Feedback for Tutorial Updates (Eterna Essentials)

Community
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Dear Eterna Community: We’d like some feedback on our planned tutorial updates (the Eterna Essentials) by October 6. Summary document here - Eterna_Essentials_puzzle_summary - Google Docs

The Eterna Essentials puzzles are intended to be a short-/medium-term update to the tutorial progression in Eterna. These ~30 puzzles should be sufficient to introduce players to the core concepts of Eterna and prepare them for starting Labs. The previous tutorial progression and quests will still remain on Eterna, but Lab access will be granted after finishing the Eterna Essentials (for players who do not yet currently have Lab access). (For extra context: Proposal_tutorial_changes - Google Docs)

We are currently playtesting and accepting feedback on these puzzles - they are a work-in-progress. Any help and suggestions are welcome! You can give feedback in any of the following ways:

We request that all feedback for this iteration be given by October 6. Thank you! Special thanks to Astromon for providing some preliminary feedback and suggestions.

Logistics: If your account is old enough, it should already exist on the dev version of the website. If your account is less than ~several months old, feel free to create a new account there.

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These new tutorials are so fantastic! Thank you Slava! I’m going to post my notes as I come across things. Other players can ‘Like’ posts if they agree.

Puzzle 5: Need to remove bracket from this text. Maybe a formatting issue?

Base pairs - how strong are they?
Base pairs - how strong are they?269×515 43.7 KB

Puzzle 6: I would remove the parentheses and make it a separate sentence.
Base pairs - swapping

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I would remove “Expanding the Toolbox” from both puzzle 3 and 7. It confused me, I was waiting for a new tool in the toolbar, which puzzle 3 does cover but not puzzle 7. I prefer a cleaner title that gets straight to the point.

Puzzle 7 isn’t flowing for me, it’s long and I didn’t know where it was heading. The hyphens need to come out, so how about numbering the text instead? (And the text boxes were so long I had to expand my browser to reach the Next button.)

Possible new text:
In this puzzle, we will describe five strategies for solving RNA puzzles. (Or, here are five steps for solving RNA puzzles.)

  1. Start by adding pairs in Target Mode. When one base in a pair is already locked, think about what the other base might/must be. Fill in stacks however you wish, keeping…
  2. <Take out the last sentence. Players don’t know how to mark a base and it’s not necessary yet.>
  3. If the structure is not forming, try switching out weaker pairs for stronger pairs or swapping pair directions. At this stage…
  4. Use Natural Mode to check if unwanted base pairs are forming, then switch back to Target Mode to try different base pairs. Be sure to vary the types of base pairs in each region. Stacks with too many of the same pairs in a row are particularly susceptible to misfolding.
  5. Solve the structure first then work on satisfying puzzle constraints, such as removing GC pairs or adding GU pairs. If you get stuck…
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Puzzle 8 - The Mission Accomplished text is not correct. GU does pair when alternating in short stretches (2-3 pairs) within long helices.
8 - GU pairs

Proposed text:
As you can see, several adjacent GU pairs can pair surprisingly well when they are aligned in the same direction, but may not bond when aligned in opposite directions.
Additionally, the specific direction the GU pairs are facing can matter and the identity of neighboring base pairs can affect which orientations work or not.

Puzzle 9 - Mission Accomplished screen. This is the first time the term ‘motif’ is used and I can see it’s going to be used going forward. Your use of the term is completely correct, I’ve often seen motif used this way in RNA structure discussions (and our own Wiki page). But there are also many other researchers who reserve this term to refer specifically to sequence patterns forming a unique chemical bond arrangement such as GNRA tetraloops. That is how players use this term. We even have a motif booster in the ribosome puzzles that identifies motif locations.

Do we all agree that ‘motif’ should be taken out of these tutorials? I don’t want to set up players for confusion down the road. We don’t need to change the Wiki page or the link to the Wiki page, that’s minor.

The Forum isn’t letting me post any more replies until someone replies to me!

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Puzzle 5: Need to remove bracket from this text. Maybe a formatting issue?

I think I was originally meaning it as an “aside” - where it wasn’t necessary for the player to read but was there for people who were interested. But I think I could remove the brackets without the sentiment being interrupted.

Puzzle 6: I would remove the parentheses and make it a separate sentence.

Yes, that can be done (and I think it breaking it up not only as a separate sentence but also a separate “paragraph” could help the player to process the info).

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I would remove “Expanding the Toolbox” from both puzzle 3 and 7. It confused me, I was waiting for a new tool in the toolbar, which puzzle 3 does cover but not puzzle 7. I prefer a cleaner title that gets straight to the point.

