2013.03.06 Dev Chat

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On Scripting, Highlighting Tools, & Theophylline Lab


jeehyung: hi all [6:00 PM]

Jieux: I try to be punctual :) [6:01 PM]

jmf028: hi jee [6:01 PM]

Eli Fisker: hi Jee :) [6:01 PM]

TomoeUzumaki: hi hee [6:01 PM]

starryjess: hi jee [6:00 PM]

TomoeUzumaki: *jee [6:01 PM]

jeehyung: it's time for the Eterna dev meeting : ] Please ask us any question [6:01 PM]

jmf028: hi jieux [6:01 PM]

jeehyung: hi Eli, Tomoe starry : ] [6:01 PM]

jeehyung: and jmf [6:01 PM]

Jieux: Hi Jee, Eli, Tomoe, J1, starry [6:01 PM]

starryjess: thanks for the updates, jee [6:01 PM]

starryjess: hi again Jieux [6:01 PM]

Jieux: ;) [6:01 PM]

starryjess: the game updates, I mean [6:01 PM]

jmf028: how are you guys doing on the cloud labs jee? [6:02 PM]

jeehyung: @starry please let me know if anything goes wrong with the update : ] [6:02 PM]

jeehyung: @jmf that [6:02 PM]

jeehyung: that's one of the main news today. There will be a news item about this too. [6:02 PM]

starryjess: not that I've seen yet :) [6:02 PM]

jmf028: alrighty [6:03 PM]

TomoeUzumaki: :D [6:02 PM]

Eli Fisker: great [6:03 PM]

TomoeUzumaki: jee, I have a question [6:03 PM]

jeehyung: Unfortunately there was a contamination of the RNAs that were synthesized from 20 cloud lab. Rhiju himself is investigating the issue, but it seems like the ETA of the results have been pushed back to March 20th [6:03 PM]

starryjess: uh oh [6:03 PM]

jmf028: oh noes [6:04 PM]

jeehyung: I'm sorry about the delay. There'll be a news item/dev article about this soon [6:03 PM]

TumbleBuzz: ouch [6:03 PM]

jeehyung: @Tomoe what is it? [6:03 PM]

jmf028: not too much of a problem for me [6:04 PM]

TomoeUzumaki: is it possible for us to view the puzzles we're solving [6:04 PM]

TomoeUzumaki: ? [6:04 PM]

Jieux: Can I ask a quesiton about the labs Jee? [6:04 PM]

jeehyung: @Tomoe Not right now, it'll be soon there. Our developer is working on an update to display 10 most recently played puzzles for every player. [6:05 PM]

jeehyung: @Jieux sure what is the question? [6:05 PM]

TomoeUzumaki: ohh [6:06 PM]

TomoeUzumaki: thanks! [6:06 PM]

TomoeUzumaki: :) [6:06 PM]

jnicol: any news on scripting? [6:07 PM]

TomoeUzumaki: what is the scripting for, actually? [6:07 PM]

jeehyung: @jnicol - Justin, our dev on the scripting, is working on a system where every "puzzle solving" script acts like a bot and try to solve player puzzles as Vienna, RNASSD and InfoRNA did. He's also adding few more basic functions like getting free energy of the structure. [6:08 PM]

Brourd: cool [6:08 PM]

jeehyung: @Tomoe, it's a little programming interface where you can build an algorithm to solve Eterna puzzles [6:08 PM]

TomoeUzumaki: ah. I can't program [6:09 PM]

jandersonlee: @Jee: A request: could the labs page display the shape string for bound and unbound forms? I need them for a tool I'm working on. [6:09 PM]

jandersonlee: (Would also be nice for puzzles too.) [6:10 PM]

jeehyung: @janderson ah, actually showing both shapes on the puzzle page is on the current week's task list. I'll ask the dev to do it on the lab page as well [6:10 PM]

Brourd: Sucks about the contamination of the cloud lab :( [6:10 PM]

jandersonlee: tqvm [6:10 PM]

jandersonlee: what about the original play project data? anything worth salvaging? [6:11 PM]

