| --- Log opened Tue Aug 06 00:00:47 2013 | ||
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| ThomasEgi | wasn't someone looking for those car-related papers to be released? | 00:40 |
|---|---|---|
| ThomasEgi | http://blog.ioactive.com/2013/08/car-hacking-content.html might be just that. | 00:40 |
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| wrldpc | Root Wolpe is a fucking idiot. | 04:07 |
| wrldpc | I'm certainly not a Kurzweil flag waver, but Wolpe is a fucking dilettante. | 04:08 |
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| nmz787 | paperbot: http://www.ingentaconnect.com/content/iafp/jfp/1999/00000062/00000002/art00016?token=004d12f99a41333c4a2f7a736a5e3b20674723773b254f6d6222346b62687630502163b172b11 | 04:34 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/5f0d29aff3dd6e90628a3bae0da6ee2a.txt | 04:35 |
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| archels | wrldpc: FUD | 04:44 |
| wrldpc | aye | 04:46 |
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| drazak | kanzure: meh, that derek guy is in victoria | 05:48 |
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| @kanzure | beep | 08:09 |
| @kanzure | victoria? that loser. | 08:09 |
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| @kanzure | heath: i still don't understand why you are obsessed with all of these broken methods | 08:12 |
| drazak | kanzure: yeah | 08:12 |
| ParahSail1n | broken methods? | 08:13 |
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| @kanzure | ParahSail1n: you aren't going to outrace a supercomputer with dna | 08:13 |
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| @kanzure | http://www.kickstarter.com/projects/mossmann/hackrf-an-open-source-sdr-platform | 08:33 |
| drazak | kanzure: you think about kickstartering the dna synth project? | 08:34 |
| @kanzure | no. money isn't the problem. | 08:36 |
| drazak | o.O | 08:36 |
| drazak | where are you getting your funding? | 08:36 |
| drazak | I will work for you | 08:36 |
| @kanzure | i work my ass off so that i can fund this shit but you guys keep giving me the finger | 08:36 |
| drazak | >.> | 08:36 |
| @kanzure | what would i pay you for btw? | 08:37 |
| @kanzure | i remember you used to be way better than me at chemistry | 08:37 |
| drazak | dunno, I'm ok at stuff, once I am not having fucked up days regarding housework and emotions I'm gonna take a good look at this | 08:38 |
| @kanzure | eww why does this require qt http://openbiometrics.org/ | 08:46 |
| drazak | lol | 08:46 |
| @kanzure | oh, for building | 08:46 |
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| chris_99 | half duplex seems quite a big limitation of hackrf | 08:49 |
| gradstudentbot | Sorry, I can't really talk right now because I'm burried in grant writing. | 08:50 |
| superkuh | For some applications, I guess. I'll be picking one up for solar radio astronomy due to the excellent frequency coverage. | 08:54 |
| chris_99 | i'm hoping to get bladerf when it's out | 08:55 |
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| heath | kanzure: it's just something to work on | 10:18 |
| * heath enjoyed Anne Condon's talk last night | 10:19 | |
| @kanzure | but why not work on other things? go make that brain zapper gun. | 10:19 |
| ParahSailin | brain zapper? | 10:19 |
| heath | tdcs i'm assuming | 10:20 |
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| @kanzure | i was being intentionally vague because any working brain zapper is probably better than trying to force dna to do things that it doesn't do | 10:20 |
| heath | working on dna folding pathways isn't a terrible idea | 10:21 |
| heath | it naturally folds | 10:21 |
| ParahSailin | can you disable certain lobes of the brain using tdcs? | 10:21 |
| heath | i'm not sure, that's something i don't care to try | 10:22 |
| ParahSailin | wimp | 10:22 |
| heath | kanzure: maybe you're being sarcastic and i'm not picking it up through IRC. what else are you going to use the oligos for once you finally have a machine to synthesize them? | 10:23 |
| ParahSailin | make teh genes | 10:24 |
| heath | :) for? | 10:24 |
| superkuh | It is really lame that, "The NCBI web site requires JavaScript to function." | 10:24 |
| ParahSailin | put dna constructs into teh things | 10:24 |
| ParahSailin | you have any idea how long "routine cloning" takes? | 10:25 |
| @kanzure | heath: primers. genes. genomes (not really, but theoretically you can eventually make genomes). | 10:25 |
| ParahSailin | huge waste of time and bottleneck in molecular biology | 10:25 |
| @kanzure | hell, just primers would be worth it | 10:26 |
| ParahSailin | maybe | 10:28 |
