Dear all,
EteRNA dev team had a long discussion about how EteRNA will change with the new high-throughput synthesis pipeline. Here are the details about the new EteRNA, which is temporarily called EteRNA 2.0 ~ Cloud Lab~ (If you have other ideas for the name, let us know!)
1. Roadmap based website
The new EteRNA 2.0 ~ Cloud Lab~ website will be focused around a concept of “roadmap.” The roadmap lists list of things you can clear and learn in an orderly fashion - so that the new players can simply follow the roadmap to become EteRNA experts. You may have seen similar concept in many other video games, or websites like “Khan Academy”
(A mock up of what a roadmap might look like)
Each node (or a stage) in the roadmap will have associated conditions and rewards which can be points, badges, and sometimes unlocking of game features.
The roadmap consists of 4 zones (only 2 showing up in the mock up)
i) Game & Puzzles : This is a part where you focus on learning basics of RNA folding, clearing challenges, making puzzles. This zone will embrace tutorials, challenges, and player puzzles.
ii) Cloud Lab :This is a part where you really get into player lab (or player projects) and rna synthesis. This zone comes after “Game & Puzzles”
This zone will have extensive nodes (stages) that will walk you through from participating in other players’ projects to creating your own project and succeeding on it.
iii) Paper & Publication : This is a zone which you can access when you have at least 1 “successful” player project. Stages in this zone will walk you through to create a scientific write up of what you discovered in your project. The write up will be published to “EteRNA Library” which will be an archive of all researches in EteRNA. Also, a few very good write ups will be encouraged to submit to scientific journals - (more details on cloud lab section)
iv) Bot Factory : This is still in discussion - but this part will focus on beating bots like Vienna, InfoRNA and RNASSD as we currently do in player puzzles. Furthermore this zone will focus on creating a new algorithm from “Player scripting interface” that can beat all other bots.
2. Cloud Lab
“Cloud Lab” is another term for “Player Projects” which will replace the entire lab section. Unlike current lab section, in which we developers propose one challenge at a time, players will propose their own lab projects and use up to 20,000 synthesis slots.
i) Project proposal
Any player who’s about half way through the Cloud Lab Zone will be able to propose a project. There are several things the player will have to prepare, but the most important thing is a “hypothesis” the player wishes to prove with the project.
A hypothesis should be a clear (and brief) statement that you want to test with your project. 1 good example would be “RNA won’t fold successfully if it has more than 90% GC pairs.” In the project you (and participants) will focus on proving that the hypothesis is true (or false)
In the early stage, we will restrict the number of active projects to 20 at a time. When a player propose a project, the project goes into “proposed projects” roster. All lab members will be able to vote on the proposed projects. If an active project finishes and a slot opens up, the project with the most votes at the time will go take the slot.
ii) Finishing a project
An active project can be finished in 2 circumstances. a) P.I (Principal Investigator, the project proposer) declares the project done. P.I moves on to “Paper and Publication Zone.” b) The project have been inactive for a certain amount of time
iii) Participating in a project & rewards
Any lab member can participate in a project by submitting a sequence. When a player submits a sequence to the project, he has to decide whether the sequence will “prove” or “disprove” the project hypothesis. For example, if a project’s hypthesis is “RNA won’t fold successfully if it has more than 90% GC pairs.”, you could create an RNA with 100% GC pairs and say that the rna will “prove” the hypothesis. Or, if you believe the 100% GC pairs RNA could fold successfully, you would say that the rna will “disprove” the hypothesis. You will get reward when your sequence is synthesized & the prediction is correct.
Players will also be able to comment on & “Like” other designs submitted in the projects.
iv) Synthesis
A single round of synthesis will take 2 weeks ~ 1 month time span. We are not perfectly clear how long it will take at this point. We will start by synthesizing 1,000 sequences per round, then eventually bump up to 20,000 sequences per round.
v) Synthesis slot allocation
As for the synthesis slot allocation, we decided to give full powers to players themselves.
Beginning of every round, all lab members will get approximately [total number of slots] / [number of lab members] synthesis slots in their hands.
A player can pick any sequence in active projects and choose to synthesize it (unless the sequence was already picked to be synthesized.) The player can pick his own sequence if he wants.
PIs of active projects, will get (possibly many) extra slots to spend on their projects.
These extra slots can only be spent on the PI’s project. Also, how these slots were used will be published. Technically, a PI could decide to spend the extra slots for only himself - but this will be known to all players. If offended players decide not to participate in the project anymore, the project will become inactive and get closed.
vi) Publishing to EteRNA library.
When a PI decides to finish his project, he’ll be able to enter “Paper & Publication” and formalize the outcome of the project as a scientific paper. The zone will guide the PI through step by step procedure to present the outcome of the project into a clear/concise writing.
Every finished paper will be published to EteRNA library, which will be an archive of all EteRNA researches. This will be a public archive, and the author of the paper will be fully credited.
Eventually, EteRNA team will pick 4 best papers out of EteRNA library and help the authors to further polish the papers and publish to scientific journals. We hope to do this in 1 year from now. We’ll also encourage 4 authors to help other players in polishing their papers and researches - the goal is to open the opportunity of publication to every member of EteRNA cloud lab.
3. EteRNA new website structre
(How pages in the new websites are connected to each other.)
If you have suggestions or questions about the new EteRNA, please let us know!
EteRNA team
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[2:57 PM]