| --- Log opened Tue Nov 04 00:00:40 2014 | ||
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| archels | http://journal.frontiersin.org/Journal/10.3389/fnins.2014.00349/full | 00:25 |
|---|---|---|
| archels | very pointed | 00:25 |
| fenn | .title | 00:26 |
| yoleaux | Frontiers | The tale of the neuroscientists and the computer: why mechanistic theory matters | Brain Imaging Methods | 00:26 |
| archels | A little over a decade ago, a biologist asked the question “Can a biologist fix a radio?” (Lazebnik, 2002). That question framed an amusing yet profound discussion of which methods are most appropriate to understand the inner workings of a system, such as a radio. For the engineer, the answer is straightforward: you trace out the transistors, resistors, capacitors etc., and then draw an electrical circuit diagram. At that point you have ... | 00:26 |
| archels | ... understood how the radio works and have sufficient information to reproduce its function. For the biologist, as Lazebnik suggests, the answer is more complicated. You first get a hundred radios, snip out one transistor in each, and observe what happens. | 00:26 |
| ebowden_ | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/22532431 | 00:31 |
| fenn | he's sleeping | 00:31 |
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| nmz787 | archels: we have that paper, it is good | 00:51 |
| nmz787 | erhmm, i guess i read it elsewhere http://www.uic.edu/labs/bml/BML/Stuff/Stuff_files/biologist%20fix%20radio.pdf | 00:52 |
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| ebowden_ | http://www.ncbi.nlm.nih.gov/pubmed/22532431 | 02:42 |
| ebowden_ | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/22532431 | 02:43 |
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| ebowden_ | paperbot: http://www.pnas.org/content/111/23/8458.abstract | 03:25 |
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| archels | kanzure: could you suggset any good library for working with meshes; generating shapes, geometric operations, writing to file and so on? | 04:38 |
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| kanzure | archels: meshlab? | 05:15 |
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| kjskjskjs | that's not a library | 05:29 |
| kjskjskjs | archels: I couldn't find a good one and so I wrote a bad one: https://github.com/kragen/stl3dpy | 05:29 |
| kjskjskjs | CGAL has a bunch of geometric operations (not specifically on meshes) | 05:29 |
| kanzure | salome has lots of mesh stuff | 05:30 |
| kanzure | (from the opencascade people) | 05:30 |
| kanzure | actually, opencascade... but check if salome solves your problems first. | 05:30 |
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| kanzure | http://gregegan.customer.netspace.net.au/FOUNDATIONS/ | 05:41 |
| kanzure | podcast about lack of access to academic research http://letstalkbitcoin.com/blog/post/lets-talk-bitcoin-158-ebola-and-the-body-blockchain | 05:41 |
| kjskjskjs | http://www.salome-platform.org/user-section/about/geometry mentions "Pipe creation" | 05:43 |
| kjskjskjs | do you suppose that's the operation CATIA calls "shell"? | 05:43 |
| kjskjskjs | oh, and it also has "fillet" and "chamfer". nice! | 05:43 |
| kjskjskjs | it also mentions "shell" under "topological objects" | 05:44 |
| kjskjskjs | I think this is the library I have been wishing for! | 05:44 |
| kjskjskjs | thank you very much, kanzure! | 05:48 |
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| archels | kjskjskjs: that's about the point I'm at, just some Python loops writing out a WaveFront OBJ file | 05:50 |
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| kanzure | .title http://vimeo.com/102167635 | 05:51 |
| yoleaux | DevOpsDays Brisbane 2014 - Sidney Decker - System Failure, Human Error: Who's to Blame? on Vimeo | 05:51 |
| kanzure | "... this year's keynote address focusing on the history of our understanding of system failures and the assumed role of human error." | 05:52 |
| kjskjskjs | archels: yeah. this SALOME thing looks like it could help a lot. | 05:52 |
| kanzure | meh he's just promoting his own crappy books | 05:53 |
| kanzure | nevermind | 05:53 |
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| archels | geometry to mesh? neat | 05:54 |
