| --- Log opened Mon Jan 14 00:00:30 2013 | ||
| rigel | oh who is @pdx.edu, and should i meet them | 00:00 |
|---|---|---|
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| @kanzure | rigel: almost everyone. jrayhawk, nmz787, lichen, mokbor, bioguy, the other jerks. | 00:01 |
| lichen | hmm? | 00:02 |
| * nsh hips hat at room | 00:02 | |
| @kanzure | well, you are close to pdx. | 00:02 |
| nsh | and tips tat | 00:02 |
| rigel | yes, quite close | 00:02 |
| rigel | i go to dorkbot now and again | 00:03 |
| lichen | ah, yeah, im in pdx | 00:03 |
| lichen | hello | 00:03 |
| rigel | hi | 00:03 |
| lichen | going to psu as well, heh | 00:03 |
| rigel | i am up on the hill actually | 00:04 |
| lichen | ah, neat | 00:04 |
| lichen | you at a program at ohsu? | 00:04 |
| rigel | nod | 00:05 |
| lichen | very cool | 00:05 |
| lichen | im just an undergrad still :p | 00:05 |
| bkero | Son of a bitch | 00:05 |
| bkero | More pdx people? | 00:05 |
| rigel | well i would be keen to meet up and chat | 00:05 |
| bkero | lichen: what major at psu? I have many friends there. | 00:05 |
| lichen | biomedical physics | 00:06 |
| bkero | right on | 00:06 |
| * bkero lives in PDX, but is currently traveling at the moment. Be back sometime early next month. | 00:06 | |
| rigel | i was a bench lab monkey before coming here | 00:06 |
| lichen | hehe | 00:06 |
| bkero | lolwetwork | 00:06 |
| lichen | i work at a warehouse doing manual labor bullshit | 00:06 |
| bkero | I did that back in high school. Mini/maxi-preps, PCR, glorified dishwashing. | 00:06 |
| lichen | school part time for now | 00:06 |
| lichen | always on the lookout for something more related | 00:07 |
| @kanzure | http://www.nature.com/nrn/journal/v13/n12/full/nrn3399.html | 00:08 |
| paperbot | HTTP 401 unauthorized http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf | 00:08 |
| @kanzure | what | 00:09 |
| @kanzure | WHAT | 00:09 |
| bkero | yupyup | 00:10 |
| bkero | paywallol | 00:10 |
| @kanzure | well paperbot is supposed to have access to that | 00:11 |
| @kanzure | paperbot: http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf | 00:11 |
| paperbot | error: didn't find any pdfs on http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf | 00:11 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/f4612cfb3251a43a730d64439905a0ec | 00:11 |
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| @kanzure | i think discussing scraping in public is probably okay | 00:34 |
| @kanzure | https://groups.google.com/group/science-liberation-front/about | 00:34 |
| @kanzure | sign 'em up | 00:34 |
| * nsh nods | 00:39 | |
| bkero | Wasn't there a person in the news lately who did something like that? | 00:39 |
| @kanzure | i think it's better to keep discussions on this public for the moment | 00:39 |
| @kanzure | because people are angry and are going to be trying to do some possibly mistaken things | 00:40 |
| @kanzure | and if they talk about best methods first maybe their efforts wont be as useless | 00:40 |
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| archels | what the- http://www.ncbi.nlm.nih.gov/pubmed/19197316 | 03:35 |
| archels | Carbon nanotubes might improve neuronal performance by favouring electrical shortcuts. | 03:35 |
| superkuh | Eh... that seems unlikely. | 03:43 |
| superkuh | At least the mechanism proposed. | 03:43 |
| superkuh | The electrical shortcut is only 10nm across the cell membrane. | 03:44 |
| superkuh | It's not like there are longitudinal currents. | 03:45 |
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| * Viper168 licks superkuh | 03:54 | |
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| kirka | Hi guys. | 04:41 |
| ViperMeowsworth | HO GUYS | 04:44 |
| ViperMeowsworth | -caps | 04:44 |
| kirka | Actually I wanted to talk with kanzure about intricacies of running a web forum (about nanotechnology), but he is probably sleeping now, so I'll wait. | 04:49 |
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| kirka | gene_hacker Are you a real genehacker or it's just a fancy nickname? | 04:50 |
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| kirka | Hi, eudoxia! | 04:50 |
| eudoxia | yo | 04:50 |
| eudoxia | i don't think it would take off | 04:51 |
| kirka | eudoxia Jim wants to do it. None of us has web development experience though. | 04:52 |
| ViperMeowsworth | lol | 04:52 |
| eudoxia | which jim? | 04:52 |
| ViperMeowsworth | I used to run forums | 04:52 |
| ViperMeowsworth | but computer related | 04:52 |
| ViperMeowsworth | general help, software, free and cheap internet listings | 04:52 |
| ViperMeowsworth | etc.. | 04:52 |
| ViperMeowsworth | was freeaccess.com, but the domain got sold off | 04:52 |
| kirka | eudoxia Last post here: https://groups.google.com/forum/?fromgroups=#!topic/sci.nanotech/Sjvz_Nr857U | 04:52 |
| kirka | eudoxia I think there should be at least one forum on MNT. | 04:53 |
| kirka | eudoxia To discuss design of molecular machinery, new software tools etc. | 04:53 |
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| eudoxia | yeah | 04:53 |
| kirka | eudoxia btw I'm developing MNT CAD in lisp: http://rghost.ru/43023154.view | 04:54 |
| kirka | That's very early stage though. | 04:54 |
| kirka | My goal is million atoms on screen. | 04:54 |
| eudoxia | and i'll port it to hylas :) | 04:54 |
| kirka | Heh, that's possible, I thought about it. | 04:55 |
| kirka | Hylas desperately needs documentation. | 04:55 |
| eudoxia | need to write some opengl binings | 04:55 |
| eudoxia | well i updated the readme and wrote some docs | 04:55 |
| eudoxia | it's up in github | 04:55 |
| eudoxia | there are some code examples | 04:56 |
| kirka | Yes, I have seen this. | 04:56 |
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| eudoxia | are you using CL? | 04:57 |
| kirka | I think there should be explanation of Hylas's abstractions over LLVM assembler (if tehre are any). | 04:57 |
| eudoxia | ? | 04:57 |
| eudoxia | code generation is straight to LLVM; IR | 04:57 |
| kirka | eudoxia For the first prototype model viewer I used Racket. It's too slow though, so I'm switching to CL. | 04:58 |
| eudoxia | i see | 04:58 |
| kirka | I think CL is very good language for this thing, as it demonstrates that 20 year old code (Maxima) runs well on it now. | 04:58 |
| eudoxia | needs a better gui toolkit | 04:59 |
| eudoxia | if you need help with CommonQt i have a tutorial on my blog | 04:59 |
| kirka | So this CAD will work 10-20 years into the future, without bit rot. | 04:59 |
| kirka | eudoxia I tink Qt is a monstrous dependence. | 04:59 |
| eudoxia | yeah | 04:59 |
| kirka | It's changing | 04:59 |
| kirka | API can change in a couple of years. | 04:59 |
| eudoxia | the molecular cad code shouold be separate from the interface | 05:00 |
| kirka | I will have several graphics backends, including parallel software render. | 05:00 |
| kirka | Yes, absolutely. | 05:00 |
| eudoxia | in NanoEngineer, well... | 05:00 |
| eudoxia | "User interface and code are only one, and they love each other so much they are completely glued together." | 05:00 |
| eudoxia | - a friend at work | 05:00 |
| kirka | Hehe. | 05:00 |
| kirka | Graphics backend will provide simple interface for drawing model and relaying user's input into command logic module. | 05:01 |
| kirka | eudoxia So Hylas is S-Exp version of LLVM IR? | 05:02 |
| kirka | It also does variable allocation (static by default), | 05:02 |
| eudoxia | there isn't a huge distance between assembly and the language, no | 05:03 |
| eudoxia | i intended it to combine low-level shit with macros | 05:03 |
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| eudoxia | and metaprogramming, introspection, reflection, etc. | 05:03 |
| kirka | But to program in it one should clearly understand what's done behind the scenes. | 05:03 |
| kirka | eudoxia That's cool idea. | 05:03 |
| kirka | I have been waiting for 2 years for such language to be created. | 05:04 |
| eudoxia | i won't let you down bro | 05:04 |
| kirka | That's good, heh. | 05:05 |
| kirka | For example there is a keyword "recursive", but one can write macro that infers recursiveness of function and adds this label if necessary. | 05:07 |
| eudoxia | that's actually pretty good | 05:07 |
| eudoxia | also i made the cover for the docs book (docs/res/i | 05:09 |
| eudoxia | mg) and its pretty as shit | 05:09 |
| eudoxia | tits 'n stuff | 05:09 |
| kirka | Heh | 05:09 |
| kirka | It would be good if you described primitives (like define, let etc) and memory allocation issues. | 05:10 |
| kirka | ViperMeowsworth As you can see we want to start a forum on molecular nanotechnology. | 05:12 |
| eudoxia | i'll write the function reference today | 05:12 |
| eudoxia | if i can | 05:12 |
| ViperMeowsworth | yeah I'm scanning, hopping between half a dozen channels | 05:13 |
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| gene_hacker | @kirka it's my name of course, though once the technology becomes cheap we'll see about it | 05:15 |
| kirka | eudoxia There is no need to be in a hurry, | 05:15 |
| kirka | eudoxia You are the creator of the language after all. | 05:16 |
| eudoxia | still i want to get the docs done | 05:17 |
| eudoxia | so kirka will you put your cad up on github? | 05:34 |
| kirka | eudoxia I will, when it's usable | 05:35 |
| kirka | eudoxia It's still just pdb-loader with sloow 3d-viewer. | 05:35 |
| eudoxia | areyou using opengl or something else for the 3d? | 05:35 |
| kirka | opengl | 05:35 |
| kirka | But for million of atoms, maybe I'll have to use sprites. | 05:36 |
| eudoxia | hm | 05:37 |
| eudoxia | i've heard about something like that, used, coincidentally, for a molecule viewer | 05:37 |
| kirka | I also think that in very large designs parts could be abstracted away, represented as polygonal meshes with bondpoints. | 05:39 |
| eudoxia | i was thinking about that too | 05:39 |
| eudoxia | for MNT MEMS stuff | 05:39 |
| kirka | And to see whole atomic structure one could render them offline. | 05:39 |
| kirka | Yep. | 05:39 |
| kirka | Also I want to classify parts and their structural patterns by difficulty of manufacturing. | 05:47 |
| kirka | And build complex structures with easy-to-manufacture components. (relatively "easy", of course) | 05:47 |
| eudoxia | needs afm integration | 05:48 |
| kirka | Heh | 05:48 |
| kirka | Of course, "model structures", not "build". | 05:48 |
| eudoxia | lol | 05:48 |
| kirka | E.g. look at this sorting pump: http://www.nanoengineer-1.net/mediawiki/index.php?title=File:SortingPump1.png | 05:49 |
| kirka | There are unnecessary curved surfaces | 05:49 |
| kirka | And sulfur atoms. | 05:50 |
| kirka | The design is cool. of course. | 05:50 |
| eudoxia | http://wiki.transhumani.com/index.php?title=Molecular_Machinery#Abstract_Sorting_Pump is much better | 05:52 |
| kirka | I agree. It's strange that nobody designed atomically precise version yet. | 05:53 |
| eudoxia | yeah | 05:53 |
| eudoxia | i would if i knew how to make a bidning site | 05:53 |
| kirka | Also, there is a need in springs. | 05:53 |
| eudoxia | i wouldn't be so sure | 05:53 |
| eudoxia | consider, on one side, you got actual pressure from molecules to be sorted | 05:53 |
| eudoxia | on the other side there's near vacuum | 05:53 |
| eudoxia | probability would allow the pump to work without moving binding sites | 05:54 |
| kirka | Hmph. That's a question of kT >> EnergyBarrier for sliding | 05:54 |
| kirka | If that's true then it'll work this way. | 05:55 |
