| --- Log opened Thu Aug 08 00:00:07 2013 | ||
| --- Day changed Thu Aug 08 2013 | ||
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| @kanzure | oh this is the dumbest thing i've ever seen: https://github.com/zotero/translators/blob/master/ScienceDirect.js#L88 | 06:41 |
|---|---|---|
| @kanzure | //mimetype map for supplementary attachments | 06:41 |
| @kanzure | //intentionally excluding potentially large files like videos and zip files | 06:41 |
| @kanzure | uh.. except maybe i really do intend you to download videos and zip files? | 06:41 |
| drazak | lol | 06:42 |
| -!- Rk is now known as rk[] | 06:52 | |
| Lemminkainen | paperbot http://www.reportlinker.com/p0490898-summary/Life-Science-Tools-and-Reagents-Global-Markets.html | 06:57 |
| drazak | paperbot: http://www.reportlinker.com/p0490898-summary/Life-Science-Tools-and-Reagents-Global-Markets.html | 06:59 |
| drazak | or not | 06:59 |
| Lemminkainen | it's an industry report | 07:00 |
| drazak | wonder why it can't do it | 07:00 |
| Lemminkainen | may be beyond poor paperbot's steez | 07:00 |
| drazak | indeed | 07:00 |
| @kanzure | you killed it | 07:09 |
| Lemminkainen | i love you paperbot http://psycnet.apa.org/journals/rev/93/2/119/ | 07:20 |
| paperbot | RuntimeError: maximum recursion depth exceeded in cmp (file "/usr/lib/python2.7/_weakrefset.py", line 73, in __contains__) | 07:21 |
| paperbot | RuntimeError: maximum recursion depth exceeded in cmp (file "/usr/lib/python2.7/_weakrefset.py", line 73, in __contains__) | 07:22 |
| Lemminkainen | o_o I'm so sorry Paper Bot | 07:23 |
| chris_99 | haha | 07:23 |
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| ThomasEgi | up the recursion limit! | 07:43 |
| ThomasEgi | http://cdn.memegenerator.co/instances/400x/39791605.jpg | 07:43 |
| chris_99 | heh | 07:45 |
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| archels | so this new stuff from IBM's SyNAPSE project is pretty cool | 08:25 |
| archels | https://dl.dropboxusercontent.com/u/91714474/Papers/020.IJCNN2013.Corelet.pdf | 08:25 |
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| archels | lots of applications | 08:27 |
| archels | http://www.research.ibm.com/software/IBMResearch/multimedia/IJCNN2013.algorithms-applications.pdf | 08:27 |
| archels | kurzweilai's writeup is actually relatively decent http://www.kurzweilai.net/ibm-research-creates-new-foundation-to-program-synapse-chips | 08:29 |
| chris_99 | are those chips analog? | 08:31 |
| chris_99 | in some parts | 08:31 |
| heath | kanzure: what's wrong zotero's lookup table? | 08:32 |
| heath | minus the horrible indentation | 08:32 |
| archels | chris_99: no, all-digital. weights are binary :( | 08:39 |
| chris_99 | ah | 08:40 |
| chris_99 | i'd quite like to make a simple ANN with op-amps and the like just to play with | 08:40 |
| archels | that's useless, just simulate it | 08:40 |
| archels | you'd be building a cybernetic circuit more than a neural circuit anyway | 08:41 |
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| chris_99 | i never said it'd serve much purpose, i'd have leds or something to view the weights etc ;) | 08:41 |
| archels | no, that's cool, but you'd be hard pressed calling it a neural circuit | 08:43 |
| archels | it would be an analog feedback controller | 08:43 |
| chris_99 | why couldn't i call it an ANN? | 08:44 |
| archels | because neurons do not work remotely like op-amps | 08:45 |
| chris_99 | i didn't think ANNs worked esp. like real neurons anyway? | 08:45 |
| archels | it's true that the level of realism varies considerably | 08:46 |
| archels | if you stuck a few op-amps together, you could call it a neuron in the classical McCulloch-Pitts sense | 08:46 |
| archels | but those aren't very much like real neurons either | 08:47 |
| chris_99 | it'd just be something kind of fun to play with i guess, like i could train it to act as an xor or what not | 08:48 |
| archels | well, I guess the guys at IBM got some good results with binary synapses, so we don't need over-the-top realism | 08:48 |
| * rk[] likes MP neurons | 08:51 | |
