2013-02-15.log

--- Log opened Fri Feb 15 00:00:01 2013
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eleitlspringerkink, huh01:21
@kanzurehahah01:21
@kanzureyes :)01:21
eleitlIs that a real project?01:21
eleitlIt better ber.01:21
eleitlThat would be indeed glorious to behold.01:21
@kanzureit's in the early idea phase01:21
@kanzurei'm open to suggestions01:21
eleitlI'm swamped. But Rule 34 sounds like a good start.01:27
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eleitlBolide rain over Ural. 50 people hurt.01:31
eleitlThe pressure wave broke many windows.01:32
eleitlhttp://de.rian.ru/society/20130215/265530539.html01:33
eleitlsee amateur video there01:33
@kanzurecrater: http://www.youtube.com/watch?v=XDYdh7V0vyU01:43
eleitlThat's burning coal.01:46
eleitlSorry, gas. Darvaz: http://www.hoax-slayer.com/door-to-hell.shtml01:47
eleitlThought I remembered it.01:47
@kanzuredarn.01:52
eleitlReal impact craters are different.01:53
eleitlHere's a big local one: http://passc.net/EarthImpactDatabase/ries.html01:55
eleitl24 km diameter, 14.3-14.5 MYrs01:56
eleitlcrater rim still very visible: http://en.wikipedia.org/wiki/File:Ries_Crater_Rim.jpg01:56
@kanzurehttp://www.youtube.com/watch?v=NuKtVGdPESM http://youtube.com/watch?v=-OAcrmjmHp402:02
@kanzureliving in the future is pretty neat02:02
@kanzure""We can only register stones coming from the direction of the night sky," Malkov explained." .. seems like a rather critical flaw.02:05
@kanzureeleitl: http://bettercryonics.com/BetterCryonics02:08
eleitlLuke Parrish's work02:13
eleitlNews from Parallella: http://www.parallella.org/02:14
eleitlZynq-7020 onboard, with 48 FPGA pins, with 8 GByte/s throughput02:15
jrayhawkpretty02:15
eleitlthis is begging to implement a custom MPI interface02:15
eleitlwith 6 links you'll get 8 pins/link02:16
eleitlmaybe even space for a primitive Bresenham router02:16
eleitlRoman will be publishing a guide explaining how to replace the bit stream of the default Parallella Ubuntu 12.04 SD image distribution with a custom bit stream. It is quite straightforward.(as long as the content of the FPGA bitstream is valid..)02:33
eleitlhow far can an FPGA pin drive a signal directly?02:34
eleitl10 cm?02:34
archelsIt depends on what it is that it's driving.02:35
archelsOtherwise, just stick a cheap off-the-shelf buffer on there.02:35
eleitljust FPGA to FPGA, with shorterst distance and smallest cable geometry02:35
archelsAt a GHz or so, 10 cm should be no trouble at all.02:36
eleitlcan you get 1 GByte/s with 8 pins?02:36
archelsWith the right FPGA, sure.02:36
eleitlZynq-702002:36
eleitlhttp://www.youtube.com/watch?v=RH1DpTOuheI02:38
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archelseleitl: its DDR3 interface is only 800 Mb/s02:39
eleitlif it's a switch it needs to be able to cut-through02:39
eleitlso it wouldn't need RAM02:39
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archelsits internal logic tops out at 1412 MHz for the highest speed grade02:42
archelsbut achieving 1 GB/s relies on more things than just raw speed02:42
eleitlwhat does that mean in practical terms? Less than 1 GByte/s througput through each 8 pins?02:42
eleitl800 MByte/s would be quite ok for MPI02:43
eleitlit's latency that counts02:43
eleitlthat way you could keep GBit Ethernet NIC for admin stuff02:43
archelsif it's a burst transfer and not sustained, you can probably do it02:43
eleitlthanks, archels02:43
archelssure02:44
eleitlreally looking forward to take my board for the spin02:44
eleitlif it's good I'm going to order 802:44
archelscool, any specific application plans for it or just playing around?02:44
eleitlMD and neural stuff02:45
eleitlI want to see what you can do with 32 kBytes/DSP core02:45
eleitlI think one can do plenty02:45
archelsWhat type of neurons though?02:46
eleitlAs biologically realistic as possible. I'll start small, and see how far I can get.02:46
eleitlSomething like Openworm would be great.02:46
archelsWhat can the FPGA offer you at this point that a general-purpose processor cannot?02:48
eleitlthe FPGA is just for the MPI interface02:48
eleitlthe 16-64 DSP cores are for heavy lifting02:48
archelsI don't think we're at a point yet where speed is the bottleneck for neural simulations02:48
archelswe just don't know what we're doing, mostly :)02:48
eleitlI'm going to start with the smallest numerics footprint I can, and work myself upwards02:49
archelssure, but why on the FPGA board and not on your desktop in NEURON or Moose or so?02:49
eleitlnot on the FPGA board02:50
eleitlthe FPGA is part of the Epiphany board, so it's free02:50