| eudoxia | i think drexler said it wiuld | 05:56 |
| eudoxia | would* | 05:56 |
| eudoxia | somewhere in nanosystems | 05:56 |
| kirka | Yes, I remember that. | 05:56 |
| kirka | Binding sites probably should be designed to approximate potential energy surface of target molecule. | 05:57 |
| kirka | We need to visualize PES first. | 05:59 |
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| kirka | eudoxia There is a note on complimentary surfaces on p.265 of "Nanosystems". | 06:07 |
| kirka | eudoxia http://www.zyvex.com/nanotech/bindingSites.html | 06:28 |
| kirka | They thought about it 20 years ago. | 06:32 |
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| eudoxia | that paper is almost as old as i am | 08:28 |
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| @kanzure | sigh yet another forum | 08:58 |
| kirka | kanzure Do you have better suggestion? | 08:59 |
| @kanzure | yes. the vast majority of the people from foresight institute all prefer mailing lists. | 09:01 |
| kirka | sci.nanotech is dead. | 09:01 |
| kirka | Leitl's list is also half-dead. | 09:01 |
| @kanzure | that's not what i'm talking about | 09:01 |
| @kanzure | leitl's list isn't dead. | 09:02 |
| eudoxia | postbiota/nano? | 09:02 |
| kirka | It's repost of non-related news, that's all. | 09:02 |
| kirka | *nano | 09:02 |
| @kanzure | well, then you should call him out on it | 09:02 |
| kirka | There is no mailing list of forum that's created solely for MNT-related discussions. | 09:03 |
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| @kanzure | kirka: jrayhawk created one for you | 09:05 |
| @kanzure | but you seemed to never look | 09:05 |
| kirka | I looked | 09:05 |
| eudoxia | link? | 09:05 |
| @kanzure | eudoxia: it was the sympa link | 09:05 |
| kirka | It was something scary on some unrealted domain. | 09:05 |
| @kanzure | it even has a web ui for you | 09:06 |
| eudoxia | <3 | 09:06 |
| eudoxia | http://diyhpl.us/sympa/ ? | 09:07 |
| @kanzure | yep | 09:08 |
| kirka | Actually, Jim Logajan wants to start a forum. | 09:08 |
| kirka | And we discuss software, domain and webhosting providers. | 09:08 |
| kirka | kanzure Can you give an advice on choice of good forum engine? | 09:09 |
| kirka | There are hunderds of them. | 09:09 |
| eudoxia | phpBB3 | 09:09 |
| @kanzure | they are all fucking awfl | 09:09 |
| @kanzure | phpbb is terrible and evil, you should never use it | 09:10 |
| eudoxia | hahah i'm trolling | 09:10 |
| kirka | I tried jForum, and it simply works. | 09:10 |
| eudoxia | roll your own | 09:10 |
| eudoxia | c: | 09:10 |
| kirka | I don't want to dig into web programming. | 09:10 |
| @kanzure | you should never use ikonboard, fluxbb, invisionboard, jforum, phpbb, smf, or any of the others. | 09:10 |
| kirka | Heh. | 09:10 |
| @kanzure | kirka: what do you have against email? | 09:10 |
| eudoxia | have a git repo on a server where people write their posts as yaml files and threads are folders | 09:11 |
| kirka | kanzure Nothing, but participating in mailing lists is more complex than using a forum. | 09:11 |
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| eudoxia | i don't even know how to unsubscribe from llvm-dev | 09:11 |
| kirka | Jim wants a forum and I agree with him. | 09:11 |
| @kanzure | eudoxia: llvm-dev-unsubscribe@whatever | 09:11 |
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| eudoxia | so i just send whatever email to that? | 09:12 |
| @kanzure | no, usually you have to include unsubscribe in the subject line to that address | 09:12 |
| @kanzure | otherwise it will complain | 09:12 |
| eudoxia | oh okay | 09:12 |
| eudoxia | thanks kanz+ | 09:12 |
| @kanzure | btw, this was in the instructions when you first subscribed. | 09:13 |
| eudoxia | probablyh | 09:13 |
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| ParahSailin | kirka: make it a subreddit | 09:26 |
| kirka | There is http://www.reddit.com/r/nanotech already. | 09:27 |
| kirka | 95% of unrelated information. | 09:27 |
| ParahSailin | so make another? | 09:27 |
| kirka | Maybe. | 09:27 |
| kirka | But if something happens to reddit, all discussion will be lost. | 09:28 |
| @kanzure | i think kirka doesn't believe in the existence of email | 09:28 |
| kirka | I believe. | 09:28 |
| kirka | A read different mailing lists and participate in some. | 09:29 |
| kirka | But forum with web interface is simpler. | 09:29 |
| eudoxia | i don't even know how to post to one lol | 09:29 |
| @kanzure | eudoxia: you write an email. | 09:29 |
| kirka | I use google groups. | 09:29 |
| ParahSailin | if something happens to the internet backbone, all will be lost | 09:29 |
| ParahSailin | clearly we need pigeons | 09:30 |
| kirka | We need backups. | 09:30 |
| eudoxia | dogs carrying DVDs | 09:30 |
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| @kanzure | kirka: backups of mailing lists are very easy. you just upload your mbox file. | 09:30 |
| kirka | I agree. | 09:30 |
| eudoxia | or terabyte flash drives, that might have more bandwidth than most internet connections | 09:30 |
| eudoxia | although the latency would be fucked | 09:31 |
| kirka | Backups of forums are also easy. You just copy the database. | 09:31 |
| kirka | The question is "what forum engine do we choose?"/ | 09:31 |
| @kanzure | how about mailman | 09:32 |
| @kanzure | ParahSailin: https://groups.google.com/group/science-liberation-front | 09:33 |
| kirka | kanzure Do you plan to upload a torrent with terabyte of scientific papers? | 09:33 |
| @kanzure | no | 09:34 |
| @kanzure | library genesis tried that and nobody seeded | 09:34 |
| ParahSailin | the last guy who did that did not have a very good day | 09:34 |
| kirka | I know. | 09:34 |
| @kanzure | ParahSailin: aaronsw did not use torrents | 09:34 |
| kirka | Someone could host them in I2P. | 09:35 |
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| ParahSailin | someone just needs to make a pirate marketplace for papers | 09:36 |
| eleitl | howdy bryan | 09:36 |
| eudoxia | oh jesus it's eugene leitl | 09:36 |
| * eudoxia faints | 09:36 | |
| eleitl | hi eudoxia | 09:36 |
| ParahSailin | let people run bots to sell papers for like five bitcents | 09:37 |
| @kanzure | eleitl: we are your official fan club | 09:37 |
| eleitl | :)) | 09:37 |
| @kanzure | ParahSailin: i think you should propose that to the group | 09:37 |
| * eudoxia twirls a little leitl flag | 09:37 | |
| @kanzure | ParahSailin: i was thinking of letting people rent out their student ids/passwords for bitcoins | 09:37 |
| @kanzure | ParahSailin: and make money on their student loans | 09:37 |
| @kanzure | eleitl: so, eudoxia and kirka have some complaints about the nanotech list | 09:37 |
| eudoxia | i don't just kirka | 09:38 |
| @kanzure | and they are too passive aggressive to tell you in person | 09:38 |
| eudoxia | gee thanks kanz making me look bad infront of the leitl | 09:38 |
| kirka | Well that's problem of MNT in general | 09:38 |
| eleitl | what's wrong with the list, other that it doesn't get traffic? | 09:38 |
| eleitl | machine-phase is dead in the water | 09:38 |
| ParahSailin | people dont like my ideas, and that silkroad for papers would be really low on my own to-do list | 09:38 |
| @kanzure | ParahSailin: you should post it anyway, someone else might build it | 09:39 |
| @kanzure | ParahSailin: like me | 09:39 |
| kirka | It's practiced by maybe 100 researchers in the world. | 09:39 |
| eudoxia | 100'¿ | 09:39 |
| eudoxia | you nuts | 09:39 |
| eudoxia | 5 tops | 09:39 |
| kirka | Ok, 20 | 09:39 |
| eleitl | libgen is pretty good, I hope they can start accepting BTC soon | 09:39 |
| eleitl | kirka, yes, but it's not easy to change that | 09:39 |
| eudoxia | assuming metzger plays with nanoengineer in his free time | 09:39 |
| ParahSailin | i think you're probably about 75% of the programming productivity of that entire group, kanzure | 09:39 |
| eleitl | perry is working hard, but he needs to establish himself academically first | 09:39 |
| @kanzure | ParahSailin: ah so i should tone it down..? | 09:40 |
| ParahSailin | so reposting idea there would be redundant | 09:40 |
| @kanzure | ParahSailin: please? :( | 09:40 |
| ParahSailin | ok | 09:40 |
| eleitl | kanzure, we're going to mix some VM-1 perfusate this weekend, for a test on a human cadaver | 09:40 |
| @kanzure | please elaborate | 09:40 |
| nmz787 | funny their page here doesn't list winter 2013 http://genefoo.com/blogs/news/6074124-launching-personalpcr | 09:40 |
| @kanzure | where have you acquired a human cadaver | 09:41 |
| ParahSailin | VM-1 is some kind of antifreeze? | 09:41 |
| @kanzure | nmz787: yeah that seems to be what macowell is doing | 09:41 |
| eudoxia | CI's cryoprotectant | 09:41 |
| eleitl | the human cadaver is not our own, it's a group of embalmers which klaus has dug up | 09:41 |
| eleitl | I don't know any of them, though I would like to attend, if feasible | 09:41 |
| eleitl | VM-1 is Pichugin's vitrifyable perfusate | 09:41 |
| eleitl | we start with it because it's cheap, and we've been asked to do it in a somewhat urgent fashon | 09:42 |
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| eleitl | to all: a group of kraut cryonicists are trying to establish a local cryonics provider | 09:43 |
| -!- mode/##hplusroadmap [-b dende!*@*] by kanzure | 09:43 | |
| eudoxia | i saw those pictures of your new lab | 09:43 |
| eleitl | we've rented lab space in a startup incubator | 09:43 |
| eleitl | we'll try to do some SENS and other research in there during daytime | 09:43 |
| eleitl | we're supposed to get our dewars by weekend, but it will likely take a little longer | 09:44 |
| nmz787 | eleitl: what's with all the DMSO? | 09:45 |
| eleitl | don't ask me, ask Pichugin. It's not my perfusate of choice. | 09:46 |
| nmz787 | is that for the emblaming? | 09:46 |
| eleitl | However, it's easy and cheap, and if we do fracturing research, we'll also start with VM-1, and possibly VM-1 with iceblockers. | 09:46 |
| eleitl | Not embalming, perfusion, and then thermal descent to dry ice, and transport overseas on dry ice. | 09:47 |
| eleitl | Vitrified, not frozen. | 09:47 |
| eleitl | Assuming perfect perfusion, which almost never happens with the kind of ugly cases we're getting in krautlandia. | 09:47 |
| eudoxia | tests or actual past cases? | 09:49 |
| eleitl | There have been CI cases in Germany, and they typically do not look very good, due to very conservative criteria for death declaration. | 09:50 |
| eleitl | It doesn't matter to me, since we need to be able to learn the technique, regardless where it is going to be used. | 09:51 |
| @kanzure | kirka: can you elaborate why you don't like eleitl's nanotechnology forum? | 09:53 |
| kirka | It's not that I don't like it. | 09:53 |
| kirka | There are some interesting posts. | 09:54 |
| kirka | But as in other mailing lists there is little of MNT. | 09:54 |
| eudoxia | it's not about the medium | 09:54 |
| eleitl | of course, because MNT is rare as hen's teeth | 09:54 |
| kirka | It's a global problem. | 09:54 |
| eudoxia | there just aren't many people interested | 09:54 |
| kirka | I agree. | 09:54 |
| @kanzure | then why did you want to make a separate forum? | 09:54 |
| @kanzure | i am very confused. | 09:54 |
| kirka | Molecular manufacturing has plitical burden on it, so it's doesn't get funded. | 09:55 |
| kirka | kanzure Jim Logajan wants to make a replacement for sci.nanotech mailing list. | 09:55 |
| eleitl | I'm not married to MNT. Nano is nano. All paths lead to machine-phase, eventually. | 09:55 |