| kjskjskjs | yeah! | 05:54 |
| kanzure | "This book explores complexity theory and systems thinking to better understand how complex systems drift into failure. It studies sensitive dependence on initial conditions, unruly technology, tipping points, diversity—and finds that failure emerges opportunistically, non-randomly, from the very webs of relationships that breed success and that are supposed to protect organizations from disaster. It develops a vocabulary that allows us to ... | 05:55 |
| kanzure | ... harness complexity and find new ways of managing drift." | 05:55 |
| kanzure | "you are fucked" | 05:55 |
| kjskjskjs | I'm still trying to get a handle on topology optimization in mechanical design, now that I know it exists | 05:56 |
| kanzure | if you didn't know about opencascade then i should inform you about https://github.com/tpaviot/oce | 05:56 |
| kanzure | and about http://www.pythonocc.org/ | 05:57 |
| kanzure | and https://github.com/dcowden/cadquery | 05:57 |
| kanzure | and the examples and fancypants screenshots on http://opencascade.org/ | 05:59 |
| kanzure | (context: salome and opencascade share a lot of code and history) | 05:59 |
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| alusion | http://www.abc.net.au/news/2014-11-04/scientists-reverse-ageing-process-in-mice/5865714 | 06:28 |
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| ebowden_ | Isn't that fairly old news? | 06:47 |
| kanzure | prolly | 06:53 |
| FourFire | kanzure: what about byzantine fault tolerance ? | 06:55 |
| kanzure | what about it | 06:55 |
| FourFire | which, according to my rather limited understanding of it is a design philosophy which assumes that everything in a system is fucked by default, and anyway attempts to make it work to some extent | 06:56 |
| kanzure | http://2014.igem.org/Team:SF_Bay_Area_DIYbio | 06:56 |
| kanzure | how is that diybio. fucking community labs. | 06:56 |
| chris_99 | haha | 06:57 |
| kanzure | "is a community team of more than two dozen individuals from all walks of life, sponsored by DIYbio labs Counter Culture Labs from Oakland and BioCurious from Sunnyvale." | 06:57 |
| kanzure | man i can't believe people tolerate this sort of poor reasoning | 06:57 |
| chris_99 | i'm not sure the benefits of vegan cheese, but if they can pull it off... | 06:58 |
| kanzure | er, no i mean if you use a company or organization like biocurious, that's not diybio | 06:58 |
| chris_99 | ah sorry, didn't see that | 06:58 |
| chris_99 | but how could you do this diy, without expensive synthesizers, or is it possible to easily get hold of the required plasmids somehow? | 07:00 |
| kanzure | why is it important that you do it without expensive synthesizers? | 07:05 |
| chris_99 | it's not, i guess, but they seem prohibitively expensive for most people | 07:06 |
| kanzure | yeah well that's not my fault :p | 07:06 |
| chris_99 | heh | 07:06 |
| chris_99 | could you isolate the plasmid from something already existing, or is that not possible? | 07:07 |
| kanzure | .wik plasmidome | 07:10 |
| yoleaux | "The term Plasmidome refers to the total plasmids content that is available in a certain environment. The term is a portmanteau of the two English words Plasmid and Kingdom." — http://en.wikipedia.org/wiki/Plasmidome | 07:10 |
| kanzure | .title http://www.youtube.com/watch?v=Ek49JSAiKjY | 07:11 |
| yoleaux | c_elegans.avi - YouTube | 07:11 |
| kanzure | .title https://www.youtube.com/watch?v=mM_C-AkVrDQ | 07:11 |
| yoleaux | caenorhabditis elegans, locomotion model - YouTube | 07:11 |
| kanzure | .title http://www.biomedcentral.com/1471-2202/12/S1/P363 | 07:11 |
| yoleaux | BMC Neuroscience | Full text | CLONES : a closed-loop simulation framework for body, muscles and neurons | 07:11 |
| kanzure | history of progress in simulating c. elegans https://docs.google.com/spreadsheets/d/1NclOVMRIqY_hn-aL8MdLlJrfuhDgNJyk_ChsZMjugmE/edit | 07:11 |
| kjskjskjs | "kingdom"? "genome" comes from "kingdom"‽ | 07:12 |
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| archels | no, it comes from genus + chromosome | 07:15 |
| archels | .ety genome | 07:15 |
| yoleaux | genome (n.): ""sum total of genes in a set," 1930, modeled on German genom, coined 1920 by German botanist Hans Winkler, from gen "gene" + (chromos)om "chromosome."" — http://etymonline.com/index.php?term=genome | 07:15 |
