| --- Log opened Wed May 22 00:00:34 2013 | ||
| kanzure | ugh http://bamh1.com/2013/05/22/the-renaissance-of-citizen-science-and-the-emergence-diy-bio-start-ups/ | 00:02 |
|---|---|---|
| kanzure | how is it diy if you are venture backed, ryan. | 00:03 |
| nmz787 | paperbot: http://pubs.acs.org/doi/pdf/10.1021/ed074p1055 | 00:12 |
| paperbot | error: HTTP 200 http://diyhpl.us/~bryan/papers2/paperbot/Vanillin%3A%20Synthetic%20Flavoring%20from%20Spent%20Sulfite%20Liquor.txt | 00:12 |
| nmz787 | sci-hub didn't like that link either | 00:13 |
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| kanzure | "Fpv-Uho (fpv-uho.bet) – This offers proxy access through ~20 different university libraries. It worked well on a few papers that I wasn't able to access otherwise. This should be especially useful if you don't normally have VPN access to a library. (If the current proxy doesn't have access to your paper, just click the refresh icon on the right to switch to another proxy.) Again, looks like you'll need a non-US IP." | 00:26 |
| kanzure | so sci-hub is just using 20 schools. | 00:26 |
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| gnusha_ | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=ed22907e Bryan Bishop: diybio in pittsburgh | 00:27 |
| gnusha_ | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=cd4fd2c3 Bryan Bishop: where to find pdfs | 00:27 |
| nmz787 | where could i find someone to take two images and photoshop them into an svg? | 00:49 |
| nmz787 | like for pay | 00:49 |
| nmz787 | i think $10 would be good | 00:49 |
| kanzure | fiverr? | 00:51 |
| DonnchaC | Is that site online? fpv-uho? | 00:52 |
| kanzure | DonnchaC: that's rot13 of sci-hub.org | 00:53 |
| kanzure | http://diyhpl.us/wiki/articles | 00:53 |
| DonnchaC | ah right ;) | 00:57 |
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| nmz787 | paperbot: Jonsson | 02:51 |
| nmz787 | paperbot: http://www.sciencedirect.com/science/article/pii/S0960852411008844?np=y | 02:51 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Enhanced%20resistance%20of%20.pdf | 02:52 |
| nmz787 | paperbot: http://link.springer.com/article/10.1007/s002530051233 | 02:52 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Detoxification%20of%20wood%20hydrolysates%20with%20laccase%20and%20peroxidase%20from%20the%20white-rot%20fungus%20Trametes%20versicolor.pdf | 02:52 |
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| Kliment | How does paperbot work? | 04:19 |
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| kanzure | Kliment: https://github.com/kanzure/paperbot | 09:33 |
| yoleaux | 09:55Z <sbp> kanzure: likely you've seen it already, but: https://github.com/ricardobeat/filr | 09:33 |
| kanzure | how kind of him (too bad he's slow) | 09:34 |
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| brownies | "In Canada 80% of postdocs earn $38,600 or less per year before tax—the average salary of a construction worker." | 13:30 |
| brownies | how glamorous! | 13:30 |
| kanzure | just think of all that awesome cheap science talent | 13:42 |
| kanzure | i should hire a postdoc just to sit around thinking up death rays or something. | 13:42 |
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| kanzure | "The problem with a modern web browser project is it's expensive to operate. All the ones I know of have extensive regression test suites, both correctness and performance, that get run from continuous integration systems in multiple configurations and on multiple platforms. That's not to mention the continuous fuzz testing farms looking for security bugs. I'm most familiar with the Firefox case: according to ... | 15:13 |
| kanzure | ... https://etherpad.mozilla.org/InfraLoadIdeas a full correctness test run across all platforms is about 120 hours of machine time. Adding performance tests raises that to 177 hours. Combined with the pace of development, that means a build+test farm of 3000+ machines (according to http://oduinn.com/blog/2013/03/27/at-mozilla-releaseengineering-release-automation-continuous-integration/ ) and infrastructure load is still a problem. So any ... | 15:13 |
| kanzure | ... serious project picking up Chromium development would need financial resources to at the very least maintain basic test infrastructure." | 15:13 |