eleitlthe idea is to extend the on-die fabric by MPI in FPGA, for a 3d torus02:50
eleitlthe board is credit-card sized, and air-coolable, so you could build a nice cubic latice numerics box02:51
archelsthat does sound nice, but on the other hand it's going to take a lot of time to implement this, whereas you can have NEURON up and running in about 5 minutes02:51
archelsI'm probably being dense, but I don't see the added value if the purpose is neuronal simulation02:51
archelsif the purpose is exploring hardware/firmware options for neuronal simulation, then I do see the point02:52
eleitlI need a cheap numerics box that is scalable. 99 USD/board is cheap.02:53
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eleitlI want something that can do realtime neurons02:54
eleitli.e. kHz scale events in realtime on that iron02:54
eleitlsomething that can scale O(1) by throwing hardware at it02:54
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eleitl3d lattice with local communication only02:55
eleitlthe 16 or 64 DSP cores with embedded memory are effectively local02:57
eleitlthe idea is to scale this across a 3d lattice02:57
eleitlit's basically a SHARC cluster on a die02:57
eleitlI very much doubt Neuron would scale across that, especially as O(1)02:58
eleitlO(1) meaning here that your runtime stays constant with problem size if you match that with hardware02:59
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archelsah, realtime emulation--having a scaleable solution for that would be nice.03:04
eleitlyep03:04
archelsI'm sure you could still accomplish that on a desktop for the C. elegans brain, but not for brains much larger than that03:05
eleitlI would like 20 kNeurons03:07
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archelsHmm, how many neurons are there again in an average cortical column?03:17
archelsAbout that order of magnitude?03:17
eleitlmaybe03:18
eleitlI'm looking at L. stagnalis03:18
archelsoh yes, I recall03:18
eleitlEpiphany is almost an order of magnitude more energy-efficient than Blue Gene/Q03:18
eleitland a lot cheaper, especially if you can buy them in installments03:19
archelsHere, we report the number and distribution of NeuN-positive neurons within the C2, D2, and D3 TC projection columns in P27 rat somatosensory barrel cortex based on an exhaustive identification of 89 834 somata in a 1.15 mm3 volume of cortex. A single column contained 19 109 ± 444 neurons (17 560 ± 399 when normalized to a standard-size projection column).03:20
archelsthen of course we can debate about the functional role of glia...03:22
eleitlthe glia don't seem to require a lot of crunch03:24
eleitlso cortical column, just 20 kNeurons?03:24
eleitlthat's quite small03:24
eleitlso ~1 mm^3, 20 kNeurons?03:25
archelsit's probably an underestimation, as they only looked at NeuN positive cells.03:36
eleitlstill, as an order of magnitude estimate it's a good thing to know03:37
eleitlDARPA and UPMC collaboration -- Direct control of prosthetic arm by tetraplegic individual. Electrodes wired into cortex. Watch out for tactile03:40
eleitl+feedback and wireless interface coming soon.03:40
eleitlhttp://www.yousendit.com/download/UW16YUlqMGNKV1A0WjlVag03:41
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archels"We are all interested in the future, for that's where we'll be spending the rest of our lives" --Free The Robots04:21
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* eleitl has no future04:30
eudoxiait's ok eleitl, if any of the cryo orgs go bankrupt we'll go in and steal your head04:30
eleitlit's probably going to be my own cryo org :/04:31
eleitlspeaking of which, I probably have vitrified some VM-1 yesterday. I haven't had time to look yet.04:31
Mariu:p04:32
Mariunice one, eudoxia04:32
eleitlfirst dewar fill blew through some 95 l04:32
eleitlI'm still not convinced the vacuum is very good. but, it will do for time being.04:33
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strangewarpWaking up to meteor videos is pretty weird05:24
Mariuoh05:24
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@kanzurehttp://aws.amazon.com/redshift/ seems to offer 16 TB storage for $1000/TB-year if you pay $24k up front05:53
@kanzureit's crazy how little space we have available05:59
@kanzuremega.co.nz offers 4 TB for $25/mo06:01
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@kanzureheh they are asking for 20 TB minimum per hosting offer https://mega.co.nz/#hosting06:05
@kanzureopera owns the admarvel ad network?06:12