| eleitl | sci.nanotech is a Usenet group, not a mailing list, right? | 09:55 |
| kirka | I agree, protein/foldamer engineering has very good future. | 09:56 |
| kirka | eleitl Right. | 09:56 |
| kirka | And also google group. | 09:56 |
| eleitl | oh, haven't seen that one. | 09:56 |
| kirka | But I think that nanoparticles are a dead end. | 09:57 |
| eleitl | nanoparticles are not real nanotechnology | 09:57 |
| eleitl | just inflationary use | 09:57 |
| eleitl | Just subscribed to sci.nanotech, thanks | 09:58 |
| eudoxia | eleitl, what do you think about Zyvex's epitaxy approach? | 09:58 |
| kirka | Yes, it's after creation of NNI and lobbying of Nanobusiness alliance nanoparticles research has become NNI's main focus. | 09:59 |
| eleitl | haven't look at zyvex in more than a decade | 10:00 |
| eudoxia | http://www.zyvexlabs.com/Research.html | 10:00 |
| eudoxia | http://nextbigfuture.com/2010/10/what-is-optimal-bootstrapping-pathway.html | 10:00 |
| eleitl | thanks, I will look at it | 10:01 |
| eudoxia | "Von Ehr hopes to have a primitive nanotechnology system that can create blocklike objects by 2015 and rudimentary molecular manufacturing by 2020. The big game-changer to my mind is Digital Matter. For enzymes, catalysts, and increasingly even for transistors, every atom has to be in the correct place in order for the molecule or component to function. " | 10:01 |
| eudoxia | i don't want to get my hopes up ;_; | 10:01 |
| -!- mode/##hplusroadmap [-b d3nd3!*@*] by kanzure | 10:02 | |
| nmz787 | rigel: so you're in PDX? | 10:02 |
| nmz787 | I'm gonna go tour FEI, the e-microscope and FIB company this thurs evening | 10:02 |
| kirka | There is also a promising parallel MEMS-STM firm: http://www.icspicorp.com/ | 10:02 |
| nmz787 | http://portland-or.sites.acs.org/newsletter.pdf | 10:02 |
| kirka | They are partners of Zyvex. | 10:03 |
| eleitl | I wouldn't get the hopes up too far | 10:03 |
| eleitl | the best hope is with DNA autoassembly | 10:03 |
| eleitl | which is not much | 10:03 |
| nmz787 | using modified cells seems like a reasonable way to go about APM | 10:04 |
| kirka | Recent synthetic DNA ion channel is good. | 10:04 |
| kirka | This one: http://www.sciencemag.org/content/338/6109/932.abstract | 10:04 |
| kirka | It's a DNA-origami structure that works as ion channel, designed from scratch. | 10:04 |
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| eleitl | not sure I've sent that. why don't you send such papers to the nano list? | 10:05 |
| kirka | I will, next time. I'm not used to mailing lists yet. | 10:05 |
| eleitl | Heh. What do you use? Usenet? | 10:06 |
| @kanzure | "I know Ariya used to work for Trolltech and that has obviously been fundamental in PhantomJS's success to date." | 10:06 |
| @kanzure | oh. i didn't know that. | 10:06 |
| @kanzure | paperbot: http://www.sciencemag.org/content/338/6109/932.abstract | 10:06 |
| paperbot | error: didn't find any pdfs on http://www.sciencemag.org/content/338/6109/932.abstract | 10:06 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/e92df00e68df7c336e7bf8fccf642b32 | 10:06 |
| @kanzure | hmm | 10:06 |
| archels | eleitl: do you think it would be worthwhile to look at plastification as an alternative to cryonic preservation? | 10:07 |
| @kanzure | paperbot: http://www.sciencemag.org/content/338/6109/932.full.pdf | 10:07 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/859715fc8cbb731cfe0429f2b19aba5d | 10:07 |
| nmz787 | did science change their format? | 10:07 |
| eleitl | Mike Darwin is making some very interesting noises about fixation/plastination, so I'm hanging on until he delivers. | 10:07 |
| kirka | eleitl I'm from 1990's generation, so I haven't seen age of UseNet, heh. | 10:07 |
| eleitl | oic, kirka | 10:07 |
| @kanzure | http://diyhpl.us/~bryan/papers2/paperbot/Synthetic%20Lipid%20Membrane%20Channels%20Formed%20by%20Designed%20DNA%20Nanostructures.pdf | 10:07 |
| @kanzure | there you go | 10:08 |
| @kanzure | nmz787: i guess so :( | 10:08 |
| eleitl | I think fixation/plastination might be feasible, but it's very difficult to validate. | 10:08 |
| eleitl | the no-feedback problem | 10:09 |
| @kanzure | fascinating https://github.com/laurentj/slimerjs | 10:09 |
| @kanzure | gecko-based phantomjs port | 10:09 |
| @kanzure | not so headless though | 10:09 |
| kirka | eleitl Drexler is into peptoids/foldamers these days. Probably that's a faster route than UHV-STM. | 10:10 |
| eleitl | yes, I've always been of the opinion that bootstrap by bio is easier | 10:10 |
| -!- mode/##hplusroadmap [-b *!*@*.croy.cable.virginmedia.com] by kanzure | 10:10 | |
| kirka | Good protein/foldamer engineering is rare though. | 10:10 |
| eleitl | inverse protein folding is almost solved | 10:10 |
| @kanzure | mode -b *!*@*cpc10-croy17-2-0-cust245* | 10:10 |
| @kanzure | oh god | 10:10 |
| -!- mode/##hplusroadmap [-b *!*@*cpc10-croy17-2-0-cust245*] by kanzure | 10:10 | |
| nmz787 | i think we just need to design a minimal cell that is XYZ controllable | 10:11 |
| eleitl | strangely, it is easier than straight protein folding | 10:11 |
| nmz787 | XYZ and rotate | 10:11 |
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| d3nd3 | success | 10:11 |
| d3nd3 | kanzure: ty | 10:11 |
| kirka | nmz787 But their membranes are absolutely non-stiff. | 10:11 |
| eleitl | we need an enzyme which can lay down bucky | 10:11 |
| eleitl | that might be possible | 10:11 |
| nmz787 | kirka: what's stiffness have to do with moving around to place atoms? | 10:12 |
| nmz787 | then the cell becomes the STM and STP tip with atom loader | 10:12 |
| kirka | nmz787 Stiffness matters because of thermal noise. | 10:12 |
| nmz787 | isn't that why receptors exist, to lock onto a target before manipulation? | 10:12 |
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| kirka | nmz787 So the receptor is the controlled molecular machie, floating in cell? | 10:14 |
| kirka | *machine | 10:14 |
| kirka | *in cells membrane | 10:14 |
| nmz787 | well the whole cell is the controlled machine | 10:14 |
| nmz787 | you'd tell it export receptor A to surface | 10:14 |
| kirka | eleitl is right, we need engineered enzymes. | 10:14 |
| nmz787 | export enzyme G to surface | 10:14 |
| eleitl | guys, it's very interesting, but I need to catch the train home. I'll try dropping by later today, or at least I'll read the scroll tomorrow. | 10:14 |
| eleitl | catch you laters. Thanks! | 10:15 |
| nmz787 | I guess telling the cell to move 5 hydroxyls south vs north would be hard | 10:15 |
| @kanzure | you could magnetically move the cell | 10:16 |
| @kanzure | and make it produce magnetic-responsive enzymes | 10:16 |
| nmz787 | maybe it'd have to be magneto or light -tactic... so move X atoms in J direction | 10:16 |
| nmz787 | well the moving X atoms is done already with actin filament moving | 10:16 |
| nmz787 | so somtehing could be adapted for non-polymers | 10:17 |
| kirka | I don't think it's possible to move cell as a whole with right precision (1 angstrem). | 10:17 |
| nmz787 | but movement would be too coarse I think if you didn't have an enzyme doing the positioning | 10:17 |
| kirka | It's possible for components of protein/RNA/DNA machinery though. | 10:17 |
| nmz787 | well you don't need to move the whole cell to move 1 angstom | 10:18 |
| nmz787 | since the membrane is much larger area, you can just move within the membrane | 10:18 |
| kirka | If we had an analog of Ribosome that can manufacture more complex structures than aminoacid-chains that'd be a huge step forward. | 10:18 |
| nmz787 | what other polymers would you want it to make? | 10:19 |
| kirka | There is already work on mutating ribosome to understand 4-word codons. | 10:19 |
| kirka | nmz787 Polymers with two covalent bonds for example | 10:19 |
| kirka | nmz787 They would be more predictable. | 10:20 |
| kirka | There are, for example peptoids: http://en.wikipedia.org/wiki/Peptoid | 10:21 |
| kirka | They are more stable than proteins. | 10:21 |
| kirka | There is a large space of possible monomers, with them it may be easier to build stable structures than with amino acids. | 10:24 |
| nmz787 | lacking secondary structure seems pretty limiting to make anything catalytic | 10:25 |
| archels | kanzure: you should tell paperbot to grab the supplements as well ;) | 10:25 |
| archels | the supplement on that DNA-origami-ion-channel paper is much better than the brief main publication | 10:25 |
| kirka | nmz787 >Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure | 10:26 |
| archels | I still have them on my webserver, http://www.turingbirds.com/temp/Langecker.SM.pdf | 10:26 |
| archels | paperbot: http://www.turingbirds.com/temp/Langecker.SM.pdf | 10:26 |
| archels | low hit rate :P http://diyhpl.us/~bryan/papers2/paperbot/ | 10:27 |
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| kirka | nmz787 The main problem as it seems to me is a lcak of good method to design foldamers. | 10:28 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/1e9ee8083534045e107de3879995fe45 | 10:28 |
| kirka | *lack | 10:28 |
| kirka | nmz787 There is a need in foldamer design software with real-time simplified force fields. | 10:29 |
| ParahSailin | paperbot: https://s3-us-west-2.amazonaws.com/droplr.storage/files/acc_15515/sK7z?AWSAccessKeyId=AKIAJSVQN3Z4K7MT5U2A&Expires=1358189301&Signature=7GvBHMfkgBjcBFpnQ79a0jENm7c%3D&response-content-disposition=attachment%3B%20filename%2A%3DUTF-8%27%271-s2.0-016378278990009X-main.pdf | 10:30 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/293105c6bfdc3f3d95184ef931393947 | 10:30 |
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| kirka | Drexler did Pam-3 and Pam-5 into NE1 for this purpose. | 10:30 |
| nmz787 | hmm | 10:30 |
| nmz787 | seems like it would make a lot more sense to pour resources into learning how to fold normal proteins, since we're composed of them already | 10:31 |
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| nmz787 | them modify the strategy from there | 10:31 |
| nmz787 | then* | 10:31 |
| kirka | nmz787 Folding and designing aren't inverse problems. | 10:31 |
| d3nd3 | so how do i view paperbots papers ? | 10:31 |
| nmz787 | why not? | 10:32 |
| kirka | nmz787 Structures can be designed to be easily predictable. | 10:32 |
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| nmz787 | but we care about function | 10:32 |
| kirka | E.g. this protein was designed to be easily predictable: http://www.nature.com/nature/journal/v458/n7236/full/nature07841.html | 10:33 |
| kirka | And it works. | 10:33 |
| kirka | Id on't think that all of natural protein's complexity is related to function. | 10:33 |
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| nmz787 | no but it obviosuly works | 10:34 |
| kirka | It's just evolution building complex patterns in sequental steps (it adds complexity until functionality breaks). | 10:34 |
| nmz787 | and there's a huge amount of prior art waiting to be understood and hacked | 10:34 |
| kirka | I agree | 10:35 |
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| kirka | But much of this complexity can be just random mutations. | 10:35 |
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| kirka | Drexler writes a lot abou this. | 10:35 |
| nmz787 | there's still a reason that it works | 10:35 |
| nmz787 | that isn't random | 10:35 |
| nmz787 | so PDX has this, so this /should/ work paperbot: http://www.nature.com/nature/journal/v458/n7236/full/nature07841.html | 10:36 |