| kanzure | https://news.ycombinator.com/item?id=5743024 | 15:13 |
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| xablor | Hey all. | 17:40 |
| xablor | 'bout how many lurkers do we have here? | 17:40 |
| * FooQuuxman lurks | 17:41 | |
| kanzure | xablor: hello | 17:42 |
| xablor | Heya. | 17:42 |
| xablor | Got linked to diyhpl.us on Hacker News, figured I'd drop in. | 17:43 |
| kanzure | that was probably my fault | 17:44 |
| kanzure | i regret everything | 17:44 |
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| xablor | Username matches, anyway? | 17:44 |
| xablor | But yeah, found that the stated ethos matched a lot of what I've been sorta stumbling into, so wth. | 17:45 |
| kanzure | well, see the /topic and such | 17:46 |
| xablor | Yeah, fair enough. Seems to be a fairly healthy group, at least. | 17:50 |
| xablor | Hm. Group? Movement? Temporary loose alignment of likeminded folk? | 17:51 |
| kanzure | uh, irc channel | 17:51 |
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| fenn | definitely a cult | 18:09 |
| kanzure | worst cult ever | 18:10 |
| xablor | "Happy occupant of a DHS watchlist"? | 18:10 |
| kanzure | you'd think so, but actually the FBI denies having records on me. | 18:10 |
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| kanzure | i haven't checked with DHS. | 18:10 |
| xablor | Huh. | 18:11 |
| bkero | kanzure: did you FOIA yourself? | 18:11 |
| xablor | ...are they actually legally bound to tell the truth, there? I am ign'ant of such things. | 18:11 |
| kanzure | bkero: i sent in a FOIA request yes | 18:12 |
| kanzure | xablor: there are some legal obligations, yes. there are some loopholes but they are fairly obscure. | 18:12 |
| xablor | Ah, okay. Thanks. | 18:12 |
| kanzure | like, they don't have a lot of incentive to loophole me on that one. | 18:12 |
| xablor | *nod* | 18:13 |
| xablor | Were there sufficient cause it could be done, but no visible reason to in this case. | 18:13 |
| kanzure | what? | 18:13 |
| kanzure | oh, ok sure. | 18:13 |
| kanzure | this was their response: http://diyhpl.us/~bryan/irc/fbi/foipa/response.html | 18:15 |
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| xablor | Huh. Interesting of itself. | 18:20 |
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| kanzure | wow when did virustotal become a subsidiary of google? https://www.virustotal.com/en/about/ | 18:39 |
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| xablor | Last Sept, apparently? | 18:49 |
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| heath | if dna origami isn't worth the time, then what (outside of some javascript soon)? | 19:01 |
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| kanzure | heath: well i would start here http://diyhpl.us/wiki/declaration | 19:04 |
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| heath | "molecular nanotechnology" | 19:06 |
| heath | http://diyhpl.us/~bryan/papers2/nanotech/ | 19:06 |
| kanzure | heath: https://github.com/kanzure/nanoengineer could use some attention | 19:07 |
| heath | you're running into similar problems there as you you do in dna origami, no? | 19:07 |
| kanzure | the problems are related to ancient poorly written software | 19:07 |
| heath | re:molnano | 19:07 |
| kanzure | and no unit tests | 19:07 |
| heath | that's what dna origami is, molnano | 19:07 |
| kanzure | if you say so | 19:08 |
| fenn | wait, who said DNA origami isn't worth the time? | 19:09 |
| * heath rereads from last night | 19:09 | |
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| fenn | oh. i was talking about transcriptional networks, which is more like playing games with packet storms between routers on a subnet | 19:10 |
| heath | oh, kanzure just seemed to hint he didn't care for winfree | 19:11 |
| heath | and fenn stated | 19:11 |
| heath | [23:53:50] <fenn> i dont like the whole transcriptional logic idea though, it's trying to draw an analogy where there really isnt one | 19:11 |
| heath | and for some reason i had it in my head there was a log from years ago where you guys were discussing this and cast it in a bad light due to how large a single strand had to be to make anything useful, but that might be my imagination | 19:12 |