| heath | "put dna constructs into things", e.g. cells.. making genomes, and then putting them into... cells. isn't this synthetic biology, an despised around here? | 10:29 |
| heath | an +area | 10:29 |
| heath | superkuh: w3m seems to work on ncbi's site | 10:29 |
| ParahSailin | didnt know we despised biology | 10:29 |
| @kanzure | wha? | 10:33 |
| * kanzure scratches his head | 10:33 | |
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| @kanzure | grr i think the http://n.tkte.ch/ commit bots are blocked on freenode | 10:48 |
| @kanzure | ParahSail1n: https://github.com/kanzure/papermonk and https://npmjs.org/package/papermonk | 10:49 |
| @kanzure | ParahSail1n: i know it's not much for now, but i'm busy doing other things for the next few hours | 10:49 |
| heath | power went out briefly | 11:10 |
| heath | once you make some constructs using dna, it's logical to place them inside cells, i'm definitely not opposed to working with cells, i was confused about the feelings toward synthetic biology | 11:20 |
| heath | looking through the logs, it looks like it's more toward biobricks and igem | 11:20 |
| heath | https://gist.github.com/heath/03347981b8c466e28e09/raw/6b3feebb906b9bd6c432a8835a29b8db87f5d08a/gistfile1.txt | 11:20 |
| @kanzure | there's definitely a lot of hype around synthetic biology that is unwarranted | 11:20 |
| @kanzure | .title https://news.ycombinator.com/item?id=6166292 | 11:20 |
| yoleaux | Security advisory: Breach and Django | Hacker News | 11:20 |
| ParahSailin | kanzure: so the downloaders should be able to do dom selectors, compose functions with results of dom selectors, and maybe do arbitrary javascript functions that are aware of page dom? | 11:23 |
| @kanzure | well, i have a few thoughts about that | 11:23 |
| @kanzure | first, you have previously convinced me that we shouldn't allow downloaders to just use phantomjs or w/e | 11:23 |
| @kanzure | second, i think some downloaders will choose to use jsdom but most will not require it | 11:24 |
| @kanzure | i am gonna try to make sure most of the downloaders use the glorious "request" library, because it seems to be a good way to do asynchronous streaming requests and pdf downloads and stuff | 11:24 |
| @kanzure | ideally most downloaders will use the same tooling as each other | 11:25 |
| ParahSailin | i think the eDSL defined by zotero is a good starting point, but could be generalized to be more complete | 11:25 |
| @kanzure | one idea was that there can be a library that all downloaders use | 11:25 |
| @kanzure | and this intermediate library will expose jsdom | 11:25 |
| @kanzure | and then all downloaders should have only that one dependency | 11:25 |
| ParahSailin | not saying use any of their stuff, but create a similar edsl | 11:25 |
| @kanzure | that way we can force people to approve extra dependencies | 11:25 |
| @kanzure | (or something) | 11:25 |
| @kanzure | because i don't want there to be 10 different dependencies that all handle dom parsing or some shit. that's going to be stupid/annoying/bad. | 11:25 |
| @kanzure | maybe i will just have a review process before accepting a new downloader into the papermonk module | 11:26 |
| ParahSailin | all of them probably will need jsdom though? | 11:26 |
| @kanzure | each module will have its own package.json file that will specify their dependencies | 11:26 |
| @kanzure | npm is smart enough to not download the same dependency twice (unless a different version is required) | 11:27 |
| @kanzure | http://breachattack.com/resources/BREACH%20-%20SSL,%20gone%20in%2030%20seconds.pdf | 11:28 |
| ParahSailin | id say make jsdom and sizzle default requires | 11:30 |
| @kanzure | it will be up to each individual module | 11:32 |
| @kanzure | what is sizzle? | 11:32 |
| ParahSailin | sizzle is the dom selector library used in everything else | 11:33 |
| @kanzure | i think people will just use jsdom + jquery | 11:33 |
| ParahSailin | yeah sizzle is the selector that jquery uses | 11:34 |
| @kanzure | didn't know. cool. | 11:34 |
| ParahSailin | you dont need the other jquery stuff like dom manipulation and fancy traversal bla etc | 11:34 |
| @kanzure | also i should rewrite pdfparanoia into javascript for streaming watermark removal reasons | 11:35 |
| ParahSailin | how fast is pdfparanoia | 11:35 |
| superkuh | I have disabled compression on his nginx http, https, and https tor hidden service. No more problems with BREACH, right? | 11:35 |
| superkuh | s/his/my/ | 11:36 |
| @kanzure | don't you run lighttpd somewhere? | 11:36 |
| superkuh | Nope. I used to use thttpd but I've moved on. | 11:37 |
| @kanzure | the only other thing i can think of is that you might want to be cautious about what you do over HTTPS in the near future (as a user) | 11:38 |
