Evolutionary biology with the Azoarcus ribozyme
Today marks an exciting milestone in Eterna's progress: We are launching our first international collaboration!
French researchers have been studying a ribozyme capable of reproducing itself, and they are curious how many variations of the sequence are also capable of self-reproduction. Finding a large number of diverse sequences could be a clue towards unraveling the mystery of how life began on our little planet.
The Azoarcus ribozyme is a bit unique for us because the starting sequence already folds into the target structure in real life. The goal is to make 10-60 mutations to the sequence while maintaining the 2D and 3D structure. A 3D model is provided to allow visualization of potentially important 3D contacts, such as the two hairpin loops that dock with internal loops.
The Monday, May 20 town hall will discuss the new lab project and update players on the status of the OpenKnot rounds. The time has been moved forward to 10am PT to encourage participation by European players. Start time is 10am Pacific/Noon Central/1pm Eastern/5pm Coordinated Universal Time. No registration needed. Simply click on the Zoom link to join.
Also want to let everyone know I will be going to the RNA Society meeting May 28-June 2 to host an exhibit about Eterna's education tools and to answer researcher questions about collaborating with citizen science.
DigitalEmbrace - Jill
https://wiki.eternagame.org/wiki/Main_Page
https://eternagame.org/about
https://eternagame.org/
https://docs.google.com/document/d/1qWW0SU42KNcRBv6xiklODl_5w1VYIovioS6KeWpFGH0/edit?pli=1#heading=h.kwp8bt8rr8ko
https://www.youtube.com/watch?v=Iq57MTprHV0&embeds_referring_euri=https%3A%2F%2Feternagame.org%2F&source_ve_path=Mjg2NjY&feature=emb_logo
Eterna is an open science platform leading to fundamental advances in RNA biomedical research.
Eterna has created current state-of-the-art technologies to aid in complex RNA design, which are now available for licensing
Gameplay Resources
- Puzzle Walkthroughs
- Player-Created Guides
- Tips and Tricks
- Puzzle Maker
- Lab - An overview of the Eterna lab process
- Educational resources
Technical Resources
General
| Name | Author | Description |
| Comprehensive guide to EteRNA | Eli Fisker, Brourd, Starry | Guide to the guides. An introduction to the game resources and how to get well started. |
| EteRNA Dictionary | Eli Fisker | A large document listing all the terms used in the other guides with pictures. |
| EteRNA Toolbox | Eli Fisker |
A list of keyboard shortcuts. |
| A Gamer’s Guide to Eterna | rna-key |
Eterna game mechanics, basic game play, tactics and scenarios, and a path to mastering the game. Appendices on science and art. Published in 2020. |
Puzzle-solving Guides (single state puzzles)
| Name | Author | Description |
| Loops guide | mpb21 | The first guide on stabilizing loops. |
| Vienna vs Eternafold | JPS838898 | A guide for Vienna vs. EternaFold |
| General strategies | Multiple players | Players sharing general puzzle solving strategies in the forum. |
| Puzzle Solving Guide (Addition) | Eli Fisker | A great introduction for players learning how to solve puzzles. |
| Loop Guide | Eli Fisker | Useful tricks for solving tricky loops. |
| Multiloop Guide | Eli Fisker | A visual overview of how energy in multiloops can be lowered. |
| Tips and Tricks | Eli Fisker | A compilation of useful tricks for solving unusual shapes. |
| Stack Guide | dimension9 | A table of nearest-neighbor energy terms for stacks. |
| Hairpin Guide | mat747 |
A picture of successful hairpin sequences in mat747's lab designs. |
| Boost guide (New slide show version) | Brourd | A fine guide on how to stabilize loops. |
| Advanced Puzzle Solving Guide | Drake | A guide to puzzle solving that goes at puzzle solving from an energy perspective. |
| Puzzle solving guide |
Brourd | A fundamental guide that will show you the basics of puzzle solving. |
| Beginner's to Puzzle Solving | Brourd | A fundamental guide that will show you the basics of puzzle solving. |
| Challenge Puzzles Quick Solve Guide | Jennifer Pearl |
A visual guide showing good and bad puzzle solving style beside each other. |
Puzzle-solving Guides (switches)
| Switch Puzzle Guide |
Eli Fisker | Collection of switch puzzle guides, walkthroughs and solving methods. |
| Switch Training Series | Nando | Fantastic walkthrough giving the reasoning behind solving switches. |
| How to solve a switch |
JR | Great walkthrough on how to solve a switch puzzle. |
| Hand and Finger Walkthrough | Meechl | Visual walhthrough on how to solve a switch puzzle and get ready for lab. |
| A TRIPLE SWITCH WALKTHROUGH for EteRNAddicts everywhere | Jieux | Awesome guide for dealing with 3 state switch puzzles. |
Lab Guides
| Name | Author | Description |
| Lab Guide | Eli Fisker | Strategies for making successful designs in lab. |
| Lab Guide for new players | Eli Fisker | More strategies for making successful designs in lab. |
| Lab Guide | mpb21 | Strategies for making successful designs in lab. |
| A guide to using Vienna RNA fold | Eli Fisker | A guide to using Vienna - for assessing potential Lab designs. |
| GC Pairs in Lab | ccccc | Why you don't want to make Christmas trees in lab. |
| Mat's lab design strategy | Mat747 | Strategies for good lab designing. |
| Quick guide to the lab | Eli Fisker | Quick introduction to the lab tools. |
| Ways to deal with voting in huge labs [1] [2] | Eli Fisker | Lab voting methods. |
| Ways to deal with designing in huge labs | Eli Fisker | Methods for improved lab designing. |
| Switch Lab Guide | Eli Fisker | Collection of info on switches and advice for the switch lab designing. |
| General lab info and lab tech details | Eli Fisker | Collection of info from chat, forum, devs etc. relevant to labs and lab designing. |
| CSE using LabDataMiner for Lab "Late Bulge" | JandersonLee | A demonstration of how to use the LabDataMiner for lab designing. |
| CSE for Reversed G-C Multibranch Loop Closing Base Pairs | JandersonLee | A demonstration of how to use the LabDataMiner for lab designing in designs with multiloops. |
| Reading the lab results - Intro to SHAPE data | Eli Fisker | Intro on how to read lab results and SHAPE data. |
| Lab Manual - The Eterna History Tour | Eli Fisker | Learn how to do lab work. This lab guide is connected to the ongoing lab project for lab introduction. |
| MS2 - Thoughts about the lab data | Eli Fisker | Mixture of analysis, chat discussions on the lab and highlighting areas of interest for designing and analysis. |
| Different types of switches | Eli Fisker | Boiled down Switch lab Guide. Intro to switch tendencies and what has worked for them so far. |
| Switch Lab Intro | Eli Fisker | Quick intro to main tendencies for working lab switches. |
| MS2 Lab Intro | Eli Fisker | Introduction on how to start solving a switch lab puzzle in an MS2 lab. |
| MicroRNA Intro [3] | Eli Fisker | Introduction to microRNA, Eterna Medicine and the Feynman challenge. |
| Doing Math with RNA | Eli Fisker | Simple approach for doing math with RNA. |
| A Tutorial for A/B Ramp-up puzzles | Omei, Eli Fisker | Introduction to puzzles and lab for the A/B switch labs. |
| Logic Gates | Eli Fisker | Pointers for the logic gates lab. |
| A*B/C^2 neutral Design for both DEC and INC TB puzzles | AndrewKae | Tips for designing for the hard TB A*B/C^2 DEC and INC puzzles. |
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