| fenn | actually most dna origami is made of short strands these days | 19:13 |
| kanzure | fenn wasn't talking about origami. | 19:13 |
| fenn | oh, right. so, i was talking about the address length required to reliably target a specific promoter (i think) | 19:14 |
| fenn | maybe it was a scheme for using pcr primer tricks to do dna synthesis | 19:15 |
| heath | https://www.youtube.com/watch?v=T7A35Je5Y3U | 19:16 |
| heath | the latest video from rothemund, i think | 19:16 |
| kanzure | .title | 19:16 |
| yoleaux | Recent Advances in the Use of DNA as a Building Material - YouTube | 19:16 |
| heath | it's the same ol' stuf up until around the 20min mark | 19:16 |
| kanzure | the stuff about transcription networks is not very related to the "building objects with dna fragments". | 19:16 |
| heath | ~25 | 19:17 |
| kanzure | you can link to different timestamps with #t=whatever | 19:17 |
| kanzure | https://www.youtube.com/watch?v=T7A35Je5Y3U#t=25m | 19:17 |
| heath | http://yanlab.asu.edu/Research.html | 19:18 |
| heath | .t | 19:18 |
| yoleaux | Thu, 23 May 2013 02:18:29 UTC | 19:18 |
| heath | poop | 19:18 |
| heath | http://yanlab.asu.edu/Publication.html is the better link | 19:19 |
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| heath | yoleaux: fetch all the titles of papers linked to, do it. | 19:19 |
| fenn | yay i love dead tree bibliographies | 19:19 |
| fenn | someone remind me why this is still considered acceptable | 19:20 |
| fenn | isnt there a wikipedia bot that automatically links references like this to their DOI? | 19:21 |
| fenn | http://en.wikipedia.org/wiki/User:DOI_bot/Sandbox | 19:21 |
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| heath | .paper "Complex Archimedean Tiling Self-Assembled from DNA Nanostructures" | 19:25 |
| heath | .fetch it! | 19:26 |
| heath | paperbot: http://pubs.acs.org/doi/abs/10.1021/ja4035957 | 19:26 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Complex%20Archimedean%20Tiling%20Self-Assembled%20from%20DNA%20Nanostructures.txt | 19:26 |
| fenn | that would be pretty cool eh | 19:26 |
| * heath likes to think paperbot is jamming away to https://www.youtube.com/watch?v=JIOE_pSTEH4&list=FL_E3LyNEq65lOQPDe0sSJlw and ignoring my requests | 19:27 | |
| fenn | i wonder why it failed. anyway, http://fennetic.net/irc/complex_archimedean_tiling_self-assembled_from_DNA_nanostructures.pdf | 19:29 |
| kanzure | how did you have access? | 19:30 |
| fenn | gnusha | 19:31 |
| kanzure | it would be great if some of you could fix paperbot bugs once in a while. | 19:32 |
| kanzure | or throw out my code | 19:32 |
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| heath | fenn: thanks | 19:36 |
| fenn | that disneyland video is pretty cool | 19:36 |
| fenn | i want a nuclear tunnel borer :( | 19:37 |
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| fenn | what most people don't understand is that EPCOT was for real, and disneyland just sorta took over after walt died | 19:38 |
| kanzure | so apparently this is how i met lion kimbro originally: | 19:40 |
| kanzure | http://web.archive.org/web/20020607133707/http://2dnow.zenzer.net/memberlist.php | 19:40 |
| kanzure | i always thought i met him somewhere else.. my first recorded interaction is 2008-04-17 | 19:40 |
| kanzure | i remember emailing him because of his journals or notebooks | 19:41 |
| kanzure | but not about meeting him in 2002. | 19:41 |
| heath | http://research4.dfci.harvard.edu/shih/SHIH_LAB/Publications.html :: more dead links | 19:44 |
| kanzure | oh and lion seems to work for pokemon these days | 19:45 |
| kanzure | fascinating. | 19:45 |
| fenn | i was just about to ask | 19:45 |
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| fenn | "how to make a complete map of every thought you think" error meta meta stack overloaded | 19:47 |
| heath | .paper http://pubs.acs.org/doi/abs/10.1021/ja310454k | 19:49 |
| heath | .paper http://pubs.rsc.org/en/Content/ArticleLanding/2013/BM/c2bm00154c | 19:49 |
| heath | .paper http://pubs.rsc.org/en/Content/ArticleLanding/2013/CC/C3CC38804B | 19:49 |
| heath | paperbot: http://pubs.acs.org/doi/abs/10.1021/ja310454k | 19:50 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Direct%20and%20Real-Time%20Observation%20of%20Rotary%20Movement%20of%20a%20DNA%20Nanomechanical%20Device.txt | 19:50 |