| kirka | Yep, core structure, functional folds, etc. | 10:36 |
| kirka | But look at that O2 transport protein - it doesn't contain dpecial folds that natural one has. | 10:37 |
| kirka | And it works. | 10:37 |
| nmz787 | yeah but all that says is that evolution either had a reason to keep that fold, or it's just prehensile | 10:38 |
| nmz787 | err no | 10:38 |
| nmz787 | s/prehensile/hanging around/ | 10:38 |
| nmz787 | o | 10:39 |
| nmz787 | oO big snow flakes outside :D | 10:39 |
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| @kanzure | ParahSailin: what kinda link was that | 10:39 |
| kirka | nmz787 http://metamodern.com/2009/03/30/a-revolution-in-de-novo-protein-engineering/ | 10:39 |
| kirka | The point is that evolation adds complexity until something breaks. | 10:40 |
| kirka | *evolution | 10:40 |
| @kanzure | brownies: "January Events at Genspace - Glow Your Mind!"..... you got what you wanted, are you happy now? | 10:40 |
| nmz787 | "Protein engineering is often approached as if it were part of biology. Imagine approaching aerospace engineering as if it were part of ornithology: " | 10:41 |
| nmz787 | isn't a bird still more efficient than a plane? | 10:41 |
| kirka | Actually, no. | 10:41 |
| kirka | Though that's complex to measure | 10:41 |
| nmz787 | yeah esp if you are talking mass being moved, or just a single being moving aroun | 10:42 |
| nmz787 | like person per fuel or mass per fuel spent in the air | 10:42 |
| kirka | There is an article about this: mb-soft.com/public3/birdeff.html | 10:43 |
| brownies | kanzure: not until i have a glowing cat of my own | 10:43 |
| kirka | But looks like it's down. | 10:43 |
| brownies | kanzure: but i do applaud their innovative focus | 10:43 |
| nmz787 | kanzure: is this list any good diyresearch-bounces@inventati.org] | 10:44 |
| nmz787 | ? | 10:44 |
| @kanzure | kirka: http://web.archive.org/web/20120407104406/http://mb-soft.com/public3/birdeff.html | 10:44 |
| @kanzure | nmz787: not sure. it's just diyresearch@inventati.org | 10:44 |
| kirka | kanzure Thanks. | 10:44 |
| @kanzure | nmz787: it's probably people stalking diy people, and pertending it's research | 10:44 |
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| kirka | btw I haven't found any good book on protein engineering. | 10:52 |
| ParahSailin | books are for topics that are 30+ years old | 10:55 |
| kirka | Yes, looks like I have to dig papers on the subject. I'm doing it anyway. | 10:56 |
| nmz787 | kanzure: none of the PDX people you told me to email got back :( | 10:57 |
| nmz787 | no one wants to be my for realz friend | 10:57 |
| @kanzure | whaat | 10:57 |
| @kanzure | bunch of jerks | 10:57 |
| nmz787 | it's probably my fault for being so weird | 10:58 |
| @kanzure | no they are the weirdos | 10:59 |
| @kanzure | human decency is to at least reply | 10:59 |
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| rigel | nmz787: yes | 10:59 |
| nmz787 | rigel: have you ever gone to The Circuit climbing gym? | 11:00 |
| rigel | no | 11:01 |
| rigel | i am fat | 11:01 |
| @kanzure | fat monkeys are also capable of climbing | 11:02 |
| nmz787 | if it weren't for my epigenetics (I think) I'd probably be fat too | 11:02 |
| nmz787 | my mother was bulemic when she was pregnant, and I think that might have something to do with me not adding weight | 11:03 |
| nmz787 | my body thinking i'm born to starve or something | 11:03 |
| rigel | doubtful | 11:03 |
| rigel | probably the other direction | 11:03 |
| rigel | limited resources, fetus works hard to keep as many calories etc as possible | 11:04 |
| nmz787 | i dunno, i read something about this regarding starving during pregnancy causing the kids to be insensitive to insulin | 11:04 |
| nmz787 | meaning they wouldn't store sugar | 11:04 |
| rigel | its all speculative horseshit anyway | 11:04 |
| rigel | i am in a foul mood | 11:04 |
| nmz787 | plus is that if you're really starving you brain gets all the sugar it can, since sugar is never stored where the brain cant get it | 11:04 |
| rigel | i probably do not need to be having this conversation right now. yes i am in portland. | 11:04 |
| bkero | oh dear | 11:05 |
| nmz787 | downside if you're well fed, you can easily become too sweet and start to damage organs | 11:05 |
| nmz787 | rigel: what brings you here? | 11:09 |
| nmz787 | i see you do something at OHSU | 11:09 |
| rigel | aaron swartz | 11:11 |
| nmz787 | so the sanyasin (where OSHO the rolls royce guru stayed in E Oregon) ranch is now a christian youth ranch | 11:11 |
| nmz787 | even though the Sheela lady commited bioterrorism, I think the christian camp is probably worse overall | 11:11 |
| nmz787 | well i take that back | 11:12 |
| rigel | thats kind of bigoted | 11:12 |
| @kanzure | "Identifying the DNS server used to fulfill a HTTP request" http://5f5.org/ruminations/dns-debugging-over-http.html | 11:13 |
| nmz787 | i googled bigtoed | 11:13 |
| rigel | lots of different kinds of religious folks, some good some bad | 11:13 |
| nmz787 | well neither creed is mine, so i don't think i'm a bigot | 11:13 |
| rigel | of course you dont | 11:14 |
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| nmz787 | by technical definition i'm not a bigot in this case | 11:15 |
| nmz787 | rigel are you interested in touring FEI with me this Thurs evening? | 11:15 |
| @kanzure | nmz787: https://groups.google.com/group/science-liberation-front | 11:15 |
| nmz787 | kanzure: wasn't the first message in there 'can we change the name of this group to avoid being targeted' | 11:16 |
| @kanzure | sure | 11:17 |
| eudoxia | it's okay guys | 11:17 |
| @kanzure | nobody suggested an alternative name | 11:17 |
| eudoxia | we're all already in multiple watchlists | 11:17 |
| @kanzure | "OH MY GOD WE'RE TALKING ABOUT READING?" | 11:17 |
| eudoxia | just for the record I think the DHS provides many useful services like their C vulnerabilities database | 11:17 |
| eudoxia | America <3 | 11:17 |
| nmz787 | C vulnerabilites eg? | 11:18 |
| nmz787 | eh? | 11:18 |
| nmz787 | I was reading about CODIS a few weeks ago | 11:18 |
| nmz787 | they don't have protocols listed | 11:18 |
| @kanzure | 00:36 <+nsh> ARCHIVISTS OF THE WORLD UNITE! YOU HAVE NOTHING TO LOOSE BY YOUR INSTITUTIONAL ACCESS! | 11:18 |
| nmz787 | so I called their office, but they didnt get back to me | 11:18 |
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| kirka | eudoxia So, for C2H2 buckytube (9,0) seems to be a good pocket. | 11:32 |
| eudoxia | yep | 11:32 |
| eudoxia | it's in nanosystems too | 11:32 |
| eudoxia | actuall i think the picture from that old paper was a figure in NS | 11:33 |
| kirka | eudoxia To make a srting pump we should think how to bond it with diamond rotor (without inducing too much strain). | 11:33 |
| eudoxia | buckytube can be grown on some diamond surfaces, and has been grown | 11:33 |
| nmz787 | wasn't someone saying nanoengineer isn't realistic at all? | 11:34 |
| eudoxia | http://img405.imageshack.us/img405/1253/nanotube60onc111.png | 11:34 |
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| kirka | eudoxia That;s good, but we need large diameter and hole for rod to slide. | 11:35 |
| kirka | nmz787 In what sense "unrealistic" ? | 11:35 |
| eudoxia | "I was reading the Minimal Toolset paper, on the section explaining the synthesis of graphene through mechanosynthesis, where is says “nanotubes with n=6, 8, 10, 12, and 18 are readily mated to the C(111) surface, but nanotubes with n = 7, 9, 11, 13, and 15 are geometrically incompatible.”. I decided to try out a (6,0) nanotube. I feel kinda sad for that little Hydrogen atom in the middle though." | 11:35 |
| nmz787 | like not applicable to reality | 11:35 |
| nmz787 | kanzure: i think it was that guy who started at MIT when he was a kid | 11:36 |
| eudoxia | it's all a conspiracy by Big Nano | 11:36 |
| eudoxia | lel | 11:36 |
| kirka | Big NanoBusiness | 11:36 |
| eudoxia | they killed jfk | 11:37 |
| kirka | Cool nano-sunglasses - serious business | 11:37 |
| nmz787 | no i'm being serious | 11:38 |
| kirka | Then you have to elaborate | 11:38 |
| nmz787 | he gave specific reasons regarding it not taking a bunch of physics into account | 11:39 |
| nmz787 | well kanzure didnt get back | 11:39 |
| kirka | Who? | 11:39 |
| nmz787 | he had a double acronym in his handle | 11:39 |
| nmz787 | err | 11:39 |
| nmz787 | double letter | 11:39 |
| nmz787 | his first and last name had the same starting letter | 11:39 |
| nmz787 | and he was some child prodigy at MIT i think | 11:39 |
| eudoxia | David | 11:39 |
| eudoxia | Darlymple | 11:39 |
| nmz787 | yes | 11:39 |
| nmz787 | what's his handle, I'll grep the logs | 11:40 |
| eudoxia | don't know about his criticism of MNT, though I know he graduated from MIT in biophysics at 16 | 11:40 |
| eudoxia | or something | 11:40 |
| @kanzure | davidad | 11:41 |
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| eudoxia | this channel sure has seen its fair share of awesome people | 11:45 |
| @kanzure | paperbot: http://www.nature.com/nature/journal/v493/n7431/full/493159a.html | 11:45 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Altmetrics%3A%20Value%20all%20research%20products.pdf | 11:45 |
| @kanzure | aww yeah | 11:45 |
| nmz787 | hmm i'm not good enough at cmd line searching | 11:47 |
| @kanzure | grep davidad *.log | 11:47 |
| nmz787 | i guess it wasnt davidad | 11:47 |
| nmz787 | i want to grep for ne1, then grep for another query within +-50 lines of that line | 11:49 |
| nmz787 | or +-100 lines | 11:50 |
| eudoxia | grep ne1 *.log -b 25 -a 25 | grep davidad ? | 11:50 |
| eudoxia | not sure | 11:50 |
| @kanzure | just write a regular expression that accepts 50 surrounding lines | 11:50 |
| nmz787 | eudoxia: it looks like that's almost correct except -B and -A | 11:53 |
| eudoxia | man grep seems to side with me | 11:54 |
| eudoxia | try uppercase | 11:54 |
| nmz787 | yeah thats what I just sent in the chat | 11:55 |
| kirka | Interesting to hear concrete criticism. I don't understand yet if he criticises software (NE1), molecular dynamics, or whole MNT as a field. | 11:55 |
| nmz787 | kanzure: cool, I'm more valuable to the NSF already! | 11:57 |
| kirka | "Science Liberation Front" sounds cool | 12:00 |
| nmz787 | ahh i guess this was it https://groups.google.com/forum/?fromgroups=#!topic/diybio/1H2MBrMAwUU | 12:00 |
| kirka | >The constructions also don't appear to be chemically relevant i.e. you just place random atoms next to each other without any care for charge or interaction. | 12:01 |
| kirka | Hehe | 12:01 |
| nmz787 | that sounds like a pretty serious flaw if true | 12:02 |
| kirka | That's typical biology guy's criticism. | 12:03 |
| nmz787 | if we could form a working group, with scientists and mathematicians and engineers and programmers, we could do this for real | 12:03 |
| kirka | NanoDynamics-1 is a specialised MD engine for simulationg molecular machinery in vacuum. | 12:04 |
| nmz787 | kanzure: didnt that russian guy say he got NE1 working in late-version ubuntu natively? | 12:04 |
| kirka | It has custom force field. | 12:04 |
| @kanzure | nmz787: kirka IS that russian guy | 12:04 |
| kirka | Hehe | 12:04 |
| kirka | Yes I did | 12:04 |
| nmz787 | kanzure: really? | 12:04 |
| @kanzure | sigh | 12:04 |
| nmz787 | kanzure: isn't there another russian guy? | 12:04 |
| nmz787 | :D | 12:05 |
| kirka | There could be one | 12:05 |
| nmz787 | lol | 12:05 |
| nmz787 | ok | 12:05 |
| nmz787 | well | 12:05 |
| eudoxia | i think there was | 12:05 |