| rk[] | i have been considering making a led lattice, implementing a ANN and viewing the weights with LEDs | 08:52 |
| nsh | ugh, speaking of neurons... | 08:55 |
| nsh | anyone read this: http://www.wired.com/opinion/2013/07/die-links-die-stop-worrying-about-link-rot/ | 08:55 |
| nsh | synopsis: the web is a brain! it's a brain! no really, it's just like a brain! so therefore links that aren't used should rot and die and that will make it work better! | 08:55 |
| nsh | signed, brain scientist and all-round genius guy | 08:56 |
| nsh | i'm really tempted to irl stalk this person and engineer getting trapped in an elevator with him so i can savagely apply the cluestick for several hours without him being able to escape in his personal helicopter | 08:57 |
| @kanzure | heath: the code is poorly tested | 08:57 |
| @kanzure | heath: and it's hard to decipher what it's doing | 08:57 |
| @kanzure | heath: and it's not a state machine | 08:57 |
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| eudoxia | paperbot: http://dl.acm.org/ft_gateway.cfm?id=378823&ftid=120666&dwn=1&CFID=238345090&CFTOKEN=34506872 | 09:09 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/9c9eeacbe850042d120452c5348dab19.pdf | 09:10 |
| eudoxia | yisss paperbot | 09:10 |
| eudoxia | paperbot: http://dl.acm.org/ft_gateway.cfm?id=1065042&type=pdf&coll=DL&dl=GUIDE&CFID=238345090&CFTOKEN=34506872 | 09:11 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/7923b3a1efd5c07d3830d4a844850c75.pdf | 09:11 |
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| archels | The brain has two types of links: inbound (axons) and outbound (dendrites), and sometimes two neurons are connected by both an inbound and an outbound link — two-way links. | 09:33 |
| archels | wait--what? | 09:33 |
| @kanzure | they are just bad at describing basic neuroscience | 09:37 |
| chris_99 | that article looks crap in all respects | 09:37 |
| chris_99 | 'Our greatest technological network to date — the World Wide Web — is approaching a breakpoint, at which it will shrink.' | 09:37 |
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| nmz787 | anyone in here actually have success with ANNs? | 09:49 |
| @kanzure | once or twice. | 09:50 |
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| nsh | define success | 09:58 |
| nsh | some weights changed and now desired classification is occurs with higher frequency? or oh yeah, goldbach conjecture, solved that before breakfast | 09:59 |
| nmz787 | dunno what goldbach is | 10:08 |
| nmz787 | i guess i mean real world success, better at classification | 10:08 |
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| chris_99 | have you played with weka, that's pretty cool to compare a number of different classifiers | 10:35 |
| nmz787 | no | 10:39 |
| nmz787 | fenn: sortof related to the zeolite water from air http://www.youtube.com/watch?v=FWwii1dX4v8 | 10:39 |
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| @kanzure | http://learningthreejs.com/blog/2013/08/02/how-to-do-a-procedural-city-in-100lines/ | 12:24 |
| @kanzure | http://www.mrdoob.com/lab/javascript/webgl/city/01/ | 12:25 |
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| @kanzure | heh http://blog.typeracer.com/2013/08/08/typeracer-5th-anniversary-and-1-million-users/ | 12:38 |
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| @kanzure | well, zotero-translators sure is an active project https://github.com/zotero/translators/pull/606 | 13:23 |
| @kanzure | https://github.com/zotero/translators/pulls | 13:23 |
| @kanzure | ParahSail1n: apparently crossref returns more metadata than dx.doi.org https://github.com/zotero/translators/pull/452 | 13:24 |
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| ParahSailin | kanzure: what url do you request from for crossref | 13:35 |
| @kanzure | no idea, i'd have to look at their implementation | 13:36 |
| ParahSailin | i guess you can use http://www.crossref.org/guestquery | 13:42 |
| childcorn | Korean scientists have used lazers to perforate a cell and then optical tweezers to put foreign DNA into them. | 13:50 |