| archels | .ety gene | 07:15 |
| yoleaux | gene (n.): "1911, from German Gen, coined 1905 by Danish scientist Wilhelm Ludvig Johannsen (1857-1927), from Greek genea "generation, race" (see genus). De Vries had earlier called them pangenes. Gene pool is attested from 1950." — http://etymonline.com/index.php?term=gene | 07:15 |
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| kanzure | gene pool is from 1950? | 07:15 |
| pasky | ah maybe i should add some comments there | 07:18 |
| kanzure | hm? | 07:18 |
| pasky | wrt. nemaload | 07:19 |
| pasky | already did | 07:19 |
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| archels | oh, great. "university branch organisation VSNU in The Netherlands terminates negotiations with Elsevier over open access policies. potential disruptions in the usual way in which you access articles in these journals. we apologize for the inconvenience." | 07:24 |
| kanzure | haha you are boned | 07:25 |
| kjskjskjs | hopefully they were trying to pressure Elsevier for more open access and so the end result will be that we are all less boned | 07:36 |
| kanzure | a $7 billion gorilla like this is really problematic | 07:37 |
| kanzure | i mean, $7 billion can tolerate a lot of er, disruption, or whatever it's called | 07:37 |
| kjskjskjs | yeah. RIP Aaron. | 07:39 |
| kanzure | it's funny how aaronsw gets all the credit for gmaxwell's monster jstor torrent dump | 07:41 |
| kanzure | i can see how it might seem confusing | 07:41 |
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| kjskjskjs | well, gmaxwell wouldn't have done it without aaronsw to give him the courage or outrage or whatever | 07:44 |
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| heath | augur: :) | 08:43 |
| kanzure | http://datassette.net/content/datashat-businessfunk2.mp3 | 08:43 |
| heath | i guess the amount of work is piling up on your end around this time | 08:43 |
| nmz787_i1 | kanzureis there a reason you didn't recommend salome to me? just forgot? | 08:45 |
| kanzure | what was i supposed to recommend it to you for? | 08:47 |
| nmz787_i1 | CAD stuff | 08:48 |
| kanzure | lots of salome is just opencascade | 08:48 |
| justanotheruser | If publishers had no incentive to pay their editors then what would scientists end up doing to get published? | 08:52 |
| kanzure | dingo: there should be a thing to make simple summaries of strace log output, like collapsing similar messages or sequences or something | 08:55 |
| kanzure | justanotheruser: most editors are currently not paid anyway | 08:55 |
| kanzure | http://online.wsj.com/articles/mark-wetjen-bringing-commodities-regulation-to-bitcoin-1415060058 | 08:56 |
| justanotheruser | kanzure: What do you think of this model? Authors self publish to some set of websites, peers review it and sign a hash of the paper plus their comments, users of these websites construct a WoT for peer reviewers to determine the legitemacy of the paper. | 08:57 |
| justanotheruser | paperbot: http://online.wsj.com/articles/mark-wetjen-bringing-commodities-regulation-to-bitcoin-1415060058 | 08:58 |
| kanzure | i very strongly doubt that it is a problem of technology at this point | 08:58 |
| kanzure | it's entirely a problem of reputation | 08:58 |
| kanzure | and career metrics | 08:58 |
| kanzure | there was a whole fad about "alt metrics" that was trying to get launched around 2007-2011 but never went anywhere | 08:59 |
| justanotheruser | alt metrics? | 08:59 |
| kanzure | you know, other than isi web of knowledge impact factor | 08:59 |
| kanzure | btw you can get access by querying google for "wsj wetjen cftc bitcoin" or clicking one of their url redirection link thingies | 09:00 |
| yorrick | kanzure: got a record on gmaxwell's torrent? | 09:02 |
| kanzure | .wik impact factor | 09:02 |
| yoleaux | "The impact factor (IF) of an academic journal is a measure reflecting the average number of citations to recent articles published in the journal. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones." — http://en.wikipedia.org/wiki/Impact_factor | 09:02 |
| kanzure | yorrick: https://thepiratebay.se/torrent/6554331 | 09:02 |
