Discussion on new lab system with 20,000 synthesis per month

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As some of you may already know, EteRNA is expecting a groundbreaking change in the very core of the lab. Until now we could only synthesized 16 sequences every 2 weeks. However, Das lab (biology side creators of EteRNA) at Stanford University is developing a major breakthrough which would allow us to synthesize 20,000 sequences every month. This would mean that basically EVERYONE could get at least 20 RNA sequence synthesized each month if 1000 people participate in the lab.

We are planning 3 major updates along with the change



1. Massive RNA lab puzzles



With so many synthesis slots available, it wouldn't be the best idea to use entire 20,000 synthesis for solving 1 lab puzzle at a time as we do now. Instead, we'll ask research labs around the world and YOU to propose your own RNA lab puzzle and use synthesis slots. Every month 20,000 synthesis slots will be distributed to every active lab puzzle. For example if you have a specific shape of RNA you want to try synthesize, you could propose it as a lab puzzle - you'll soon be assigned synthesis slots, and you can submit any sequences you want to get them synthesized.

2. synthesis database



Every synthesis result from every lab puzzle will be publicly available. We'll deploy a database and appropriate interface in which you can search/review experimental results. You'll be able to search synthesis results by sequences, secondary structures, and in many other metrics.

3. Scripting

We'll provide a scripting interface with which you can design your own computer algorithms for solving puzzles, designing good lab submissions, scoring lab submissions ..whatever you want to do. (This is a generalized version of "Strategy Market" in which algorithms were limited to scoring lab submissions.) Scripting itself will be a fairly expert feature since it requires programming skills, but we'll develop a way for players to share scripts so that everyone can benefit from the expert effort.

As we are planning these massive changes to the game, there remain many important questions that are yet to be answered, and we would love to hear our players' opinions.

1. What will a lab puzzle look like?

Now that everyone can submit their own lab puzzle, what will it look like? Should each lab be public so that everyone can participate and submit sequences? or should it be private so that only the puzzle owner can submit a sequence?

If a lab puzzle can be public, how do we pick sequences for synthesis from each lab? Does the owner of the project decide which sequences get synthesized..or do we still want to keep voting interface in each lab?

Can other players review/rate the project? If so, what would be the best way to represent them? Also, can more than 1 players be co-admins of 1 lab project?

How do we know when a lab puzzle is done? Does the puzzle owner decide that?

2. How do we allocate synthesis slots?

Say we have 2,000 active lab puzzles. How do we assign 20,000 synthesis slots to those lab puzzles? We could just evenly distribute 10 slots per each lab - but is there a better way to do it? Is there a way that we allocate more synthesis slots to those who are good and can make more efficient usage out of the slots? If so, is it possible to still give newbies a chance to get synthesis slots?

One idea we had was we could again entirely leave this to the community. If we have 1000 lab members, we could simply give 20 synthesis slots to each person, and everyone can decide how they will 'donate' their synthesis slots to projects. This is as transparent we can get with the resource allocation, but will share same cons with the current voting method.

Another idea is we come up with an resource allocation algorithm that will consider lab puzzle owners' performances, current community rating of each lab projects, number of submissions in each process, etc and automatically decide allocation. The obvious downside is that this process is not transparent, and we have no idea what kind of things the algorithm needs to consider at this point. However, if we tune the algorithm well, it would be perfectly objective allocator which could maxmize the outcome.

3. Lab rewards?

What is the best way to reward players for creating/pariticipating in lab projects? Until now, everyone got rewarded for submitting/voting in the lab, even if the designs they submitted/voted for did not get synthesized. This turned the lab rewards to be more like a weekly income that is not as exciting as it should be. Perhaps the lab rewards should be big/hard to earn such that good lab players can easily climb up the rank and the entire rankboard has more dynamic movements. On the other hand, the lab rewards shouldn't be to hard to earn as new players might get scared away.

These are some of the main issues that the dev team has been actively discussing lately.

Let us know what you think!

EteRNA team
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Jeehyung Lee, Alum

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Posted 8 years ago

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Eli Fisker

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Lab interface improvements

I would be very happy that each time I want to hide the dot and meltplot away, I wouldn't have to click cancel. It would be much easier if I could just press escape and it disappeared.



It would be even better if we could get a hot key to drag forth and pack it away, without having to do all the mouse clicking.
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jandersonlee

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Further on this vein, when doing labs, I keep exporting the sequence to RNAfold and RNAshapes to get better feedback on the overall design strength and the location of weak spots. This is an area where the lab tools are currently weak.

RNAshapes gives alternative foldings with probabilities.

RNAfold gives per-nucleotide local entropy values as well as fMFE and ED.

Now in *theory* some of this data is present in the dot plot, but in practice it's hard to interpret it or to see the plot and relate the points in it to the nucleotides in the structure.

Assuming that the EteRNA model can compute some of this data, some thoughts on how to present it:

a) Include fMFE and ED (or near equivalents) on the dot/melt plot page or even on the main lab screen near the FE.

b) Add a positional entropy graph (like that of RNAfold) under (or beside) the dot-plot with the positions aligned with the dot plot columns (or rows). When hovering over a position in the graph, highlight the node in the structure.

c) Allow optional coloring or shading of the rings around the bases to indicate positional entropy values (and/or allow the use of more degrees of colors or shading rather than just red/white in the bonding status icon). Also, when hovering over a spot in the bonding status icon, highlight the same region in the main structure.

d) provide a(n optional?) mode where hovering over a nucleotide with say SHIFT-MOUSE-DOWN would show radiating lines of various colors or shades to indicate relative probabilities of bonding between that nucleotide and others. The ring around the nucleotide would then indicate the probability of remaining unbonded. Hovering over a node may also draw a vertical line on the dot-plot and/or entropy plot for the region that represents that node when both are visible, and/or

(e) provide a mode where hovering over a dot in the dot plot would draw a line between the two related pairs that was colored or shaded to indicate the probability of those two bases bonding.

(f) provide a slider to adjust the *temperature* of the model to see what happens to the bonding as the simulated temperature changes. This might also help to indicate weak spots as they would be the first to break as the temperature rises.

(g) something I've not yet thought of which occurs to you based on how to make the data available in the model or parameters that can be reasonably tweaked made more accessible to the user.

Any way to improve the feed back on where the weak spots are in a design would be greatly appreciated!!
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jandersonlee

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(h) When marking a node with CTRL-CLICK, also mark the same node in the dot-plot and bonding status icon.

BTW, I *love* this game - I just want to make it even *better*!
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jandersonlee

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And just to be clear here, I'm *not* talking about integrating RNAfold or RNAshapes into the game. I just want to get a better fix on the information that the EteRNA model already *has* about the design. If it can draw a dot-plot it *must* have some idea of positional entropy and probabilities of pair-bonding and I want to expose that in a better fashion to the end-user. Likewise if it can draw melt-plot, it must be able to vary the temperature....
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jandersonlee

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It's about making it available in real-time to the user withought having to go through a submit/wait/look cycle. Also the UI of the game makes it possible to flip back and forth from the structure to the graphs in ways that the external resources cannot (but it doesn't do that yet)
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Eli Fisker

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I would like easy access to the dot bracket structure, just like I can get the RNA sequence in one click. Make a button like the "Copy the current sequence", but for the secondary structure.