| childcorn | ABSTRACT http://www.opticsinfobase.org/boe/fulltext.cfm?uri=boe-4-9-1533&id=260009 | 13:51 |
| @kanzure | there is also laser-induced ultrasonic poration | 13:52 |
| gradstudentbot | Dude, you contaminated my experiment. | 13:53 |
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| yorick | kanzure: on your site, most useful qr code ever? | 14:04 |
| @kanzure | it's a honeypot for people silly enough to scan a qr code on a website | 14:05 |
| yorick | dammit | 14:05 |
| @kanzure | you're the only person it has ever trapped | 14:05 |
| @kanzure | congratulations! :confetti: | 14:05 |
| yorick | what do I win? | 14:05 |
| ParahSailin | what qr code | 14:06 |
| @kanzure | eternal shame | 14:06 |
| yorick | yay | 14:06 |
| @kanzure | ParahSailin: http://heybryan.org/ | 14:06 |
| yorick | kanzure: also your name thingy on github is going offscreen | 14:07 |
| @kanzure | my what? | 14:08 |
| yorick | http://dl.dropbox.com/u/22989236/temp/2013080824.png | 14:08 |
| yorick | or does it just say 'e' | 14:08 |
| @kanzure | it used to say "HIRE ME" but then i realized i didn't want to work | 14:08 |
| yorick | you could've made it 'kanzure' | 14:08 |
| @kanzure | https://github.com/gelstudios/gitfiti | 14:09 |
| @kanzure | also this guy did something else https://github.com/will | 14:09 |
| yorick | it would've been nice if it actually committed every day | 14:10 |
| @kanzure | it did. | 14:10 |
| yorick | it didn't cheat and commit in the past? | 14:10 |
| @kanzure | it committed in the future | 14:10 |
| yorick | that's *also* cheating | 14:11 |
| @kanzure | cheaters gonna cheat | 14:11 |
| @kanzure | i would rather just do actual work anyway | 14:12 |
| @kanzure | https://github.com/substack still trying to figure out which drugs he's on | 14:12 |
| yorick | kanzure: well it's his only job | 14:13 |
| yorick | I don't think he's on any drugs | 14:13 |
| yorick | he just does modules for a living | 14:13 |
| yorick | and sometimes combines them into moderately-well-working awesome virtualization things | 14:13 |
| @kanzure | "only job".. same with me, right? i just write code. | 14:16 |
| @kanzure | but i don't pump out 200 modules/year | 14:16 |
| yorick | kanzure: he writes modules to call mkdir -p | 14:17 |
| yorick | https://github.com/substack/node-mkdirp <-- he really does | 14:17 |
| @kanzure | yeah, i'm aware | 14:17 |
| yorick | and also, he doesn't maintain anything really | 14:17 |
| @kanzure | writing small modules is an okay thing | 14:17 |
| chris_99 | lol | 14:17 |
| @kanzure | being aware of code boundary issues is commendable because it lets you focus on the actual work | 14:18 |
| yorick | kanzure: or on infinite subprojects "hmm my mkdir -p needs a callback on every created dir, and to be able to automatically mount volumes according to fstab if mkdir -ping across it, and automatically calling sudo" | 14:23 |
| @kanzure | callbacks on each created directory would be cool | 14:24 |
| @kanzure | but your file system isn't async anyway | 14:24 |
| @kanzure | so it's a bit of a loss | 14:24 |
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| ParahSailin | sure, any syscall could be considered async | 14:30 |
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| drazak | wtf is an MFC? | 14:52 |
| @kanzure | mere field communicator | 14:56 |
| drazak | I... I don't think so | 14:56 |
| drazak | refering to this https://groups.google.com/forum/#!msg/diybio/2LiRM1OCwIA/8bbD2r0CUNAJ | 14:57 |
| drazak | is it.. a battery? | 14:58 |
| ParahSailin | microbial fuel cell | 14:58 |
| @kanzure | fuel cell | 14:58 |
| @kanzure | damn it he beat me | 14:58 |
| ParahSailin | really shitty sort of batter | 14:58 |
| ParahSailin | y | 14:58 |
| drazak | gotcha | 14:58 |
| ParahSailin | well, not shitty, but nobody's figured out how to make it useful yet | 14:58 |
| drazak | seems awful | 14:58 |
| chris_99 | what do the microbes do in it? | 14:59 |
| ParahSailin | electron donors to an electrode | 14:59 |
| chris_99 | intriguing | 14:59 |
| chris_99 | what sort of microbes? | 14:59 |
| drazak | this idea just seems awful | 14:59 |