TomoeUzumaki: Brourd, it is [6:11 PM]

jeehyung: @Brourd things happen when you are dealing with new technologies : [ [6:11 PM]

Brourd: Yeah, do they have any idea what it was? [6:12 PM]

jeehyung: @janderson the 1500 sequences data from the original lab is fine and good to go. We just need a way to display them now - we'll probably need about a week to do this [6:13 PM]

jeehyung: @Brourd Unfortunately no. That's where they are spending time now - finding the cause. [6:13 PM]

Brourd: okay, thanks [6:13 PM]

jandersonlee: np. I'm not ready to sift through 1500 seqeunces righ now anyways [6:13 PM]

mat747: jee - a list of results would be fine for now [6:14 PM]

Brourd: how have you been Jee? Some great updates in the last few days [6:14 PM]

Jieux: Sorry about that, my robot is not feeling well again. [6:14 PM]

TomoeUzumaki: Jieux, that's a shame [6:14 PM]

jeehyung: @mat list of results as in text file? [6:14 PM]

mat747: yes [6:14 PM]

jandersonlee: or .csv [6:14 PM]

jnicol: were these the original player project designs you are talking about? [6:15 PM]

jmf028: bye all [6:15 PM]

jeehyung: @Brourd bit busy as alaways but good : ] I hope new updates are not causing any new problem [6:15 PM]

TomoeUzumaki: sorry folks, have to go to swim practice [6:15 PM]

jeehyung: @jnicol yes the original player proejcts from last year [6:15 PM]

TomoeUzumaki: state meet is this weekend [6:15 PM]

TomoeUzumaki: bye.. [6:15 PM]

jnicol: bye tomoe [6:15 PM]

Jieux: Thanks for the sentament Tomoe.... @ Jee: Did my request for a question get rhough? [6:15 PM]

Jieux: take care. [6:15 PM]

TomoeUzumaki: bye [6:15 PM]

Brourd: see ya tomoe [6:15 PM]

jnicol: did thes designs need to add the barcode? [6:16 PM]

TomoeUzumaki: I'll be back in 3 hours [6:15 PM]

TomoeUzumaki: so see you then [6:15 PM]

TomoeUzumaki: bye jee [6:15 PM]

Jieux: Great J1, my question was about the barcode. [6:16 PM]

jeehyung: @mat I can ask Rhiju about the text file. He'll definitely go with it I think [6:16 PM]

jandersonlee: @Jieux. You dn't need to hold up your hand. Just throw it out when there seems to be a gap in the conversation [6:16 PM]

mat747: jee - great thx [6:16 PM]

jeehyung: @Jieux, sorry can you remind me what the question was again? [6:16 PM]

Jieux: Crashed before I could ask :) [6:17 PM]

jeehyung: @jnicol for the last year's player project design, yes, I think Rhiju automatically added barcodes to them later [6:17 PM]

Jieux: I wanted to know how the proximity of the barcode to the open tail loop is determined. [6:17 PM]

Jieux: did I crash again? [6:19 PM]

Brourd: on the 3' side there is a base before the 20 bases needed for synthesis [6:19 PM]

jeehyung: I'm really sorry Jieux. I might have completely skipped out on the question. Can you elaborate the question? what do you mean by proximity? [6:20 PM]

Brourd: on the 5' side, it's based on the shape of the lab [6:20 PM]

Jieux: the closeness between the open pair of the barcode to the next nearest open pair. [6:21 PM]

Jieux: open pair is a pair that enters into a loop rather than another pair. [6:21 PM]

TomoeUzumaki: bye folks [6:22 PM]

jnicol: thought you left already, i'm not saying bye again :) [6:22 PM]

jandersonlee: @Jieux: that all depends on how you design the 63 bases we can specify [6:22 PM]

starryjess: lol [6:22 PM]

Brourd: yes, if I understand Jieux correctly, there will be no bases between the barcode stack and the first stack of your design if you do not specify it [6:23 PM]