| yorrick | kanzure: gracias | 09:02 |
| yorick | oh god why is there a yorrick | 09:02 |
| yorrick | yorick, sorry dude, I'll drop this nick. Didn't realize a "yorick" existed at the time | 09:03 |
| kanzure | i hired him to replace you | 09:03 |
| yorick | yorrick: nah, it's okay | 09:03 |
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| yorick | kanzure: what was my function anyways | 09:03 |
| kanzure | who knows, that's why you're fired | 09:04 |
| justanotheruser | is yorick a bot? | 09:04 |
| yorick | not that I know of | 09:04 |
| justanotheruser | yorick: what is the 2nd derivative of acceleration | 09:06 |
| PoorYorrick | lel | 09:06 |
| yorick | I know the 2nd integration, that's location | 09:07 |
| yorick | is that good enough? | 09:07 |
| PoorYorrick | justanotheruser: the 1st derivative of a jerk? ;) | 09:07 |
| PoorYorrick | 3rd* | 09:07 |
| PoorYorrick | There's supposed to be a pun in there somewhere. | 09:08 |
| yorick | jounce! | 09:08 |
| yorick | https://en.wikipedia.org/wiki/Jounce do people just make this up | 09:08 |
| justanotheruser | PoorYorrick: the guy who shakes hands with the guy who shakes your hand. | 09:08 |
| yorick | "snap", "crackle", "pop" | 09:08 |
| PoorYorrick | kanzure: dem ads on piratebay... | 09:08 |
| justanotheruser | yorick: are you from a former soviet country? | 09:10 |
| yorick | no. | 09:10 |
| justanotheruser | is your name yorick? | 09:10 |
| yorick | yes | 09:10 |
| justanotheruser | are you a descendant of a viking? | 09:10 |
| yorick | probably? | 09:11 |
| justanotheruser | are you > 72 inches tall? | 09:11 |
| yorick | yes | 09:11 |
| justanotheruser | ok | 09:11 |
| yorick | but so is everyone here | 09:11 |
| justanotheruser | really? | 09:11 |
| PoorYorrick | Yeah, I'm like 90 inches soft. | 09:11 |
| yorick | netherlands | 09:11 |
| justanotheruser | oh | 09:11 |
| justanotheruser | I thought you meant ##hplusroadmap | 09:12 |
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| chris_99 | http://nextglass.co/beer-census/ | 09:15 |
| justanotheruser | If that really works its strange that they limit it to beer | 09:17 |
| chris_99 | spectrometize everything! | 09:17 |
| chris_99 | can't see why it wouldn't work | 09:17 |
| chris_99 | you can get stuff like IBU etc. via mass spectrometery iirc | 09:18 |
| PoorYorrick | Anyone ever read this before? | 09:23 |
| PoorYorrick | http://en.wikipedia.org/wiki/User:Asmodeus/pseudosciencerfarb | 09:23 |
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| kanzure | http://datassette.net/content/datashat-businessfunk3.mp3 | 09:31 |
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| heath | "Naples is one of the wealthiest cities in the United States, with the sixth highest per capita income in America,[5] and the second highest proportion of millionaires per capita in the US" | 09:48 |
| heath | seems like we need a startup scene here :) | 09:48 |
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| heath | neat, coworking space downtown has fiber | 10:08 |
| heath | http://zincubate.com/venture-x-coworking-offices | 10:08 |
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| FourFire | PoorYorrick: I'm not going to read all of that | 10:57 |
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| PoorYorrick | FourFire: I have. At least twice. Entertaining stuff. :P | 10:57 |
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| kanzure | .d will | 11:21 |
| yoleaux | kanzure: Sorry, that command (.d) crashed. | 11:21 |
| kanzure | "expressing the future tense." | 11:21 |
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| heath | https://www.kickstarter.com/projects/chaibio/open-qpcr-dna-diagnostics-for-everyone | 11:32 |
| heath | mac cowell | 11:33 |
| heath | hm, schloendorn even?.. | 11:35 |
| heath | it doesn't look like opentrons is going to meet their goal | 11:36 |
| delinquentme | heath, what about these guys?? | 11:52 |
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| delinquentme | COOL | 11:55 |
| heath | delinquentme: eh? | 12:25 |
| heath | those two are associated with the open-qpcr it looks like from the vid | 12:25 |
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| kanzure | http://opencores.org/project,bluespec-80211atransmitter | 12:30 |