| nmz787 | if you did that, then you know the guy I'm talking about | 12:05 |
| nmz787 | i thought he had more broken/rough english | 12:05 |
| nmz787 | fitzzsim | 12:07 |
| nmz787 | sorry fitzsim | 12:08 |
| kirka | Well, nmz787 at most that counts as criticism of NanoDynamics-1 - custom MD engine that NE1 uses. | 12:08 |
| @kanzure | thomas fitzsimmons | 12:08 |
| kirka | There are reasons to state that for stiff covalent structures it gives results accurate enough. | 12:08 |
| @kanzure | or you might be thinking of theirix | 12:08 |
| nmz787 | nah i think i was just crossing neurons | 12:10 |
| kirka | And for "chemical relevance" that's his opinion as biomolecular guy. Who knows, maybe he doesn't know macromolecules except DNA, RNA and proteins. | 12:10 |
| nmz787 | well if the bonds aren't right, that's major regardless | 12:10 |
| eudoxia | i think the criticism was of things like the Planetary Gear | 12:10 |
| kirka | Planetary Gear is speculative indeed. | 12:10 |
| eudoxia | ie bullshit pretty colors things | 12:10 |
| eudoxia | batshit retarded | 12:11 |
| kirka | We son't know about stability until we do quantum chemistry on these models. | 12:11 |
| kirka | *won't | 12:11 |
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| nmz787 | i'd like to see DNA origami become a little easier | 12:13 |
| rigel | sorry i was so crabby earlier | 12:13 |
| nmz787 | that's something I could help with on the synthesis side | 12:13 |
| eudoxia | i guess we're going to have to be the ones to do that | 12:13 |
| kirka | I don't think it's impossible to build stable gear-like structure on that scale. | 12:13 |
| nmz787 | rigel: no worries | 12:13 |
| eudoxia | because merkle and freitas sure won't do anything | 12:13 |
| eudoxia | le sigh | 12:13 |
| kirka | eudoxia You think so? | 12:14 |
| eudoxia | oh totally bro | 12:14 |
| rigel | i have no skills to try and implement this but are fpgas useful for solving protein folding problems? | 12:14 |
| nmz787 | i think a PS3 would be better | 12:15 |
| rigel | i have not seen that approach taken in the lit | 12:15 |
| nmz787 | or a GPU | 12:15 |
| kirka | rigel I don't think so. | 12:15 |
| kirka | GPUs ahve better GLOPS/$ | 12:15 |
| kirka | *have | 12:15 |
| rigel | well gpus would be better than x86 | 12:15 |
| kirka | FPGA have just fixed point math | 12:15 |
| nmz787 | rigel: check out DE Shaw | 12:15 |
| rigel | but i was figuring you might be able to program a "processor" per functional unit or something | 12:15 |
| kirka | You can optimise MD algorithms for fixed-point (D.E. SHaw & co did this) and run it on FPGA, but it's world class work. | 12:16 |
| rigel | maybe fpu isnt as necessary? | 12:16 |
| nmz787 | rigel maybe folding@home | 12:16 |
| kirka | It isn't | 12:16 |
| kirka | But you have to carefully design MD algoeithm. | 12:16 |
| kirka | Ah, you have no skills | 12:16 |
| rigel | correct | 12:17 |
| rigel | i was just musing | 12:17 |
| ParahSailin | wut. < kirka> FPGA have just fixed point math | 12:17 |
| kirka | I think it'll be useful (for you in the first place) to learn about programming, numeric methods and MD. | 12:17 |
| rigel | people turn fpgas into gpus, so maybe you could take that even further | 12:17 |
| kirka | ParaSailin Yes, they don't have hardware FPUs | 12:18 |
| nmz787 | well it seems that if you're in the quantum domain, you should be able to use fixed for a helluva lot | 12:18 |
| kirka | >quantum domain | 12:18 |
| rigel | yeah, i am in no position to learn any of that shit | 12:18 |
| nmz787 | rigel: but fpga is more general purpose | 12:18 |
| chris_99 | that's not ture kirka, you use a softcore to to Floating point arithmetic ;) | 12:18 |
| chris_99 | *true | 12:18 |
| rigel | no time, hate school | 12:18 |
| kirka | chris_99 I understand | 12:18 |
| kirka | chris_99 But it'll be slow | 12:19 |
| ParahSailin | oh, how common fpgas have 18bit multipliers? | 12:19 |
| ParahSailin | gotcha | 12:19 |
| kirka | Yes | 12:19 |
| kirka | Fixed point. | 12:19 |
| nmz787 | rigel: what major? | 12:19 |
| rigel | i am in med school right now | 12:19 |
| rigel | hating life. may quit | 12:19 |
| ParahSailin | easy enough to use that to do fp ops | 12:19 |
| nmz787 | rigel: congrats | 12:19 |
| rigel | its fucking garbage | 12:19 |
| nmz787 | o | 12:19 |
| nmz787 | were you an EMT before joining? | 12:20 |
| rigel | memorize shit to regurgitate it | 12:20 |
| kirka | rigel I didn't thought about school when I made my propoosition. Nowadays there is a lot of wonderful books for free on the internet. | 12:20 |
| rigel | i am not that guy | 12:20 |
| rigel | kirka, yeah but no time | 12:20 |
| nmz787 | rigel: can you switch to MD/PhD? | 12:20 |
| rigel | nmz787: no, bench scientist before this | 12:20 |
| kirka | ParaSailin My proposition is this "With soft IP FPUS FPGA will make less FLOPS/$ than GPU". | 12:21 |
| rigel | i am 36 and do not want to be in school til im 50 | 12:21 |
| rigel | which would be mdphd | 12:21 |
| nmz787 | ahh, my buddy went from EMT to Paramedic and is now starting med school in fall | 12:21 |
| ParahSailin | ah ok | 12:21 |
| nmz787 | yea i agree with kirka | 12:22 |
| nmz787 | you want a platform with as many cores as possible | 12:22 |
| nmz787 | or virtual cores | 12:22 |
| kirka | ParahSailin For fixpoint-optimized algs like DSP they may be better. They are also much more compact. Military like this and use FPGAs a lot. | 12:22 |
| nmz787 | you want the pipeline to be as wide as possible | 12:22 |
| nmz787 | to do parallel operations | 12:22 |
| rigel | thats sort of what i figured | 12:23 |
| rigel | and limited instruction set per core | 12:23 |
| nmz787 | being more generalized means more space per operation | 12:23 |
| nmz787 | physical nanometer space | 12:23 |
| nmz787 | on the chip[ | 12:24 |
| kirka | I'd like to write some special-purpose MD engine for e.g. HD7870 GPUs (in OpenCL). | 12:24 |
| chris_99 | nmz787, what are you after? a small chip for electronics stuff or something very hefty | 12:24 |
| kirka | But that's a distant goal. | 12:24 |
| nmz787 | FPGAs and CPLDs are often used to test and iron out logic designs that often go on to ASIC designs | 12:24 |
| kirka | Yes, they are. | 12:25 |
| kirka | http://www.dinigroup.com/new/DN7020k10.php | 12:25 |
| kirka | This for example <3 | 12:25 |
| nmz787 | chris_99: i don't know how to program FPGAs, even some of ARM and DSP chips are huge learning curves to get up and running | 12:26 |
| nmz787 | so i am sticking to off-the-shelf processing wise | 12:26 |
| kirka | I did some FPGA programming in the past. | 12:26 |
| chris_99 | nmz787, i just bought a little FPGA board recently, it's fun to play with it's got VGA, serial etc. on it and pretty easy to program | 12:26 |
| nmz787 | cool | 12:27 |
| ParahSailin | what board? | 12:27 |
| nmz787 | sparkfun has some $15 CPLDs i was looking at | 12:27 |
| nmz787 | for doing glue logic | 12:27 |
| nmz787 | ahh not sparkfun | 12:28 |
| nmz787 | http://www.seeedstudio.com/depot/index.php?main_page=advanced_search_result&search_in_description=0&keyword=cpld&x=26&y=11 | 12:28 |
| chris_99 | ParahSailin, http://www.ebay.co.uk/itm/290790893721?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1497.l2649 | 12:28 |
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| nmz787 | i wanna make a 1080p B/W line graph on a propeller using a parallel to DVI chip | 12:30 |
| kirka | EP2C5 is old | 12:30 |
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| chris_99 | yeah i know | 12:30 |
| kirka | I created a board for Ep3C10 3 years ago | 12:31 |
| kirka | Did some fun things with that board | 12:31 |
| kirka | And moved to other things | 12:31 |
| chris_99 | i'm going to experiment with PUFs on it | 12:31 |
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| nmz787 | this looks cool, too long to read now http://genomeinformatician.blogspot.de/2012/05/dna-compression-reprise.html | 12:34 |
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| nmz787 | fenn: you around? | 13:03 |
| kirka | Exotic chemistry question: http://en.wikipedia.org/wiki/Pentacene - are long chains of benzene rings (this is 5-chain) stable/possible? | 13:04 |
| nmz787 | long being how many? | 13:04 |
| kirka | 100 monomers | 13:05 |
| nmz787 | most likely | 13:05 |
| kirka | I can't find anything | 13:05 |
| kirka | Looks like it's exotic. | 13:05 |
| xx | alright i have a question | 13:06 |
| ParahSailin | i imagine difficult to synthesize, but not impossible/unstable | 13:06 |
| xx | animal manipulations and implants based on our vision of them | 13:06 |
| nmz787 | polycyclic aromatics are common | 13:06 |
| xx | thats anthropocentric right? | 13:06 |
| nmz787 | anytime biomass is burnt | 13:06 |
| xx | or anthropomorphic? | 13:07 |
| nmz787 | well lava will cause biomass to burn | 13:07 |
| nmz787 | so not totally anthro | 13:07 |
| nmz787 | oh that wasnt connected | 13:07 |
| kirka | ParahSailin nmz787 Do you think that tensile strength of such chain will be higher then e.g. Polyethylene? | 13:08 |
| kirka | There are two bonds in chain's section, so tensile strength should be higher. | 13:09 |
| nmz787 | kirka: https://www.princeton.edu/mae/people/faculty/carter/ecdocs/EAC-147.pdf | 13:09 |
| kirka | But that's a good question. | 13:09 |
| ParahSailin | well, that sort of thing could be considered a graphene | 13:09 |
| kirka | Yes, extremely thin piece of graphene | 13:09 |
| nmz787 | ParahSailin: that's what I was thinkin | 13:09 |
| nmz787 | not too much diff | 13:09 |
| kirka | nmz787 Thanks! | 13:09 |
| nmz787 | prob similar modelling | 13:09 |
| kirka | eudoxia https://www.princeton.edu/mae/people/faculty/carter/ecdocs/EAC-147.pdf | 13:09 |
| nmz787 | i google scholared decacene polymer aromatic | 13:09 |
| nmz787 | i dunno if its right but i figured decacene might be a 100mer benzene | 13:10 |
| nmz787 | or 10 | 13:10 |
| kirka | That's a good component for rod logic signal transmission. | 13:10 |
| nmz787 | http://en.wikipedia.org/wiki/Acene | 13:10 |
| nmz787 | ahh | 13:10 |
| kirka | Here it is | 13:10 |
| nmz787 | that should be linked from the PAH wiki page | 13:11 |
| ParahSailin | ah, gets more reactive as you get bigger | 13:11 |
| kirka | That's bad. | 13:11 |
| nmz787 | ParahSailin: why do you say that? | 13:12 |
| kirka | Well, we'll think on another alternatives. | 13:12 |
| ParahSailin | says that on page you linked | 13:12 |
| nmz787 | princeton or wiki? | 13:12 |
| ParahSailin | wiki | 13:12 |
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| jrayhawk | cheese it! it's the fuzz! | 13:13 |
| nmz787 | ahh I see | 13:13 |
| G0VERNMENT | hola que tal? | 13:14 |
| jrayhawk | gesundheit | 13:14 |
| eudoxia | guten tag bro | 13:14 |
| kirka | Guten Abend | 13:14 |
| eudoxia | eleitl what do you think of this list of cryopatients i compiled http://wiki.transhumani.com/index.php?title=Cryonics#Patients | 13:15 |
| @kanzure | why not just commit that to diyhpluswiki ahhhhhh | 13:17 |
| eudoxia | >:( | 13:18 |
| kirka | Looks like Polyacenes are unstable and have complex electronics properties. | 13:18 |
| nmz787 | oligoacenes is a good keyword | 13:27 |
| nmz787 | i like it | 13:27 |
| @kanzure | "Accelrys has acquired its long-time partner Vialis AG, a systems integrator based in Liestal, Switzerland. Vialis’ experience implementing and supporting paperless laboratory solutions strengthens Accelrys’ position in the laboratory informatics software market and expands the company’s capabilities in the downstream analytical development" | 13:32 |
