2015.01.12 Ebbe & Cody 3D RNA Chatlog

From Eterna Wiki

jandersonlee: popup meeting link... [10:50 PM]

jandersonlee: Eterna Presentation Cody and Ebbe [10:50 PM]

TomoeUzumaki: yesss [10:50 PM]

Eli Fisker: Thx, JL :) [10:50 PM]

jandersonlee: np [10:51 PM]

StillBrees: Hi all [10:51 PM]

TomoeUzumaki: hey [10:52 PM]

StillBrees: This game is fun already [10:51 PM]

TomoeUzumaki: that's good :) [10:53 PM]

Eli Fisker: Hi StillBrees [10:54 PM]

StillBrees: hi [10:54 PM]

Eli Fisker: I see you found our old game tutorials. Try out these new and better .nova ones: [10:56 PM]

LinkBot: http://www.pbs.org/wgbh/nova/labs/lab/rna/ [10:56 PM]

rhiju: hi everyone [11:00 PM]

rhiju: hi linkbot [11:00 PM]

TomoeUzumaki: yo, rhiju [11:00 PM]

Eli Fisker: hi Rjiju :) [11:00 PM]

rhiju: we're having technical difficulties getting ebbe & cody up [11:00 PM]

TomoeUzumaki: ah [11:00 PM]

rhiju: but are reaaallllly close [11:00 PM]

TomoeUzumaki: that's okay, take your time :) [11:00 PM]

Eli Fisker: Crossed fingers [11:01 PM]

machinelves: hello! thanks for making it possible! :D [11:01 PM]

TomoeUzumaki: hey machinelves :D [11:01 PM]

Eli Fisker: Hi Elf and Tomoe :) [11:01 PM]

machinelves: hey Tomoe & Eli :D [11:01 PM]

TomoeUzumaki: Eli, quick PM [11:01 PM]

Eli Fisker: Tomoe, checking [11:02 PM]

StillBrees: what do the different colors of naes mean? [11:00 PM]

TomoeUzumaki: hah wait I have to write it first XD [11:02 PM]

Eli Fisker: They are just so we can tell each other apart [11:02 PM]

jandersonlee: no meaning - just easier to separate them visually [11:02 PM]

jandersonlee: (unless you are color blind I guess) [11:04 PM]

TomoeUzumaki: Eli, sent [11:04 PM]

rhiju: ok almost there [11:05 PM]

TomoeUzumaki: haha [11:05 PM]

StillBrees: ah. That's smart [11:04 PM]

machinelves: technological difficulties unites us across platforms lol [11:06 PM]

TomoeUzumaki: lol [11:06 PM]

Eli Fisker: Elf :) [11:06 PM]

Brourd: we're live. [11:06 PM]

jandersonlee: there is an echo - can you mute your speaker? [11:06 PM]

TomoeUzumaki: yep [11:06 PM]

machinelves: i see video but have echo [11:07 PM]

TomoeUzumaki: yeah same [11:07 PM]

hoglahoo: oo neat. how long is the presentation? [11:07 PM]

rhiju: is the echo better now? [11:07 PM]

jandersonlee: headphomes for the presenter - so no speaker feedback? [11:08 PM]

janelle: Can this be posted in wiki, must leave in 10 [11:08 PM]

machinelves: echo seems better [11:08 PM]

rhiju: OK we're about to go live for real, sorry for the craziness [11:08 PM]

rhiju: @elves thanks [11:08 PM]

StillBrees: wats happening? [11:07 PM]

machinelves: :D thank you everybody! [11:08 PM]

rhiju: sounds better to me too [11:08 PM]

Brourd: no problem, Dr. Das. [11:09 PM]

machinelves: hi janelle, will try to post under monthly eterna lab meetings [11:09 PM]

jandersonlee: better! [11:09 PM]

machinelves: and thanks for coming to say hi :) [11:09 PM]

janelle: thanks machine, and sound is fine [11:09 PM]

StillBrees: whats happening [11:08 PM]

StillBrees: ?? [11:08 PM]

Eli Fisker: This: [11:10 PM]

Eli Fisker: http://eterna.cmu.edu/web/news/5474894/ [11:10 PM]

Eli Fisker: We are going to get a presentation [11:10 PM]

Eli Fisker: on RNA [11:10 PM]

