tool #1 from worseize

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I created script for Eterna https://worseize.github.io/Eternagame/

Any issues are welcome
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worseize

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Posted 1 year ago

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worseize

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update: now it search automatically for longest possible RNA sequence from 2 oligos.
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worseize

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update:
Second edition better structure of code (automatically find longest rna from 2 oligos "V" and "N" to navigate thru memory array that stores all possible variants)
App:
https://worseize.github.io/EternagameScript2018/
Repository:
https://github.com/Worseize/EternagameScript2018
(Edited)
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worseize

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-Folding added to 2D engine at second page.
-Bot added - brute force algorithm - only 1 loop (does not predict states where is more than 1 loop) 85 bases =  around 450k variations of rna folding  = 1 around second to solve
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worseize

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Manual playlist
https://www.youtube.com/watch?v=dYDxDWK1A4U&list=PL7CHTefBrBuj3EMghG_MJ-AuV1Hwmrab6

v. 2.3.1
In manual mode: 
   Shift + mouseClick => change letter on Page2.
   Alt + mouseClick => remove letter on Page2.
   Ctrl + mouseClick => add letter on Page2.
In auto mode:
   V | N => change memory position.
Shift + [page number] => choose Page.
(Edited)
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MasterStormer

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Nice one! I think that an option to remove bases from the oligos would be nice. for example, with these 2:
UAUAUAUUAUAU
UAUAUAUAUAUA
You app will show the longest is the sequence up until the double Us, although with a bulge of the second U the entire oligo can be used.

[EDIT]: Adding spaces would be better than removing bases for that use imao.

Your project seems to fall under the same umbrella of a project I am currently working on, so I will probably find algorithms or features in my project that I could send to you and vice versa (such as algorithm for the best matches) .

Is it open source? Or just hosted on github?
(Edited)
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Eli Fisker

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Worseize, this looks interesting.

Could you shot a few images from an example along with an explanation of how to use your tool?
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Astromon

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Does this tool give you complementary sequences to the puzzles olegos?
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whbob

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yes it will create a kernal sequence where  there is a common attractor to the two oligo's. You can step one oligo along while leaving the other in place and look for the most sequential bases common to the two oligo's. nice tool.
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Eli Fisker

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Hi Worseize!

I really like what you are up to. It reminded me that jandersonlee, mat and I had an early effort from OpenTb round 2. It is hereby dusted off. It is my hope this will help.

Jandersonlee and I threw together a spreadsheet that can help to generate starting sequences. It has the TB RNA oglio sequences at the top in two different color schemes: base and oglio. Really it is mainly his work. :)

OPENTB_R2-generator.xls

jandersonlee also wrote an intro on how to use the spreadsheet.

Sequence Generator Starter Kit Intro

Basically one can copy the input or the inverted version (input complement) of an input and dump it in a line that will do the RNA math of making a complement sequence to whatever is dumped.
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Eli Fisker

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jandersonlee made an even more through guide to use the input calculator spreadsheet. Here it comes:

OpenTB Designing with RABC-Design
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worseize

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I am back . I need a vision of whole program or structure . If anyone have time please send me how you imagine best tool.  It could be explained like that :
Inputs [4] : A, B, C, r -->  [process (Inverse Input) ] -- > Output [4] 
This is only what I see at the moment. So I will do it today. What next ?

Big problem is space . I could make 2 page program but it would be less efficient. I`d like to see entire structure on one page then it is efficient.

Best if you send screenshot of what kind of information where should I put.
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Eli Fisker

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Worseize, I really like what you are up to.


Ok, I have an idea. I will use a concrete lab that I have been working on as an example. Please say if I am not making myself understandable, and I shall try explain better.


Here is an image from the lab.



The puzzle is not stable. It is from this series. If anyone is capable of making it stable, please do.


In this puzzle I am not using any overlap between the input sequences. Instead I make both the A and the B input each fold up with itself. I use some bases at each end of the input complements to help this.


Basically what I would really like to be able to do in your tool is to use it to explore how I can best make an input complement pair up with itself, without altering too many of the original bases.


I have tried draw what I wish on the image and show how I wish the bases to be related.



I basically wish for a way to check how one can make a match inside the same input complement (can also be any other stretch of sequence where one may wish this). But still I want the input to also be related to the input. So if I can have this sequence line I drew with dots, below the actual B input but still get allowed to somehow test for pairup posibilities inside the sequence, I would love to be able to.


Here is one puzzle that is representative for the series. They are called Input complements selffolded in the ABC2DEC lab. Or Seastar in the ABC2INC lab.


This selffolding strategy could also be used for designing sites where the reporter needs to be turned off against one input complements.


Background post on why this is really helpful.


Andrew’s Key: Reporter turnoff proximity matters


I have explained more about this lab puzzle strategy on making an input complement pack itself away against itself.


Input concentrations matter - length of inputs complements too

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worseize

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https://worseize.github.io/EternagameScript2018/ Finally I did it . Is it ?
https://github.com/Worseize/EternagameScript2018 - manual .
What Next ? Maybe auto Search but what to search ? Maybe mouseClick to element and change it value as in page 1 ? 
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Eli Fisker

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I really like what you have done with your tool!

Also the visual video demonstration is really helpful.

I love the hairpin option that is formed between inputs and that I can see how many pairs are formed in it.