User:Eli Fisker/EEE

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Eli's

Encyclopædia EteRNA

 

 

 

Contents

 

 

GUIDES

GUIDE TO THE GUIDES

A comprehensive guide to EteRNA

 

DICTIONARY AND FAQ

EteRNA FAQ

Eterna dictionary

 

ETERNA TOOLBOX

Keyboard shortcuts

 

EDUCATIONAL RESOURCES

Want to level up on your knowledge about RNA too? Check these videos and articles

 

PUZZLE GUIDES

Brourd's Beginner's Guide to Puzzlesolving

Puzzle solving guide

Puzzle solving guide addition

Brourd's Loop boosting guide - New slide version

Brourd's Loop boosting guide

Mpb21's Loops guide

Jennifer Pearl's Challenge Puzzles Quick Solve guide

Brourd's Puzzle solving guide

Drake's Advanced puzzle solving guide

 

PUZZLE WALKTHROUGHS

Hoglahoo's Reverse Spore Walk-through

The Spiral's Hog's Folly Revealed

 

SWITCH PUZZLE GUIDES

Switch puzzle guide

EINando888's Switch Training Series 1.1 Walkthrough

How to create FMN switch puzzles by EINando888.

How to Create a Switch Puzzle by Jnicol.

How to Create a Switch Puzzle as a Cloud Lab Candidate by Jnicol.

JMF028's Guide to mirroring part 1

 

LAB GUIDES

SINGLE SHAPE LAB

Quick Guide to the Lab

Lab guide for new players

My strategy guide to the lab

Mat’s lab design strategy

 

SWITCH LAB GUIDES

Switch lab guide

How to read the raw switch data

Visual guide to the new scoring system

For more on lab tools, go see under the tool section.

 

OTHER GUIDES

Understanding Free Energy (using Legos)

Tips and trick guide

Brourd's Zigzag Catalog

Jennifer Pearl's How To Write Clean looking technical documents using Google Docs

Rhiju's How to write a paper draft

Loops guide addition

EteRNA Script Intro

Gaming methods

Teaching and tutorial puzzles

Player strategy guides in general

 

 

TOOLS

PUZZLE TOOLS

Eterna Toolbox - Keyboard shortcuts

How to make a puzzle

How to create FMN switch puzzles by EINando888.

How to Create a Switch Puzzle by Jnicol.

 

LAB TOOLS

What to use melt plot for

How to use dot plot in single shape lab

How to use dot plot in switch lab

How to read shape data - basics

How to read shape data - extended

Quick guide to Eterna Bot


LAB DATA ANALYSIS TOOLS

Computationally Selected Elements

You can use this tool to help you with the lab data analysis and when you are designing for lab. With it you can pick out good sequences for a particular element in a design. You can look at certain type of loops, bulges or strings. 

How to use Computationally Selected Elements Tool

The tool is programmed by Jnicol. He based it on Mat's idea for a lab data analysis tool, Computationally Selected elements. The intention is helping us all make better use of the lab data we are getting back. And help us with the growing amount of lab data we will get.

For Mat's description of his tool idea, go see the forum post Computationally selected elements - analysis tool for lab data

 

DOT PLOT CAPTURE APP

Jennifer Pearl has made an app to capture dot plot. Here is her description: Dot Plot Capture Beta v1 of a new automated screenshot app for capturing dot plots of EteRNA. It allows everyone to perform simple analysis on the dot plots and also do screen captures of the different states. Same tool I used for screen shot for the cataloges I created.

Lab Results Image Capture and Analysis Tool

This is the manual describing how to use the tool. For links to the program go see: 

Jennifer Pearl's profile

 

CURRENT LAB - Theophylline Ribozyme Switch

There has been a lot of discussions and talks about the new Theophylline Ribozyme Switch lab. We are still trying to figure how to best take a go on it. I have collected some fine chatlogs and some of the official material on the lab in a doc, to help aid our efforts. Especially EINando888 has been contributing some fine intros, both to the lab but also to the 3D RNA viewer Chimera. 

Discussions on the Theophylline Ribozyme Switch lab

 

ETERNA SCRIPTS

EteRNA Script Intro

 

 

OUTSIDE TOOLS

HOW TO USE OUTSIDE TOOLS

Quick guide to Vienna RNA fold

Intro to Rfam - database over natural RNA

Quickstart with Chimera 1.7 by EINando888

 

LINKS TO OUTSIDE TOOLS

RNA folding algorithms

NUPACK

Rosetta

INFO-RNA

Vienna

 

Structure Databases

SCOR

 

TEST OF OUTSIDE TOOLS

EINando888 shared a link to a site that holds up many current RNA structure prediction algorithms with the aim of rating which is best. 

Comparna

As he also said: "Have you seen the list of competing algorithms on that website I linked? Specially, its length? What does it tell us ? To me, it's a very clear sign that no single algorithm, no software, no method, not even a global approach is overwhelmingly better than the others.

