--- Log opened Fri Feb 15 00:00:01 2013 | ||
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eleitl | springerkink, huh | 01:21 |
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@kanzure | hahah | 01:21 |
@kanzure | yes :) | 01:21 |
eleitl | Is that a real project? | 01:21 |
eleitl | It better ber. | 01:21 |
eleitl | That would be indeed glorious to behold. | 01:21 |
@kanzure | it's in the early idea phase | 01:21 |
@kanzure | i'm open to suggestions | 01:21 |
eleitl | I'm swamped. But Rule 34 sounds like a good start. | 01:27 |
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eleitl | Bolide rain over Ural. 50 people hurt. | 01:31 |
eleitl | The pressure wave broke many windows. | 01:32 |
eleitl | http://de.rian.ru/society/20130215/265530539.html | 01:33 |
eleitl | see amateur video there | 01:33 |
@kanzure | crater: http://www.youtube.com/watch?v=XDYdh7V0vyU | 01:43 |
eleitl | That's burning coal. | 01:46 |
eleitl | Sorry, gas. Darvaz: http://www.hoax-slayer.com/door-to-hell.shtml | 01:47 |
eleitl | Thought I remembered it. | 01:47 |
@kanzure | darn. | 01:52 |
eleitl | Real impact craters are different. | 01:53 |
eleitl | Here's a big local one: http://passc.net/EarthImpactDatabase/ries.html | 01:55 |
eleitl | 24 km diameter, 14.3-14.5 MYrs | 01:56 |
eleitl | crater rim still very visible: http://en.wikipedia.org/wiki/File:Ries_Crater_Rim.jpg | 01:56 |
@kanzure | http://www.youtube.com/watch?v=NuKtVGdPESM http://youtube.com/watch?v=-OAcrmjmHp4 | 02:02 |
@kanzure | living in the future is pretty neat | 02:02 |
@kanzure | ""We can only register stones coming from the direction of the night sky," Malkov explained." .. seems like a rather critical flaw. | 02:05 |
@kanzure | eleitl: http://bettercryonics.com/BetterCryonics | 02:08 |
eleitl | Luke Parrish's work | 02:13 |
eleitl | News from Parallella: http://www.parallella.org/ | 02:14 |
eleitl | Zynq-7020 onboard, with 48 FPGA pins, with 8 GByte/s throughput | 02:15 |
jrayhawk | pretty | 02:15 |
eleitl | this is begging to implement a custom MPI interface | 02:15 |
eleitl | with 6 links you'll get 8 pins/link | 02:16 |
eleitl | maybe even space for a primitive Bresenham router | 02:16 |
eleitl | Roman 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 |
eleitl | how far can an FPGA pin drive a signal directly? | 02:34 |
eleitl | 10 cm? | 02:34 |
archels | It depends on what it is that it's driving. | 02:35 |
archels | Otherwise, just stick a cheap off-the-shelf buffer on there. | 02:35 |
eleitl | just FPGA to FPGA, with shorterst distance and smallest cable geometry | 02:35 |
archels | At a GHz or so, 10 cm should be no trouble at all. | 02:36 |
eleitl | can you get 1 GByte/s with 8 pins? | 02:36 |
archels | With the right FPGA, sure. | 02:36 |
eleitl | Zynq-7020 | 02:36 |
eleitl | http://www.youtube.com/watch?v=RH1DpTOuheI | 02:38 |
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archels | eleitl: its DDR3 interface is only 800 Mb/s | 02:39 |
eleitl | if it's a switch it needs to be able to cut-through | 02:39 |
eleitl | so it wouldn't need RAM | 02:39 |
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archels | its internal logic tops out at 1412 MHz for the highest speed grade | 02:42 |
archels | but achieving 1 GB/s relies on more things than just raw speed | 02:42 |
eleitl | what does that mean in practical terms? Less than 1 GByte/s througput through each 8 pins? | 02:42 |
eleitl | 800 MByte/s would be quite ok for MPI | 02:43 |
eleitl | it's latency that counts | 02:43 |
eleitl | that way you could keep GBit Ethernet NIC for admin stuff | 02:43 |
archels | if it's a burst transfer and not sustained, you can probably do it | 02:43 |
eleitl | thanks, archels | 02:43 |
archels | sure | 02:44 |
eleitl | really looking forward to take my board for the spin | 02:44 |
eleitl | if it's good I'm going to order 8 | 02:44 |
archels | cool, any specific application plans for it or just playing around? | 02:44 |
eleitl | MD and neural stuff | 02:45 |
eleitl | I want to see what you can do with 32 kBytes/DSP core | 02:45 |
eleitl | I think one can do plenty | 02:45 |
archels | What type of neurons though? | 02:46 |
eleitl | As biologically realistic as possible. I'll start small, and see how far I can get. | 02:46 |
eleitl | Something like Openworm would be great. | 02:46 |
archels | What can the FPGA offer you at this point that a general-purpose processor cannot? | 02:48 |
eleitl | the FPGA is just for the MPI interface | 02:48 |
eleitl | the 16-64 DSP cores are for heavy lifting | 02:48 |