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@kanzurehosted phantomjs scraping http://tubes.io/09:06
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archelsBetteridge's law of headlines is an adage that states, "Any headline which ends in a question mark can be answered by the word no."11:08
@kanzurethere's a law of laws that says that invariably someone will bring that up in response to a headline like that11:09
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@kanzuredelinquentme: have you met SphericalMouse at biocurious yet?11:09
delinquentmenah havn't b een down there yet11:10
delinquentmejust attempted to join the langton labs group11:10
delinquentmekanzure, also does anyone in SF that you know need a roomie?11:10
@kanzurelangton labs is chronically overbooked11:11
@kanzureklafka might want a roommate. josh gourneau asks often too, i think.11:11
klafkai'm full up atm11:12
nmz787delinquentme: how's SF so far?11:12
delinquentmenmz787, wild11:13
delinquentmei need to do moar11:13
nmz787so there's a kid in the science class I'm teaching who has diabetes... should I mention genetic engineering to him?11:13
nmz787delinquentme: i found SF was too expensive for me to get out much11:13
Mariudelinquentme: what does SF stand for ?11:14
nmz787whether it was taking the train, or paying for parking...11:14
delinquentme*shrug*11:14
@kanzureMariu: san francisco11:14
Mariuthanks, kanzure11:14
@kanzurenmz787: which diabetes?11:14
@kanzureactual diabetes or the other one?11:14
nmz787i think type 111:14
nmz787cause he can't eat the snacks the other kids get11:15
nmz787i dunno if it's connected at all, but his dad is blind too11:15
nmz787he sits outside the classroom, I think to give him meds before or afterwards11:15
nmz787i think11:15
nmz787he could just be paranoid after all that shooting crap11:16
nmz787hah, on that topic... the school nor volunteer agency ever asked for any paperwork or IDs11:16
nmz787they know my email address and name from that11:16
klafkai've never been asked for anything either for any job11:18
klafkamy work now apparently thought i had a phd for a month after i joined11:18
klafkaeven though i explicitly told several people i never finished it11:18
nmz787lol11:18
nmz787do u?11:18
klafkai didn't finish it11:18
klafkait's listed on my resume but it's like 2 years11:19
nmz787ur extra smrt, finish phd in 2 years11:19
klafkaunless i'm stephen wolfram11:19
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chris_99with companies that hold plasmids, do they use PCR to replicate the DNA?11:59
@kanzurethere's a popular yeast method of copying plasmids12:03
chris_99ooh interesting12:03
chris_99is there a way to know what DNA will actually function in different cells, for instance with http://2007.igem.org/Edinburgh/Yoghurt/Design#Lemon_Flavour_Production how do they know it'll function in lactobacillus and ecoli, do they actually have to test it, or is there a clever way to know12:09
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yashgarothwho uses yeast for amplifying plasmid?12:12
@kanzuremaybe i am misremembering12:13
@kanzurechris_99: the answer to your question is yes ;)12:13
yashgaroth"Unfortunately all three of the genes responsible for lemon flavour synthesis have three or more forbidden restriction sites, making their isolation and insertion into biobricks impossible within a short period of time" pffft haha12:13
@kanzureyes they have to test it12:13
chris_99oh12:13
chris_99darn12:13
chris_99that's a bit of a pain surely12:13
@kanzureand yes there is a "clever way to know".. this looks like only one or two enzymes they need to insert.12:14
yashgarothyou can make an educated guess, there are maps of what precursors a species will have, so you gotta make sure those are present12:14
@kanzurechris_99: this is less painful than the majority of other things in biology12:14
@kanzureyep.. but then you also run the risk of things not folding because ph or something12:14
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@kanzureor maybe it doesn't get expressed because you forgot to do codon optimization12:14
yashgarothtrue, but you can factor those in12:14
yashgarothmostly this stuff is metabolic engineering; even if it works and expresses, you're probably only gonna get femtograms of product12:15
yashgarothso you're tweaking a hundred other genes to generate more substrate, which each require tweaking of their upstream genes, etc12:15
chris_99gotcha12:16
yashgarothe.g. they eventually got yeast to make arteminisinininin but their final expression was a million-fold higher than when they just shoved the genes in12:17