Jieux: here's an example: [6:23 PM]

Jieux: http://eterna.cmu.edu/sites/default/files/chat_screens/48170_1362612224.png [6:23 PM]

jeehyung: @Jieux the only specification we have on the puzzle is that the puzzle must have 63 length - after than it's the barcode hairpin and 21 bases loop (tail) [6:23 PM]

Jieux: the long one is the barcode. [6:24 PM]

firedrake969: Hi all [6:24 PM]

Jieux: the pentaloop is the rest of the design. [6:24 PM]

Eli Fisker: hi Fire :) [6:24 PM]

jnicol: hi fire [6:24 PM]

firedrake969: Hi all [6:24 PM]

Jieux: how is the space between them determined? It varies from puzzle to puzzle. [6:24 PM]

wateronthemoon: hi all [6:25 PM]

Eli Fisker: hi Moon :) [6:25 PM]

wateronthemoon: missed a bunch but will read after [6:25 PM]

jnicol: hi wotm [6:25 PM]

jeehyung: @Jieux It solely depends on the puzzle designer. After the barcode it's just 21 loop bases so no open loops after barcode. The distance to first open loop before the barcode, depends on the puzzle strucuture, not by us. [6:25 PM]

Brourd: @ Jieux [6:25 PM]

hotcreek: eli i liked your lastest puzzle [6:25 PM]

jeehyung: hi wateronthemoon, firedrake [6:25 PM]

jeehyung: hotcreek [6:26 PM]

hotcreek: latest [6:26 PM]

ElNando888: @Jieux: if the original has a tail on the 3' side, there will be some space, otherwise not [6:26 PM]

hotcreek: and hello jee [6:26 PM]

Jieux: (by the way, I'm going to try to make something like this into a switch later :) [6:26 PM]

firedrake969: I'm going, see ya all. [6:26 PM]

wateronthemoon: so we determine where the barcode goes by our design? [6:26 PM]

Jieux: take care firedrake. [6:27 PM]

wateronthemoon: bye fire [6:27 PM]

Brourd: yes [6:27 PM]

Eli Fisker: happy to hear, Hotcreek [6:27 PM]

jeehyung: @wateronthemoon the cloud lab puzzle is always like this [6:27 PM]

Jieux: hi hotcreek. [6:27 PM]

jeehyung: 5 tail bases = 63 "free bases" = 19 barcode bases = 20 tail bases [6:27 PM]

jeehyung: You decide what 63 bases' structure is like, the rest is completely fixed [6:28 PM]

jnicol: missed the shift key :) [6:28 PM]

jeehyung: So barcode is always at the end of the structure followed by the 20 bases tail [6:28 PM]

Jieux: got it. thanks. [6:29 PM]

Jieux: never noticed that. [6:29 PM]

wateronthemoon: yes, thanks [6:29 PM]

Jieux: probably too busy k'vetching :) [6:29 PM]

Jieux: Will help in future designs. [6:29 PM]

wateronthemoon: XD [6:29 PM]

jandersonlee: so if you want unbonded bases before the hairpin leave base 63 (and 62 ...) unbonded in your puzzle [6:29 PM]

wateronthemoon: or more [6:30 PM]

Jieux: right, the longer the tail, the wider the distance. [6:30 PM]

TumbleBuzz: do scripts run on the client? (sorry im new) [6:30 PM]

Brourd: @ Jee - wasn't here for the beginning, but about how long will we have to wait for theophylline ribozyme results? [6:30 PM]

jeehyung: @TumbleBuzz they do run on your browser. [6:30 PM]

jeehyung: @Brourd I'm hoping we get results by tomorrow. We can publish right away when we get them [6:31 PM]

TumbleBuzz: okay thanks! [6:31 PM]

Brourd: great [6:31 PM]

jeehyung: We also added in small changes for the theophylline results display to show individual cleavage ratios - that might add few more insights to the data so please check them out : ] [6:31 PM]

jandersonlee: @jee: does that mean you have code for a javacript rna FE evaluator? [6:32 PM]