| ParahSailin | shewanella | 14:59 |
| @kanzure | hahah funny to see mark hamalainen at synthego. basically he's jumping ship now. | 15:00 |
| drazak | chris_99: please tell me you're not 13 | 15:00 |
| @kanzure | wasn't he working at halcyon molecular | 15:00 |
| chris_99 | i'm not heh | 15:00 |
| @kanzure | and immunepath | 15:00 |
| ParahSailin | lol | 15:00 |
| @kanzure | and mitosens | 15:01 |
| chris_99 | http://en.wikipedia.org/wiki/Microbial_fuel_cell has lots of info | 15:01 |
| ParahSailin | mfcs tend not to be very useful | 15:01 |
| ParahSailin | if you want to get usable energy out of microbial fermentation, protip is methanogenesis | 15:01 |
| ParahSailin | you can put the methane into a fuel cell if you want | 15:02 |
| drazak | mfcs seem awful, you're probably better off using some sort of enzyme than an actual bacterium. | 15:02 |
| ParahSailin | loose "enzymes" tend to be even less productive | 15:03 |
| drazak | it just seems like a losing value | 15:04 |
| drazak | er, battle | 15:04 |
| drazak | it's my bed time | 15:04 |
| ParahSailin | the cool thing about bacteria is that they recycle their degraded enzymes for you | 15:04 |
| drazak | but I can't think of a way in which something biological magically gets you more energy out of electrons skipping levels | 15:04 |
| ParahSailin | drazak: it actually works, its just low power denisty | 15:04 |
| ParahSailin | its not "magic" | 15:04 |
| drazak | to be frank low power density is the same as not working at all | 15:05 |
| drazak | and what do you get, like, 100mv extra per cell? | 15:05 |
| @kanzure | what does power density mean in units? | 15:05 |
| drazak | come off it | 15:05 |
| @kanzure | huh? | 15:05 |
| nmz787 | pfft | 15:06 |
| nmz787 | ya'll are nuts | 15:06 |
| nmz787 | there are lots of interesting research directions that MFCs are the intersection of | 15:07 |
| drazak | show me papers | 15:07 |
| @kanzure | ha ha http://www.theverge.com/2013/8/7/4595876/kickstarter-founder-yancey-strickler-explains-ban-GMOs | 15:07 |
| nmz787 | hooking up wires to bio stuff, speeding up water treatment, sludge powered sensors | 15:07 |
| ParahSailin | kanzure: power density = W/ m2 of electrode area in this case | 15:07 |
| nmz787 | drazak: use google scholar | 15:07 |
| drazak | nmz787: if you think it's cool show me papers to prove it | 15:08 |
| gradstudentbot | The autoclave smells really good. | 15:08 |
| ParahSailin | kanzure: do we like drazak for some reason? | 15:08 |
| drazak | probably not, I'm kind of an asshole | 15:10 |
| chris_99 | look at all the cool stuff they can do on the wikipedia article | 15:10 |
| @kanzure | ParahSailin: he knows chemistry things sometimes | 15:10 |
| drazak | ParahSailin: also electronics things | 15:10 |
| nmz787 | drazak: i don't think it's cool enough right now to show you papers | 15:11 |
| drazak | nmz787: ok so it's not that cool yet, that I can understand | 15:11 |
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| nmz787 | it's more my mood | 15:11 |
| drazak | let me rephrase things so that I'm less of an asshole | 15:11 |
| nmz787 | my interest in MFCs lies in that some species grow wires from themselves to their electrode | 15:12 |
| nmz787 | and I think that could be useful in other applications | 15:12 |
| drazak | I don't think MFCs are a good research path if you're a small lab and it's your only thing you're researching | 15:12 |
| nmz787 | and the idea of charge separation | 15:12 |
| drazak | nmz787: I like bateria growing their own wires | 15:12 |
| drazak | that's cool and somethign with a lot of applications that doesn't lock you into a hard to fight battle | 15:12 |
| nmz787 | drazak: MFCs are cheap and easy though, why wouldn't they be a good hit for small labs? | 15:13 |
| drazak | nmz787: because it's hard to get somewhere with it in a constructive way, you make little improvements, but there's never an ah-hah moment, and it's going to take a LOT of time | 15:13 |
| drazak | nmz787: I think small labs want to have a lot of small projects | 15:13 |