archels | I don't think we're at a point yet where speed is the bottleneck for neural simulations | 02:48 |
archels | we just don't know what we're doing, mostly :) | 02:48 |
eleitl | I'm going to start with the smallest numerics footprint I can, and work myself upwards | 02:49 |
archels | sure, but why on the FPGA board and not on your desktop in NEURON or Moose or so? | 02:49 |
eleitl | not on the FPGA board | 02:50 |
eleitl | the FPGA is part of the Epiphany board, so it's free | 02:50 |
eleitl | the idea is to extend the on-die fabric by MPI in FPGA, for a 3d torus | 02:50 |
eleitl | the board is credit-card sized, and air-coolable, so you could build a nice cubic latice numerics box | 02:51 |
archels | that 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 minutes | 02:51 |
archels | I'm probably being dense, but I don't see the added value if the purpose is neuronal simulation | 02:51 |
archels | if the purpose is exploring hardware/firmware options for neuronal simulation, then I do see the point | 02:52 |
eleitl | I need a cheap numerics box that is scalable. 99 USD/board is cheap. | 02:53 |
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eleitl | I want something that can do realtime neurons | 02:54 |
eleitl | i.e. kHz scale events in realtime on that iron | 02:54 |
eleitl | something that can scale O(1) by throwing hardware at it | 02:54 |
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eleitl | 3d lattice with local communication only | 02:55 |
eleitl | the 16 or 64 DSP cores with embedded memory are effectively local | 02:57 |
eleitl | the idea is to scale this across a 3d lattice | 02:57 |
eleitl | it's basically a SHARC cluster on a die | 02:57 |
eleitl | I very much doubt Neuron would scale across that, especially as O(1) | 02:58 |
eleitl | O(1) meaning here that your runtime stays constant with problem size if you match that with hardware | 02:59 |
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archels | ah, realtime emulation--having a scaleable solution for that would be nice. | 03:04 |
eleitl | yep | 03:04 |
archels | I'm sure you could still accomplish that on a desktop for the C. elegans brain, but not for brains much larger than that | 03:05 |
eleitl | I would like 20 kNeurons | 03:07 |
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archels | Hmm, how many neurons are there again in an average cortical column? | 03:17 |
archels | About that order of magnitude? | 03:17 |
eleitl | maybe | 03:18 |
eleitl | I'm looking at L. stagnalis | 03:18 |
archels | oh yes, I recall | 03:18 |
eleitl | Epiphany is almost an order of magnitude more energy-efficient than Blue Gene/Q | 03:18 |
eleitl | and a lot cheaper, especially if you can buy them in installments | 03:19 |
archels | Here, 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 |
archels | then of course we can debate about the functional role of glia... | 03:22 |
eleitl | the glia don't seem to require a lot of crunch | 03:24 |
eleitl | so cortical column, just 20 kNeurons? | 03:24 |
eleitl | that's quite small | 03:24 |
eleitl | so ~1 mm^3, 20 kNeurons? | 03:25 |
archels | it's probably an underestimation, as they only looked at NeuN positive cells. | 03:36 |
eleitl | still, as an order of magnitude estimate it's a good thing to know | 03:37 |
eleitl | DARPA and UPMC collaboration -- Direct control of prosthetic arm by tetraplegic individual. Electrodes wired into cortex. Watch out for tactile | 03:40 |
eleitl | +feedback and wireless interface coming soon. | 03:40 |
eleitl | http://www.yousendit.com/download/UW16YUlqMGNKV1A0WjlVag | 03:41 |
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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 Robots | 04:21 |
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* eleitl has no future | 04:30 | |
eudoxia | it's ok eleitl, if any of the cryo orgs go bankrupt we'll go in and steal your head | 04:30 |
eleitl | it's probably going to be my own cryo org :/ | 04:31 |
eleitl | speaking of which, I probably have vitrified some VM-1 yesterday. I haven't had time to look yet. | 04:31 |
Mariu | :p | 04:32 |
Mariu | nice one, eudoxia | 04:32 |
eleitl | first dewar fill blew through some 95 l | 04:32 |
eleitl | I'm still not convinced the vacuum is very good. but, it will do for time being. | 04:33 |
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strangewarp | Waking up to meteor videos is pretty weird | 05:24 |
Mariu | oh | 05:24 |