Brourd: Told you, tomoe. The weather almost requires long sleeve shirts. [11:10 PM]

janelle: Still click on the link and watch live [11:10 PM]

machinelves: (Post link to meeting here later) [11:10 PM]

rhiju: its on! you'll see it in a few minutes [11:11 PM]

jyesselm: (Post link to meeting here later) [11:11 PM]

machinelves: thanks! live for me [11:11 PM]

machinelves: :D awesome cartoon [11:12 PM]

Eli Fisker: Agree, this is amazing [11:12 PM]

janelle: Sound is Perfect! [11:13 PM]

hoglahoo: reminds me of bacon [11:13 PM]

Eli Fisker: Lol [11:13 PM]

rhiju: hey everyone do you see the feature on youtube to 'join the conversation'? [11:14 PM]

rhiju: its cool, you can directly give thumbs up/down to parts of the seminar [11:14 PM]

hoglahoo: I don’t see that. must I be signed in? [11:14 PM]

janelle: yes [11:15 PM]

rhiju: yea you may need to be signed in [11:15 PM]

janelle: Don't want to click and turn on the mic and disrupt the talkkk [11:16 PM]

Eli Fisker: Lol, on the dolphin [11:16 PM]

machinelves: hahaha smiley face totally sweet. omg that dolphin!!! [11:16 PM]

hoglahoo: oh, I see it now. That was there before I signed in too, but I didn’t even look at it. I thought it was an ad and I immmediately closed it [11:16 PM]

machinelves: :D never seen that before :D [11:16 PM]

rhiju: if you join via that link to the 'hangout audience' you'll actuall see a live stream without delay [11:17 PM]

jandersonlee: losing the sound from time to time [11:17 PM]

machinelves: me too on the sound loss [11:17 PM]

Eli Fisker: haha, on molecular spider [11:17 PM]

Eli Fisker: Yes, sounds fall out [11:17 PM]

Eli Fisker: Sound fall out now [11:18 PM]

rhiju: i've tried to move the mic closer to ebbe [11:20 PM]

machinelves: hahaha translation cartoon :D and awesome history on ribo [11:20 PM]

Eli Fisker: Good [11:20 PM]

Eli Fisker: Cool RNA visualizing [11:21 PM]

machinelves: lol pirate protein [11:21 PM]

machinelves: or what is risc? [11:21 PM]

machinelves: lost sound + video briefly again but back [11:22 PM]

Nando: RNA-induced silencing complex [11:23 PM]

machinelves: thanks nando! [11:23 PM]

Nando: np [11:23 PM]

janelle: Thank you Dr. Das and Eterna [11:24 PM]

machinelves: awesome comparative slide with all the representations of structure :D [11:27 PM]

jandersonlee: I'd not seen the arc diagrams before [11:28 PM]

machinelves: that caught my eye too, haven't seen before [11:28 PM]

machinelves: hahaha stapled origami [11:30 PM]

rhiju: ebbe is about to finish [11:30 PM]

rhiju: any q&a for him? [11:30 PM]

Eli Fisker: Ebbe, big thx for your lecture. It was awesome. [11:30 PM]

Eli Fisker: These RNA cartoon images are simply amazing. Are they published in a book anywhere? [11:30 PM]

jandersonlee: so when does this get added to EteRNA ;) [11:31 PM]

machinelves: thank you Ebbe, agree with Eli, cartoons were simply beautiful and hilarious [11:31 PM]

Eli Fisker: Also Ebbe, did you draw them? [11:31 PM]

jandersonlee: informative and entertaining - thanks! [11:31 PM]

Nando: I think he did [11:31 PM]

Eli Fisker: I thought the nano scientist looked like Cody :) [11:31 PM]

Nando: I saw some of them signed [11:31 PM]

machinelves: so cool. i agree with janderson would love to see more about the arc structure representation [11:32 PM]

Eli Fisker: They are simply fantastic and very helpful, they would be lovely for a book [11:32 PM]

machinelves: wow! amazing, the cartoons are so helpful. really well done [11:32 PM]

machinelves: really stellar - both funny and educational, and pretty too. we love educational materials that bridge the gap from scientist to citizen scientists [11:33 PM]

jandersonlee: we'd love a tile lab! [11:33 PM]

machinelves: the phrase "temperature ramp" was interesting, would like to hear a sentence about that [11:33 PM]

machinelves: yay! comparative slide between rna & dna so helpful [11:35 PM]

machinelves: wow i had no idea there were different helical structures between the two [11:36 PM]

machinelves: "the shapes themselves are carrying the function" :D [11:36 PM]

jandersonlee: Q: what non-watson crick pairs? any beyond GU/UG? [11:37 PM]