Brourd: yes, and thanks for that as well :) [6:32 PM]

Eli Fisker: cool, Jee [6:32 PM]

jeehyung: @janderson we do have a javascript code for RNA fold/FE evaluator. only the fold function is public, but our dev is working on getting FE function out too [6:32 PM]

jandersonlee: would be appreciated :) [6:33 PM]

jeehyung: To be fair, it's not actually javascript, but a flash lib accessed by javascript [6:33 PM]

jandersonlee: Ah. [6:33 PM]

Hyphema: hi jee, if the scripts can be used to solve puzzles what keeps players from using it to cheat? Or am i confused. [6:34 PM]

stevetclark: when are the results from the cloud labs coming out [6:35 PM]

Brourd: @ Steve, there was a contamination, so it is now delayed [6:35 PM]

Brourd: eta, later this month [6:36 PM]

jandersonlee: @steve mar 20++ [6:36 PM]

jeehyung: @Hyphema currently we don't have a way to prevent cheating. That's something we are brainstorming at this point [6:36 PM]

jeehyung: There isn't a script that'll solve all puzzles for you yet, so it's not a problem at the moment. But we realize it could get tricky once the scripts get good [6:37 PM]

jandersonlee: the foldit philopsophy says it is not cheating to use scripts -- it's technolgy building :) [6:37 PM]

wateronthemoon: and re hyphema's question--will computer idiots like me be at a big disadvantage? [6:37 PM]

Hyphema: can you design a sort of entrance test to be able to use the scripts? [6:37 PM]

jeehyung: @stevetclark, there was a contamination in the RNA we synthesized. The ETA of the data is 3/20 now. We are sorry about the delay [6:37 PM]

Brourd: will the dev be delaying the date they pull the switch cloud lab designs now? [6:37 PM]

mat747: JL - i agree [6:38 PM]

Hyphema: or a history of solving challenging puzzles [6:38 PM]

jeehyung: @Hyphema yes that's definitely one option - requiring certain amount of points before being able to use scripts on other puzzles [6:38 PM]

starryjess: good idea [6:38 PM]

jeehyung: @Brourd in fact, yes. We'll discuss about that more in few days, but there'll be at least 1 week delay for the switches lab. [6:39 PM]

Brourd: will all scripts be public? [6:39 PM]

Brourd: nice, and thanks [6:39 PM]

wateronthemoon: and/or a simple-minded tutorial too? [6:39 PM]

jeehyung: @Brourd - yes every script will be public, for modification and improvements by others. That's our plan now, unless we find major issues [6:39 PM]

jeehyung: @wateronthemoon for the scripting? [6:39 PM]

stevetclark: when will lab tutorials be available [6:39 PM]

wateronthemoon: yes, am confessing to illiteracy [6:40 PM]

mat747: jee - have all scripts public is a good idea [6:40 PM]

wateronthemoon: and what steve said too [6:40 PM]

Eli Fisker: I agree with mat [6:40 PM]

Eli Fisker: Will be a help for those who can't program [6:41 PM]

jeehyung: @stevetclark we are pushing back on the lab tutorials as we will soon reform lab a bit for the cloud lab. The tutorials will probably come after the cloud lab system settles in [6:41 PM]

Jieux: Public except for Nando who has the Vinnie script ; ) [6:41 PM]

starryjess: anybody who wants to learn javascript can do this http://www.codecademy.com/tracks/javascript but it's not "simple minded" I don't think [6:41 PM]

jeehyung: @wateronthemoon, Eli, yes we could try walkthrough for creating very basic bot. I'll ask the scripting dev if he could do that.. [6:42 PM]

Eli Fisker: Great Jee. Thx! [6:42 PM]

jeehyung: @starryjess - I second this. codeacademy is a good place to begin learning javascript [6:42 PM]

Jieux: Jee, will we ever get to spend our coins on anything? [6:42 PM]

wateronthemoon: yes, thanks starry. [6:42 PM]