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@kanzure | http://aws.amazon.com/redshift/ seems to offer 16 TB storage for $1000/TB-year if you pay $24k up front | 05:53 |
@kanzure | it's crazy how little space we have available | 05:59 |
@kanzure | mega.co.nz offers 4 TB for $25/mo | 06:01 |
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@kanzure | heh they are asking for 20 TB minimum per hosting offer https://mega.co.nz/#hosting | 06:05 |
@kanzure | opera owns the admarvel ad network? | 06:12 |
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@kanzure | hosted phantomjs scraping http://tubes.io/ | 09:06 |
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archels | Betteridge'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 |
@kanzure | there's a law of laws that says that invariably someone will bring that up in response to a headline like that | 11:09 |
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@kanzure | delinquentme: have you met SphericalMouse at biocurious yet? | 11:09 |
delinquentme | nah havn't b een down there yet | 11:10 |
delinquentme | just attempted to join the langton labs group | 11:10 |
delinquentme | kanzure, also does anyone in SF that you know need a roomie? | 11:10 |
@kanzure | langton labs is chronically overbooked | 11:11 |
@kanzure | klafka might want a roommate. josh gourneau asks often too, i think. | 11:11 |
klafka | i'm full up atm | 11:12 |
nmz787 | delinquentme: how's SF so far? | 11:12 |
delinquentme | nmz787, wild | 11:13 |
delinquentme | i need to do moar | 11:13 |
nmz787 | so there's a kid in the science class I'm teaching who has diabetes... should I mention genetic engineering to him? | 11:13 |
nmz787 | delinquentme: i found SF was too expensive for me to get out much | 11:13 |
Mariu | delinquentme: what does SF stand for ? | 11:14 |
nmz787 | whether it was taking the train, or paying for parking... | 11:14 |
delinquentme | *shrug* | 11:14 |
@kanzure | Mariu: san francisco | 11:14 |
Mariu | thanks, kanzure | 11:14 |
@kanzure | nmz787: which diabetes? | 11:14 |
@kanzure | actual diabetes or the other one? | 11:14 |
nmz787 | i think type 1 | 11:14 |
nmz787 | cause he can't eat the snacks the other kids get | 11:15 |
nmz787 | i dunno if it's connected at all, but his dad is blind too | 11:15 |
nmz787 | he sits outside the classroom, I think to give him meds before or afterwards | 11:15 |
nmz787 | i think | 11:15 |
nmz787 | he could just be paranoid after all that shooting crap | 11:16 |
nmz787 | hah, on that topic... the school nor volunteer agency ever asked for any paperwork or IDs | 11:16 |
nmz787 | they know my email address and name from that | 11:16 |
klafka | i've never been asked for anything either for any job | 11:18 |
klafka | my work now apparently thought i had a phd for a month after i joined | 11:18 |
klafka | even though i explicitly told several people i never finished it | 11:18 |
nmz787 | lol | 11:18 |
nmz787 | do u? | 11:18 |
klafka | i didn't finish it | 11:18 |
klafka | it's listed on my resume but it's like 2 years | 11:19 |
nmz787 | ur extra smrt, finish phd in 2 years | 11:19 |
klafka | unless i'm stephen wolfram | 11:19 |
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chris_99 | with companies that hold plasmids, do they use PCR to replicate the DNA? | 11:59 |
@kanzure | there's a popular yeast method of copying plasmids | 12:03 |
chris_99 | ooh interesting | 12:03 |
chris_99 | is 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 know | 12:09 |
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yashgaroth | who uses yeast for amplifying plasmid? | 12:12 |
@kanzure | maybe i am misremembering | 12:13 |
@kanzure | chris_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 haha | 12:13 |
@kanzure | yes they have to test it | 12:13 |
chris_99 | oh | 12:13 |
chris_99 | darn | 12:13 |
chris_99 | that's a bit of a pain surely | 12:13 |
@kanzure | and yes there is a "clever way to know".. this looks like only one or two enzymes they need to insert. | 12:14 |
yashgaroth | you can make an educated guess, there are maps of what precursors a species will have, so you gotta make sure those are present | 12:14 |
@kanzure | chris_99: this is less painful than the majority of other things in biology | 12:14 |
@kanzure | yep.. but then you also run the risk of things not folding because ph or something | 12:14 |
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@kanzure | or maybe it doesn't get expressed because you forgot to do codon optimization | 12:14 |
yashgaroth | true, but you can factor those in | 12:14 |