Would something like “Strategies” be a helpful descriptor? And/or are there other phrasings that you think could be useful?

Numbering does sound good. And it can help to use numbering if we want to break down the text boxes further and thus make individual text boxes smaller.

Additional idea - currently, puzzle 22 probably has the most text of all. I’m thinking it could be useful to cut out all of the text that it shares with puzzle 7 and to just focus on the boosting-related strategies for puzzle 22. At least within the puzzle gameplay - it could potentially be nice to go ahead and keep all of the text in the puzzle description page just in case someone wants to refer to it all at once.

As you can see, several adjacent GU pairs can pair surprisingly well when they are aligned in the same direction, but may not bond when aligned in opposite directions.
Additionally, the specific direction the GU pairs are facing can matter and the identity of neighboring base pairs can affect which orientations work or not.

Yes, this wording change can be made.

Side note - as I was preparing the text for all of these puzzles, I noticed that I originally was using “pair” and “bond” interchangeably. Within the context of Eterna, should these terms be used interchangeably? If so, should I explicitly explain that somewhere? If not, should I explicitly explain the nuance (whatever that may be) between the two words?

Puzzle 9 - Mission Accomplished screen. This is the first time the term ‘motif’ is used and I can see it’s going to be used going forward. Your use of the term is completely correct, I’ve often seen motif used this way in RNA structure discussions (and our own Wiki page). But there are also many other researchers who reserve this term to refer specifically to sequence patterns forming a unique chemical bond arrangement such as GNRA tetraloops. That is how players use this term. We even have a motif booster in the ribosome puzzles that identifies motif locations.

You are correct that I used this wording because it was used on the Wiki :slight_smile: - but if we should use other terminology, then we can come up with another phrasing.

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Completely agree, change puzzle 22 text.

I was wondering why the term “bond” wasn’t being used. Use “bond” wherever the term is scientifically correct. I’m not aware of eterna idiosyncrasies.
From nucleotidemixer 3: The bases bond with each other to make different shapes. Target mode shows you the shape that will solve the puzzle.
Definitely use the term here: GC bonds are the strongest…

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FWIW, I would say the (hydrogen) bond is what holds two bases together in a pair/to form a pair/to make them “paired”.

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Puzzle 24 - Blocking
We need to lock all but the two bases in play in order to demonstrate blocking. Otherwise it can form a whole bunch of different structures.
And I prefer the hint in the original puzzle: “You have to prevent the Us from pairing with the As. Experiment with G and C on the open bases (which don’t form strong pairs with U.)”

Puzzle 26 - Sliding
I prefer the original hint: “You need to prevent the slide by orienting the center AU pairs correctly.”

Puzzle 28 - Short Stacks is a tough puzzle. A lotta players get stuck on that one in the current progression. Either add the hint from the original puzzle or put an easier puzzle in this slot.

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Wow, just tested the puzzles. They are great! A huge improvement over the current ones!

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The only problem I see with the tutorials, and this was there before, is that the skills learned in the tutorials do not translate much into labs. I understand that labs change very often, and it is not practical to change every month or two, but what I am suggesting is a quick tutorial that covers information about labs that are applicable to all, because even though there is a direction slide at the end, it doesn’t provide much of a clear direction, and many players are left unsure of how they can contribute. Those are just my two cents, and the new progression is definetly an improvement. I think what I’m suggesting is kind of similar to this video that Nicole made:

I think a link to the video would suffice.

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I think a link to the video would suffice.

Great idea! Will plan on adding a link to this lab intro video.

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For reference, here are the slides I presented at today’s Town Hall on the Eterna Essentials progress: 20211018_Town_Hall - Google Slides

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Great, Slava, thanks!

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Puzzle 1: This text box is using a different verb tense than the other text. Change the first sentence to “Finally, these boxes display objectives for the puzzle”.

Puzzle 1
Puzzle 1395×507 39.2 KB

Puzzle 3: This tripped me up as a reader. How about “how the RNA is currently folding”. It’s good the current text for the puzzle implies it’s the most likely folding but we don’t to be completely technically correct in each text box at the cost of clarity for new players. Plus, it is currently folding that way in our engine if not necessarily nature.

Puzzle 3

Possible puzzle 7 hint: You’ll need a strong pair at base 10 to help the stack fold.

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Free energy puzzle: Better grammar and more clear to say “higher free energy means a less stable structure”

free energy

Need a closing parenthesis
parantheses

1 Like