What's the plan?

  • 1
  • Question
  • Updated 8 years ago
  • Answered
I'm sorry if this has been answered already - I tried a search but could get anything meaningful to this topic.

I just fail to see a plan in all this work that is going.

As far as I understood, Eterna is making a library of synthetic RNA's. They choose every week some candidates, synthesize in lab and store the results in database.

Some molecules are stable, some aren't. My question is, what could be the use of this database? Is it that lab will get the stable molecules, get its properties, and try to test on different reactions to see if a drug could be created from this?

Is the database open to outside world?

Can we get some videos from lab, with some explanations on how the tests are done, and why the conclusion is like this?

What do you plan to do as the database gets bigger and has more important data, what is the next step?

I'm not from biology field, so I apologize if some questions don't make sense or have too complicated answers to be meaningful.

Thanks,
Photo of igorcov

igorcov

  • 2 Posts
  • 0 Reply Likes

Posted 8 years ago

  • 1
Photo of rhiju

rhiju, Researcher

  • 403 Posts
  • 123 Reply Likes
Hi igorcov -- this is an important question. When we released EteRNA we weren't sure if this new scientific model -- giving thousands of non-expert players access to high-throughput experimentation -- would even work, so we purposefully kept the initial mission statement a bit limited, to the creation of a library of designs & data. We can change this now, due to much good news!

Now, we're finding that top players can fold RNAs in silico faster than computers. More importantly, the community has found rules for designs that actually work in the test tube that have eluded prior algorithms and experts, and we have just finished experiments to rigorously test these ideas. As a first milestone for the project, the developers are writing what we hope will be considered a major scientific paper.

Because of these successes, we're planning several major updates to EteRNA in the next few months, including a more detailed mission statement.

The main advance that we expect will be a massive increase in experimental throughput so that essentially all players will get their designs synthesized and biochemically validated/falsified in the lab. We are still working out this protocol, so it might take a little time, but this is a top priority. In terms of scientific goals, the project's aims will expand from creating a library of designs, one-by-one, to more generally finding and rigorously testing new rules for RNA folding & design in 2D and 3D, and eventually for testing in living cells. Please stay tuned for a month; in addition to summarizing the advances we've made so far, we'll lay out a plan for the future of EteRNA.
Photo of Adrien Treuille

Adrien Treuille, Alum

  • 243 Posts
  • 33 Reply Likes
Looks like we both wrote responses at the same time! :)
Photo of Adrien Treuille

Adrien Treuille, Alum

  • 243 Posts
  • 33 Reply Likes
And they're pretty identical! :)
Photo of Eli Fisker

Eli Fisker

  • 2236 Posts
  • 495 Reply Likes
Hi Igorcov!

About the RNA library, see here under Science data on our game.

To hear about the plan of Eterna and for the future check out the first 15 minutes of this video, that Mat sent to me:

Open education and the future of science education

For more videos and news about Eterna, see News about eterna. This should be easy understandable as most of is written by outside journalists not into biology.

Don't be sorry for asking. Most of us are not in biology either.
Photo of Adrien Treuille

Adrien Treuille, Alum

  • 243 Posts
  • 33 Reply Likes
This is a great question. Currently we are preparing our first paper on EteRNA results, and we hope that reviewers will agree with our assessment of two important results:

(1) The community has learned insights into RNA folding to the point that it now soundly outperforms state-of-the-art algorithms.

(2) The community has been able to express (to a certain degree) these insights as "strategies" which can automatically design RNAs better than existing algorithms -- although not quite as well as the players themselves. We expect this community-designed "ensemble strategy" to improve over time as more and better strategies are submitted.

These results are very exciting on several levels. First of all, RNA design is a biologically important problem that EteRNA is rapidly advancing. Second, this project demonstrates that non-expert citizen scientists can formalize successful and empirically repeatable rules that describe a natural phenomenon -- perhaps the core aim of science.

I hope that this helps answer your question. (Also, yes: the database of designs will be made publicly available, although we're still working on the interface.)

Your post has inspired us to think that it would be good for us to publish a two year scientific roadmap for the future of EteRNA on-line so that the community could see what we're doing and comment.
Photo of Eli Fisker

Eli Fisker

  • 2236 Posts
  • 495 Reply Likes
Two year scientific roadmap for the future of eterna. Now I'm really excited too - okay, already was. :)