| kanzure | http://opencores.org/project,bluetooth | 12:30 |
| kanzure | https://github.com/RangeNetworks/openbts | 12:30 |
| kanzure | https://github.com/travisgoodspeed/80211scrambler | 12:30 |
| kanzure | https://github.com/ewa/802.11-data | 12:30 |
| kanzure | openbts is curious http://openbts.org/ | 12:31 |
| kanzure | "The OpenBTS software is a Linux application that uses a software-defined radio to present a standard 3GPP air interface to user devices, while simultaneously presenting those devices as SIP endpoints to the Internet. This forms the basis of a new type of wireless network which promises to expand coverage to unserved and underserved markets while unleashing a platform for innovation, including offering support for emerging network ... | 12:32 |
| kanzure | ... technologies, such as those targeted at the Internet of Things." | 12:32 |
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| kanzure | that's really unfortunate because i thought 3gpp was an mpeg container format | 12:37 |
| kanzure | .wik 3gp | 12:37 |
| yoleaux | "3GP (3GPP file format) is a multimedia container format defined by the Third Generation Partnership Project (3GPP) for 3G UMTS multimedia services. It is used on 3G mobile phones but can also be played on some 2G and 4G phones." — http://en.wikipedia.org/wiki/3gp | 12:37 |
| kanzure | "OpenBTS-GSM (2.5G) supports SDRs from vendors such as Ettus Research, Fairwaves, and Nuand, as well as Range Networks’ SDR1, which is found in its development kit and base station products, and whose design files have been open-sourced and can be found below and at Github. If you choose a product which connects via Ethernet, make sure your Linux server has a dedicated Ethernet port for the radio." | 12:38 |
| kanzure | "The Range Networks SDR1 consists of two individual PCBs that work in tandem, referred to as the SDR module and the RF module (or board). The SDR module provides signal processing and digital data transfer between the RF signals and the host. The RF module provides the wireless transmission of the data. The SDR and RF module boards are each on a 5.5″ x 3.25″ PCB outline. This is a stacked design with a single interface connector between ... | 12:39 |
| kanzure | ... them. The RF module uses the same PCB layout with different component stuffing options and is capable of supporting the following frequency bands: 850, 900, 1800, 1900 MHz. The SDR1 is based in large part on the USRP1 design." | 12:39 |
| kanzure | pcb stuff https://github.com/RangeNetworks/hardware-designs | 12:40 |
| kanzure | http://openbts.org/site/wp-content/uploads/2014/07/OpenBTS-4.0-Manual.pdf | 12:41 |
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| chris_99 | are there any sites specifically for manuals of old random pieces of lab equipment out of interest | 13:45 |
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| kanzure | yes i think it's called hplusroadmap | 13:58 |
| kanzure | drethelin might know, actually | 13:58 |
| jrayhawk_ | i am sure if you link to it somewhere, kanzure will compulsively shove it in his papers repository | 14:01 |
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| chris_99 | heh, i just found this www.ebay.co.uk/itm/Mass-Spectrometer-Waters-Micromass-Tof-Spec-2E-/281482569637 was just curious to find the manual for it, to see what it could do | 14:07 |
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| kanzure | hello eudoxia | 14:20 |
| eudoxia | hey kanz | 14:20 |
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| kanzure | .tw https://twitter.com/xor/status/529428190729478144 | 14:47 |
| yoleaux | Now that Sherlock is in the public domain I guess the FBI is free to make an adaptation where he can't figure out crimes because of crypto (@xor) | 14:47 |
| chris_99 | heh | 14:48 |
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| heath | upvotes welcome https://www.reddit.com/r/robotics/comments/2lb63h/opentrons_opensource_rapid_prototyping_for_biology/ | 15:19 |
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| chris_99 | 'there doesn't seem to be anything here' | 15:21 |
| heath | chris_99: it's a link to the kickstarter page | 15:25 |
| chris_99 | oh i thought there was supposed to be a comment | 15:25 |