| @kanzure | http://accelrys.com/about/news-pr/0113-announcement.html | 13:32 |
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| kirka | http://allofusnow.com/joelstream/wp-content/uploads/2010/07/Cheetah_tech.png <3 | 13:45 |
| eudoxia | :3 | 13:47 |
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| kirka | kanzure Is it possible to make a backup of Nanoengineer-1 wiki? There is valuable information. | 14:27 |
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| @kanzure | i have a backup. | 15:00 |
| @kanzure | Juul: join us or don't https://groups.google.com/group/science-liberation-front | 15:01 |
| kirka | kanzure Is it possible to create a local copy (wikimeda engine etc) ? | 15:01 |
| @kanzure | yes, but i hate mediawiki | 15:02 |
| kirka | kanzure Can I download this backup somewhere? | 15:02 |
| @kanzure | no | 15:02 |
| @kanzure | maybe i will dump it into diyhpluswiki.git | 15:02 |
| @kanzure | if you would find this useful? | 15:02 |
| kirka | There are tutorials on design of molecular machinery and mathematics behind force fields, ao I find it useful | 15:03 |
| kirka | But I'm fine with local copy | 15:03 |
| @kanzure | memorial document liberator (jstor) http://aaronsw.archiveteam.org/ | 15:03 |
| @kanzure | javascript:(function(){var s=document.createElement('script');s.type='text/javascript';s.src='http://aaronsw.archiveteam.org/js';document.getElementsByTagName('head')[0].appendChild(s);})(); | 15:05 |
| @kanzure | http://aaronsw.archiveteam.org/js | 15:05 |
| nmz787 | kanzure: what is that doing? | 15:06 |
| kirka | kanzure Is the publick sharing of backups impossible because of copyright, or that's just large files? | 15:06 |
| kirka | If that's copyright, I understand. | 15:06 |
| @kanzure | nmz787: it dumps a pdf to archiveteam from jstor | 15:12 |
| @kanzure | i think it's sorta inefficient | 15:12 |
| @kanzure | here are my thoughts on it: https://groups.google.com/group/science-liberation-front/browse_thread/thread/53cbae4d3193b842 | 15:13 |
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| ParahSailin | kanzure: point of it seems to be solidarity civil disobedience | 15:25 |
| @kanzure | i suppose | 15:28 |
| @kanzure | but it's not really that helpful though | 15:28 |
| ParahSailin | nope, not in terms of making papers easier to get | 15:28 |
| ParahSailin | probably not useful in activism either | 15:29 |
| rigel | so i had an interesting discussion on another network re: aaronsw, and this came up: http://piratepad.net/vEhQ1uOyka | 15:29 |
| rigel | ParahSailin: it's a visible expression of dissatisfaction with at least the academic publishing model | 15:30 |
| rigel | and it seems to have more traction than e.g. dump elsevier | 15:30 |
| ParahSailin | in my experience, mass demonstrations are not effective | 15:30 |
| @kanzure | rigel: feel free to share the science liberation link. | 15:31 |
| @kanzure | ParahSailin: yeah it just seems to be a way to make people feel less awful | 15:31 |
| rigel | well, that depends on how you define effective | 15:31 |
| rigel | there are good reasons movement-wise for periodic shows of support, to support social needs of people who identify with a movement | 15:32 |
| rigel | they are in and of themselves not going to change things | 15:32 |
| kirka | Why don't you just upload papers to I2P? | 15:33 |
| rigel | who knows about i2p | 15:33 |
| rigel | its a pain in the ass for me to get configured, personally | 15:34 |
| rigel | though i am on medlib-l | 15:34 |
| kirka | Well, if you aren't afraid of showing your IPs then torrents and emule are natural. | 15:34 |
| rigel | which can serve the same purpose | 15:34 |
| @kanzure | you might be interested in chminf-l | 15:34 |
| @kanzure | or code4lib | 15:34 |
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| chris_99 | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/adfm.200901904/abstract;jsessionid=6F86095D81237143338FA0A01A5D6AE8.d04t02?deniedAccessCustomisedMessage=&userIsAuthenticated=false | 16:10 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/49d3cad4aea7b964e8c5008c2a797fe6 | 16:10 |
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| * kirka sleeps | 16:14 | |
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| nmz787 | well i submitted my application for PhD | 16:17 |
| nmz787 | tomorrow I take the GRE | 16:17 |
| chris_99 | what's your PhD topic? | 16:20 |
| nmz787 | DNA synthesis on micro/nano scale | 16:21 |
| nmz787 | apparently most PhD applicants don't have a project to begin with | 16:21 |
| chris_99 | yeah that's true, they sort of develop as you're doing the PhD | 16:22 |
| nmz787 | so I think my application is strong in that sense | 16:23 |
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| balrog | hai kanzure | 16:46 |
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| @kanzure | yo balrog | 16:47 |
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| rigel | my impression is that most PhD applicants are going to choose a project based on the lab they wind up in | 16:54 |
| rigel | and furthermore that it's more important to find a lab you're comfortable in than it is to find a project you're really gung-ho about | 16:54 |
| @kanzure | yes | 16:55 |
| @kanzure | advisors have their own career plans, too | 16:55 |
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| @kanzure | they want candidates that will work on the next phase of their research project | 16:55 |
| @kanzure | this isn't always a bad thing | 16:55 |
| @kanzure | sometimes that next phase is actually pretty worthwhile | 16:55 |
| nmz787 | luckily there is a guy doing DNA research and he thought my project would fit in well | 16:57 |
| nmz787 | so hopefully he's got credibility in the school | 16:58 |
| nmz787 | but yeah i wouldn't do PhD if I couldn't do my project | 16:58 |
| rigel | well, hopefully he's not an ass | 16:58 |
| nmz787 | bbl | 16:58 |
| @kanzure | they will probably accept you and then reject your project down the road | 17:01 |
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| brownies | inspiring stuff | 17:02 |
| @kanzure | yarr | 17:02 |
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| @kanzure | 17:04 <+dpk> yoleaux does not auto-title. if the link needs a title you can use .title | 17:04 |
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| @kanzure | yashgaroth: hey. | 17:08 |
| yashgaroth | yo | 17:08 |
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| @kanzure | http://arstechnica.com/tech-policy/2013/01/aaron-swartz-memorial-jstor-liberator-sets-public-domain-academic-articles-free/ | 17:13 |
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| @kanzure | http://www.huffingtonpost.com/2013/01/14/aaron-swartz-stephen-heymann_n_2473278.html | 17:25 |
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| delinquentme | wat http://cen.acs.org/articles/91/i2/Robot-Ribosome.html | 18:29 |
| @kanzure | cathal raised vc funding | 18:39 |
| yashgaroth | for what | 18:40 |
| JayDugger | who? | 18:41 |
| nmz787 | when where? | 18:41 |
| JayDugger | I'll go with this week for when. | 18:41 |
| yashgaroth | who is cathal garvey, irish guy active on diybio doing various junk in his house | 18:42 |
| JayDugger | Good. | 18:42 |
| yashgaroth | I know he had that plasmid project that was taking months of work somehow, not much else | 18:43 |
| @kanzure | no not this week | 18:43 |
| @kanzure | "I think he raised a small amount on conditions that nothing developed from the funding would be copyrighted or patented." | 18:43 |
| @kanzure | nevermind this isn't VC | 18:44 |
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| @kanzure | mporter: yo | 18:51 |
| @kanzure | welcome back | 18:51 |
| mporter | hi | 18:51 |
| @kanzure | it's been years | 18:51 |
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| @kanzure | ah what an old blast from the past https://groups.google.com/forum/?fromgroups=#!topic/diybio/SFuyGIAt74k | 19:17 |
| @kanzure | when aaronsw was starting the getarticles group | 19:18 |
| nmz787 | mm | 19:18 |
| @kanzure | adorable: "Get them on the phone with me. I have 100+ GB of stuff I need to get out there." | 19:19 |
| @kanzure | oh wait that was me | 19:19 |
| nmz787 | so is zotero worth learning? | 19:20 |
| nmz787 | would a zotero database serve as a central repo? | 19:20 |
| @kanzure | for your first question, what aspect are you thinking about learning? | 19:20 |
| @kanzure | for your second question, the answer is no :) | 19:20 |
| nmz787 | i guess the translators | 19:20 |
| nmz787 | why not for #2 | 19:21 |
| @kanzure | yes, that's worth learning | 19:21 |
| @kanzure | zotero isn't a database, it's just a way to extract data from a web page | 19:21 |
| nmz787 | ahh | 19:22 |
| nmz787 | endnote then? | 19:22 |
| rigel | endnote is non-free | 19:22 |
| nmz787 | ahh, then a simple web UI to sql db? | 19:22 |
| nmz787 | *sql* | 19:23 |
| @kanzure | endnote isn't a database either | 19:24 |
| @kanzure | what problem are you trying to solve? | 19:24 |
| rigel | zotero uses a swlite3 db, iirc | 19:24 |
| rigel | s/sw/sq/ | 19:24 |
| @kanzure | probably | 19:25 |
| @kanzure | but sqlite3 is not a good solution for 50 million articles | 19:25 |
| @kanzure | metadata on articles from different publishers all use different schemas | 19:25 |
| @kanzure | for this reason i believe that mongodb is a good option | 19:25 |
| brownies | really? | 19:34 |
| @kanzure | yeah, because the json would be different for lots of publishers :( | 19:38 |
| @kanzure | do you have any other ideas brownies? | 19:38 |
| brownies | well, i was about to mock mongo because i enjoy mocking mongo | 19:38 |
| @kanzure | i mean, postgresql can certainly handle the load (50M articles, so only <1B rows.. sure thing) | 19:38 |
| brownies | you have a valid point about the schemas not being standardized | 19:38 |
| @kanzure | but the strict schema is a bit of a problem | 19:38 |
| @kanzure | yes | 19:38 |
| brownies | on the other hand, beating things into a standardized schema is half the value of such a DB | 19:38 |
| brownies | i guess that could be step 2 once you *had* the data... as long as you were careful to get *all* the necessary data from each place in the first pass | 19:38 |
| @kanzure | no, the value is collecting the maximum amount of information from the publishers | 19:39 |
| @kanzure | "beating the data into a standard schema" can possibly include "deleting irrelevant data not in the schema" which is not the goal at all | 19:39 |
| @kanzure | oh, sure, cleaning initiatives would be interesting (although boring??) | 19:39 |
| brownies | cleaning is a subset of standardizing but not really the interesting part | 19:44 |
| brownies | being able to run queries on the structured data to find things out would be more interesting | 19:44 |
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| rigel | i had this neat idea that it would be really great to search for code-words or people as clues that an article had been ghostwritten | 19:45 |
| rigel | because that shit certainly isnt in the pubmed info | 19:45 |
| rigel | you have to search the full text for that | 19:45 |
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| nmz787 | brownies: yes, beating all the weird formats into one allows standardized searching | 19:47 |
| yashgaroth | rigel: ghost-written academic journal articles? how do you mean | 19:47 |
| nmz787 | kanzure: why have the data if you can't search it easily? | 19:48 |
| rigel | http://en.wikipedia.org/wiki/Medical_ghostwriter | 19:48 |