Eli Fisker: Wow [11:37 PM]

Eli Fisker: on the twisted square [11:38 PM]

machinelves: agree [11:38 PM]

jandersonlee: (sweet!) [11:38 PM]

Eli Fisker: Hehe, I forsee RNA valentine [11:38 PM]

machinelves: hehe :D [11:39 PM]

machinelves: wow the top right image that is grey what is that? [11:39 PM]

Eli Fisker: I think the grey part are done with the grey tiles [11:40 PM]

machinelves: electron microscopy photo of rna? [11:40 PM]

jandersonlee: The grey parts are done by EteRNA players (sometimes) [11:40 PM]

Eli Fisker: Wow on the angle loops too [11:40 PM]

jyesselm: we'l ask cody to pause and answer some questions [11:40 PM]

Eli Fisker: haha, good one, JL [11:40 PM]

jyesselm: after this awesome movie [11:40 PM]

machinelves: are the angle loops certain motifs then? [11:40 PM]

Eli Fisker: thx, Joe [11:41 PM]

jandersonlee: got to run to another meeting - thanks for sharing this online! [11:41 PM]

Eli Fisker: Bye JL [11:41 PM]

machinelves: bye JL! :) [11:41 PM]

machinelves: would also like to know a sentence more on "polishing" [11:42 PM]

machinelves: awesome explanation of temp ramp, thanks! annealing, lol perfect word [11:43 PM]

Nando: has work started on dynamic RNA origamis? for instance a change in pH would cause a conformational change [11:45 PM]

machinelves: wow on polishing procedure [11:48 PM]

Nando: structure minimization [11:48 PM]

machinelves: i heard of chimera a long time ago and didn't realize it was still used! thanks for the tip! [11:48 PM]

Nando: ok cool :) [11:49 PM]

Eli Fisker: We have some intro guides to chimera [11:49 PM]

machinelves: wow cool, thanks Eli! [11:49 PM]

Eli Fisker: One by Nando: [11:49 PM]

Eli Fisker: https://docs.google.com/file/d/0B8EEBMO3fRaUTDFMSDdmZm5INm8/edit [11:49 PM]

Eli Fisker: And one by Omei: [11:49 PM]

Eli Fisker: https://docs.google.com/document/d/1Ebb0b3lGHALGkTYS_9w9-9m3YTA7Zhf6XUB4dP7hGko/edit#heading=h.edkaw71jve03 [11:50 PM]

machinelves: very cool, thank you! [11:50 PM]

Eli Fisker: np [11:50 PM]

rhiju: sound has been ok? [11:53 PM]

machinelves: yes, occasionally cuts out but working now [11:53 PM]

machinelves: truly there is an order to formation helices hairpins - junctions - tertiary? [11:54 PM]

machinelves: or is that what we are aiming for? [11:54 PM]

Eli Fisker: Haha, loves the realtime image video [11:54 PM]

Eli Fisker: This is crazy fast [11:55 PM]

machinelves: yes img that's awesome [11:55 PM]

machinelves: *omg [11:55 PM]

machinelves: { so awesome can't even type lol } [11:55 PM]

Eli Fisker: RNA football [11:55 PM]

machinelves: lol [11:55 PM]

Eli Fisker: If it could curve [11:55 PM]

machinelves: good point [11:55 PM]

Nando: awesome [11:55 PM]

Eli Fisker: RNA honeycomb [11:55 PM]

machinelves: how strong is the nano rna mesh? [11:56 PM]

rhiju: will ask all q&a at end -- keep typing in questions [11:56 PM]

machinelves: wow those images are *phenomenal* [11:56 PM]

machinelves: thanks rhiju!! [11:56 PM]

machinelves: omg you can see the heximesh [11:57 PM]

machinelves: :D [11:57 PM]

machinelves: atomic force microscopy thank you, that's what i was wondering :D that 500nm photo, wowzers! [0:00 AM]

machinelves: 15 minutes!!! [0:01 AM]

machinelves: like magic! [0:01 AM]

