Lab submission 'evolutionary tree'

  • 4
  • Idea
  • Updated 5 years ago
I would like to be able to see a higher archival parenting of lab submissions, to be able to see where 'mods of mods' come from (and on the flip side, how designs are adjusted down the line)
Photo of LFP6

LFP6, Player Developer

  • 639 Posts
  • 109 Reply Likes

Posted 5 years ago

  • 4
Photo of bekeep

bekeep, Learning Researcher

  • 98 Posts
  • 20 Reply Likes
Interesting idea.  I think this goes hand in hand with improving the lab interface, generally.  The "one-design-at-a-time" is a really inefficient way for people to navigate submissions.  It would also make it clearer where ideas come from (which would be helpful for IP issues).
Photo of Astromon

Astromon

  • 204 Posts
  • 30 Reply Likes
This is a great idea. I would also like to be able to go back to the beginning while looking at someone's designs so I can see the line of thought that helped design the RNA. Just get the site to record all lab submissions and delete un-submissions work in the labs. the program will automatically record all painted nt's in the labs and delete all but the submitted designs that get synthesized.
(Edited)
Photo of rhiju

rhiju, Researcher

  • 416 Posts
  • 125 Reply Likes
@LFP6 (or other players), do you have a draft of what this looks like for previous labs? We'd like for this kind of figure also in publications from eterna, but don't have a dev with the cycles to put together, color in a pretty way, interpret results. 
Photo of LFP6

LFP6, Player Developer

  • 639 Posts
  • 109 Reply Likes
Hmmm... I could give that a shot at some point.
Photo of rbierman

rbierman

  • 5 Posts
  • 0 Reply Likes
This reply was created from a merged topic originally titled Ancestry System (Mod-of).

Formalizing the 'mod-of' system.

It could be beneficial to create an ancestry system in labs, where mod-ing information is automatically stored for the player.

The current idea is that when a user presses [view/copy] on a design from the voting screen, their mod will automatically be linked to the original design in a child-parent relationship without any user intervention.

Can anyone comment on this system, propose a new system, spot any problems/difficulties?

Thanks!
-Rob
(Current Das Lab rotation student)
Photo of rbierman

rbierman

  • 5 Posts
  • 0 Reply Likes
I might be able to help. I have a list of puzzles with the same secondary structures that occur over multiple rounds. Is this what you mean?
Photo of Omei Turnbull

Omei Turnbull, Player Developer

  • 1026 Posts
  • 332 Reply Likes
@LFP6: Can you show me an example that illustrates your understanding?

@rbierman: What I think we're discussing right now is what changes it would take in the game code and/or database design to let players easily see all the solutions for a "puzzle" (also called lab or sub-lab in some contexts) in the Eterna UI.  If and when a decision is made to do that, then your list will be very useful for updating the database for puzzles that weren't originally coded that way.
Photo of rbierman

rbierman

  • 5 Posts
  • 0 Reply Likes
Great, thanks for explaining @Omei!
Photo of LFP6

LFP6, Player Developer

  • 639 Posts
  • 109 Reply Likes
@Omei:

Here's a lab that actually uses rounds as they were designed: http://www.eternagame.org/web/lab/3553469/
Photo of Omei Turnbull

Omei Turnbull, Player Developer

  • 1026 Posts
  • 332 Reply Likes
Thank you.  This is the first time I have seen both levels of "puzzles" properties used in a project.  I've wondered what they were intended for.  For the discussion, here's a selected section of the response to your query:


So you're right that two rounds are encoded here.  But this way of representing round number in the API doesn't really address the problem of retrieving designs from "equivalent" labs across rounds.  If you expand each of the lower-level "puzzle" properties, you see things like

and

Notice that the two nids for "Motif Assembled GAAA tetraloop binders - Shape 0" are different.  This means there is no existing way to get designs from those two labs into the same browser window.  Before projects were introduced, we had instances of multiple rounds within the same lab nid.

For all I know, there is still a reasonable way to set up a new project without requiring a new set of lab nids, in which case we can again have exactly what Nando was suggesting. But I don't think there have been any examples of that since projects were introduced.
(Edited)