Jieux: perhaps a Java scropter? [6:42 PM]

jeehyung: @Eli, mat glad you agree on the public scripts [6:43 PM]

Eli Fisker: np [6:43 PM]

jandersonlee: @jee: likewise on public [6:43 PM]

stevetclark: will there be a new blog post soon [6:43 PM]

jeehyung: @Jieux I really hope we could. but we can't think of anything we can "sell" at this point. I'm all open for the idea. [6:44 PM]

Brourd: About how long do we plan on running the theophylline riboswitch before we move on to a new one? [6:44 PM]

jeehyung: @stevetclark, yes there'll be one about the contamination in the cloud lab once the cause is determined. [6:44 PM]

Jieux: Do I get a kickback for my ideas 8P [6:45 PM]

jeehyung: @Brourd That depends on the current round results. If we see good results we may move on to the version with bigger degree of freedom right away [6:45 PM]

Brourd: is it going to be "we got the best design, so move on" [6:45 PM]

jandersonlee: For the tutorial writers: I'd like to see one on designing switches... [6:45 PM]

Brourd: or "we need the top 10, so you all better have good ideas" [6:46 PM]

starryjess: RNA jewelry :D jk [6:45 PM]

jandersonlee: what make it easy, what makes it hard, ... [6:46 PM]

wateronthemoon: sell hints to difficult puzzles [6:46 PM]

jeehyung: @Brourd to be honest, we are still figuring that out. We'll have to have a discussion with Brent once we get the results. [6:46 PM]

Eli Fisker: JL, Jnicol and Nando has written tutrials on how to make switch puzzles lately [6:47 PM]

wateronthemoon: you could clean up on spugs jieux [6:47 PM]

Jieux: starry... wait for an answer to the kickback question! (great idea btw!) [6:47 PM]

jandersonlee: 200 coins to solve a 100 coin puzzle? [6:47 PM]

Brourd: @ janderson - as in solving, or just creating one? [6:47 PM]

jandersonlee: @Brourd: creating first [6:47 PM]

Mike Reynolds: Jieux, I ?modified your solution on the Bistable lab. Yours was by far the best, next to Meechl and Eli Fisker. [6:46 PM]

Brourd: elnando put together a guide on creation via suboptimal designs [6:47 PM]

jeehyung: @Jieux Maybe synthesis slots : ] ? [6:47 PM]

Brourd: however, doesn't help with solving ;P [6:48 PM]

jandersonlee: I think we need more exploration there, as some of the lab switches seem too hard to get both states cleanly [6:48 PM]

Jieux: Spugs are free and open to the public [6:48 PM]

Jieux: Thanks Mike! [6:48 PM]

wateronthemoon: bribing the devs? [6:48 PM]

Eli Fisker: JL, link here: [6:48 PM]

Jieux: not sure how you judge the best, but I'm working a theory. [6:48 PM]

Eli Fisker: https://docs.google.com/file/d/0B8EEBMO3fRaUWVBEc3RqSUNhSFE/edit [6:48 PM]

Brourd: @ janderson - those were the subotimal design switches ;P [6:48 PM]

wateronthemoon: but if you sold hints? [6:48 PM]

wateronthemoon: @jieux :D [6:48 PM]

jandersonlee: ah missed. that. tx for the link [6:48 PM]

Mike Reynolds: But your first solution was better than your second. The 2nd state dot plot was cleaner. It is too bad it is getting fewer votes than your 2nd solution. [6:47 PM]

Jieux: Maybe each player should be albe to set up their own store like starting a group [6:49 PM]

Eli Fisker: JL and Jnicol have made two, one for creating a cloudSwitch puzzle in particular: [6:49 PM]

Eli Fisker: https://docs.google.com/document/d/14vWQwVx6jpqceC6Z75yIQ92sw4gcCUG40UUDvb7UerE/edit [6:49 PM]

wateronthemoon: yes, Eli's link is a good one [6:49 PM]

starryjess: sell airline miles so we can meet each other "{ [6:50 PM]

starryjess: :P [6:50 PM]