| nmz787 | there's research into basically adding a wire in waste treatment plants that simply dumps current to ohmic resistance (resistance makes heat) | 15:13 |
| drazak | nmz787: shotgun vs sniper | 15:13 |
| nmz787 | so it speeds up waste treatment simply by heating itself | 15:14 |
| drazak | yep | 15:14 |
| nmz787 | it's more of optimization | 15:14 |
| ParahSailin | theres some reason why mfcs seem to be a dead end | 15:14 |
| nmz787 | ah hahs don't happen often in isolated science | 15:14 |
| nmz787 | these days at least | 15:14 |
| ParahSailin | lots of labs throw lots of money into them and it never seem to go anywhere | 15:14 |
| nmz787 | there's some collaboration or knowledge transfer | 15:15 |
| drazak | yes, optimization projects are almost always of diminishing returns | 15:15 |
| drazak | nmz787: yes, which is why the shotgun approach is great | 15:15 |
| drazak | nmz787: you get to collaborate with a lot of people on a lot of things | 15:15 |
| @kanzure | drazak: it's hard to tell what other people are in diybio for | 15:15 |
| nmz787 | they don't seem mutually exclusive | 15:15 |
| ParahSailin | if you want to get energy out of waste sludge, methane fermentation is well proven and scalable | 15:15 |
| chris_99 | i just saw the wiki page 'Electrohydrogenesis' know anything about that? | 15:17 |
| drazak | kanzure: dunno, I thin you know I'm in it to help people make actual science happen and not pseudoscience or just science for show, which is why I'm an asshole | 15:17 |
| ParahSailin | electrolysis? | 15:17 |
| nmz787 | ParahSailin: more like methanogenesis | 15:17 |
| chris_99 | http://www.sense.nl/graduations/2648 is the paper they cite | 15:18 |
| ParahSailin | nmz787: that was to chris_99 | 15:18 |
| chris_99 | ' biocatalyzed electrolysis ' | 15:18 |
| ParahSailin | if you're electrolysing water, you're already doing something dumb in most cases | 15:19 |
| nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/es803531g | 15:19 |
| ParahSailin | exceptions would be a nuclear submarine making oxygen for human crew and other weird applications like that | 15:19 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1021%2Fes803531g%26pubId%3D340422328 | 15:19 |
| ParahSailin | http://sci-hub.org/pdfcache/cb4cc1b556cc422eac80ed3f495ed704.pdf | 15:20 |
| ParahSailin | well thats garbage | 15:20 |
| @kanzure | drazak: "actual science". i see. that's not entirely why i'm here. | 15:20 |
| ParahSailin | hey im pretty sure my former pi is the editor of that journal | 15:20 |
| @kanzure | drazak: i mean, i certainly don't mean pseudoscience. but spending $100M to prove that a certain drug isn't effective.. doesnt' matter to me. | 15:21 |
| drazak | kanzure: heh, well, for some value of actual science, it's kind of a moving target | 15:21 |
| @kanzure | ParahSailin: got anything in the black book against him? you can bribe him into publishing.. er.. something. | 15:21 |
| drazak | kanzure: yeah that's not the type of science I'm talking about, and I think you know that | 15:21 |
| ParahSailin | ah, associate editor | 15:21 |
| @kanzure | associate editor means he does all the work, i think | 15:21 |
| ParahSailin | theres like 10 of those | 15:21 |
| drazak | kanzure: I simply mean doing things to some sort of standard, and that projects like lets make a kit to show off bioluminescent bacteria that a 5 year old can do don't interest me and I think they're a waste of time | 15:22 |
| drazak | if ou're not documenting hat you're doing it's useless, etc | 15:23 |
| @kanzure | ParahSailin: haha. i wonder how that works. | 15:23 |
| ParahSailin | http://pubs.acs.org/page/esthag/editors.html | 15:23 |
| drazak | nobody will take diy bio seriously if thing saren't documented well, if it's not repeatable, etc | 15:23 |
| ParahSailin | diybio is already a joke | 15:23 |
| drazak | ParahSailin: yeah well | 15:24 |
| drazak | ParahSailin: I can only do what I can do to help fix that | 15:24 |
| @kanzure | avery is finally pushing code up via git | 15:24 |
| @kanzure | https://github.com/AveryLouie/BlogDocs/tree/master/DNACrusher | 15:24 |
