great idea. a home for volunteer developers?!
Volunteers should not have any fear of writing faulty code. Years ago, my computer programming instructor told our class, “You will never write a computer program correctly the first time. The very first time you test it, it will crash.” For what my two cents is worth, I think the description above is pointing in the right direction. Fear should be completely removed from the equation. Credit to you guys! This is a very challenging undertaking.
I’ve been playing with some alternative interfaces, like a “Switch Ring” view of the sequence and bonds:
It would be nice to have a home where I could put these so that others could try them and help develop them further.
Do you want demonstrably professional coders or do you also want people like me who like to code for fun and come up with some nifty things every now and then? Would breaking up significant coding assignments into small pieces and distributing to the “crowd” be useful? I have a feeling I would be the low guy on the totem poll given the kinds of high-quality coders you seem to have access to.
I think we need a (1) build/test/development server, and (2) (git?) repository server, and (3) suitable “sandboxes” for people to play in. If it is reasonably sandboxed, then all skill-levels are welcome. (AKA crowd-sourced development.)
I’m tickled that you guys are even considering this…just delighted!
Uhh. Who is “you guys”? I’m just a player. 
Oh sorry. My tickledness still stands though. You said “all skill levels welcome”. I interpreted that to mean you were one of the promoters.
I think the basics of crowd-sourcing are much like that of chat: by default, you are welcome to join, unless you make a nuisance of yourself, in which case you are banned.
Sandboxing development makes it harder to interfere with one another. You could still become a nuisance by suggesting all kinds of weird and unnecessary changes, but that doesn’t often happen.
Typically one or two people will become the final arbiters of what changes are included in the “master” version line, but beyond that, people do their own thing, knowing that that have to play by certain rules to get their changes folded back into “master”.
And here is a alternative Dot Plot Viewer that lets you step through sub-optimal foldings and see the dot-plot in a ring:
So far. I leveraged the Vienna tools of course, but most of it is Javascript and runs in the browser. I do need a server to serve up the JavaScript and run RNAsubopt on demand though (as I don’t have a JS version of that.) Gotta love HTML5 w/ Canvas!
Wow. There’s some serious thinking going on in this community. Kudos to all involved! I’m still getting my “sea legs” around here but seeing topics like this is very motivating for digging into the deeper science of it all (papers, research, etc.).
I only hope I can catch up before it (EteRNA) comes out in 3D at a theater near me :).
Great tool, love the color use. did you know there was a similar concept posted in the forum–but you have made it glorius!
I think jnicol has laready made the RNAsubopt port to javascript, or is working on it. If not, ElNando is trying Emscripten. Let’s hope it goes well–he could possibly port all of either or both versions of Vienna. Or show that it really is possible.
Fantastic tool. How do I get to use it?
Did you see this post https://getsatisfaction.com/eternagam… ?
Or did you develop this great tool unaware the technique had been mentioned?
Home for volunteer developers - like that thought, JL.
Spacefolder, thx for sharing this advice for novice programmers. Great teacher you had.
I may have been influenced by that forum thread. I don’t remember. I was working on it around the same time.
Check my profile for a list of some papers that might be of interest, as well as all the top players–most have something somewhere on the site or the wiki.
SCRIPTING SANDBOX
If you want a place to play and not having your temporary and perhaps not working scripts among the published scripts, Brourd suggested you can post them on the test server. Our former beta test site.
Hoglahoo tested it out. It seems that every script that gets posted in the our regular Eterna page, turns up on the beta test site. But everything posted on the dev beta test side, doesn’t get mirrored on the main site. From Hoglahoo’s testing out:
hoglahoo: oh ok, so whatever is published on .com shows up on .org but not other way around?
hoglahoo: Eli, I created on .org but I don’t see it on .com. So I guess it’s a one way copy machine or something?
Eli Fisker: Great
hoglahoo: yep, so this should work
Eli Fisker: So we have our script playground
Eli Fisker:
Hmm. I created http://eterna.cmu.edu/web/script/2839… but there is no http://kws.eternadev.org/web/script/2….