Nucleotide Numbering

  • 5
  • Idea
  • Updated 8 years ago
  • Implemented
I think it would possibly be a great convenience to have the Nucleotides numbered. This occurred to me when I finally got around to the lab, and started working back and forth between the Sequences in the Voting Window - and the Pairs in the Graphic Display. It is, of course, doable without numbering, but to my way of thinking, this would make things significantly easier and more fluid.

In the Sequences column of the Voting display, the Nucleotides could be numbered across the top perhaps, or via "tool-tip" type display, while in the Graphic Display, they could also be accessed in "tool-tip" fashion - or as in Fold-it: via a hot-key while hovering over the target.

This would make it much more convenient to see which Sequence Column Nucleotide letters match-up to which colored Nucleotide Graphics in the Display.

I think this would particularly facilitate the process of analyzing and evolving others' RNA solutions in the Lab.
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dimension9

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  • happy

Posted 9 years ago

  • 5
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Adrien Treuille, Alum

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Dimension: This is a great idea. It's marked #225 in the bug tracker, and we'll discuss it during our next developer's meeting.
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Jeehyung Lee, Alum

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Hi d9, this feature is now in the game. Check it out!
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Adrien Treuille, Alum

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Jee: None of us can find this feature. Can you please explain how we can access it? Is it in the design game itself, or in the solution browser?
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Matt Baumgartner [mpb21], Alum

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Bump.
What is the way to see the numbers on the nucleotides? I haven't found it anywhere.
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dimension9

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Hi all, just wanted to "goose" this topic to bring it back to the top of the list, and keep it current, since I think it is going to be one of the best, most important improvements for lab analysis aid in the whole list of planned upgrades.

Also, I was thinking how much easier it will be to communicate about a lab design when we can say for instance, " I swapped the G-U pair at sequence location '46 - 105' ... instead of " the third G-U in the bulge next to the second big loop." It'll be like having street addresses instead of descriptions like "the blue house third from the corner." :)

Best Regards,

-d9
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dimension9

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Hi all,

Just re-goosing this topic to the top of the list again, as it is becoming more and more important to me as time goes on. I have already begun referring to pairs and bases in my lab-design descriptions by their sequence numbers - but to get them, I have to manually sketch out the whole RNA, and label the drawing.

Then, for the lab interface, I printed out a list of the sequence numbers on a strip of paper, which I then hold up to the screen so see the sequence numbers there.

These measures work - but they are very labor intensive and primitive, and I doubt many others will go to these lengths for this convenience.

I imagine many players look at my sequence numbers in my lab design descriptions, and are either just baffled and give up, or are faced with the tedium of manually counting out the bases to follow what I have said - not so much fun.

Anyway, just hoping to re-kindle interest in this at the Dev Level.

A million thanks, for all you guys do!

Sincerely,

-d9
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Adrien Treuille, Alum

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D9: Thanks again for the really good idea. We really will do this! Promise! I just increased it's priority to "unconfirmed" which forces us to talk about it in meetings. Please be patient, though. The team is completely swamped getting ready for the launch.
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dimension9

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Hi Adrien - Just returned from the Bug Tracker - this item is indeed in there at #225; however, it is marked both "Done" and "Open." - but not "Unconfirmed" ... could this be affecting the attention it receives in Dev meetings?
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Jeehyung Lee, Alum

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D9 it's "open". "Done" means a response to the request in this forum has been made. The feature will be added to the game in few days
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Jeehyung Lee, Alum

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The feature has been added to the game.

Let us know if it doesn't work!

- EteRNA team
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dimension9

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jee, thanks so much for the nucleotide numbers!!! - they are very, very helpful in the graphic interface; however I do not see how to make the corresponding numbers visible in the Sequence Column in the Lab List Window. (So it is still difficult to relate the Sequence to the Graphic) Has that part not been implemented yet? ... or perhaps I just didn't figure out how to activate it?
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dimension9

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Hi Jee, also, just noticed in larger puzzle (telomerase), no numbers after 495 are printed; instead, every 5th base after #495 is marked with a letter "N." There are 11 "N's" at the end of telomerase.
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Jeehyung Lee, Alum

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Thanks d9, will come up with a fix ASAP
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chaendryn

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How do I get the numbers to show?
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Jeehyung Lee, Alum

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Chaendryn, there's a "view options" button in the bottom action bar.

See http://eterna.cmu.edu/news/274738 for details!
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chaendryn

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Awesome, thank you :)
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Jeehyung Lee, Alum

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Fix for displaying N over 500 has been fixed. Let us know if you still see the problem

EteRNA team
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dimension9

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Thanks Jee, but a question: Has the other half of the numbering idea been deferred? (The part about also adding the numbers to the Sequence Column in th Lab-Listing)?
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Jeehyung Lee, Alum

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That issue has already been added as case #403 and will be discussed in the dev meeting : )
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Jeehyung Lee, Alum

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This issue has been finally solved. You can now find sequence numbers in the lab listing

EteRNA team