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| ParahSailin | kanzure: instead of allowing people to write arbitrary and verbose javascript for each scraper, we should nudge them into writing maintainable ones in this style https://gist.github.com/rcallahan/0748c6b40f590d43e096 | 12:12 |
| @kanzure | the only argument i can see in favor of that is that testing becomes more discrete over the keys that they expose | 12:13 |
| @kanzure | but that's the only benefit i can think of | 12:14 |
| @kanzure | and the downside is that.. you can't write plain javascript anymore. isn't that whta went wrong with zotero? and everything else? | 12:14 |
| ParahSailin | well zotero exposes their dsl as well as plain freeform javascript | 12:15 |
| @kanzure | their dsl is silly. what's the point of the zotero dsl? | 12:15 |
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| ParahSailin | for the most part, their translators only need to do xpath selectors and compositions of functions on those | 12:15 |
| ParahSailin | so it makes it more concise and readable for the majority of the translators | 12:16 |
| ParahSailin | and enforces a uniform style | 12:16 |
| @kanzure | how would this handle things like, "scraping an index of an issue of a journal"? | 12:16 |
| ParahSailin | so, page navigation? | 12:17 |
| ParahSailin | i think that could be written in a nonspaghetti way as well | 12:17 |
| @kanzure | well, maybe.. i think zotero does it without navigating to each paper's page. this is maybe a dumb idea. | 12:17 |
| heath | "Animations with eCommerce is an attempt by companies to make the intangible tangible - Heath Matlock #fowd" | 12:17 |
| heath | what? i never said that | 12:17 |
| heath | "Consider caching vectors drawn by canvas as a bitmap to help with performance - Heath Matlock #fowd" | 12:18 |
| @kanzure | heath: you probably got hit by a js exploit | 12:18 |
| heath | i never said that either | 12:18 |
| heath | http://eventifier.co/event/fowdnyc/hellohynes | 12:18 |
| heath | i don't know what's going on | 12:18 |
| @kanzure | your twitter account might have been hijacked | 12:18 |
| @kanzure | either through cookie stealing, an xss attack, password guessing, etc. | 12:18 |
| heath | oh that's possible, i have a weak password | 12:18 |
| heath | *had* a weak password, now | 12:21 |
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| @kanzure | heath: quick, arguments against a javascript dsl for writing paper scrapers? | 13:02 |
| @kanzure | heath: context is https://github.com/kanzure/papermonk https://npmjs.org/package/papermonk https://gist.github.com/rcallahan/0748c6b40f590d43e096 | 13:03 |
| heath | it isn't coffeescript or livescript :) | 13:04 |
| @kanzure | both coffeescript and livescript can write in that dsl | 13:05 |
| @kanzure | you're lying | 13:05 |
| heath | :) | 13:05 |
| @kanzure | like, there's no way you don't know that about coffeescript | 13:06 |
| heath | i like this | 13:07 |
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| heath | what is the ddDoi? | 13:08 |
| heath | i know what doi is, but i don't know what dd stands for | 13:09 |
| heath | ah | 13:09 |
| @kanzure | me either | 13:11 |
| @kanzure | why do you like it though | 13:11 |
| heath | is the .bind you're own method or are you using Function.prototype.bind? | 13:11 |
| @kanzure | i have no idea | 13:12 |
| @kanzure | (this is why i am objecting to it) | 13:12 |
| ParahSailin | i didnt know that was a reserved word in javascript | 13:12 |
| @kanzure | it's for scope binding | 13:12 |
| ParahSailin | its (>>=) in haskell | 13:12 |
| heath | as is .call | 13:12 |
| heath | that's for binding to a monadic context, similar, but not exactly the same | 13:13 |
| ParahSailin | no i mean what im defining | 13:14 |
| heath | oh, i didn't notice rcallahan | 13:14 |
| ParahSailin | oh, yeah my github is under a "professional" name | 13:14 |
| heath | i just saw kanzure/papermonk and assumed the gist was from the same person | 13:15 |
| @kanzure | i wonder what this package is: jhove - JSTOR/Harvard Object Validation Environment | 13:16 |
| @kanzure | http://hul.harvard.edu/jhove/ | 13:16 |
| nmz787 | heath: I think you have it backwards somehow... we love synBio in here, we despise iGem | 13:19 |
| heath | nmz787: i kind of figured that out, but thanks for clarifying, it's always nice to have a little more feedback | 13:22 |
| @kanzure | to be fair, there's a lot of BS in synthetic biology that's not worth liking | 13:23 |
| nmz787 | i don't really despise iGem, actually, it's just really annoying how it's unavailable to anyone with less than $2.5-5k... and good teams probably get $5-20k spent total (depending if they get transport to the iGem jamboree, and if they get a sumnmer work stipend) | 13:24 |