| ParahSailin | it will be a joke until methods come within the reach of diyers | 15:24 |
| @kanzure | ugh he had images dumped into the repo whaaaat | 15:24 |
| nmz787 | drazak: you must not value enhancing the educational effectiveness for coming generations | 15:24 |
| @kanzure | and .pyc files argh | 15:24 |
| ParahSailin | lol pyc | 15:24 |
| @kanzure | oh it's his blogdocs repo wtf | 15:25 |
| @kanzure | still.. pyc :( | 15:25 |
| @kanzure | and .tar files | 15:25 |
| ParahSailin | i think that guy has not heard of biopython which basically makes all that code he just pushed redundant | 15:25 |
| @kanzure | well, at least it's python. so now instead of cathal and avery making crap in different languages, i only have to fix their crap in one. | 15:26 |
| @kanzure | win-win-lose... :| | 15:26 |
| drazak | nmz787: not really, no | 15:27 |
| gradstudentbot | I could never be a PI. | 15:27 |
| nmz787 | drazak: well that stuff matters, so just know that some projects you might think are stupid, but it's more stupid to worry about them, unless they're causing trouble | 15:28 |
| ParahSailin | lol ^I tabs ftw | 15:28 |
| drazak | nmz787: that's why those projects I don't comment on | 15:28 |
| drazak | nmz787: I just let them go | 15:28 |
| nmz787 | glowing gfp ecoli with an elecron microscope to accompany would be an awesome kit for a 5 yr old | 15:28 |
| drazak | nmz787: I do comment on bad science | 15:28 |
| drazak | why do you need an electron microscope o.O | 15:28 |
| nmz787 | seems avery could have done what he did with biopython, but i guess that would be heavier? | 15:29 |
| ParahSailin | heavier but kanzure wouldnt have to fix it | 15:29 |
| @kanzure | biopython is poorly written in a bunch of places, but at least the general community has agreed to maintaining it or something | 15:29 |
| ParahSailin | also his fasta file parser is probably broken | 15:30 |
| nmz787 | i can't really tell what it's use is really supposed to be... or rather what his graph is showing... I've only sequenced stuff like twice, and used sequencher once and can't remember the second time | 15:32 |
| drazak | nmz787: I know a guy in ##chemistry who do some awesome sythetic chemistry stuff in their garage, can't remember his f-ing name but kanzure probably remembers who it is | 15:32 |
| nmz787 | or what's wrong with phred phrap consed? | 15:32 |
| drazak | nmz787: he has a legit lab notebook and could probably publish if that was to his liking if he had a novel method for his synthesis | 15:33 |
| drazak | UC235 | 15:33 |
| drazak | derp | 15:33 |
| nmz787 | was it synbio? | 15:35 |
| @kanzure | no i don't remember the person | 15:35 |
| nmz787 | or for synbio? | 15:35 |
| drazak | nmz787: no he has youtube vids | 15:35 |
| drazak | he posted images of his lab notebook a couple time sin ##chemistry | 15:35 |
| drazak | nmz787: http://www.youtube.com/watch?v=-PGtoZEZnzc is a good one, he has better chemistry in his other ones | 15:36 |
| drazak | he had some cool new synthesis pathways and stuff | 15:36 |
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| drazak | oh | 15:37 |
| drazak | nmz787: didn't realize you were nathan | 15:37 |
| @kanzure | tequals0: hi there | 15:38 |
| @kanzure | tequals0: do you know about biopython? | 15:38 |
| tequals0 | hi | 15:38 |
| tequals0 | yep | 15:38 |
| @kanzure | are you aware that your git repo has a .pyc file in it? | 15:38 |
| tequals0 | yes | 15:38 |
| @kanzure | these are precompiled python files that usually aren't distributed around | 15:38 |
| @kanzure | okay cool. welcome to the fold. | 15:38 |
| tequals0 | it also has the source, or it should | 15:38 |
| nmz787 | tequals0: hi! | 15:39 |
| tequals0 | hey nathan (?) | 15:39 |
| gradstudentbot | If I break my arm, do I still have to present tomorrow? | 15:40 |
| nmz787 | ea | 15:40 |
| nmz787 | yea | 15:40 |
| nmz787 | i just replied on the list | 15:40 |
| @kanzure | gradstudentbot: yes, go write that paper | 15:40 |
| gradstudentbot | The paper was rejected. | 15:40 |
| nmz787 | can't tell what your plot is supposed to be helpful for | 15:40 |
| nmz787 | lol | 15:40 |
