2016.03.25 Dev Chat
Astromon: heloo everyone are we having a DEV chat todaY? [12:02 AM]
calebgeniesse: hey [12:07 AM]
Astromon: hi cal [12:07 AM]
calebgeniesse: whats up [12:07 AM]
Astromon: just getting started for the daY!! [12:08 AM]
Astromon: i love fridays<< [12:08 AM]
johana: hello [12:08 AM]
Astromon: hi johana [12:08 AM]
Astromon: been working on studying the old A/B results and trying to apply them for the current ones [12:09 AM]
Astromon: guess we have 2 more days to work on the current ones<> [12:10 AM]
Astromon: mostly changing my best designs from that first A/B and tweeking them with strethening the non-static -switching area [12:11 AM]
Astromon: jenninfer P and Eli noticed designs score better that way [12:12 AM]
Jennifer Pearl: hi [12:13 AM]
Astromon: Hi jen [12:13 AM]
Jennifer Pearl: Some of my analysis last night is pointing more towards the exclusions and the same state puzzles behaving differently in some aspects [12:14 AM]
Astromon: cool [12:14 AM]
Jennifer Pearl: I think static loop is one of them. I think the same states like it but the exclusions might not care [12:14 AM]
Astromon: i guess we have to go where the data is pionter towards! :) [12:15 AM]
Jennifer Pearl: need to look at teh rest of the labs though [12:16 AM]
Jennifer Pearl: only looked at EXNG1 and EXNG2 last night [12:16 AM]
Astromon: are same state 2 state puzzles? [12:16 AM]
Astromon: i forget< [12:17 AM]
Astromon: oH [12:17 AM]
Jennifer Pearl: for the exclusions but EXNG2 is kinda hard casue the static stem can have a 1-1 loop in teh middle and still do good so those designs are included in teh bad predictions I realized for NG2 labs I think [12:17 AM]
Astromon: is that round 98 your referring to jen? [12:17 AM]
Astromon: hmm [12:18 AM]
Jennifer Pearl: round 101 the FMN lab..most recent [12:18 AM]
Astromon: oH [12:18 AM]
Astromon: the ones we worked on [12:18 AM]
Astromon: way cool [12:19 AM]
Jennifer Pearl: but the observation about a 1-1 loop being ok in teh middle is from Round 1 and 2 analysis for the FMN ribiswitch labs [12:19 AM]
Astromon: my 90 has a loop in the middle [12:19 AM]
Astromon: of the staticNSarea [12:20 AM]
Astromon: for sensor B off [12:20 AM]
Astromon: a 1-1 loop btw [12:20 AM]
Jennifer Pearl: I have a theorry that becasue there is no harpin at the end of the NG2 labs it is a stronger binding on that stack thus it can allow more unwanted stuff [12:21 AM]
Astromon: im going to open that at the data browser [12:21 AM]
Jennifer Pearl: and a 3 pair long large loop does fine but not in other labs so much [12:22 AM]
Jennifer Pearl: @caleb adnb johan you guys have anything to go over? [12:22 AM]
Astromon: oH hmm [12:22 AM]
Jennifer Pearl: I dont want to hog all the time [12:22 AM]
calebgeniesse: not really, do you guys have anything you'd like to talk about? [12:23 AM]
johana: @Jennifer: I have been reading all the discussions again on the forum. It looks very interesting. It seems like you're onto something with Sarabot and the latest Round (R101) [12:24 AM]
johana: I have to read up on it even more but I appreciate you sharing the analysis in the posts. [12:24 AM]
Astromon: BTW here is my 53 im moding with the static hypotyhesis added in [12:24 AM]
Astromon: http://prntscr.com/ajz59h [12:25 AM]
Astromon: to see how it will score. :) [12:25 AM]
Astromon: it has the non switching stack in all 3 states :D [12:25 AM]
Jennifer Pearl: @Johan I am working on putting together plots for the EX and the SS labs for teh dynamic vrs static stack thing [12:26 AM]
Astromon: yeaH i like though explanitory type posts jen makes also<> [12:26 AM]
Jennifer Pearl: Iv'e always worried I havnt been putting enough info in the posts. Is there anything else you would like to see in them Johan?> [12:27 AM]
Jennifer Pearl: FYI, SaraBot uses data derived from DPAT so it is more DPAt doing the heavy lifting and Sara just uses that info [12:28 AM]
Jennifer Pearl: Sara uses alot of code from DPAT [12:28 AM]
Jennifer Pearl: @caleb did you see my email about the GoFundMe' [12:30 AM]
johana: @Jennifer: Good to know. There definitely seems to be signals in there. This is the great part about people trying different things. The difficulty is to understand what everyone was thinking at the time:-). Is it easy to find which puzzles are included in each analysis based on the hashtags? [12:32 AM]
Jennifer Pearl: Teh hashtags jsut give what I was doing at the time. [12:33 AM]
Jennifer Pearl: I can send you all my raw data [12:33 AM]
Jennifer Pearl: The predictions are all posted in the forum and I list the designID's [12:33 AM]
Jennifer Pearl: the designs submitted by Sarabot I have raw data for those [12:34 AM]