| @kanzure | well, their policies have changed to allow non-institutional teams (i think) | 13:24 |
| @kanzure | jonathan has some more specific criticism that i'm sure he would be happy to share | 13:24 |
| heath | see the beginning of 07-04-2013.log | 13:24 |
| nmz787 | yeah but to get the shit (plasmid/DNA) you have to pay a few thousand, then you'd need to drop out to not have to pay to attend the jamboree | 13:24 |
| heath | "engines": { "node": ">0" } | 13:26 |
| heath | :) | 13:26 |
| gradstudentbot | Don't mess with me, I'm a world pipetting champion 14 years running. | 13:29 |
| @kanzure | heath: because sometimes i write things for phantomjs | 13:29 |
| @kanzure | heath: and it's a different engine | 13:29 |
| @kanzure | wow "Amazon Web Services (AWS) (hosting) allows customers to run any type of Tor servers provided abuse complaints are handled in a timely manner" | 13:32 |
| @kanzure | https://trac.torproject.org/projects/tor/wiki/doc/GoodBadISPs | 13:32 |
| @kanzure | haha what "RoadRunner (TimeWarner) (USA): Very reliable service. Been running web server on 80 for several years. IP changes when cable modem reset (almost never for me). No ports blocked (that I know of). No BW limits, only speed caps. I've got 5Mbps down/384kbps up. Definitely recommend. Running Tor since Jan 06. -- MichaelAnsel" | 13:35 |
| heath | link comes from a short email exchange on diybio between nmz and zayner | 13:36 |
| heath | https://groups.google.com/forum/#!search/diybio$20resource$20utilization/diybio/uwYWESC4kpY/fKOq0Ev2SygJ | 13:36 |
| heath | paperbot: http://www.jbioleng.org/content/3/1/11/abstract | 13:36 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1186%2F1754-1611-3-11 | 13:36 |
| gradstudentbot | Coffee? Never tried it. | 13:39 |
| nmz787 | heath: that's open access http://www.jbioleng.org/content/pdf/1754-1611-3-11.pdf | 13:39 |
| nmz787 | detail | 13:40 |
| nmz787 | ! | 13:40 |
| * heath imagines something like this as scienceDirect: {doi: "#foobar", doiExtraction: function() {}, paperLink: "#bazqux", supplementary: [], suppExtraction: function (){} } | 13:48 | |
| heath | not sure if a json would ever be preferential | 13:49 |
| heath | a json +format | 13:50 |
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| @kanzure | heath: the bibliometricdata object is always json serializable. it must be. | 13:53 |
| @kanzure | heath: and if we're lucky we could maybe maintain compatibility with zotero's json output | 13:54 |
| cogitokat | when did it become bibliometricdata instead of bibliometadata? d: | 13:55 |
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| @kanzure | cogitokat: oops | 14:11 |
| @kanzure | well, bibliometricmetadata sounds a little bit cooler maybe | 14:12 |
| cogitokat | Isn't bibliometrics a thing that is something slightly different? http://en.wikipedia.org/wiki/Bibliometrics | 14:14 |
| @kanzure | "Bibliometrics is a set of methods to quantitatively analyze scientific and technological literature." | 14:14 |
| @kanzure | oh.. citation analysis. | 14:14 |
| @kanzure | damn why do all of the cool terms have to be taken | 14:14 |
| cogitokat | hahaha | 14:14 |
| cogitokat | I wouldn't care except it might confuse people. | 14:15 |
| @kanzure | it's fine, i should use a different term | 14:15 |
| cogitokat | Papermonk needs bibliometric data to work? Hrmm.. | 14:15 |
| @kanzure | no | 14:15 |
| cogitokat | lol | 14:15 |
| cogitokat | I should have wrapped that in quotes. | 14:16 |
| @kanzure | it extracts metadata, authors, titles, institution addresses/names, email addresses, abstracts, etc. | 14:16 |
| @kanzure | ah okay | 14:16 |
| ParahSailin | well, if you get from dx.doi.org with the correct headers you will get metadata serialized in json, rdf, xml, whatever | 14:23 |
| @kanzure | can you show me some of the json output? | 14:23 |
| @kanzure | i am curious how thorough/accurate/correct it is | 14:24 |
| ParahSailin | curl -LH "Accept: application/rdf+xml;q=0.5, application/vnd.citationstyles.csl+json;q=1.0" http://dx.doi.org/10.1126/science.169.3946.635 | 14:25 |
| @kanzure | cool | 14:26 |
| @kanzure | {"volume":"169","issue":"3946","DOI":"10.1126/science.169.3946.635","URL":"http://dx.doi.org/10.1126/science.169.3946.635","title":"The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance","container-title":"Science","publisher":"American Association for the Advancement of Science","issued":{"date-parts":[[1970,8,14]]},"author":[{"family":"Frank","given":"H. ... | 14:26 |
| @kanzure | ... S."}],"editor":[],"page":"635-641","type":"article-journal"} | 14:27 |
| @kanzure | how is there no editor? | 14:27 |
| @kanzure | also, how should we handle utf8 and latin1 abstracts? | 14:27 |
