2014.01.15 Dev Chat

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On PNAS, NOVA, & Press Interviews


jeehyung: hi all [3:08 PM]

jeehyung: welcome to the bi-weekly dev meeting [3:09 PM]

mseetin: Hi jee, and thanks again for promoting my labs [3:07 PM]

Brourd: thanks Matthew! Look forward to the results from your experiments. [3:08 PM]

Brourd: Hi Jee [3:08 PM]

Brourd: how is your day going so far? [3:08 PM]

mat747: Hi Jee [3:08 PM]

Eli Fisker: hi Jee :) [3:08 PM]

jeehyung: Hi matt, brourd, mat, Eli [3:11 PM]

jeehyung: @Brourd I'm good : ] thanks [3:11 PM]

jeehyung: @mseetin no problem I hope we get a lot of submissions [3:11 PM]

Brourd: So matthew, looking at your favoring equivalent structure lab. [3:10 PM]

Brourd: http://prntscr.com/2jolcw [3:10 PM]

jeehyung: Before we begin, we are aiming for some more press releases about our new paper. Again, some of the presses will want to talk to our players [3:11 PM]

jeehyung: If you are willing to help - please message me. I'll post a news item about this soon! [3:12 PM]

Brourd: are mutations for this area off limits? [3:11 PM]

Eli Fisker: Jee, cool that our paper will come soon. I look forward to it. [3:11 PM]

Brourd: Will do Jee, can you disclose the entity that wants to do the interviews? [3:11 PM]

jeehyung: @Brourd actually we don't know exactly who they'll be yet. CMU is talking to various media, so they'll let us know. Of course, you'll have a chance to decline the talk when you are contacted. [3:14 PM]

hoglahoo: :) [2:12 PM]

Brourd: excellent [3:13 PM]

Eli Fisker: It was really PNAS who took our paper? [3:14 PM]

jeehyung: @Eli - yes, our paper will be on PNAS [3:16 PM]

Brourd: yes (as indicated in the EteRNA certificate) [3:14 PM]

Eli Fisker: hehe, awesome [3:14 PM]

Eli Fisker: Ah, yes. [3:15 PM]

Eli Fisker: I'm just still very happy it will come soon [3:15 PM]

mseetin: @Brourd, no, mutatiosn there are not off limits. I made that area larger than in the original lab so that people could mess with it. Is there perhaps a bug in the test script that says that cannot be changed? [3:15 PM]

Brourd: oh, no, I was just wondering. [3:15 PM]

mat747: Jee - can you tell us what the title is [3:15 PM]

mseetin: I was hoping people would have some hypotheses about what to do in that area [3:16 PM]

Brourd: Since mutations there could potentially shift the state of the RNA. [3:16 PM]

mseetin: yepp [3:16 PM]

Brourd: ah, okay then! [3:16 PM]

mseetin: We should design it to be unpaired, but maybe we can find some key kinds of mutations [3:16 PM]

Eli Fisker: Matthew, I saw your awesome graphics at the Eterna Monthley meeting. However the pics on the lab are small. Could you add a bigger pic somewhere below the lab info? [3:17 PM]

Eli Fisker: (On the new labs) [3:17 PM]

mseetin: I'm actually not sure how to do that. Do I just use HTML code? [3:17 PM]

Eli Fisker: I think that question is for Jee [3:18 PM]

mseetin: What did you do to post the images you posted for me in my first lab? [3:18 PM]

Eli Fisker: I think I used some Html code to put mine up [3:18 PM]

mseetin: ah, ok [3:18 PM]

Eli Fisker: Let me check and send you a message afterwards [3:18 PM]

Brourd: @ mat - the title of the paper would be "RNA Design Rules from a Massive Open Laboratory" [3:20 PM]

mat747: brourd - thx [3:20 PM]

jeehyung: @mat sorry about the delay. Our paper title is "RNA design rules from a massive open laboratory" [3:23 PM]

Brourd: So Jee, how is development of the Flash embedded design browser going? [3:22 PM]

Brourd: Any suggesions from players yet for the beta? [3:23 PM]

mat747: Jee - np - did you/dev use the "Strategy market" to gather the rules of RNA design of players ? [3:23 PM]

jeehyung: @Brourd there are lots of bugs to fix..but we think it's pretty useful in that you never have to leave a screen to vote & browse through sequences [3:25 PM]

jeehyung: @mat yes the rules are from the strategy market [3:25 PM]

mat747: Jee - so its the eternaBot then [3:24 PM]

Brourd: Well, good thing that progress is being made on that! How about the semi open source EteRNA protocol? [3:25 PM]

jeehyung: @mat yes - eternabot is used to evaluate the quality of player discovered strategies [3:27 PM]

jeehyung: @Brourd we haven't had a chance to re-visit it yet. I really hope to find some time to do this sometime this weekend. [3:29 PM]

Brourd: Jee, I noticed that a high number of issues on github were recently closed, was that just to clean up the issue tracker? [3:28 PM]

Brourd: Since there were 300+ open issues before that. [3:29 PM]

jeehyung: @Brourd yes we cleaned old issues and marked them "revisit later" to focus on on-going issues now [3:31 PM]