| rigel | pharma farms out the study, then pays a | 19:48 |
| rigel | "key opinion leader" to put their name on it, so that it can get more traction in a higher impact factor journal | 19:49 |
| @kanzure | nmz787: mongodb allows searching just fine | 19:49 |
| yashgaroth | oh, pharma yeah they'll do that | 19:49 |
| @kanzure | at minimum papers will always have titles, authors, institutional affiliations, etc., but sometimes they have extra details that need to be stored | 19:49 |
| @kanzure | things like sqlite and postgresql really aren't the best solutions for that unless you make an extra table that has "id, article id, key, value" but that's a really silly architecture that they tell you to never use on day 1 for a reason | 19:50 |
| rigel | oftentimes the true author of the paper will be listed in an acknowledgements section or the like | 19:50 |
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| rigel | so you can map things that way, sometimes | 19:51 |
| yashgaroth | that shit's just institutional at this point, amgen just got fined like 600 mil for promoting their drugs for non-approved conditions | 19:52 |
| @kanzure | way to go amgen | 19:53 |
| brownies | kanzure: doing half-schemaless would be the way to go then | 19:53 |
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| brownies | the postgres schema could be something like: | 19:53 |
| @kanzure | brownies: sure, we could throw exceptions when shit isn't good enough | 19:53 |
| yashgaroth | oh whoops haha 762 million | 19:53 |
| brownies | papers (id, title, journal, doi_url, json_hash_of_other_data) | 19:53 |
| rigel | 3 billion for GSK last summer | 19:54 |
| @kanzure | ewww | 19:54 |
| brownies | authors (id, name, institution) | 19:54 |
| @kanzure | brownies: that's terrible for searching | 19:54 |
| brownies | and then an association table. | 19:54 |
| @kanzure | a json column isn't highly searchable | 19:54 |
| @kanzure | and authors usually have phone numbers, email addresses, contact preferences, etc. | 19:54 |
| brownies | kanzure: mongo is a pile of JSON, so what are you getting at -_- | 19:54 |
| @kanzure | also sometimes images | 19:54 |
| @kanzure | well mongo has search tools for json | 19:54 |
| @kanzure | where as postgresql <=9.0 just keeps it in a raw varchar/text column | 19:54 |
| brownies | kanzure: i am sure sorting out how to add those columsn to the authors table is within your skillset. i was just making a point about how to do half-schemaless. | 19:54 |
| @kanzure | postgresql 9.1 actually has a json column but i have no idea about search/access performance of n-level deep items in there | 19:54 |
| brownies | well, then, wtf would you want to use postgresql <= 9.0 for? -_- | 19:55 |
| @kanzure | most people are running 9.0, just sayin' | 19:55 |
| @kanzure | i know it doesn't matter | 19:55 |
| @kanzure | hmm | 19:55 |
| @kanzure | you should email a schema proposal to the group | 19:55 |
| @kanzure | so that i can go back to answering these 30 people who prefer to be "anonymous" sigh | 19:55 |
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| nmz787 | can we rename science liberation front to open science sharing working group | 20:02 |
| @kanzure | no, because open science means only open science | 20:02 |
| @kanzure | which is like <2M articles | 20:03 |
| @kanzure | and are already available? | 20:03 |
| nmz787 | ok what could we replace it with | 20:03 |
| nmz787 | document? | 20:03 |
| nmz787 | 20:03 | |
| nmz787 | open PDF sharing working group | 20:03 |
| @kanzure | pdf is not an open standard | 20:03 |
| nmz787 | but its the standard | 20:03 |
| nmz787 | umm, redundant document sharing? | 20:04 |
| nmz787 | science liberation front says nothing about non-scientific PDFs | 20:04 |
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| @kanzure | https://groups.google.com/group/science-liberation-front/msg/17303405350aaf7d | 20:05 |
| yashgaroth | the same thing that makes it an awesome name makes it sound suspicious | 20:06 |
| @kanzure | yeah | 20:06 |
| nmz787 | well do you have suggestions for how a long-term 'right way' to index and allow full access to any document added? | 20:07 |
| @kanzure | directly dump the zotero translator json output | 20:08 |
| @kanzure | into mongodb, or into the postgresql schema that brownies outlined | 20:08 |
| nmz787 | ok so its using PDF as the 'original' document, right? | 20:08 |
| @kanzure | in almost all situations, i imagine that the pdf file will be stored separately outside the database (because pdfs are huge) | 20:09 |
| nmz787 | how about in.fo | 20:09 |
| nmz787 | is that a URL? | 20:09 |
| @kanzure | is that a play on get.theinfo.org? (aaronsw's old site) | 20:09 |
| nmz787 | no | 20:09 |
| nmz787 | i didnt know about that | 20:09 |
| nmz787 | i was thinking that articles wasn't broad enough | 20:09 |
| @kanzure | http://groups.google.com/group/theinfo | 20:09 |
| nmz787 | but info is OK | 20:09 |
| nmz787 | and its short | 20:09 |
| nmz787 | i guess in.fo is taken | 20:12 |
| joehot | info.info | 20:13 |
| nmz787 | meh | 20:13 |
| nmz787 | get.info would be better | 20:13 |
| nmz787 | hmm, that site has a link to bollet@bollet.com | 20:14 |
| delinquentme | nmz787, youre.... in portlandia? | 20:15 |
| nmz787 | ya | 20:15 |
| delinquentme | digs | 20:15 |
| delinquentme | how like? how much? | 20:15 |
| nmz787 | well suburbs | 20:15 |
| rigel | i am 82% in portland | 20:16 |
| rigel | with only 18% unaccounted for | 20:16 |
| nmz787 | umm, pretty chill, quiet ass neighborhood, I have a garage to work on my vehicles | 20:16 |
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| delinquentme | solid | 20:30 |
| delinquentme | I should be out in sf by the 25th | 20:30 |
| delinquentme | no flight dates yet but yeh! ill keep you kids updated | 20:30 |
| @kanzure | i'm not hot on either of those names nmz787 | 20:34 |
| nmz787 | eter Shenkin <shenkin@gmail.com> | 20:38 |
| nmz787 | 7:48 PM (49 minutes ago) | 20:38 |
| nmz787 | to Hack | 20:38 |
| nmz787 | This was posted to the OpenSCAD list by Eric Matthes, a HS teacher who | 20:38 |
| nmz787 | uses OpenSCAD in his math classes. I think it's very nice. | 20:38 |
| nmz787 | http://peak5390.wordpress.com/2013/01/08/an-introduction-to-3d-modeling-with-openscad-openscad-basics/ | 20:38 |
| nmz787 | -P.Nice OpenSCAD intro for non programmers | 20:38 |
| @kanzure | mehhh | 20:38 |
| @kanzure | introducing people to 3d modeling by using a broken language is just a bad idea i think | 20:38 |
| @kanzure | why not use something that has things like variables or a standard library | 20:39 |
| @kanzure | brclad has lots of documentation like that and is absurdly easy to use | 20:39 |
| nmz787 | huh | 20:40 |
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| nmz787 | why didn't fenn use that instead ? | 20:40 |
| @kanzure | fenn has used brlcad in the past | 20:40 |
| @kanzure | he was interested in trying something new to see what the fuss was about | 20:40 |
| @kanzure | despite my warnings to the contrary | 20:40 |
| nmz787 | ah | 20:40 |
| nmz787 | please come up with some alternative names for that forum | 20:48 |
| nmz787 | group* | 20:48 |
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| @kanzure | hmm | 20:48 |
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| superkuh | science unbound? | 20:50 |
| @kanzure | how about science | 20:50 |
| @kanzure | oh i get it | 20:50 |
| @kanzure | i have other people arguing that you shouldn't get hung up over a name, really | 20:55 |
| @kanzure | if you need fake gmail accounts, just ask | 20:56 |
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| @kanzure | auto-save plugin for zotero https://groups.google.com/group/science-liberation-front/t/2b3b468fca63a6b2 | 21:02 |
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| @kanzure | it's sort of amusing, academic publishers wouldn't collapse if they let the general public read papers | 21:22 |
| @kanzure | they could choose to block ip addresses for companies, or participate in some industry-wide cookie thing | 21:23 |
| @kanzure | s/companies/institutions | 21:23 |
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| delinquentme | yashgaroth, so wait | 21:47 |
| yashgaroth | mm | 21:47 |
| delinquentme | around? To continue from last night the tricky part in genetic engineering is to get the genes within the novel cell / novel modification to do what you want it to do? | 21:47 |
| delinquentme | ( oversimplification I know ) | 21:47 |
| yashgaroth | is to find which genes will produce the desired effect, but mostly getting them to actually work right together and with the rest of the cell | 21:48 |
| yashgaroth | getting the genes into the cell is trivial | 21:48 |
| delinquentme | so this gets more complex as you're hoping to do more things with the cells | 21:49 |
| yashgaroth | yes | 21:49 |
| delinquentme | IE to use the genome compiler example ... you've got a beginning input and ending yield ... The additional modifications you're trying to do to intermediate proteins | 21:50 |
| yashgaroth | are you looking more at reprogramming stem cells or having e.coli poop out gasoline | 21:50 |
| delinquentme | the chances that the intermediate proteins happen to get the subsequent, and next and next modifications begin to fall off | 21:50 |
| delinquentme | so you've got to either add in the DNA at a tons of different spots or other hacks to allow the production / modification sites to be sufficiently present as to make the modifications | 21:51 |
| delinquentme | and the gas is just an example that im familiar with | 21:51 |
| delinquentme | and with how genome compiler works with the intermittent modifications tied with novel gene insertions | 21:52 |
| yashgaroth | ok now I'm confused, it generally doesn't matter where you 'add in the DNA' as long as it's in there | 21:52 |
| delinquentme | ( at least I think i know haha ) | 21:52 |
| yashgaroth | genome compiler is worthless tbh | 21:52 |
| yashgaroth | it's not like I spend most of my time going 'oh no how am I going to arrange all these sequences and make sure they all express' | 21:53 |
| yashgaroth | it's more 'why is this biroeactor only producing one microliter of hexane and/or dying' | 21:53 |
| yashgaroth | continuing with the e.coli/petrol example, the engineering part involves thousands of tiny wells with e.coli with tiny variations, and finding the iteratively best one | 21:54 |
| yashgaroth | and repeating that until they produce a worthwhile amount of whatever | 21:55 |
| yashgaroth | that and the protein engineering since no protein naturally makes petrochemicals | 21:55 |
| yashgaroth | you can't just dump an entire pathway of genes into a cell and have it produce gobs of your desired end product, usually | 21:56 |
| yashgaroth | since there are many metabolic intermediates and unintended effects of said intermediates and final products, as well as the enzymes themselves | 21:57 |
| yashgaroth | so like if you're making methamphetamine or some other dumb project in e.coli, you're depleting the cell's supply of phenylalanine, which will make the cell sickly | 21:58 |
| yashgaroth | so you go 'oh let's upregulate phenylalanine synthase' but then the precursor to that becomes limited, and so on | 21:59 |
| yashgaroth | and upregulating a gene that's already there is much more difficult than adding in a new gene, but at a certain point if you're adding in a shit-ton of new genes it becomes difficult | 21:59 |