| chris_99 | is that your kickstarter? | 15:25 |
| heath | chris_99: nope | 15:26 |
| heath | i want it to succeed though | 15:26 |
| chris_99 | :) | 15:27 |
| nmz787_i | https://www.youtube.com/watch?v=_VFsdPAoI1g | 15:47 |
| nmz787_i | .title | 15:48 |
| yoleaux | Make It Wearable Finalists | Meet Team Nixie - YouTube | 15:48 |
| nmz787_i | 'Team Nixie (http://flynixie.com) is developing the first wearable drone camera, which can be worn around your wrist.' | 15:48 |
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| chris_99 | how does it do object detection tho? | 15:57 |
| nmz787_i | https://www.kickstarter.com/projects/chaibio/open-qpcr-dna-diagnostics-for-everyone | 16:23 |
| nmz787_i | 'releasing cad designs and software' | 16:31 |
| nmz787_i | oh, wait, that's just what their video said, the text lower down says "The hardware design, including BOM, SolidWorks files, and Eagle CAD will all be released as open source when the machine ships, and are available sooner as an early access reward." | 16:35 |
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| nmz787 | kanzure: know anyone in pdx that would be a lab tech for us? | 17:36 |
| nmz787 | I have to assume that the quality of that qPCR machine is good enough now, since they're trying to kickstart it... but I wonder if it isn't for some applications, and whether if I got it, would I even have the time to prep and run the thing | 17:37 |
| kanzure | "fr us"? | 17:42 |
| kanzure | *for | 17:42 |
| kanzure | i would consider pestering lichen, i guess, depending what "us" is | 17:42 |
| kanzure | .title https://github.com/iimarckus/pokered/pull/61 | 17:44 |
| yoleaux | Charmaps by stag019 · Pull Request #61 · iimarckus/pokered · GitHub | 17:44 |
| kanzure | there goes my preprocessor. oh well. | 17:44 |
| kanzure | it sucked anyway | 17:44 |
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| nmz787 | idk, someone to throw monotonous bio tasks at | 18:18 |
| kanzure | try lichen first | 18:19 |
| nmz787 | lichen: hi | 18:20 |
| nmz787 | what is a fair rate for bio technicians? | 18:20 |
| nmz787 | or range | 18:20 |
| nmz787 | for like making media | 18:20 |
| nmz787 | and plating cells | 18:20 |
| kanzure | apparently $10-$20/hour | 18:20 |
| nmz787 | running qpcr | 18:21 |
| nmz787 | mm | 18:21 |
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| ParahSailin_ | qpcr is so old fashioned | 18:51 |
| ParahSailin_ | some biologists apparently need to be dragged into the ngs age kicking and screaming | 18:51 |
| nmz787 | how does it compete with it for on-site diagnostics? | 18:54 |
| nmz787 | I could put this in a lab room at my farmers new building and he could use it on-site just after he milks, for example | 18:55 |
| sheena | blah | 19:06 |
| sheena | nmz787: did we talk about my chicken diagnostic problem? | 19:09 |
| nmz787 | no, but I think I saw something about it in the logs at one point | 19:12 |
| sheena | there is a chicken disease that can be transmitted through eggs | 19:12 |
| sheena | mycoplasma | 19:12 |
| nmz787 | ok, yeah, i've tested for that before | 19:12 |
| sheena | ok | 19:12 |
| sheena | is on-farm testing something that owuld be worth even considering for it? | 19:12 |
| nmz787 | qpcr /should/ be able to tell you yes/no | 19:13 |
| sheena | thats an emphatic should... | 19:13 |
| nmz787 | well it will, if the primers work | 19:13 |
| nmz787 | but i'm not sure how much reagents are these days | 19:13 |
| nmz787 | i think i used to get qpcr kits for free | 19:14 |
| nmz787 | as samples | 19:14 |
| sheena | oh hm | 19:15 |
| sheena | we'd be needing to test flocks.. would we be able to mix samples? | 19:15 |
| nmz787 | but yeah i did qpcr and it's the standard protocol, or was | 19:15 |
| nmz787 | you could mix samples, but then you would only know if someone in the mix had it, but not who | 19:15 |
| nmz787 | the unit has 8 or 16 wells | 19:16 |
| nmz787 | but the description of it is worded a bit strangely | 19:16 |
| nmz787 | 'The software supports amplification curve Ct thresholds, presence/absence detection, melt curve analysis, and relative quantification. Software support for absolute quantification may be ready by the shipping date, or will otherwise be made available shortly thereafter as a free downloadable update. It's a bit tricky to do absolute quantification with a 16 well block, but we've got some ideas.' | 19:17 |
