RNA picture library + new idea on The RNA sequence search tool

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We were a bunch of players that were just about planning building a RNA library of pictures. So we had a collecton of shared photoshoot of the labs to be able to scroll through lab designs, instead of have to painstrikingly have to click several times each time one wants to see a design and jump the waiting time as well.

What originally kickstarted the idea was Brourd writing to me the other day:

I was chatting with another player about designs for the current lab, and the main point of interest was a design "kiwi." Here, the central multiloop has the GC pairs all situated going around, however, I pointed out that designs like that may misfold. I then mentioned that I believe I saw it in the Cross lab, and he said that the amount of time would be too high. He then mentioned that it would be nice to see a list of designs/sequences that failed or succeeded.

Brourd suggested the idea to that we players should worked together on making a RNA picture library.

I discussed the idea with Mat to get more input on how this could be done. Here is a quick cut from our discussion:

mat747: i have ask for next/back tab/buttons for the lab
Eli Fisker: That will be great, I would really love this, it would by far be the easiest solution
Eli Fisker: Instead that we have to screenshoot all, especially if we want the shapedata and estimate mode in too
mat747: and a perview of the designs from the list
Eli Fisker: Exactly
Eli Fisker: I hope we get it some day
mat747: "483 MEDIUM Next/Back button to browse through lab designs in the design browser"
Eli Fisker: And we sort of need this as a training for when we get the ton of data from 10000 slots

So a piture library was the plan in combination with a next back button. Untill Jee threw in the big game changer later wto days ago. We just got the great news from Jee of the 1000 slots comming and synthesising of old data from previous labs.

With all these data comming our way soon, our picture library would be hopelessly outdated even before it could be made.

An automated solution will be much better than us photo shooting thousands of old results. It will help us all handle the many more results. Especially for old lab.

So this is what I suggest get incorporated into the game. The option to scroll through pictures of all designs in one lab.

Or as I found Soulrush saying in a recent chatlog: ”Would be nice to be able to highlight a portion of your structure, and have it search by position”.

That is the even better solution to a similar idea of mine about a visual RNA sequence search tool.
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Eli Fisker

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Posted 8 years ago

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mat747

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We need a shape search (dot-bracket) tool.
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Eli Fisker

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I really like the idea, Mat. I also wished for an element search, but shape search will be very important too. Especially if they could be combined. Else people will have to do a lot experiments to get the data, instead of analysing the data that is already there. When the flood of data is comming, no one will be able to have the overview of what everybody else is doing, so dragging out just the ones we are interested in will save time. The main reason for the wish is so we use our time analysing and not sifting through tons of data in an unintelligent way. Though I admit that the random viewing often did gave me an idea or two. :)
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Freywa

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It may be possible to use DU notation rather than the normal dot-bracket notation. DU notation is a RLE encoding of dot-bracket; the NUPACK web server design page has an overview of DU notation. In this way, repetitive sequences can be shortened.
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rhiju, Researcher

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EteRNAlists: I very much like the idea of the picturebook, for at least a few of the labs.

Even if we need to create a much more elaborate, automated search interface over the next year, it well help the devs immensely to have a 'mockup' that we know is designed by players and valuable to players!
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Eli Fisker

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Hi Rhiju!

One more idea on that account.

Outline from chatlog:
Eli Fisker: Jennifer have been making a nice page where all the dot plots and meltplots from the same lab are together in a document
mat747: great
mat747: maybe we should have asked dev for a comparison view for dot plots and meltplots as well
Jennifer Pearl: That would be a nice feature to have [9:59 AM]
Eli Fisker: Yes, I would love to be able to scrool through them, just like I can in Jennifers document
Eli Fisker: https://dl.dropbox.com/u/87351147/RNA...
Eli Fisker: here is the link
Jennifer Pearl: the ability to do a quick side by side of two designs
Eli Fisker: yes, that is helpfull too
mat747: yes we have asked for a side by side
Jennifer Pearl: we could use a format similar like you were saying

Just a sum up of the above. We would like to be able to scroll between the dotplot and meltplot as in Jennifers document and then be able to pick out two for closer comparison.
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mat747

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Here is a post from the past.

Split-Screen in Lab to Allow Side-by-Side Design Comparisons

https://getsatisfaction.com/eternagam...
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mat747

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Here is mockup I did in the past of how I think Side-by-Side Design Comparisons could look/function.

"Next/Back button to browse through lab designs in the design browser.
The Buttons would be hidden until the mouse was moved near/over them.

Link
http://img545.imageshack.us/img545/96...
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Eli Fisker

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Sounds good.

I have a few labs as screenshot. Right now they are in open office. I can't copy them direct into Google docs, only one picture at a time.

Also the pictures can't be shown in Google docs the way I prefer it. I want to view two pages at the time, which is usefull as I can better compare shapedata and estimate.

Is there any way I can publish a open office document as it is?

Anyway, here is a small taste of what I got, with this example from the lab Things to test.
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Eli Fisker

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In an other lab I have screenshots from, I have the name and the picture of the design on the left page and the shapedata on the page to the right. That is a view I find very useful, as I can see which colorpatterns and formation that is potentially bad, at the same time. That improves my ability to compare. In the game I can't see this information as once, and that was what originally made me do some screenshots.

The chalk outline lab.
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Eli Fisker

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My technical problems should be solved. I had to download an application that makes Google and Open office understand each other.

Here is a contribution to EteRNA lab picturebook:

The chalk outline lab, complete.

Things to test lab, complete.
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Eli Fisker

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Mat came with a suggestion to me the other day.

As he said: I think it would have been a lot easier is there was a save image to desktop game feature.

I really like it. It would be useful for much more than being the first helping step towards a RNA picture library.

I think it will mean more players will write posts and earlier. Posts with pictures are easier to understand too. Then the new don't have to mess with installing screen shot tools - which are not all easy to use. It would save time too. Hereby it is suggested as game feature.

Not all screen shot tools include all layers of the eterna pictures. If someone after reading this wants to install a screenshot tool I can recommend LightShot as an add on to the Firefox browser. [It now works with Google chrome too]
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mat747

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whbob

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Sometimes I like to print out state 3 & 4 of the OpenTB lab puzzles.  Just like to hold a paper in my hands.  Because the puzzles are on a blue background, it uses a lot of printer ink.  Trying to change the picture extension, mask the design shape to change the background to white is not efficient. Has anyone come up with a simple way to change the blue background to white for printing purposes?