Eli Fisker: JL, and Johns guide on designing switches in general: [6:50 PM]

Eli Fisker: https://docs.google.com/document/d/1N-8rvyCGSbMyTWqKy0HsYh65FWhWpPb4o2e1B56Y1GA/edit [6:50 PM]

Mike Reynolds: People aren't checking their 2nd state dot plot. Particularly in the Bistable lab I saw 90% of the entries with bad 2nd state dot plots. You should tell people there is a 2nd dot plot, they don't seem to know. [6:49 PM]

jandersonlee: @Mike dotplot is teh same in both states (or used to be) [6:51 PM]

starryjess: dot plots are iffy anyway [6:51 PM]

Jieux: We can start an EteRNAconomy... I actually was thinkng about that yestersay [6:51 PM]

wateronthemoon: no not the same [6:51 PM]

starryjess: whether or not they're a good indication of a good design [6:51 PM]

Eli Fisker: lol, Jieux [6:51 PM]

Mike Reynolds: No longer, the dot plot for the 2nd state is quite distinct from the 1st. [6:50 PM]

wateronthemoon: that's the challenge, getting them closer [6:52 PM]

jandersonlee: ah. good news [6:52 PM]

Jieux: I hat that problem in one of the first switch labs Mike... I scored somewhere around a 50 I think. [6:52 PM]

wateronthemoon: getting 2nd state to even show up [6:52 PM]

Eli Fisker: yep, Mike is correct [6:52 PM]

jandersonlee: missed that upgrade notice :) [6:52 PM]

wateronthemoon: so that brings up questions of what they're indicating [6:53 PM]

Eli Fisker: :) [6:53 PM]

Mike Reynolds: People should be told, it is clearly not widely known. [6:52 PM]

Jieux: by the way, I like the new little green and red boxes on the camera posting button thingy. [6:53 PM]

Eli Fisker: Water, best way to find out what you want to see in the dot plots and not want to see is watch the old switch winners and some of the loosing designs [6:54 PM]

jeehyung: @Mike our plan is to have both plots to show up instead of one at a time. It'll take time since it's behind other tasks, but it'll be done [6:54 PM]

wateronthemoon: good idea. Thanks Eli [6:54 PM]

Eli Fisker: Love that idea, Jee [6:54 PM]

Eli Fisker: np, Moon [6:54 PM]

starryjess: yeah good idea [6:54 PM]

wateronthemoon: Jieux has been pointing out the importance of looking at 2nd state dot, bringing it up [6:55 PM]

Mike Reynolds: I think it tells a lot. In the Bistable lab ?a lot of people went to ?great efforts to remove the 2nd state stacks appearing in the 1st state dot plot, which effectively removed them from the 2nd state plot where they belong. So lots of people were coming up with really bad solutions based on only the 1st state dot plot. [6:54 PM]

Brourd: sad part is, I have nothing to contribute because I don't look at the dot plot :/ [6:56 PM]

wateronthemoon: So shadow of each state appears in the other? [6:56 PM]

Mike Reynolds: Yes. [6:55 PM]

Eli Fisker: Water, yes, or even lines [6:57 PM]

Eli Fisker: I have a section on it in one of the lab guides [6:57 PM]

wateronthemoon: Thanks, Mike. That's enlightening. [6:57 PM]

randl: Jee, did you see my Forum suggestion for a tool to freeze nucleotides while solving a puzzle? [6:57 PM]

Mike Reynolds: Bistable was unique in the two way shadowing, I only saw one way shadowing anywhere else (1st stack appearing in the 2nd state) [6:56 PM]

jnicol: yes, its really just intuition and feel at this point, the dot plot should not be relied on too heavily [6:58 PM]

Brourd: indeed, except to tell you your design isn't folding the way it should [6:58 PM]

jnicol: not until a better energy model can make better evaluations [6:59 PM]