| ParahSailin | seems reasonable | 14:28 |
| heath | "each mL of sea water has about a million bacteria and on the order of 10 million viruses" | 14:28 |
| heath | i wonder if surfers have a healther immune system then myself | 14:28 |
| @kanzure | only if they are bad at it | 14:28 |
| gradstudentbot | Blah, I'm going to quit. | 14:29 |
| nmz787 | http://www.whitehouse.gov/blog/2013/06/25/biocurious-hackerspace-biology | 14:30 |
| @kanzure | it's just a guest post by eri | 14:33 |
| @kanzure | "One of the biggest challenges I’ve faced is how to become involved in science as a non-scientist." that's the stupidest shit i've ever heard | 14:33 |
| @kanzure | "A hackerspace devoted to biology had never been attempted before" except for, you know, hackteria | 14:34 |
| nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/nl401219v | 14:34 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/44c12c90f608fde59b5c777c75f8a160.pdf | 14:34 |
| @kanzure | "Many said it wouldn’t work. It doesn’t simply work – it thrives." yeah.. if by "thrive" you mean "has 30 members and can't pay its bills". whatever. | 14:35 |
| nmz787 | wait so can anyone blog on the whitehouse's page? | 14:35 |
| @kanzure | dunno, it just seems like a submit-a-person thing http://www.whitehouse.gov/blog/2013/07/31/nominate-white-house-champion-change-public-health-and-prevention | 14:35 |
| @kanzure | i like how eri gets around with so many lies | 14:36 |
| @kanzure | it's amazing | 14:36 |
| nmz787 | paperbot: http://www.opticsinfobase.org/abstract.cfm?id=119210 | 14:37 |
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| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/79e32ccbfb4a62674cd9396fc7e6ac61.txt | 14:38 |
| @kanzure | "One of the biggest challenges I’ve faced is how to become involved in science as a non-scientist." | 14:38 |
| @kanzure | "One of the biggest challenges I’ve faced is how to become involved in science without actually calling myself a scientist." | 14:39 |
| gradstudentbot | Well, I can't really talk about it because I'm trying to get it published in Science or Nature. | 14:39 |
| nmz787 | paperbot: http://www.opticsinfobase.org/as/viewmedia.cfm?uri=as-60-11-1341&seq=0 | 14:39 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/3389688efed025a60657600e88ba567.txt | 14:39 |
| nmz787 | kanzure: you can't really call bullshit on someone's opinion though, she was making an 'I feel' statement of sorts, so it can't really be *wrong* | 14:40 |
| @kanzure | opinions can definitely be wrong | 14:40 |
| nmz787 | not in 'I feel' though | 14:40 |
| nmz787 | at least that's something therapists and help groups tell people... use 'I' statements so you don't offend people, etc | 14:41 |
| nmz787 | 'I feel you're being too harsh, Bryan' etc | 14:41 |
| nmz787 | rather than 'You're being too harsh Bryan' | 14:41 |
| @kanzure | there's zero difference between those two. in either case you would have to show evidence of harshness unless you want me to start discounting your opinions. | 14:41 |
| nmz787 | the latter is an absolute statement, while the former is relative to the person's internal state | 14:42 |
| nmz787 | the difference is the 'I' component, changing fact to opinion... | 14:42 |
| @kanzure | "i feel like it was okay to kill that person" | 14:43 |
| nmz787 | supposedly it makes a difference in group therapy, comes off as less pernicuous | 14:43 |
| nmz787 | pernicious* | 14:43 |
| cogitokat | This is a really strange argument. | 14:44 |
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| ParahSailin | yes, it has higher likelihood to trigger empathy circuits when you rephrase things certain ways | 14:45 |
| @kanzure | i will choose to be emphatic when and if i deem necessary. covering up lies that eri posted on whitehouse.gov is not one of those times.. | 14:45 |
| ParahSailin | so biocurious has the support of the whitehouse now? | 14:45 |
| nmz787 | :P | 14:45 |
| @kanzure | ParahSailin: depends on what you mean support. but yeah, i remember they were pretty chill with the testimony from the bioethics committee and that resulting pdf from a while back. | 14:46 |
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| @kanzure | microryza is only up to 39 funded projects. hah. | 15:14 |
| nmz787 | we're thinking of doing one of those for a year or two of rent for a local space | 15:27 |
| @kanzure | why? i suggest coming up with an alternative model, something that's not "rely on donations and membership fees" | 15:27 |
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| @kanzure | cool "Nobody has ever been sued for running a Tor node." | 15:27 |
| @kanzure | noisebridge provides 7% of tor's total exit node bandwidth? wtf. | 15:31 |