yashgaroth | mostly this stuff is metabolic engineering; even if it works and expresses, you're probably only gonna get femtograms of product | 12:15 |
yashgaroth | so you're tweaking a hundred other genes to generate more substrate, which each require tweaking of their upstream genes, etc | 12:15 |
chris_99 | gotcha | 12:16 |
yashgaroth | e.g. they eventually got yeast to make arteminisinininin but their final expression was a million-fold higher than when they just shoved the genes in | 12:17 |
yashgaroth | sorry, artemisinin, that word gives me a stroke | 12:17 |
chris_99 | had to google, that, anti-malaria drug right | 12:17 |
@kanzure | burnhousesdownisin | 12:17 |
yashgaroth | chris_99 yep it was previously only made by some shitty plant in small quantities | 12:19 |
chris_99 | heh | 12:19 |
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." pity | 12:28 |
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nmz787 | chris_99: generally the first educated guess is to try promoters from other gram-similar species | 12:37 |
nmz787 | a 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 works | 12:38 |
nmz787 | then lots of tweaking and shit like yashgaroth said | 12:38 |
chris_99 | what's gram-similar mean? | 12:40 |
nmz787 | well like you have gram-negative | 12:44 |
nmz787 | and gram-positive | 12:44 |
nmz787 | so a plasmid from a gram-negative will sometimes work in other gran-negatives, just like that | 12:45 |
nmz787 | i mean, unmodified | 12:45 |
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nmz787 | so you could theorhetically just be grabbing plasmids from moldy crap in your fridge :P | 12:46 |
nmz787 | rotten but not moldy stuff would work too | 12:46 |
nmz787 | since mold refers to eukaryotes | 12:46 |
yashgaroth | going to LA, bbl | 12:48 |
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chris_99 | gotcha, that's interesting | 12:49 |
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nmz787 | what's the belgian biohack space? | 14:01 |
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streety | has 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 |
@kanzure | paperbot: http://genomebiology.com/2013/14/1/104 | 15:42 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/f8014bac78038f967709f7cc939d0bd8.txt | 15:42 |
@kanzure | paperbot: http://genomebiology.com/content/pdf/gb-2013-14-1-104.pdf | 15:42 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9290087e7f8e79bbfc211b17b085bf8a.txt | 15:42 |
juri_ | ugh. my reading list could kill a small child. | 15:46 |
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abetusk | Did you guys see this: http://www.kickstarter.com/projects/254134422/finding-genes-to-create-perennial-crops | 16:12 |
ParahSailin | hes not gonna do anything useful with that experiment | 16:14 |
abetusk | ah, no? | 16:18 |
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abetusk | why not? | 16:20 |
abetusk | ParahSailin | 16:23 |
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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 |
ParahSail1n | abetusk, wetlab intuition | 17:02 |
ParahSail1n | or maybe that disillusionment is just the reason i didnt make it through grad school | 17:03 |
@kanzure | win 81 | 17:03 |
@kanzure | ack. | 17:03 |
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@kanzure | SphericalMouse: welcome back | 17:37 |
@kanzure | Juul: sup | 17:37 |
Juul | kanzure, learning about oxy-acetylene cutting. Do you have expertise in that area? | 17:37 |
illusive | get a decent mask | 17:38 |
illusive | goggles wont keep your beard from catching fire | 17:39 |
@kanzure | i screwed up a part once, but that's the only time i used an oxy-acetylene torch. | 17:39 |
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Juul | hehe yeah | 17:39 |
Juul | i'm trying to figure out if the connections are standardized | 17:40 |
illusive | well if you have to diy | 17:40 |
illusive | at least youll know whats best to use | 17:40 |
Juul | mmm | 17:42 |
Juul | i'm a total noob at this. i didn't even know there was a specific cutting attachment | 17:42 |
SphericalMouse | yoyo | 17:44 |
@kanzure | hah 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 |
@kanzure | weird "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 |
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@kanzure | it's too bad that pastebins fail for data with weird character encodings | 19:06 |
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delinquentme | yeeeeee | 19:08 |