Brourd: @ Jee - I was wondering [6:59 PM]

jeehyung: @randl Sorry I might have missed it what do you mean by freezing? [6:59 PM]

jeehyung: @Brourd what is it? [6:59 PM]

Brourd: is there any plan to change the score for a winning design? [6:59 PM]

Mike Reynolds: What I want is MUTIPLE HIGHLIGHT COLORS! It is so hard following the chains of propegation, where swaping a base pair effects a whole chain of bases when switch between the two states. [6:58 PM]

Brourd: example, you said about the FMN binding shapes lab that the synth team was happy with the results [6:59 PM]

Jieux: @ Eli, looking at your and Dr. Drax's FMN Aptamer 2.0 results, I am more confident in my theory. [6:59 PM]

randl: When solving a switch, I'd like to "fox" certain nts while I am searching for the solution' [6:59 PM]

randl: *fix [7:00 PM]

wateronthemoon: randl's question and Mike's are similar [7:00 PM]

Brourd: @ Jieux - the results for the old switch labs may not still be considered winners [7:00 PM]

Jieux: then perhaps my hope is misplaced. [7:00 PM]

Brourd: Drax's design remained a winner [7:01 PM]

Brourd: Eli's dropped [7:01 PM]

jeehyung: @Brourd I think the problem is, there is no one perfect number that can describe how good RNA is. We use the synthesis score as a reasonable assessment, but sometimes they disagree slightly with the experts. [Like in the switch lab - experts say good enough even when the score is not very high] [7:01 PM]

Brourd: and GnatStomper's went up in score [7:01 PM]

starryjess: @Jee, i think he means, since some of the bases are locked, the pair of those bases are locked as well, but they are not physically locked. It would be nice to mark them in a way that is different than the usual marking (black circle) [7:01 PM]

jandersonlee: @mike - or a way to link related nodes by a set of lines/loops [7:01 PM]

Jieux: they both read 95 in the lab. [7:01 PM]

jeehyung: So no matter where we set the score, that kind of "call" will always made by players [7:01 PM]

jeehyung: @randl, starry got it. Let me add that to the issue tracker. [7:01 PM]

starryjess: so mike's is the same suggestion really....multiple colors [7:01 PM]

Brourd: @ Jee - yes, I was wondering about the switch lab, perhaps we can change what a winning score can be considered [7:02 PM]

wateronthemoon: Help with getting lost in long chains of cause/effect in switches. Need a marking system or way to fix some nts [7:02 PM]

Brourd: to 90, instead of 94 [7:02 PM]

Brourd: or something along those lines [7:02 PM]

Jieux: @ brourd: I'm not going to look at the other past switch labs. I'm going to contain my misplaced hope to one puzzle :)_ [7:02 PM]

Mike Reynolds: @Janderson, I think mulitple highlight colors would be much more easy to implement than fixing base pairs, and would be much more useful. [7:03 PM]

jeehyung: @Brourd I'll bring the issue to the meeting with the synthesis team [7:03 PM]

wateronthemoon: e.g, you have a U that must stay a U because in one state it's paired with a locked A. [7:03 PM]

Brourd: great, and thanks [7:03 PM]

wateronthemoon: and you keep forgetting and going around in circles [7:04 PM]

jeehyung: All - I'll have to run in 6 minutes. Please throw in final concerns / questions [7:04 PM]

randl: no exactly what I had in mind but a good idea also. Sometimes a locked nt has a one and only one nt that can be place there, however, this nt falls in a different place in the alternate puzzle. I would like to be able to "lock and unlock" real time, while I am solving the puzzle. [7:04 PM]

Brourd: Btw Jee, on the matter of the past switch lab results, are they going to be delayed for updating in the game? [7:04 PM]

Mike Reynolds: Water, yes exactly, having mutliple hightlight colors would make locked bases much easier to deal with in switch puzzles. [7:05 PM]

Brourd: due to the 20 cloud lab beta [7:05 PM]

jeehyung: @Brourd I'm still waiting for the response from the analytsis team. Apparently they got lot of stuff on their hand too. I'm not sure if that's related to the contamination issue. [7:05 PM]