| nmz787 | gradstudentbot: you're getting smarter! | 15:40 |
| gradstudentbot | Oh that's interesting, do you want to write a paper together? | 15:40 |
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| tequals0 | its supposed to give you a hint as to where the two overlap | 15:44 |
| tequals0 | The advantage vs other things is that it has less documetnation to read | 15:45 |
| @kanzure | tequals0: btw what are the items you are selling? | 15:45 |
| tequals0 | ? | 15:45 |
| tequals0 | the gel box? | 15:45 |
| @kanzure | you started to sell a transilluminator i think? | 15:45 |
| @kanzure | oh a gel box | 15:45 |
| @kanzure | okay | 15:45 |
| nmz787 | tequals0: you defintely want a good diffuser | 15:46 |
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| nmz787 | mac posted some pics on facebook a while back of some illuminator he was testing and it looked horrible (he had no diffuser) | 15:46 |
| nmz787 | the image looked horrible i should say | 15:46 |
| nmz787 | you would have a harder time extracting data from it, such as peak intensity | 15:47 |
| tequals0 | yea | 15:47 |
| nmz787 | tequals0: it would be great if you could re-imagine a plate gel system | 15:47 |
| tequals0 | I am working one | 15:47 |
| tequals0 | you can read details here https://tequals0.wordpress.com/2013/08/04/gelis-illuminator/ | 15:48 |
| nmz787 | that iphone screen simon mentioned sounded good, as they should be aiming for equal illumination, though they can def bleed or be uneven | 15:48 |
| nmz787 | tequals0: i actually stopped doing gels because i don't have capillaries or thin lanes between plates | 15:48 |
| tequals0 | illumination experiments here https://tequals0.wordpress.com/2013/08/03/the-guide-to-diy-gel-illumination/ | 15:48 |
| tequals0 | i had a capilary design, but it's not what I am going with for the time being | 15:49 |
| nmz787 | gels in long glass pipette tips might work, but it might be better to have a flat capillary for imaging | 15:49 |
| tequals0 | http://tequals0.files.wordpress.com/2013/08/img_4577.jpg | 15:50 |
| tequals0 | flat 1 ml gel/channel | 15:50 |
| nmz787 | i would beta test that | 15:51 |
| tequals0 | good | 15:52 |
| nmz787 | if tomkinsc were idling here, he'd have some optics input | 15:52 |
| tequals0 | The transluminator/psu/gel box are going to get rolled out together first, but after that I want to play with different gel boxes, like half-gel box for running fewer samples, capilaries etc. | 15:53 |
| tequals0 | I thought about a circular gel box, but that might be too avant-garde | 15:55 |
| nmz787 | realistically you could just make it automated completely. with a lased or LED at the end and a photodiode detector | 15:55 |
| nmz787 | and not worry about diffusers | 15:55 |
| nmz787 | laser* | 15:55 |
| nmz787 | or work up to that | 15:56 |
| drazak | nmz787: anyway I'm gonna get some sleep, but we can talk about this more later | 15:57 |
| tequals0 | i like the laser/led idea | 15:58 |
| tequals0 | I agree that is how it should be done | 15:58 |
| tequals0 | like a drum scanner | 15:58 |
| tequals0 | but unfortunately people are fixated on SEEING THE DNA | 15:59 |
| tequals0 | i mean, ideally, robots would do it all | 15:59 |
| tequals0 | you would just do something like | 16:01 |
| nmz787 | drazak: see ya | 16:02 |
| tequals0 | gel_electrophoresis(100v, 50ma, 2h, DNA_SAMPLES) and then in 2 hours you would have a picture+metadata | 16:02 |
| nmz787 | drum scanner? | 16:02 |
| nmz787 | i was thinking more like a sanger sequencer or RFLP analyzer | 16:02 |
| nmz787 | plain capillary gel electrophoresis | 16:03 |
| tequals0 | http://www.luminous-landscape.com/reviews/scanners/drum_scans.shtml | 16:03 |
| nmz787 | has a single detector like all the other chromatographs | 16:03 |
| tequals0 | right, but "drum scanning" with a head instead of a photo | 16:03 |
| tequals0 | much higher resolution | 16:03 |
| tequals0 | even illumination | 16:04 |
| tequals0 | etc. good stuff | 16:04 |
| nmz787 | i don't get it | 16:04 |
| nmz787 | no | 16:04 |
| tequals0 | we are talking about the same thing, i think | 16:04 |