| kanzure | heath: https://github.com/kanzure/paperbot | 19:53 |
| fenn | hmm. "Example project: neural network computation with DNA" | 19:54 |
| heath | http://onlinelibrary.wiley.com/doi/10.1002/smll.201101212/full | 19:55 |
| heath | .title | 19:55 |
| yoleaux | Surface-Driven DNA Assembly of Binary Cubic 3D Nanocrystal Superlattices - Noh - 2011 - Small - Wiley Online Library | 19:55 |
| heath | http://pubs.rsc.org/en/content/articlelanding/2011/cp/c0cp02815k | 19:56 |
| heath | .title | 19:56 |
| yoleaux | DNA mediated assembly of single walled carbon nanotubes: role of DNA linkers and annealing - Physical Chemistry Chemical Physics (RSC Publishing) | 19:56 |
| heath | http://dna.caltech.edu/Papers/stacking-bonds2011.pdf | 19:57 |
| heath | .title | 19:57 |
| yoleaux | heath: Sorry, that doesn't appear to be an HTML page. | 19:57 |
| heath | " Programmable Molecular Recognition based on the Geometry of DNA nanostructures" | 19:57 |
| kanzure | heath: you can use .title with the url on the same line, like ".title http://awfulurl.com/" | 19:57 |
| heath | non dead-tree links: http://dna.caltech.edu/DNAresearch_publications.html | 19:58 |
| heath | Theory of Algorithmic Self-Assembly: http://dna.caltech.edu/Papers/algorithmic_tiles2012doty.pdf and http://vimeo.com/54214122 | 20:00 |
| fenn | it's nice to have at least an abstract in your list of published works | 20:01 |
| kanzure | .title http://vimeo.com/54214122 | 20:01 |
| yoleaux | Theory of Algorithmic Self-Assembly on Vimeo | 20:01 |
| kanzure | oh look heath was kind enough to specify it | 20:01 |
| fenn | it would be great if all science papers came with explanatory videos like this | 20:05 |
| kanzure | you want *video*? | 20:05 |
| fenn | given a choice, i'd rather have the text format, but sometimes video is easier to understand | 20:07 |
| heath | will someone eventually pay me to work on this and not patent every bit of the work? | 20:07 |
| kanzure | to work on what? | 20:07 |
| heath | building stuff with dna | 20:08 |
| heath | fenn, launch a startup, i'll intern until i'm useful | 20:08 |
| fenn | um. it's a little premature | 20:08 |
| kanzure | that's not how you make money | 20:08 |
| kanzure | you say: "i want to be paid x" then people pay you "x" | 20:08 |
| kanzure | if you say "i'll intern until" then you will not be paid, or if you are paid, it will be insulting. | 20:09 |
| kanzure | or illegal | 20:09 |
| fenn | you could go work in winfree's lab | 20:09 |
| kanzure | why are you suddenly interested in dna origami projects? | 20:09 |
| heath | dunno, it's one of the two things i've been consuming a lot | 20:10 |
| heath | the other thing is market making bots | 20:11 |
| kanzure | if you are looking for some small project ideas to make a few bucks, i have a large ~/lists/startup-ideas file | 20:12 |
| heath | .link | 20:12 |
| fenn | market making bots? | 20:12 |
| heath | .link startup-ideas | 20:12 |
| heath | for bitcoin | 20:12 |
| kanzure | yesterday i added two entries. first is a textbook lookahead site to see if a new edition of your textbook is coming out before class starts (so that you can buy the textbook ahead of time if there's no new edition; otherwise, prices will spike). | 20:13 |
| heath | haven't launched a one | 20:13 |
| fenn | i regret to inform you that ".link startup-ideas" doesn't actually paste a link in here | 20:13 |
| heath | fenn: yeah, i'm aware, i just figured bryan would suddenly link though | 20:13 |
| kanzure | second idea was a personal analytics site for tracking down stalkers. you can use lots of different tracking methods to identify who your stalker is. you could even give the stalker a fake android app that reports their gps location to you so that you can be notified when they are physically near you and maybe you are in danger. | 20:13 |
| kanzure | bitcoin ideas.. uh.. uh.. black market for organs and mad science. | 20:14 |
| kanzure | including antibodies. | 20:14 |
| fenn | when you said "analytics site for stalkers" i immediately thought that it was for use by stalkers to determine who/where their victim is | 20:17 |
