Gas station without pumps

2016 February 8

New statistics game

Filed under: Uncategorized — gasstationwithoutpumps @ 19:56
Tags: , , is a game (with very retro graphics) to guess correlations from scatter plots. It is surprisingly difficult to do well, especially since Pearson’s r is so heavily dominated by the outliers, while our visual perception is more attuned to the group.

I’d like to thank Robert Jernigan for his post that pointed me to the game.  (My current high score is 163.)

2011 January 12

EteRNA, an Online Game

Filed under: Uncategorized — gasstationwithoutpumps @ 02:48
Tags: , , , ,

An article in today’s New York Times introduced a new “citizen science” game: EteRNA, an Online Game, Helps Build a New RNA Warehouse.

This game, following in the model of FoldIt for protein folding, has players designing RNA molecules.  Some of the designers of FoldIt helped design EteRNA.  The difference here is that the game is 2D (RNA secondary structure, rather than protein tertiary structure) and the task is to design RNA sequences rather than to fold given protein sequences.  (FoldIt has a protein design mode for researchers, but it isn’t part of the on-line game.)

EteRNA seems to be rather addictive.  There’s a bunch of crap on the screen (like a chat box that can’t be removed completely, and buttons that throw you out of the puzzle you are working on, which you can accidentally click when trying to color a base), but overall the interface is easy to learn and not too difficult to use.  There are times when I’ve wished for a more powerful operator that allows swapping the two bases of a pair, or replacing them with the other Watson-Crick pair, since it takes a lot of mousing back to the color palette to change two bases to different colors.

One cool thing about EteRNA is that the developers plan to synthesize some of the RNA designs that gamers come up with, in an attempt to check and improve the models used for folding RNA in the game.

It would be useful for gamers to know something about the base stacking model in EteRNA.  Luckily, one of the players has reverse-engineered the model so that the stacking contributions to the energy are available in a table.  It might be good to have some visual cues about stacking energy, though.

FoldIt and EteRNA seem to be fairly successful attempts to harness game players to do interesting optimization.  A different attempt, Phylo, which attempts to use humans to do sequence alignment, is a failure.  It is not fun to play, and the puzzles that people are given are small enough that would be faster to do the combinatorial optimization than to present the puzzles to the humans.  In short, Phylo is useful neither for gamers nor for science.

Additions: 12 Jan 2011

I played EteRNA for entirely too long last night (up until 4 a.m.).  I realized that there is a swap-bases tool, and that it isn’t the tool I want.

What I want is to have 5 tools selectable by typing a key: A, C, G, U, W for the 5 recognized base pairs (W for UG).  Clicking on a loop base would behave as now, putting in the A,C,G,U or U.  But on a paired base it would also fill in the other base appropriately with U,G,C,A, or G.  It shouldn’t matter whether the current display is the target structure or the current minimum-energy structure—the pairing is always part of the target design.

Two other things I’d like to see:

  1. a “randomize” option that can give me a random start (with all 5 tools applied randomly to a range of the RNA sequence)
  2. a bin of anti-design stems: pairs that formed in some incorrect minimum-energy structure but not in the desired structure.  I should be able to click on bases in the anti-design and have the tool applied to the base selected.  I would probably need to empty the bins occasionally as changes to the sequence make some anti-design stems no longer likely to appear in any minimum-energy structure.

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