yashgarothsorry, artemisinin, that word gives me a stroke12:17
chris_99had to google, that, anti-malaria drug right12:17
@kanzureburnhousesdownisin12:17
yashgarothchris_99 yep it was previously only made by some shitty plant in small quantities12:19
chris_99heh12:19
chris_99"We analyzed this first beer for limonene content via headspace (SPME needle) GC-MS. Unfortunately we could not yet proof a significant difference between the beer containing limonene and the negative control beer." pity12:28
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nmz787chris_99: generally the first educated guess is to try promoters from other gram-similar species12:37
nmz787a lot of these bugs have small plasmids naturally, so you can often isolate them, then try shoving them in some similar (or not so similar) species to see if it works12:38
nmz787then lots of tweaking and shit like yashgaroth said12:38
chris_99what's gram-similar mean?12:40
nmz787well like you have gram-negative12:44
nmz787and gram-positive12:44
nmz787so a plasmid from a gram-negative will sometimes work in other gran-negatives, just like that12:45
nmz787i mean, unmodified12:45
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nmz787so you could theorhetically just be grabbing plasmids from moldy crap in your fridge :P12:46
nmz787rotten but not moldy stuff would work too12:46
nmz787since mold refers to eukaryotes12:46
yashgarothgoing to LA, bbl12:48
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chris_99gotcha, that's interesting12:49
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nmz787what's the belgian biohack space?14:01
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streetyhas anyone pulled datasets from https://www.ncbi.nlm.nih.gov/geo/ and repeated the analyses presented in the papers the dataset was taken from?15:20
@kanzurepaperbot: http://genomebiology.com/2013/14/1/10415:42
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/f8014bac78038f967709f7cc939d0bd8.txt15:42
@kanzurepaperbot: http://genomebiology.com/content/pdf/gb-2013-14-1-104.pdf15:42
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9290087e7f8e79bbfc211b17b085bf8a.txt15:42
juri_ugh. my reading list could kill a small child.15:46
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abetuskDid you guys see this: http://www.kickstarter.com/projects/254134422/finding-genes-to-create-perennial-crops16:12
ParahSailinhes not gonna do anything useful with that experiment16:14
abetuskah, no?16:18
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abetuskwhy not?16:20
abetuskParahSailin16:23
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@kanzure"The market is relatively small compared to  smart phones for example but is a huge market ( about 40 BB for life science tools and probably 200BB for diagnostics)"16:36
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@kanzure$40B sounds pretty huge to me.16:46
ParahSail1nabetusk, wetlab intuition17:02
ParahSail1nor maybe that disillusionment is just the reason i didnt make it through grad school17:03
@kanzurewin 8117:03
@kanzureack.17:03
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@kanzureSphericalMouse: welcome back17:37
@kanzureJuul: sup17:37
Juulkanzure, learning about oxy-acetylene cutting. Do you have expertise in that area?17:37
illusiveget a decent mask17:38
illusivegoggles wont keep your beard from catching fire17:39
@kanzurei screwed up a part once, but that's the only time i used an oxy-acetylene torch.17:39
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Juulhehe yeah17:39
Juuli'm trying to figure out if the connections are standardized17:40
illusivewell if you have to diy17:40
illusiveat least  youll know whats best to use17:40
Juulmmm17:42
Juuli'm a total noob at this. i didn't even know there was a specific cutting attachment17:42
SphericalMouseyoyo17:44
@kanzurehah i didn't know this part,18:01
@kanzure"This power was used to raise money for the Crown, and was widely abused, as the Crown granted patents in respect of all sorts of common goods (salt, for example). Consequently, the Court began to limit the circumstances in which they could be granted."18:01
@kanzure"After public outcry, James I of England was forced to revoke all existing monopolies and declare that they were only to be used for "projects of new invention". This was incorporated into the Statute of Monopolies in which Parliament restricted the Crown's power explicitly so that the King could only issue letters patent to the inventors or introducers of original inventions for a fixed number of years."18:01