| kanzure | nope, other way around | 20:17 |
| kanzure | whostalksthestalkers.com | 20:17 |
| fenn | but wouldnt it work equally well either way? | 20:17 |
| kanzure | no, because as a stalker you can't coerce your victim to click your link | 20:18 |
| fenn | that's a totally ungrounded statement, and it's false :P | 20:18 |
| kanzure | you can do phishing i guess | 20:18 |
| kanzure | anyway, stalkers are already quite capable of doing that | 20:18 |
| kanzure | there is no product marketed to people who are actively trying to identify who their creep is | 20:19 |
| kanzure | or who is the person following them around the internet making death threats | 20:19 |
| yashgaroth | there's a girl from diybio san diego who has some stalker trying to contact people from the group and claiming to be her | 20:21 |
| kanzure | is it rachel? | 20:21 |
| kanzure | oh wait, no. ok good. let's never speak that name again. | 20:21 |
| yashgaroth | yeah no | 20:21 |
| kanzure | anyway, yeah, if that's a real stalker, the goal would be to use this tool to help fix those situations. | 20:22 |
| kanzure | the idea would be to figure out as much information as possible, then maybe take that to the police or make recommendations about how to block that person for good. | 20:22 |
| yashgaroth | I figured if the stalker is contacting people, that they could reply with a link that IDs the stalker's IP address or something | 20:23 |
| yashgaroth | like 'hey here's a personal photo etc check it out' and then bam | 20:23 |
| kanzure | yes | 20:26 |
| kanzure | there are other things you can do as well | 20:26 |
| kanzure | for instance, you can look at the headers of the emails that were sent to you | 20:26 |
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| kanzure | this could provide additional information like what mail servers the creep is using | 20:26 |
| kanzure | or possibly which mail client | 20:26 |
| yashgaroth | I'm guessing they just use some random gmail account, but I have few details from her | 20:27 |
| kanzure | there are two critical problems with this idea as a business | 20:27 |
| kanzure | first, you would be putting yourself in physical danger because stalkers will fucking hate you | 20:27 |
| kanzure | second, it might be a little unethical to charge for this sort of protection/identification service | 20:27 |
| kanzure | "oh sorry about your stalker but since you're poor i can't do fuck all about it" | 20:28 |
| fenn | re first, they're already in danger if they're being stalked (assuming the stalker was a violent person in the first place) | 20:28 |
| kanzure | no, i mean the person running the site. | 20:28 |
| fenn | and second, that applies to any other business | 20:29 |
| kanzure | fair point | 20:29 |
| fenn | well, you'll just have to play pen test games to see if you can figure out who owns the company | 20:30 |
| fenn | mumble mumble corporate veil | 20:30 |
| kanzure | best way would be to make it bitcoin only and just make it a highly anonymized service | 20:30 |
| kanzure | but then you would be cutting off a lot of people that need the service because they don't understand bitcoin, even if you use coinbase or w/e the easiest thing is of the day. | 20:31 |
| fenn | nah anybody with enough savvy to use bitcoin already knows how to reverse-stalk | 20:31 |
| kanzure | no | 20:31 |
| kanzure | coinbase makes it really dead simple to pay in bitcoins on sites | 20:31 |
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| kanzure | there are many sites integrating bitcoin these days not because they want to appease the technical hordes of nerds but because there's legitimately easy flows to sign people up through bitcoin (although it's not as seamless as "type in your credit card number".. there's like 2 or 3 more clicks). | 20:32 |
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| heath | whotalkstostalkers.com | 20:34 |
| heath | maybe you should purchase that one? :) | 20:35 |
| kanzure | anyway, that was just because you asked | 20:36 |
| kanzure | i don't think i am strongly motivated to work on either one | 20:36 |
| heath | i want an idea around dna computing | 20:37 |
