a look at https://docs.google.com/document/d/1IV3om4-qMY5xZ1uYa7kFF16qdfSVqj6t6dgzIy_cmik/edit#heading=h.jkxxf..., where I tried both.  (This document is not about solving puzzles, but finding kernel attractors to work with. But the two are very closely related, at least with the way I design switches.) I discovered I could visually process the suitability of an alignment much more quickly with the two colors than the four.  

Even with player switch puzzles, my approach is to first construct a rough solve in R/Y classes (while in target mode) and then fine-tuning the solve by changing pairs to R/Y an R/Y equivalent.  (For example changing a GC pair to an AU pair to weaken an overly strong folding.)

I'll be interested to hear if that changes your perspective some.
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bekeep, Learning Researcher

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That makes a lot of sense.  It's a very different way of thinking about things (different, at least, from the way I was thinking about things).  Visually, the individual base colors are also more distracting.

Seems like a very powerful tool that let's people think about the problem in far more productive ways than the standard Eterna representation.  Going to try solving a few puzzles this way. : )