Nearest neighbor, partition functions and centroids, maximum expected accuracy, local optimas, mixes of these, etc, everyone will tell you that they are doing better than the others. Truth is, they (and we) are still poking in the dark..."

Some of our players have made their own test of some of the available structure prediction algorithms. 

How useful is structure prediction software in lab

I will advice you, if you use outside tools, to test them with some known structures. I don't use the outside tools, but I sometimes do run a test when the name of a RNA structure prediction tool pops up in chat. I then throw the tool the sequences of some winners from lab to get an idea of its strength on predicting the structure. I also throw it the sequence some bad designs to check that the tool is not too optimistic. Thus properly warned, go forth and play.

 

VISUALISATION TOOLS

Chimera

RNA Composer 3D

 

 

OTHER PLAYER RESOURCES

Catalyst points by Starry

Tutorial: The Barriers Webserver by Quasispecies

Tetraloop reference table by Dimension9

Loop and bulge energy chart by Jnicol

John has made some fine charts of loop and bulge energy. Shift between the different energy sheets in the left bottom of the document.

See also mpb21's page. He is eterna crew and have some great tips for the game on his profile.

Check out Alan.Robot's profile too. He is a computational biophysicist and have a great collection of links. Warning: Some of it is pretty complicated stuff, so DON'T feel bad for not understanding. I especially recommend his two posts, which are guides on how to use Vienna RNA fold: 

RNA fold and positinal entropy and free energy and kinetic barriers

 

 

LAB AND PUZZLE DATA SPECIAL

Jennifer have been making some nice pages with all the dot plots and meltplots from our second and third switch lab. Go check out her profile.

Jnicol have been extracting lab data so it is ready to dump in a spreadsheet for further analysis. He has a link to it all and a nice explanation on how to use it. Take a look at it the forum post Lab Data now available in spreadsheet and go make some analysis with it. Good luck!

Stlnegril9 has collected the Switch Shape Notation for both states of the switch puzzles. Find thim on his profile.

 

 

FUN RNA AND DNA SCIENCE

Fun RNA and DNA science

 

EDUCATIONAL RESOURCES

Here is a collection of things about RNA and related topics. Plus some fun science stuff too.

 

ARTICLES AND VIDEO'S ABOUT EteRNA

News about EteRNA

 

QUOTE AND JOKE COLLECTION

This is a collection with quotes and jokes about RNA, about our game and by us players.

 

EDUCATIONAL BIOLOGY GAMES

Game collection

 

SCIENCE NEWS ABOUT RNA

New collection

 

 

LAB GUIDE EXTENSION

Here is a link collection to some of my getsat posts. Compared to my lab guide, they include more explanations, pictures plus a few datasheets. Again I should remind you that this is tendencies in RNA designing as I noticed them and some of the rules could be a bit modified in the future or proven wrong. So be skeptic, but take it as a help to discover more in this wonderful world of RNA. Welcome!

 

ORIENTATION OF GC-PAIRS IN MULTILOOPS

Energy forces at work in multiloops

Same directional rule for GC-pairs in multiloops

Multiloop size and asymmetric multiloops

Update on my theory about GC-pairs in multiloop

Rulebreaking ensemble winner

Our kid robot

Adjacent multiloops

Small multiloops behaves different from bigger ones


NUCLEOTIDE PLACEMENT

Placing of nucleotides in multiloop area

Blue, green and red nucleotides in multiloop ring

Small multiloops - to boost or not to boost

Clean halo in multi loop ring

 

Placing of nucleotides in hook area

Placement of nucleotide at closing basepair for hook & neck

Nucleotides on the hook

 

Placing of nucleotides in strings

Why AU’pairs should alternate in strings

Energy strings

Repetitive patterns in strings

Placements of GU-pairs

Rulesensitivity according to length of string

The making of a string

 

Placement of nucleotides in loops

Mat's and Eli's tri-loop tendency

Internal loops

 

Placement of nucleotides in bent shapes

Bent shapes

 

THEORY OF EVEN ENERGY DISTRIBUTION

Energy, structure and symmetric colors

Even energy distribution continued

Even energy distribution revisited

 

About even energy in multiloops and tetraloops

Tetraloops, multiloops and mirrortwins

Something loopy - energy in multiloops

 

Energy jumps and their relation with mispairings (even energy on quad level)

Is energy jumps the cause of mispairing?

 

Even energy distribution, with slightly skewed energy level right after the middle of the designs 

Slightly skewed energy tendency for the whole lab

 

NECK AREA

What's so special about the neck area?

Energy in the neck area

Repetitive pattern in neck

Different types of necks and their effects on the main design

Energy in neck aligned with energy spots in the design

This is special about the neck area

 

ENERGETICALLY PRESSURED DESIGNS

Pressurized versus unpressurized lab puzzles

More on energetically pressured designs

 

OTHER

Thoughts on switch puzzles

Switch diary

Cloud Lab notes

Personal tools
Main page
Introduction to the Game