| sheena | right, we'd be testing flocks, so if anyone comes back positive, we'd test that flock for individuals? | 19:19 |
| kanzure | you could just assign one well per unit-mammal | 19:19 |
| sheena | the place we sent samples to says they use 3 tests.. ELisa, Hemagglutination inhibition and molecular diagnostic services.. | 19:20 |
| nmz787 | prices for 'mastermix' (not including primers) from VWR is (t# ests : price) "100 : $187.68 , 500 : $849.66 , 2000 : $3,165.06" | 19:20 |
| nmz787 | #tests * | 19:20 |
| nmz787 | this would be the latter | 19:20 |
| nmz787 | 'molecularz' | 19:20 |
| nmz787 | ELISA is a good one too | 19:21 |
| nmz787 | always good to have more data, unless you're cheap | 19:21 |
| sheena | indeed | 19:21 |
| sheena | cheap wou ldbe the issue | 19:21 |
| nmz787 | but at the prev posted prices, qpcr from VWR isn't too cheap | 19:21 |
| sheena | so less than $2/test, but an initial $1500 outlay for the machine? | 19:22 |
| nmz787 | $1300 today | 19:22 |
| nmz787 | so one local machine could be running stuff for you and my farmer buddy... now we just need someone to run it and also to get more farmer buddies who need stuff tested | 19:23 |
| nmz787 | i wonder if it showed up at one of the hackerspaces, if someone would be enticed into running samples | 19:23 |
| nmz787 | $1300 is a lot to drop for me personally right now | 19:24 |
| sheena | we have a hackerspace working on opening up at ht emoment | 19:28 |
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| nmz787 | ctrl-h? | 19:29 |
| sheena | at the? | 19:29 |
| sheena | moment | 19:29 |
| sheena | ugh | 19:29 |
| nmz787 | is it ctrl-h? | 19:29 |
| nmz787 | wait, are you in pdx? | 19:29 |
| sheena | um | 19:30 |
| sheena | i dont think im any of those things | 19:30 |
| sheena | lol | 19:30 |
| sheena | im in kamloops bc | 19:30 |
| sheena | if pdx is a geographical location | 19:30 |
| sheena | brand new "innovation centre" with a modlab (robot things?) and some other stuff in the works here | 19:31 |
| nmz787 | it is an airport code | 19:32 |
| nmz787 | ah, cool | 19:32 |
| nmz787 | i'm in portland OR | 19:33 |
| nmz787 | well, just outside there | 19:33 |
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| sheena | YKA is my airport code :) | 19:50 |
| sheena | if that helps | 19:50 |
| nmz787 | :) | 19:51 |
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| fenn | pretty awesome military/technical library http://archive.hnsa.org/doc/ | 19:59 |
| fenn | the foundry manual is basically the source information for the gingery series | 20:01 |
| kanzure | haha http://www.ultrasound-autism.org/ | 20:03 |
| fenn | lame | 20:03 |
| kanzure | an entire web page for every possible idea | 20:04 |
| fenn | "Effects noted in two other research projects are low birth size and increased left-handedness." | 20:04 |
| fenn | cure left-handedness, write the FDA today! | 20:04 |
| kanzure | "it was never proven safe!!!" | 20:05 |
| fenn | your children are at risk of not being able to use scissors | 20:05 |
| kanzure | "Non Structural Closures, 2005" | 20:10 |
| kanzure | "Photography (Advanced), 1995" | 20:10 |
| fenn | "Through synthetic biology, we engineer our yeast to become milk-protein factories. Our milk proteins will then be combined with water and vegan oil to make Vegan Milk, which will ultimately be converted into Real Vegan Cheese through standard cheese-making processes" once upon a time i might have thought this was a good idea | 20:13 |
| fenn | "Another Soviet contribution to genetics in these years was the concept of gene pool. The Russian geneticist A. S. Serebrovskii first formulated the concept in terms of genofond (gene fund), a word that was imported to the United States from the Soviet Union by Theodosius Dobzhansky, one of the members of Chetverikov’s group, who translated it into English as “gene pool.” Today few people | 20:22 |
| fenn | know that this term, so common in biological discourse the world over, has a Russian origin. Chetverikov, Serebrovskii, Filipchenko, Dobzhansky, Karpechenko, and Romashov were among the many pioneering Russian biologists of the 1920s." | 20:22 |