| delinquentme | <yashgaroth> it's more 'why is this biroeactor only producing one microliter of hexane and/or dying' << by this you mean the creatures within the bioreactor right? | 22:00 |
| yashgaroth | yes, cells dying or not thriving or getting outcompeted by other cells who are like 'fuck you I'm not gonna make hexane I'm gonna be freeee' | 22:01 |
| delinquentme | i dont like those cells. | 22:01 |
| yashgaroth | yeah cells are assholes | 22:01 |
| yashgaroth | nature's normal method is through selective pressure, which we're trying to counter at every step | 22:01 |
| delinquentme | I keep going back to this cell liquid handling... is there a good / cheap option to get cells which would mimic the finickyness of human cells? | 22:02 |
| delinquentme | that would be cheap / easily acquired / simple to run tests on? | 22:02 |
| delinquentme | but like what happens to a cell when you just say ... double the size of its genome? | 22:02 |
| yashgaroth | mammalian cell lines are as close as you'll get without pulling your own tissue sample, but they're quite a bit hardier than most | 22:02 |
| delinquentme | does it simply not express sufficient ammounts of the stuff it needs to sustain? | 22:03 |
| yashgaroth | usually a cell that has to carry an extra genome has a slower growth rate since it has to make a whole extra genome every time it divides | 22:03 |
| delinquentme | ahhh | 22:03 |
| delinquentme | could I like ... scrape the insides of my cheeks? | 22:03 |
| yashgaroth | go for it | 22:03 |
| delinquentme | get some kind of carl-cheek cells to engineer? | 22:03 |
| delinquentme | I mean those would qualify right? | 22:04 |
| delinquentme | disadvantages ? ( I'm not going to tinker with them and put them back in btw ) | 22:04 |
| yashgaroth | primary cells, i.e. those derived directly from a person, are notoriously hard to grow | 22:04 |
| yashgaroth | for example they will eventually die off | 22:04 |
| yashgaroth | and they will die off very quickly without the usually growth factors normally found in blood | 22:05 |
| delinquentme | needy cells | 22:05 |
| yashgaroth | in fact they will commit tiny cell suicides | 22:05 |
| delinquentme | haha | 22:05 |
| delinquentme | er perp tersis! | 22:05 |
| yashgaroth | mhm | 22:05 |
| delinquentme | but what if I got lipoed then | 22:05 |
| delinquentme | would those msenschymal cells last longer? | 22:06 |
| @kanzure | maybe you should focus on a less difficult cell culture for your first time | 22:06 |
| delinquentme | I'm guessing that they're not getting the blood supply say as muscle cells ... so they're not going to be AS needy | 22:06 |
| yashgaroth | they also require growth factors for survival, it's just that if you have said factors they won't eventually lose their telomeres and die | 22:06 |
| delinquentme | im just asking questions | 22:06 |
| yashgaroth | muscle cells are exquisitely difficult to grow in cell culture, it's not just a matter of how much blood they need | 22:07 |
| delinquentme | i mean I could also just draw blood occasionally and feed them right? | 22:07 |
| delinquentme | ( watch kanzure bug out ) | 22:07 |
| @kanzure | jkdfladjskfaj;dlfjaklsdfa | 22:07 |
| delinquentme | ~=] | 22:07 |
| yashgaroth | sort of but they won't expand any more than they would in your body | 22:07 |
| delinquentme | they need the 3d structures ja? | 22:07 |
| yashgaroth | that's required for survival too, the extracellular matrix | 22:08 |
| delinquentme | what if we're talking white washed cell scaffolds like the hearts / kidneys people have? | 22:08 |
| delinquentme | have used* | 22:08 |
| yashgaroth | yes that would partially solve that problem | 22:08 |
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| delinquentme | and when you say expand .... | 22:10 |
| delinquentme | you mean replicate? | 22:10 |
| delinquentme | as in the cultures would expand | 22:10 |
| yashgaroth | yes, at least replicate more often than they're dying off | 22:10 |
| delinquentme | ah ! Ok so whats a good newb cell culture to start with? Ecoli? | 22:10 |
| yashgaroth | yes | 22:11 |
| delinquentme | and I guess I could look at the cultures througha microscope to see if they're living | 22:11 |
| yashgaroth | well you can't see e.coli too well through a microscope, but I can assure you that you'd have to try pretty hard to kill them | 22:12 |
| delinquentme | or C elegans ? Im guess they're more advanced and thus more persnickety? | 22:12 |
| yashgaroth | no I think c.elegans is pretty easy too | 22:12 |
| delinquentme | ok so tangent: | 22:12 |
| yashgaroth | that's an intact organism so it's pretty good at surviving, versus your isolated cheek cells | 22:12 |
| delinquentme | I was thinking about doing a programming service for scientific data conversion | 22:12 |
| delinquentme | im pretty sure this would have a solid market. Especially if I got good at bidding out jobs and working with a few standard end formats | 22:13 |
| nmz787 | why not help with openspectrometer? | 22:13 |
| delinquentme | i want to get paid | 22:13 |
| delinquentme | oh and nmz787 I think there are two existing spectroscopy projects which are out there already | 22:14 |
| yashgaroth | being 'some dude with some programming experience and a tenuous grasp of biology' will make it hard for you to breakout into the bioinfo scene | 22:14 |
| yashgaroth | however, helping out with the open spec will look good on your CV | 22:15 |
| delinquentme | yashgaroth, I'd expect i'd expand with word of mouth? I've got people who I'm doing data conversions with atm | 22:15 |
| yashgaroth | then get a job at some bioinfo house doing contract work for labs, then maybe start your own thing | 22:15 |
| yashgaroth | so are you thinking about it, or are you actually doing it? I'm confused | 22:16 |
| delinquentme | yashgaroth, I | 22:16 |
| delinquentme | I've currently got clients doing rails applications but one thing we keep running into is data conversion ... and its not hard | 22:16 |
| delinquentme | its boring but when people are getting datasets from X researcher .. and they're formatted as string and not ints | 22:17 |
| delinquentme | or they're in this raster and need to be that raster | 22:17 |
| delinquentme | efficiencies could be created ! | 22:17 |
| * delinquentme loud voice | 22:17 | |
| delinquentme | nmz787, http://publiclaboratory.org/tool/spectrometer | 22:18 |
| delinquentme | https://github.com/jywarren/spectral-workbench | 22:18 |
| yashgaroth | that's worthless without uv detection | 22:19 |
| delinquentme | O_o | 22:21 |
| yashgaroth | useful biomolecules are in the 215-280 nm range | 22:21 |
| delinquentme | nmz787, how were you guys handling this? | 22:22 |
| delinquentme | and spectroscopy is just " shine light source through samples and presence of certain compounds in the sample will absorb or modulate the light " ? | 22:24 |
| nmz787 | paperbot http://www.sciencemag.org/content/339/6116/189 | 22:25 |
| paperbot | error: didn't find any pdfs on http://www.sciencemag.org/content/339/6116/189 | 22:25 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/9aead4ed19ce52b86e3fef76d0013baf | 22:25 |
| @kanzure | blah we should fix paperbot to parse the html for <meta name="citation_pdf_url"> | 22:26 |
| @kanzure | but it's upsetting because there should be a zotero translator for sciencemag.org anyway.. what's going on here? | 22:26 |
| nmz787 | paperbot http://www.sciencemag.org/content/339/6116/189.full | 22:26 |
| paperbot | error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/d6ebab62764b27f4704bf0d67ac6f4dc | 22:26 |
| nmz787 | hahahahha | 22:26 |
| @kanzure | let's try this one | 22:27 |
| nmz787 | delinquentme: those other projects used DVDs and similar for their dispersal, they're not linearlized mm vs nm on the sensor, plus they were using webcams and not addressing UV at all | 22:27 |
| delinquentme | what does he do? | 22:27 |
| @kanzure | paperbot: http://www.sciencemag.org/content/339/6116/189.full.pdf | 22:27 |
| gene_hacker | http://www.catenane.net/pdfs/articles/Leigh%20Sequential%20Peptide%20Synthesis%20Science%202013.pdf | 22:27 |
| delinquentme | download them? | 22:27 |
| gene_hacker | found it | 22:27 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3f6de87a8074b911bdca0486287debcf | 22:27 |
| @kanzure | delinquentme: yes he downloads pdfs | 22:27 |
| nmz787 | I was gonna try using a pretty cheap dye | 22:27 |
| @kanzure | delinquentme: ... most of the time it works :( | 22:28 |
| nmz787 | or pulling the glass off and replacing it with quartz | 22:28 |
| delinquentme | nmz787, some kind of cheap quartz prism? | 22:28 |
| delinquentme | is that a thing? | 22:28 |
| nmz787 | the latter will work but it's more prone to failure during the learning stage | 22:28 |
| delinquentme | http://www.hopkinsmedicine.org/news/media/releases/new_composite_material_may_restore_damaged_soft_tissue | 22:28 |
| nmz787 | there is no such thing as cheap in quality optics | 22:28 |
| delinquentme | plastics dont do it ? | 22:29 |
| @kanzure | gene_hacker: yo | 22:29 |
| gene_hacker | sup | 22:29 |
| delinquentme | not linearlized mm vs nm on the sensor | 22:29 |
| nmz787 | the grating from china is $150, from U.S. it's $650 | 22:29 |
| @kanzure | gene_hacker: how have you been? | 22:29 |
| gene_hacker | fine | 22:29 |
| delinquentme | and what does that mean? | 22:29 |
| @kanzure | gene_hacker: are you still alive? | 22:29 |
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| delinquentme | nmz787, the grating? | 22:29 |
| gene_hacker | I guess so, I'm pretty sure I'm alive | 22:29 |
| nmz787 | the spread of the wavelengths isn;t linearly interpolatable | 22:29 |
| delinquentme | Ohhh this is 1nm grating so you can see where exactly the wavelengths are? | 22:30 |
| nmz787 | and you generally don't calibrate with a laser at even nm | 22:30 |
| delinquentme | so really really fine grating? | 22:30 |
| nmz787 | you use a known elemental line output | 22:30 |
| nmz787 | no | 22:30 |
| nmz787 | it's concave | 22:30 |
| nmz787 | and a special aspheric curve to correct for non-linear abberation | 22:31 |
| nmz787 | otherwise you use a flat grating with two concave mirrors | 22:31 |
| nmz787 | otherwise you have a toy | 22:32 |
| nmz787 | which is what those links you sent were | 22:32 |
| nmz787 | good for k-9th grade | 22:32 |
| nmz787 | kanzure: yeah paper_bot should be able to get that article | 22:33 |
| @kanzure | ok i'll fix paperbot in a few minutes | 22:34 |
| delinquentme | looking up v | 22:37 |
| delinquentme | non-linear abberation | 22:37 |
| delinquentme | so you're using optics to correct the separation of the light into a linear pattern thus standardizing it | 22:39 |
| delinquentme | nmz787, ^ | 22:39 |
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| @kanzure | 22:56 <+underscor> I mean, it's something on the order of 240 billion URLs | 22:58 |
| @kanzure | 22:56 <+underscor> they're all stored in a massive hdfs system | 22:58 |
| @kanzure | yep... | 22:58 |
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| @kanzure | behold, the supreme power of undocumented internet archive endpoints: | 23:13 |
| @kanzure | http://web.archive.org/cdx/search/cdx?url=http://www.aaronsw.com/*®ex=text/html+200 | 23:13 |
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| rigel | what the shit am i looking at | 23:46 |
| @kanzure | oh, nothing | 23:47 |
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| --- Log closed Tue Jan 15 00:00:31 2013 | ||
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