| kanzure | plus the stalker thing has only like 20M potential users/year, and maybe only 50% of those are going to be cyberstalking victims, and then if you get 1% of that market it's just pretty small, etc. | 20:37 |
| kanzure | why do you want dna computing? | 20:37 |
| heath | the guys who did the glowing tree for kickstarter are actually a startup | 20:37 |
| kanzure | they are actually liars and i hate them | 20:38 |
| fenn | oh, they're actually a startup! woohoooooooooooooo | 20:38 |
| kanzure | omri is the owner of "genome compiler" except it's not a real compiler >:( | 20:38 |
| kanzure | and there's nothing "open" about his project, although everyone keeps calling it "open". | 20:38 |
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| kanzure | Juul: sup with the naming? | 20:39 |
| heath | nanomedicine, re: why | 20:39 |
| fenn | please elaborate | 20:40 |
| heath | a:"why do you like the color red?" b: "it makes me happy" a: "please elaborate" | 20:40 |
| heath | i'm not sure where this is going :) | 20:40 |
| heath | clearly it's not my specialty | 20:41 |
| fenn | how does dna origami or dna computing contribute to nanomedicine, in your opinion | 20:41 |
| fenn | (whatever nanomedicine is) | 20:41 |
| fenn | the current state of dna computing is calculating the square root of 15 | 20:42 |
| kanzure | heath: i suggest picking startup ideas based on traction or market numbers | 20:42 |
| heath | sure | 20:42 |
| kanzure | heath: go read about lean startups or something | 20:42 |
| heath | nanomedicine => drug delivery, but also i think of it as interfacing with the brain somehow | 20:43 |
| heath | my reasons will never get any less vague | 20:43 |
| heath | today | 20:43 |
| heath | re: how does it contribute to nanomeds... a very long time from now, we build stuff using these ideas | 20:45 |
| heath | we build larger things which could be used for drug delivery? i dunno | 20:45 |
| kanzure | this is not a very good startup. | 20:45 |
| kanzure | did you read the startup science transcripts? | 20:46 |
| heath | that's why i offered to be an intern :) | 20:46 |
| kanzure | http://diyhpl.us/wiki/transcripts/startup-science-2012/ | 20:46 |
| kanzure | an intern at a startup that you create? | 20:46 |
| heath | hah | 20:46 |
| heath | i haven't read the transcripts, might be something worth looking at though | 20:47 |
| heath | fenn: you making me elaborate makes me feel bad about myself :) | 20:49 |
| fenn | it isn't going to get easier than explaining to your friends in a low pressure setting | 20:51 |
| fenn | i have lots of ideas about dna origami, just wondering what yours were | 20:52 |
| heath | you have been thinking on these ideas a lot longer, it's why i was asking earlier "if not dna origami, then what", because i thought you guys had discovered a better way forward | 20:54 |
| heath | i guess we can get some immediate results with synthetic biology even though the yields are low, there aren't debuggers, etc. | 20:55 |
| heath | from what i can tell, we get higher yields of the desired produce at the genetic level than the cellular level | 20:56 |
| fenn | higher yields of what? | 20:56 |
| kanzure | better way forward for what? | 20:57 |
| yashgaroth | immediate results in what? | 20:57 |
| fenn | i assumed he meant toward something resembling drexlerian molecular nanotechnology | 20:57 |
| heath | and if we can pursue this field using techniques borrowed from computer programming, it seems mores tractable | 20:59 |
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| kanzure | i think you are more likely to make immediate impact on nanoengineer in clean up duty | 21:01 |
| kanzure | https://github.com/kanzure/nanoengineer | 21:02 |
| fenn | i tried to do that with conventional engineering where we can see and interact with the machinery | 21:02 |
| heath | so scratch [22:56:13] <heath> from what i can tell, we get higher yields of the desired produce at the genetic level than the cellular level | 21:02 |
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| heath | i just heard a guy talk about insertion yields in synthetic biology being low and for some reason that translated to "dna based computing has higher yields of THINGS!" :p | 21:03 |
| heath | re: a better way forward, transhumanism, i mean, this is what we're here for right? | 21:03 |