Eli Fisker: Hehe wow, I can see the small triangle holes [0:02 AM]

machinelves: about how many nts is a ribosome long , i forget [0:02 AM]

machinelves: omg Eli you're right [0:02 AM]

machinelves: wow [0:02 AM]

machinelves: oh haha awesome map of length [0:03 AM]

rhiju: @elves, about 5000 nts total for a ribosome [0:03 AM]

machinelves: thanks Rhiju! [0:03 AM]

rhiju: 7216 nts for human ribosomes [0:03 AM]

machinelves: ooo longer program lol [0:03 AM]

machinelves: i can see how the motif library will be so helpful for design [0:04 AM]

machinelves: and 3D viz [0:04 AM]

machinelves: aww sweet timeline of hex lattices [0:05 AM]

Eli Fisker: Oh, sweet to know that we might be helping with this [0:05 AM]

Eli Fisker: Making new kissing loops [0:05 AM]

rhiju: hohglahoo sighting comin gup [0:05 AM]

hoglahoo: whoa whoa whoa [0:06 AM]

Nando: lol [0:06 AM]

Eli Fisker: Hehe [0:06 AM]

machinelves: agree thanks for sharing your work with us, so cool that we can work together to build the future :D [0:06 AM]

Eli Fisker: :) [0:06 AM]

machinelves: lol hogla [0:06 AM]

machinelves: wow great presentation Cody! [0:07 AM]

Nando: great presentation Cody [0:07 AM]

Eli Fisker: Thx for a great lesson, Cody! This was very helpful [0:08 AM]

machinelves: agree, very illuminating to get a walkthrough like this, many thanks! :) [0:08 AM]

Eli Fisker: Amd cool! [0:08 AM]

Eli Fisker: Haha, more car analogies [0:09 AM]

rhiju: your questions next -- BTW can someone volunteer to paste in a chat log? [0:09 AM]

Eli Fisker: I love how they have a way of finding their way into RNA world [0:09 AM]

machinelves: yes, I can if needed - but have to jump to work, Eli do you have log? do you mind posting to wiki? [0:10 AM]

Eli Fisker: Elf, I can do it [0:10 AM]

Eli Fisker: I have the log [0:10 AM]

machinelves: whew! thank you :D [0:10 AM]

machinelves: awesome, just let me know if you need any pieces [0:10 AM]

Eli Fisker: Thx [0:10 AM]

Eli Fisker: I couldn't hear the question, just now [0:11 AM]

machinelves: me either [0:11 AM]

rhiju: one question was whether we really need to go big to make cool stuff [0:11 AM]

rhiju: a second question was -- have you tried to use 'chaperones' (protein enzymes which can help RNAs fold) [0:12 AM]

Eli Fisker: Thx, Rhiju :) [0:12 AM]

machinelves: ohh thanks! was the second missed [0:12 AM]

Eli Fisker: Elf, how do I make a new page to paste the log on? [0:13 AM]

machinelves: will go make page... normally you just do Name to make link [0:13 AM]

Eli Fisker: Big thx, Elf [0:13 AM]

machinelves: np! made [0:14 AM]

Eli Fisker: Sweet :) [0:15 AM]

machinelves: :) go team! [0:15 AM]

machinelves: hehe [0:15 AM]

Eli Fisker: :) [0:15 AM]

machinelves: on strong i meant how much force before breaking, vs. general resiliency. thanks for distinction [0:15 AM]

machinelves: and does the geometry of the nanostrcuture affect strength - like do triangles hold their principle of architectural strength at that level? [0:16 AM]

machinelves: getting cutting out more often now fyi [0:17 AM]

machinelves: dynamic rna motors!!! :D super cool [0:18 AM]

Eli Fisker: Yup, look forward to that [0:18 AM]

machinelves: thanks everybody!!! [0:18 AM]

TomoeUzumaki: this is super cool guys, thanks!! [0:18 AM]

Eli Fisker: Clapping on our side too :) [0:18 AM]

Nando: thanks guys [0:18 AM]

machinelves: simply beautiful and informative [0:18 AM]

machinelves: clapping here too :D [0:18 AM]

machinelves: hehe [0:18 AM]

machinelves: okay i better run back to work. thanks again, and happy journey home Ebbe & Cody! [0:19 AM]

Eli Fisker: Bye Elf! See you [0:19 AM]

machinelves: thanks for taking care of wiki post Eli! [0:20 AM]

machinelves: bye! :) [0:20 AM]

Eli Fisker: np :) [0:20 AM]

machinelves: thanks for organizing this Rhiju! [0:20 AM]

machinelves: very cool impromptu session - totally captivating. really happy we got to join in [0:20 AM]