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| nmz787 | meh, why not rely on donations if they're available? | 15:45 |
| nmz787 | otherwise we don't have other ideas for raising money | 15:45 |
| nmz787 | and i didn't say anything about membership | 15:45 |
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| streety | I think it is valid to use donations to get started. Multiple options for continuing operations would certainly be attractive though | 16:31 |
| @kanzure | i think you can get a large pile of money doing typical biotech CRO things | 16:31 |
| gradstudentbot | Who the hell stole my pipette? | 16:31 |
| @kanzure | like, do 1 or 2 projects/month to get 10-20k of income | 16:32 |
| streety | but then you're talking about salaried staff, lots of paperwork, marketing, sales etc | 16:35 |
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| @kanzure | not necessarily salaried staff, but yeah that would be helpful | 16:35 |
| @kanzure | i mean, what you basically just said "but that sounds like work"... and yes. that's the point? | 16:35 |
| @kanzure | *said is | 16:35 |
| streety | if you're not paying the staff then it is essentially donations, only of time rather than money | 16:36 |
| @kanzure | hackerspaces attract a lot of talent. i would be very surprised if that talent couldn't be used to support a space, given the rates that competent hackers can get paid at. | 16:36 |
| @kanzure | you can pay your staff and still have money leftover to run a space | 16:36 |
| @kanzure | biocurious is only $3k/mo or something stupid | 16:36 |
| @kanzure | a biotech contractor can easily earn up to 10 times as much, monthly | 16:36 |
| gradstudentbot | Let's pour a bunch of chemlights into a spinner flask and claim it's luminescent e.coli. | 16:37 |
| @kanzure | although, running an operation like that is certainly different | 16:38 |
| @kanzure | the way i see it, you give up a lot of the community bickering in exchange for resources, but you also have to do some weird prioritizing about which projects get to have time on the bench | 16:38 |
| @kanzure | which makes non-work-related-stuff a second class citizen :( | 16:39 |
| streety | yeah, essentially a business which donates space and resources when convenient to the community | 16:39 |
| gradstudentbot | The lab meeting was cancelled. | 16:40 |
| @kanzure | "when convenient" eh.. that's going a little far. | 16:40 |
| @kanzure | maybe it would do it always | 16:40 |
| streety | fair comment | 16:40 |
| @kanzure | i.e. the community projects would take priority | 16:40 |
| streety | it could be a useful model, would likely have much better resources although the startup costs would also increase | 16:41 |
| @kanzure | the startup cost for biotech consulting is mostly your time (a biotech consultant). once you can secure a contract you can lease space somewhere, and then hop around until you want your own place. | 16:42 |
| nmz787 | we essentially just want somewhere to teach workshops and screw around and work on our own startup ideas... no one really wants to run a big production | 16:42 |
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| nmz787 | kanzure: I could just add a FIB to the BOM, /Dylan has one/ | 17:01 |
| nmz787 | the FEI dual beams are pretty damn nice | 17:01 |
| @kanzure | dylan morris? | 17:02 |
| nmz787 | the SEM doesn't mill, so you can get nice imaging on precious samples | 17:02 |
| nmz787 | yes | 17:02 |
| @kanzure | he wants to sell his? | 17:02 |
| nmz787 | prob not | 17:02 |
| @kanzure | dual beam is just stereolithography? | 17:03 |
| nmz787 | it's likely their workhorse | 17:03 |
| nmz787 | nah | 17:03 |
| nmz787 | FEI's dual beam is a combo FIB + SEM | 17:03 |
| nmz787 | an e-beam and an ion beam | 17:03 |
| @kanzure | isn't that a little gratuitous? | 17:04 |
| @kanzure | hm. | 17:04 |
| nmz787 | you can get nano imagine with ions, but it mills primarily, and images with secondary ion emission... while the e-beam is just electrons so no milling | 17:04 |
| nmz787 | like I said, it's likely dylan's workhorse | 17:04 |
| nmz787 | the local company i talked to said in use they aren't that costly | 17:05 |
| @kanzure | and you said 100 nm/sec milling? | 17:05 |
| nmz787 | and it looked like they just needed a nice software overhaul to make it more CNCscripatble | 17:05 |
| nmz787 | it depends on the spot size | 17:05 |
| nmz787 | at 1 micron cubed it's 100 cubic microns per second | 17:06 |
| nmz787 | kanzure: http://www.oregon-physics.com/lab_services/images/spot_size.gif | 17:06 |
| nmz787 | bbl | 17:06 |
| ParahSail1n | kanzure, are you really desperate for something to put your money into? | 17:09 |
| @kanzure | definitely not desperate. that's why i keep rejecting all the stupid crap i'm hearing. | 17:10 |