@kanzureweird "England issued its first patents under Elizabeth I and established a patent system in the Statute of Monopolies of 1624, the country's first antitrust law as well as its first patent law (barring all monopolies except over disclosed inventions)."18:08
-!- illusive is now known as mutagen18:23
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@kanzureit's too bad that pastebins fail for data with weird character encodings19:06
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delinquentmeyeeeeee19:08
delinquentmesoo I'm now a resident19:08
delinquentmefenn,  you wan get beer??19:08
delinquentmeParahSail1n, you around?19:09
@kanzureneither of those two people live in SF19:09
delinquentmeO_o;;  really?19:09
Juuldelinquentme, where'd you end up living?19:12
delinquentmeJuul, I'm in the mission atm!19:15
delinquentmefor the next 2 months19:15
delinquentmeso I'm gonna see how that works out ... and I"ll check to see whats going on with some of the other areas19:15
delinquentmewhich is kind of what the issue is ...19:15
delinquentmeI need to see more of oakland before I move there ... like find out where the hangout spots are19:16
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delinquentmeJuul, are there any late night coffee shops?19:23
delinquentmeFarleys was decent19:23
Juuldelinquentme, where?19:23
delinquentmeoakland19:23
Juulsudo room19:24
delinquentmehaha this is true19:24
Juulthere are a couple of places that advertise 24/7 but the signs are so old that i wouldn't trust them19:25
Juullike the "24/7" burger joint outside sudo room that closes whenever they feel like19:26
delinquentmehahah19:26
delinquentmenot bad!19:26
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delinquentmeJuul, can sudo room get mail?19:30
Juuldelinquentme, hm, I don't know. why?19:31
delinquentmeFor ordering parts19:31
delinquentmeshakers , laser cut stuff19:31
Juulnah, there's no-one to receive it19:32
delinquentmeand what about cutting utensils ?  Is there anything that could chop masonite?19:32
Juulbiocurious has a package reception service19:32
ParahSail1ndelinquentme, im around19:33
Juuldelinquentme, chop it? there are power saws19:33
delinquentmeawesome.19:34
delinquentmeParahSail1n, I thought you were in SF19:34
delinquentmebut it turns out im wrong haha19:34
ParahSail1nnope19:34
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delinquentmeSO I'm trying to think of some of the kids who I should be bumping shoulders with19:42
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delinquentmeJuul, do you guys usually hang there through the weekends?19:51
Juuldelinquentme, there are generally always people there in the afternoons and evenings yeah.19:51
Juul+ sunday evening is cleanup19:51
delinquentmeok wicked19:52
ParahSail1nlol http://www.iamdann.com/2013/02/15/magnet-implants-can-actually-be-pretty-annoying19:55
@kanzurejrayhawk: which versions of linux does CVE-2013-0871 effect? it doesn't seem obvious to me.20:19
doclgrr, I can't find anything on perfusing a chicken eye.20:20
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nmz787paperbot: http://pubs.acs.org/doi/abs/10.1021/j100114a03820:46
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Analysis%20of%20resolution%20in%20DNA%20sequencing%20by%20capillary%20gel%20electrophoresis.pdf20:46
delinquentmeSO20:47
delinquentmeso called "biologics"20:47
delinquentmeare simply more complex than the normal pharma we're used to20:47
delinquentmeIE an organism vrs a chemical20:48
nmz787you gotta think about post-translational modification and shit20:49
nmz787or maybe one company uses a slightly different gene sequence20:49
nmz787mostly the same protein, but how similar does it need to be?20:49
nmz787that's the grey area of biologics20:50
nmz787paperbot: http://pubs.acs.org/doi/abs/10.1021/bi00688a01020:50
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Chain%20length%20determination%20of%20small%20double-%20and%20single-stranded%20DNA%20molecules%20by%20polyacrylamide%20gel%20electrophoresis.pdf20:50
jrayhawkhaha "cobol on cogs"21:00
ParahSail1nlol21:04
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JayDuggerGood evening, everyone.21:24
ParahSail1nhi21:25
delinquentmenmz787, a biologic is more than just a  sequence though right?21:28
delinquentmeits an actual running organism21:28
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@kanzurewhy is this private https://groups.google.com/group/biocurious-printer-hacking23:24
--- Log closed Sat Feb 16 00:00:02 2013

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