Eli Fisker: Matthew, I can't get the image upload working. I don't remember what I did. Can you ask Jee about it instead? [3:30 PM]

Eli Fisker: The html codes i have for it is not working for me [3:30 PM]

Brourd: very good. As for the errors in the puzzle descriptions, Rhiju said that needs to be done by March? [3:31 PM]

jeehyung: @Brourd hopefully yes. We want to fix errors before NOVA launches [3:33 PM]

Brourd: Right, good to know. Is there any idea how widespread the errors are? [3:33 PM]

jeehyung: @Brourd we are not sure at the moment. We assume it could span over the entire challenge series.. [3:35 PM]

Brourd: Ah [3:34 PM]

mat747: when will NOVA be launching [3:34 PM]

jeehyung: @mat they hope to launch it around March [3:37 PM]

mat747: jee - thx and talking of eternaBot will be writing up some of the strategies again ? [3:37 PM]

jeehyung: @mat do you mean if we'll open the strategy market again? [3:41 PM]

TomoeUzumaki: wait is there a dev chat today? [3:40 PM]

TomoeUzumaki: hi jee [3:40 PM]

jeehyung: We do want to. But we'll have to make it so that it's implemented in Eternascript, by players [3:42 PM]

Brourd: Yep tomoe, and you just joined it! [3:40 PM]

jeehyung: Hi Tomoe [3:42 PM]

TomoeUzumaki: dear god.. I've been too wrapped up in studying [3:40 PM]

Brourd: @ Jee - has the data for the cloud labs been incorporated into the current strategies incorporated into EteRNAbot for this recent paper? Or is the algorithm still frozen? [3:42 PM]

TomoeUzumaki: jee, when will december labs be synthed? [3:42 PM]

jeehyung: @Brourd the algorithm is frozen, for a fair comparison [3:44 PM]

jeehyung: @Tomoe they have been ordered. We are waiting for the results [3:44 PM]

Eli Fisker: Jee, then the switches are not along in the data, right? [3:43 PM]

TomoeUzumaki: oh. [3:43 PM]

TomoeUzumaki: right [3:43 PM]

jeehyung: @Eli which switches? [3:45 PM]

jeehyung: oh you mean in the paper? [3:45 PM]

Eli Fisker: yes [3:43 PM]

jeehyung: No switches are not inthe paper [3:45 PM]

Eli Fisker: Great [3:43 PM]

Eli Fisker: I remember them starting to cloud the Eternabot results [3:44 PM]

Eli Fisker: So I'm glad they are out [3:44 PM]

jeehyung: EternaBot is actually exactly opposite to designing switches. It designs a sequence that firmly stick to one structure. It's actually only natural for it to not work at switches [3:46 PM]

jeehyung: We'll need separate strategies for that : ] [3:46 PM]

Eli Fisker: Yup :) [3:45 PM]

Eli Fisker: I'm perfectly happy then [3:45 PM]

firedrake969: Hi everyone [3:45 PM]

jeehyung: All I'll have to leave in 5 minutes - please throw in questions and suggestions! [3:47 PM]

Eli Fisker: hi Fire [3:45 PM]

Brourd: What is the Das lab's, Adrien's, and your plan for the next EteRNA centric paper? Or is the goal to stick to the micropapers and player coauthorship? [3:45 PM]

jeehyung: @Brourd we' [3:48 PM]

firedrake969: jee, what's the badge Founding Member Round 2 (2013)? [3:46 PM]

jeehyung: we'll have another big paper centered around the cloud lab [3:48 PM]

TomoeUzumaki: yeah, how do you earn it? [3:46 PM]

Brourd: Very nice. [3:47 PM]

jeehyung: @firedrake It's the badge you get by being a member before Eterna cloud lab renewal [3:48 PM]

firedrake969: What does that mean? [3:47 PM]

firedrake969: Sorry, I've been away for a while [3:47 PM]

firedrake969: And is there a name to the method in which the labs are synthesized? [3:47 PM]

jeehyung: @firedrake it doesn't hold very much meaning. It's just a small present for the members who stick with Eterna [3:49 PM]

firedrake969: Oh, ok [3:48 PM]

firedrake969: And the synthesis method? [3:48 PM]

Brourd: When EteRNA switched to the high throughput synthesis pipeline back in January-February 2013. [3:48 PM]

firedrake969: I mean is there a name I should call the synthesis? If I recall it's something like in vitro? [3:49 PM]

jeehyung: in vitro means "in test tube" As for the synthesis method, you can read this paper. I don't think there's any catchy name to it [3:51 PM]

jeehyung: Seetin MG, Kladwang W, Bida JP, Das R (2014) Massively parallel RNA chemicalmapping with a reduced bias MAP-seq protocol. Methods Mol Biol 1086:95–117. [3:51 PM]

Brourd: yep [3:50 PM]

firedrake969: dang it :P [3:50 PM]

jeehyung: I'll have to go now everyone - thanks for all the discussions! [3:52 PM]

jeehyung: I'll post the chat log in the news [3:52 PM]