| @kanzure | although.. it would be nice to work on these things sooner rather than later, because future bryan is going to be angry/annoyed that he has to do it. | 17:11 |
| @kanzure | also, i'll write a downloader in a bit. i'm currently fixing cygwin/dll issues. | 17:12 |
| nsh | <---- money goes here plskthx | 17:14 |
| ParahSail1n | anannie, you there? | 17:15 |
| anannie | yes ParahSail1n | 17:15 |
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| cpopell | that class was enlightening | 17:37 |
| cpopell | I will revisit SBIR grants when we're a little better established I think | 17:37 |
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| nsh | cpopell, what was the class on? | 17:54 |
| cpopell | DoD SBIR/SBTT grants | 17:55 |
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| ParahSail1n | kanzure, pm | 18:02 |
| @kanzure | replied | 18:03 |
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| @kanzure | i wonder if affiliate commissions are enabled for amazon's online art marketplace thing. | 18:12 |
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| nmz787 | anyone know of something like https://floobits.com/ | 19:23 |
| nmz787 | but freeer? | 19:23 |
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| heath | nmz787: c9.io | 19:38 |
| @kanzure | is that going to be cloud9? god i hope not. | 19:39 |
| heath | yeah | 19:39 |
| heath | it's 'freeer' | 19:39 |
| @kanzure | ugh. i never understood cloud9... why not just use ssh -X. | 19:39 |
| heath | ick | 19:39 |
| @kanzure | "oh no you have to know commands??" | 19:40 |
| @kanzure | yes.. well.. get over it. | 19:40 |
| heath | vim scp:// | 19:40 |
| @kanzure | ah yes because you edit code that's already deployed in production? ;) | 19:40 |
| heath | :P | 19:40 |
| @kanzure | wait, what? i'm not arguing that ssh -X is a good way to edit code. | 19:41 |
| @kanzure | but if you want to use eclipse (or whatever other awful ide of the week) and "in the cloud" then -X seems to be what you want. | 19:41 |
| heath | just saying, if you have to edit remotely, i'd much rather fetch the data, edit local, and send it back using process that involves in emacs/vim land | 19:42 |
| @kanzure | what do you use for mocks in javascript? | 19:43 |
| @kanzure | i'm thinking of mockery | 19:43 |
| heath | sinon, but it may not be what you are thinking | 19:44 |
| heath | the v8 team uses a free lib specifically because of a decent mocking lib... | 19:44 |
| heath | the the lack of..* | 19:44 |
| @kanzure | this looks like jasmine? | 19:44 |
| heath | i can't talk | 19:44 |
| @kanzure | or chia or something | 19:45 |
| @kanzure | assert(callback.called); is kinda nice | 19:45 |
| @kanzure | but trivial | 19:45 |
| heath | mocha + chia + sinon is my testing suite, but it's just what i'm accustomed to | 19:45 |
| @kanzure | it doesn't seem to mock out require() ? | 19:45 |
| @kanzure | do i need to mock require()? i'm trying to decide. | 19:46 |
| gradstudentbot | Hey, let's write a paper about that. | 19:46 |
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| Not-003 | [kanzure/papermonk] kanzure pushed 2 commits to master [+0/-0/±2] http://git.io/Ev8y-A | 19:46 |
| Not-003 | [kanzure/papermonk] kanzure 3578ccc - attach the list of downloaders to Papermonk This will be helpful for investigating which downloaders are available, plus it's better to use a local variable than a global that is just aimlessly floating around. | 19:46 |
| Not-003 | [kanzure/papermonk] kanzure 93fcb2a - make require("papermonk").Papermonk work This exposes the Papermonk object immediately on the module. This is nice for playing with the constructor instead of only using whatever instance the module gives back by default. | 19:46 |
| @kanzure | i just wanna write some good tests for https://github.com/kanzure/papermonk/blob/master/index.js | 19:46 |
| @kanzure | i was thinking of using https://github.com/substack/tape | 19:48 |
| @kanzure | but also https://github.com/mfncooper/mockery seems useful | 19:48 |
| heath | a guy who has more experience than myself uses jasmine + mockery | 19:54 |
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| heath | https://github.com/arunoda/nodemock is a decent library as well | 20:00 |
| @kanzure | the other ridiculous requirement is that it must be something that can conceivably work in a browser, possibly via browserify | 20:00 |
| @kanzure | nodemock looks cool. but i worry about mocking require(). oh right i probably don't need it. i keep forgetting. | 20:01 |
| cpopell | nmz787: why not just talk to ggreer? | 20:28 |
| cpopell | he's a LWer, he may be sympathetic to your needs | 20:28 |