| fenn | one thing i've learned is that transhumanism never means the same thing to different people | 21:04 |
| kanzure | insertion yields in synthetic biology is about dna synthesis and genomic uptake and colony selection, not about dna computing. | 21:05 |
| fenn | i guess a dna computer would yield answers? | 21:05 |
| fenn | shorter/simpler computations would yield more answers because there would be more processors or more cycles per processor, so the algorithm completes N times more in the alloted reaction time | 21:08 |
| fenn | guh english is starting to fail me | 21:09 |
| fenn | on PCs we typically don't compute the answer more than once | 21:09 |
| kanzure | i think dna synthesis is a better place to work at for the moment if you are interested in making gains related to dna origami or whatever | 21:09 |
| fenn | "Maybe one day I will improve this. But that day is not today. Today is | 21:16 |
| fenn | a day for spitting text out. With God's mercy, I will learn how to | 21:16 |
| fenn | finish big projects. I pray for that ability frequently." | 21:16 |
| heath | i like to think that we can build all sorts of proteins using dnacomp (because i'm tired of typing) which we could assemble into larger structures somehow in some far future | 21:17 |
| fenn | we can already build proteins with dna.. the trick is making sure it folds the way you want | 21:19 |
| heath | https://www.youtube.com/watch?feature=player_detailpage&v=2nqHOnVTxJE#t=2259s | 21:19 |
| heath | who is this guy? | 21:19 |
| * heath wonders if he gave a talk prior/after to hers | 21:19 | |
| kanzure | 2259 seconds? is that right? | 21:19 |
| heath | yep | 21:20 |
| fenn | sounds russian? | 21:21 |
| heath | not the girl | 21:22 |
| heath | oh, yeah, he has some accent as well | 21:24 |
| heath | where's phreedom when you need him | 21:24 |
| kanzure | i scared him away | 21:24 |
| kanzure | he believed that i sucked at anonymity (and he was right) | 21:25 |
| heath | http://vimeo.com/46304267 : Sight, a short film | 21:35 |
| ParahSail1n | dude asking for electropherogram for illumina reads... | 21:51 |
| ParahSail1n | cmon get with the program, i know you're a wetlabber but what we do over here is not black magic | 21:52 |
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| heath | electropherogram: " plot of results from an analysis done by electrophoresis automatic sequencing"...google search for `illumina` yields "Illumina | sequencing and array-based solutions for genetic research" | 22:01 |
| heath | seems reasonable? | 22:01 |
| heath | ParahSail1n^ why is it unreasonable to think could get an electropherogram? | 22:03 |
| heath | not trying to knock what you are saying, this is a legitimately ignorant question on my part :) | 22:09 |
| yashgaroth | ok fine, electropherograms refer only to traditional chain-termination sequencing, whereas with illumina and others' high-throughput sequencing you only get the sequence and a quality score for each base | 22:10 |
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| heath | thanks yashgaroth | 22:27 |
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| ParahSail1n | yes | 22:29 |
| heath | http://cadnano.org/ is what winfree's lab uses | 22:29 |
| heath | https://github.com/sdouglas/cadnano2 | 22:29 |
| heath | mostly written in python too \o/ | 22:30 |
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| heath | neat: https://www.transcriptic.com/ | 23:01 |
| heath | "Transcriptic is the simplest and lowest cost way to order custom plasmids. Send us source material to start from or synthesize it for only 34 ¢ / bp, all from one workflow. Starting at $275." | 23:01 |
| heath | mentioned in http://diyhpl.us/wiki/transcripts/startup-science-2012/ | 23:02 |
| * heath didn't realize that nanoengineer, too, is mostly python | 23:10 | |
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| kanzure | heath: before cadnano they were using nanoengineer. that's why some of rothemund's work is in nanoengineer. | 23:30 |
| kanzure | heath: they stopped using nanoengineer when nanorex died. | 23:30 |
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| --- Log closed Thu May 23 00:00:35 2013 | ||
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