EteRNA Class Time - 1st session scheduled 2/5 at 6pm EST

I would like to start class time sessions for players who want to learn more details about the tools and other EteRNA related topics to advance everyone’s collective knowledge :slight_smile: I am volunteering to run the first class tomorrow 2/5 at 6pm EST. The day of week and time may change in the future, but I thought most players would be accustomed to this ‘dev chat’ schedule. The classes can take place in chat on the weeks when there is no dev chat.

The first class will be a demonstration of the javascript scripting tool using the Lib.energyOfStruct function to display an energy chart of all tetraloop energy values. I plan on this being an interactive class, so be prepared to use the scripting interface as we go through the demonstration together.

Lets see how well this session goes, and hopefully we can build some EteRNA related educational material.


Awesome initiative. I’m in. :slight_smile:

This is going to be a huge help on us getting better both at using and making resources available through scripting.

Script apprentice salutes the script master.

this is really great, thanks so much! :slight_smile:

since players were so excited about the prospect of EteRNA University, I have made a forum question to discuss which platform everyone would like to use as a curriculum repository:…

That was an awesome class :slight_smile: I hope they continue!

So then, are you taking ideas for future classes at the current time? I have an idea for a script that I am sure could teach players quite a bit :smiley:

do tell

seconded, do tell :slight_smile:

So then, the idea would be to make a lab scoring script using a strategy like jnicol’s flip strategy.…

In addition, one could also include a single, double, triple, and quadruple point mutations to the structure, and score the suboptimal structures, then use a weighted mean in order to determine the overall score of the sequence.

Various functions could probably be demonstrated in the ultimate determination of the score.

Is that a reservation for the next spot? :slight_smile:

If jnicol could reply to this, that’d be great–
What’s the name of the class he held? The wiki says Script Lesson 1 as well as the transcript, but I haven’t seen anything from jnicol confirming that name.

That’s probably just a temporary name.

Name doesn’t really matter to me, but I was trying to demonstrate how to generate the energy chart for tetraloops. Maybe “Energy Chart for Tetraloops part 1”. I would like to hold a Part 2 class after the dev chat on Wednesday.

So, to clarify how the script would be written.

Upon input of a base sequence (a target structure could be optional), the scoring script would make a predefined mutation to the sequence, then, score the predicted structure of this mutated sequence.

The image on the left represents the submitted design, with the sequence to be mutated, circled. The image in the center represents the native fold of the mutated sequence. Finally, the image on the right represents the SHAPE “score” with a score output at the bottom.

After all mutations and their scores have been determined, a final weighted mean of these scores can be calculated, which would be the output of the script.

A script like this would introduce players to many concepts, including how SHAPE scores are determined, as well as the creation of a potentially useful RNA scoring script.

Of course, this could be an advanced lesson, perhaps planned for several months from now, after players are comfortable with the scripting interface, as well as having the basic knowledge of Javascript, necessary to write the code.

Ok, thanks.

I like this idea Brourd, thanks! And I agree that this would be an advanced class.

Thanks for this great series of classes!

Although my timezone (UTC +10) make’s it hard to attend at the time, I am using them later.

wrt topics;
I’m a bit hazy about Lib.nextSequence(sequence) and Lib.nextSequenceWithBases(sequence, bases)

I’m also still not clear about multiloop energies (terminating pair, dangles, close/sparse branhces etc) so a class looking at these energies would be great.