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| drazak | kanzure: this dakota guy sounds like an idiot | 21:54 |
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| @kanzure | drazak: hah. | 22:13 |
| drazak | kanzure: why wouldn't you flame sterilie? you need a fucking lighter | 22:15 |
| drazak | and nobody does bacterial cultures in a flow hood, that's why we HAVE flame sterilization | 22:15 |
| drazak | jesus | 22:16 |
| ParahSail1n | nobody's stealing your fire, prometheus | 22:20 |
| Not-003 | [kanzure/papermonk] kanzure pushed 1 commit to master [+1/-0/±2] http://git.io/NHC3oQ | 22:26 |
| Not-003 | [kanzure/papermonk] kanzure 4638220 - write a pile of tests There will also be tests that confirm that papermonk works inside of a browser. But not yet. Run the tests with: node tests.js version bump to: v0.0.2 | 22:26 |
| Not-003 | [kanzure/papermonk] kanzure tagged 4638220 as v0.0.2 http://git.io/3m8-rg | 22:26 |
| ParahSail1n | well thats a good argument in favor of scraper dsl | 22:27 |
| ParahSail1n | if you want the same modules to work in the browser and in node or everywhere else, you dont want http.get or xhr.get stuff in the scraper code | 22:28 |
| @kanzure | that's what http://browserify.org/ is for | 22:28 |
| @kanzure | there are compatibility modules that browserify injects for http.get and request.get to work | 22:29 |
| @kanzure | including most of the core node stuff like event emitters and streams and stuff | 22:29 |
| gradstudentbot | Argh, what do you mean you don't accept LaTeX submissions?? | 22:29 |
| ParahSail1n | ah | 22:29 |
| drazak | kanzure: do you have more stuff on your dna synthesizer? | 22:29 |
| @kanzure | drazak: not really. the design is still up in the air. | 22:29 |
| ParahSail1n | have you thought more where you're going with the oligo synthesis | 22:30 |
| ParahSail1n | maybe just stick with the avastin thing | 22:31 |
| @kanzure | you mean primers versus other things? i fully expect primers to be way easier than 2 kbp proteins. | 22:31 |
| drazak | kanzure: what's your budget? | 22:31 |
| drazak | I have an idear | 22:31 |
| @kanzure | drazak: limitless. but please act like i am not a bottomless pit of money. | 22:31 |
| drazak | nah | 22:32 |
| ParahSail1n | kanzure, i mean, end goal | 22:32 |
| drazak | just thinking how I would do it on a slightly larger than micro scale | 22:32 |
| drazak | it might be worth it to prototype a somewhat more traditional method to get the physical stuff down | 22:32 |
| @kanzure | ParahSail1n: end goal is a cheap machine <$5k in parts each. uh, also at minimum, doing primer synthesis. | 22:32 |
| ParahSail1n | if you don't have a good idea how you're gonna get to bigmers, then you might as well let idt do their job | 22:33 |
| @kanzure | i don't care if it costs more than $5k to make the first one, but the point is that these machines shouldn't cost more than the reagents | 22:33 |
| drazak | right | 22:33 |
| @kanzure | i'm not targeting longmers right now | 22:33 |
| ParahSail1n | because i dont think their profit margins are very high, and they're probably cutting costs as fast as practicable | 22:33 |
| drazak | and the reagents seem expensive | 22:33 |
| @kanzure | idtdna employs a single person to build their custom synthesizers. i doubt they have explored the "let's make a cheaper synthesizer" option that well. | 22:34 |
| ParahSail1n | hm | 22:34 |
| ParahSail1n | how do you know they just have one person doing that | 22:35 |
| @kanzure | informants. to be honest i haven't confirmed it from anyone else. | 22:36 |
| @kanzure | so, possibly bad information :) | 22:36 |
| @kanzure | i bet it's cheaper for them to lease machines than it is for them to build them | 22:36 |
| @kanzure | they are a services company not a hardware engineering team | 22:36 |
| ParahSail1n | so the working theory is that idt just cobbles bits from overpriced commercial offerings | 22:36 |
| @kanzure | dunno about bits | 22:37 |
| ParahSail1n | and that we could build a cheaper machine | 22:37 |
| @kanzure | they also have a buyback program | 22:37 |
| @kanzure | well, i know the central thesis is true, but it still needs to be ("it's possible to build something cheaper than $50k that can synthesize primers") | 22:37 |
| @kanzure | not the most shocking statement to make.. but it doesn't matter. you still need the machine at some point. | 22:37 |
| @kanzure | erm *still needs to be shown | 22:38 |
| @kanzure | that's lousy reasoning | 22:43 |
| @kanzure | too much javascript tonight | 22:43 |
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| fredox | kanzure: limitless? | 22:59 |
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| --- Log closed Wed Aug 07 00:00:48 2013 | ||
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