Eli Fisker: I would want the locking option, but I wouldn't mind having different highligting colors on top on that [7:05 PM]

wateronthemoon: so jee, look at the marking issues, locked or further colors [7:05 PM]

wateronthemoon: or both [7:05 PM]

Eli Fisker: Sometimes one marks nucleotides for different reasons [7:05 PM]

Jieux: would be nice to be able to pull the sequence out of the puzzle maker, but I can understand at least some of the reasons why you can't. [7:06 PM]

jeehyung: I'm adding both lock and mutiple highlights on the issue tracker. We'll discuss this in the dev meeting and see what we should do -could end up implementing both [7:06 PM]

Jieux: Is this something you are considering changing? [7:06 PM]

starryjess: yeah, that's why we need locks or different colors: so you can do different kinds of marking at the same time and not get them confused [7:06 PM]

jandersonlee: Some folks are colorblind, but that doesn't mean those of us who can distinguish colors should ot be able to use them. [7:06 PM]

Omei: I would love to have a range of marking colors! [7:06 PM]

Eli Fisker: Sounds promising, Jee [7:06 PM]

Brourd: thanks Jee, I like to have the correct results before I go and start making my crazy theories [7:06 PM]

jeehyung: @Jieux - yes actually that should have been added in this update [pulling sequences from puzzle maker]. I'm not sure what happend, I'll check with the devs. [7:07 PM]

Hyphema: has anyone asked about trying to save a puzzle in the middle of making one. so that you can go back later to it? [7:07 PM]

Jieux: Orange and Purple circles to wrap around the nucleotides. [7:07 PM]

wateronthemoon: maybe for colorblind a way to switch on color letters. Might be too confusing? [7:07 PM]

Jieux: those would be nice in addition to black. [7:07 PM]

jandersonlee: Palate of 8 colors? [7:08 PM]

mat747: foldit has a colorblind mode [7:08 PM]

jandersonlee: (including black) [7:08 PM]

wateronthemoon: mat, how does it work? [7:08 PM]

Eli Fisker: cool, Mat [7:08 PM]

jeehyung: @Hyphema, auto-save on puzzle maker is actually on the issue tracker too. But it has not been assigned to the devs yet. [7:08 PM]

Jieux: I'd be happy with a pallete of 4 [7:08 PM]

wateronthemoon: different textures of the circles? [7:08 PM]

firedrake969: Wow, devchat's still going on? xD [7:08 PM]

Brourd: Actually, we already have 4 colors to mark with :P [7:09 PM]

Jieux: we do? [7:09 PM]

mat747: water - i`ll pm you about it [7:09 PM]

wateronthemoon: I'm not colorblind but know folks who are [7:09 PM]

Brourd: yes, have you tried to fill a switch puzzle with G-U, then mutate to A-U ye? [7:09 PM]

wateronthemoon: thanks mat. [7:09 PM]

firedrake969: I'd like to suggest saving structures that we're working on to the server, so we can work on multiple computers. [7:09 PM]

Jieux: I just started using them in Infinity Supernova. 8P [7:09 PM]

firedrake969: Unless Chrome copies cookies to each logged-in instance. [7:09 PM]

mat747: Jee - message [7:09 PM]

jeehyung: @firedrake I'll add that as a comment to the puzzle maker autosave task [7:10 PM]

starryjess: what are you talking about Brourd? [7:10 PM]

jandersonlee: as long as color marking is optional, not manditory for play I think using colors is OK [7:10 PM]

firedrake969: @jee OK [7:10 PM]

jeehyung: @mat got it - will do. [7:10 PM]

jeehyung: All I must run now. I'll post the chat log on the news item. [7:11 PM]

wateronthemoon: lost in the chat, never to be seen again . . . [7:11 PM]

jnicol: bye jee, thanks [7:11 PM]

jeehyung: Thanks all for the discussion today! [7:11 PM]