| tequals0 | well, basically the same thing | 16:04 |
| nmz787 | sanger and normal capillary and other chromatograms don't move the sensor | 16:05 |
| nmz787 | you just get elution time | 16:05 |
| tequals0 | ah | 16:05 |
| nmz787 | which happens to corellate to lenght | 16:05 |
| nmz787 | length | 16:05 |
| tequals0 | but it is the same idea | 16:05 |
| tequals0 | that you have a single read head | 16:05 |
| tequals0 | instead of many | 16:05 |
| nmz787 | this also eases purification of said band | 16:05 |
| nmz787 | cause it just dumps out the end | 16:05 |
| tequals0 | that has identical illumination/sensing | 16:05 |
| nmz787 | sure | 16:05 |
| tequals0 | instead of vingetting/pixels | 16:06 |
| tequals0 | yea | 16:06 |
| nmz787 | i'm saying move it with electrics | 16:06 |
| nmz787 | not mechanics | 16:06 |
| tequals0 | right | 16:06 |
| nmz787 | well it's still pixels | 16:06 |
| nmz787 | just a single row in that scanner | 16:06 |
| nmz787 | but yeah no lens falloff | 16:06 |
| tequals0 | right, but your pixels are arbitrarily close together instead of whatever sensor you have | 16:06 |
| nmz787 | a drum scanner might still have a diffuser, but more likely a bar fluoro lamp | 16:07 |
| nmz787 | tube | 16:07 |
| tequals0 | mmhm | 16:08 |
| gradstudentbot | You know, I hear you make more money being a garbage man. | 16:08 |
| tequals0 | gradstudentbot: also, health benifits and $20 on xmas | 16:09 |
| gradstudentbot | She keeps talking about her Nature paper, but she was only third author. | 16:09 |
| gradstudentbot | Well, you can't guarantee that. | 16:10 |
| gradstudentbot | Yeah, it's significant. | 16:10 |
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| cpopell | I missed the MFC discussion | 16:22 |
| cpopell | but if you guys want I can put you in touch with one of the people working on it... | 16:22 |
| cpopell | err, at a business scale | 16:23 |
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| tomkinsc | Anyone know of good free software for doing image stacking for astrophotography? | 16:37 |
| @kanzure | sudo apt-get install gcx | 16:42 |
| tomkinsc | thanks | 16:52 |
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| tomkinsc | Registax seems to also be popular, and can run under wine apparently http://www.astronomie.be/registax/ | 16:56 |
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| @kanzure | "The National Security Agency, hit by disclosures of classified data by former contractor Edward Snowden, said Thursday it intends to eliminate about 90 percent of its system administrators to reduce the number of people with access to secret information." | 18:36 |
| gradstudentbot | I think the centrifuge is broken. | 18:36 |
| cpopell | wut | 18:42 |
| cpopell | but Snowden was Booz | 18:42 |
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| @kanzure | "Looks like there are going to be 900 disenfranchised sysadmins out in the wild.... I wonder what information they'll have." | 20:08 |
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| heath | hrm | 22:03 |
| heath | https://www.ourlab.net/Default.asp | 22:03 |
| heath | https://www.youtube.com/watch?v=ZeL1nrt76V4 | 22:03 |
| heath | .title | 22:03 |
| yoleaux | OURLab Intro.mov - YouTube | 22:03 |
| heath | oppenheimer offered his lab for the diybio meetup :) | 22:03 |
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| * brownies pokes gradstudentbot | 22:18 | |
| gradstudentbot | When are you going to publish? | 22:18 |
| * brownies pokes gradstudentbot | 22:18 | |
| gradstudentbot | Well, it looks better if you see it through a UV scope. | 22:18 |
| heath | gradstudentbot: you can't like brownies poke you around like that | 22:20 |
| gradstudentbot | Well, the IRB rejected that, so I'm going to rewrite it and try again. | 22:20 |
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| heath | gradstudentbot: you | 23:27 |
| gradstudentbot | Blah, I'm going to quit. | 23:27 |
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| --- Log closed Fri Aug 09 00:00:50 2013 | ||
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