Jennifer Pearl: the predictions are listed by feature configuation not good or bad. that is given in the paper and the summary at teh start of each prediction [12:35 AM]
Jennifer Pearl: for each sublab [12:35 AM]
Jennifer Pearl: I can put together a list of all teh designs if that helps [12:35 AM]
johana: Let me check the posts again. I'll try to find the right forum topics. [12:37 AM]
calebgeniesse: yes @jennifer, i got your email! thanks for setting that up [12:37 AM]
Astromon: yeah it looks professional! nice going [12:38 AM]
Jennifer Pearl: they should be on the second page of the forum now. I include a link to my paper I wrote for idea binding site lenghts [12:39 AM]
Jennifer Pearl: since caleb andastro both like it I will make it live [12:39 AM]
Jennifer Pearl: release it [12:39 AM]
Astromon: release the cracken [12:40 AM]
Jennifer Pearl: Here is the Eternacon GoFundMe for praising money for player travel [12:41 AM]
Jennifer Pearl: https://www.gofundme.com/fgv2qu6c [12:41 AM]
Jennifer Pearl: praise the money yeay [12:42 AM]
Jennifer Pearl: lol [12:42 AM]
Jennifer Pearl: i meant raise [12:42 AM]
Astromon: :D [12:43 AM]
johana: @Jennifer: I will keep reading the google docs etc. again to catch up. I may contact you on the chat if I need more expanations. It's great work! [12:43 AM]
Astromon: i think its funny when someone says to raise the window down [12:43 AM]
Astromon: indeed great work Jen and ill look forwards to your presentation also. :) [12:44 AM]
DevChat T-15m
Jennifer Pearl: @johan thanks. have fun reading. If you cant get ahold of me email is a good method to reach me [12:45 AM]
Jennifer Pearl: email is probably the best method to contact me [12:46 AM]
Jennifer Pearl: @johan since I have your attention I have a big question about the labs [12:47 AM]
johana: @Jennifer: Sure [12:47 AM]
Jennifer Pearl: its here [12:47 AM]
Jennifer Pearl: https://getsatisfaction.com/eternagame/topics/request-for-verification-on-a-method-to-check-multi-oligo-sublabs-with-vienna-2 [12:47 AM]
Jennifer Pearl: not sure if I understand if I need to use the conentrations program in NUPACK for all of this or if I can just model the states with their respective oligo tha shoud be bound [12:48 AM]
Astromon: you integrating dpat and sara to nupak [12:49 AM]
Jennifer Pearl: yep [12:49 AM]
Astromon: thats awesome gl jen [12:49 AM]
Jennifer Pearl: wokring on it but if I dont need to right now then I would like to stick with Vienna since it is a shorter development time [12:49 AM]
Astromon: i would love some predictions in the nupaK labs<< [12:49 AM]
Jennifer Pearl: I am out of time....No more to pass around [12:50 AM]
Astromon: oH i c [12:49 AM]
Jennifer Pearl: seriously considerinf releasing teh source code for DPAT and Sara and seeing if the community wasnt to take up developmet [12:50 AM]
Jennifer Pearl: development [12:50 AM]
Astromon: wow [12:50 AM]
Jennifer Pearl: wants to [12:51 AM]
Astromon: propose it at omeis player/tool group [12:51 AM]
Jennifer Pearl: I would liek to manage it but just dont have time to code up everything. I spent 7 months straight just getting what little I have now [12:51 AM]
Astromon: no doubt [12:51 AM]
johana: @Jennifer: I'm not sure about Vienna. The A/B puzzles need the concentrations and the presence of both the A and B oligos so I have my doubts about it being possible in Vienna. [12:52 AM]
Jennifer Pearl: ok. So I do need to do the concentrations then. [12:52 AM]
johana: I think that the whole reason we moved to Nupack was that Vienna could not be extended. [12:52 AM]
Jennifer Pearl: at least for now [12:53 AM]
Jennifer Pearl: makes sense. [12:53 AM]
Astromon: cant wait for the day siri can code up ideas for us haha [12:53 AM]
johana: Without concentrations, the relative energies of the states is different. [12:53 AM]
Jennifer Pearl: ok. can someone send me some sample code for me to look at for how you guys are doing concentrations wiht nupack? [12:54 AM]
Jennifer Pearl: I have NUPACK compiled for windows now and would like to use it [12:54 AM]
DevChat T-05m
Astromon: Yay its almost DEV chat time!! [12:55 AM]
Jennifer Pearl: its been devcaht time [12:56 AM]
Astromon: :P [12:55 AM]
Jennifer Pearl: nando needs to fix the clock [12:56 AM]
Astromon: and send you code for consentraitions :) [12:57 AM]
johana: Yep. Have to go. Great chatting with you Astromon and Jennifer! See you next time. [12:57 AM]
Astromon: Thanks Johana [12:57 AM]
Jennifer Pearl: See you have a good day [12:58 AM]
Jennifer Pearl: I need to go as well [12:58 AM]
Astromon: great chatting with you too seeya [12:57 AM]