delinquentme | soo I'm now a resident | 19:08 |
delinquentme | fenn, you wan get beer?? | 19:08 |
delinquentme | ParahSail1n, you around? | 19:09 |
@kanzure | neither of those two people live in SF | 19:09 |
delinquentme | O_o;; really? | 19:09 |
Juul | delinquentme, where'd you end up living? | 19:12 |
delinquentme | Juul, I'm in the mission atm! | 19:15 |
delinquentme | for the next 2 months | 19:15 |
delinquentme | so I'm gonna see how that works out ... and I"ll check to see whats going on with some of the other areas | 19:15 |
delinquentme | which is kind of what the issue is ... | 19:15 |
delinquentme | I need to see more of oakland before I move there ... like find out where the hangout spots are | 19:16 |
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delinquentme | Juul, are there any late night coffee shops? | 19:23 |
delinquentme | Farleys was decent | 19:23 |
Juul | delinquentme, where? | 19:23 |
delinquentme | oakland | 19:23 |
Juul | sudo room | 19:24 |
delinquentme | haha this is true | 19:24 |
Juul | there are a couple of places that advertise 24/7 but the signs are so old that i wouldn't trust them | 19:25 |
Juul | like the "24/7" burger joint outside sudo room that closes whenever they feel like | 19:26 |
delinquentme | hahah | 19:26 |
delinquentme | not bad! | 19:26 |
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delinquentme | Juul, can sudo room get mail? | 19:30 |
Juul | delinquentme, hm, I don't know. why? | 19:31 |
delinquentme | For ordering parts | 19:31 |
delinquentme | shakers , laser cut stuff | 19:31 |
Juul | nah, there's no-one to receive it | 19:32 |
delinquentme | and what about cutting utensils ? Is there anything that could chop masonite? | 19:32 |
Juul | biocurious has a package reception service | 19:32 |
ParahSail1n | delinquentme, im around | 19:33 |
Juul | delinquentme, chop it? there are power saws | 19:33 |
delinquentme | awesome. | 19:34 |
delinquentme | ParahSail1n, I thought you were in SF | 19:34 |
delinquentme | but it turns out im wrong haha | 19:34 |
ParahSail1n | nope | 19:34 |
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delinquentme | SO I'm trying to think of some of the kids who I should be bumping shoulders with | 19:42 |
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delinquentme | Juul, do you guys usually hang there through the weekends? | 19:51 |
Juul | delinquentme, there are generally always people there in the afternoons and evenings yeah. | 19:51 |
Juul | + sunday evening is cleanup | 19:51 |
delinquentme | ok wicked | 19:52 |
ParahSail1n | lol http://www.iamdann.com/2013/02/15/magnet-implants-can-actually-be-pretty-annoying | 19:55 |
@kanzure | jrayhawk: which versions of linux does CVE-2013-0871 effect? it doesn't seem obvious to me. | 20:19 |
docl | grr, I can't find anything on perfusing a chicken eye. | 20:20 |
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nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/j100114a038 | 20:46 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Analysis%20of%20resolution%20in%20DNA%20sequencing%20by%20capillary%20gel%20electrophoresis.pdf | 20:46 |
delinquentme | SO | 20:47 |
delinquentme | so called "biologics" | 20:47 |
delinquentme | are simply more complex than the normal pharma we're used to | 20:47 |
delinquentme | IE an organism vrs a chemical | 20:48 |
nmz787 | you gotta think about post-translational modification and shit | 20:49 |
nmz787 | or maybe one company uses a slightly different gene sequence | 20:49 |
nmz787 | mostly the same protein, but how similar does it need to be? | 20:49 |
nmz787 | that's the grey area of biologics | 20:50 |
nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/bi00688a010 | 20:50 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Chain%20length%20determination%20of%20small%20double-%20and%20single-stranded%20DNA%20molecules%20by%20polyacrylamide%20gel%20electrophoresis.pdf | 20:50 |
jrayhawk | haha "cobol on cogs" | 21:00 |
ParahSail1n | lol | 21:04 |
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JayDugger | Good evening, everyone. | 21:24 |
ParahSail1n | hi | 21:25 |
delinquentme | nmz787, a biologic is more than just a sequence though right? | 21:28 |
delinquentme | its an actual running organism | 21:28 |
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@kanzure | why is this private https://groups.google.com/group/biocurious-printer-hacking | 23:24 |
--- Log closed Sat Feb 16 00:00:02 2013 |
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