| fenn | it's true, i read it in a book | 20:24 |
| kanzure | "A cost analysis of intraoperative microelectrode recording during subthalamic stimulation for Parkinson's disease." http://www.ncbi.nlm.nih.gov/pubmed/21674622 | 20:43 |
| kanzure | "The average cost for subthalamic nucleus deep brain stimulation implantation with microelectrode recording per patient is $26,764.79 for unilateral, $33,481.43 for simultaneous bilateral, and $53,529.58 for staged bilateral. For unilateral implantation, the cost of microelectrode recording is $19,461.75, increasing the total cost by 267%. For simultaneous bilateral implantation, microelectrode recording costs $20,535.98, increasing the total ... | 20:43 |
| kanzure | ... cost by 159%. For staged bilateral implantation, microelectrode recording costs $38,923.49, increasing the total cost by 267%. Microelectrode recording more than doubles the cost of subthalamic nucleus deep brain stimulation for Parkinson's disease and more than triples the cost for unilateral and staged bilateral procedures." | 20:44 |
| kanzure | "... a mean operating room time of 223.83 minutes for unilateral and 279.79 minutes for simultaneous bilateral implantation." | 20:44 |
| kanzure | i wonder if that means in malaysia or thailand that it's $5,000. | 20:47 |
| fenn | what are they recording? | 20:47 |
| kanzure | not really sure, i was more interested in the stimulation | 20:48 |
| fenn | also how does adding 25% to the operating time increase cost by 267%? | 20:49 |
| fenn | o wait i read that wrong | 20:50 |
| fenn | tangentially related to libraries and gene pools http://genofond.ru | 20:51 |
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| fenn | nmz787 sheena regular PCR would be just fine for detecting presence/absence of pathogen DNA | 21:23 |
| fenn | although that machine is cute | 21:23 |
| fenn | you would have to run a gel for regular pcr, though that's not as hard as it sounds | 21:24 |
| fenn | getting the primers and making sure they work would be a small hurdle for either PCR or qPCR | 21:25 |
| sheena | fenn: cost? | 21:26 |
| fenn | i guess you could use the qPCR dsDNA dye instead of a gel for presence/absence | 21:26 |
| fenn | not sure about cost, to me PCR means anything from buckets of water to a zillion dollar robot | 21:26 |
| fenn | i do think $599 for openpcr is too much; the light bulb pvc pipe thingy looked about right | 21:27 |
| fenn | http://www.russelldurrett.com/lightbulbpcr.html | 21:27 |
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| fenn | i'd say $50 for the materials and electronics, plus $2 per test, and primers are like $30(?) | 21:30 |
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| fenn | you'll also need a p200 micro pipettor and eppendorf tubes | 21:33 |
| fenn | .title http://www.sigmaaldrich.com/catalog/product/sigma/mp0035?lang=en®ion=US | 21:35 |
| yoleaux | LookOut® Mycoplasma PCR Detection Kit Optimized for use with JumpStart™ Taq DNA Polymerase, D9307. | Sigma-Aldrich | 21:35 |
| fenn | impossible to get prices on anything | 21:35 |
| fenn | apparently those tubes are "pre-coated with nucleotides, primers, and internal controls" | 21:37 |
| fenn | this is probably intended for testing cell cultures, not chickens; the mycoplasma species may be too different, or it may just be close enough to work | 21:40 |
| nmz787 | i see prices for sigma | 21:43 |
| fenn | how much is the kit? | 21:43 |
| nmz787 | $253.50 | 21:43 |
| fenn | that's a bit much for just one test | 21:44 |
| nmz787 | yes but it is more than that | 21:44 |
| nmz787 | http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/mp0035bul.pdf | 21:44 |
| fenn | how is it more than just one test? | 21:45 |
| fenn | oh, maybe it's 3 tests | 21:45 |
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| fenn | i wonder why it says "use of the PCR process requires a license" | 21:48 |
| fenn | PCR has been out of patent protection for decades | 21:48 |
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| fenn | After the publication of the first PCR paper, the United States Government sent a stern letter to Randy Saiki, admonishing him for publishing a report on "chain reactions" without the required prior review and approval by the U.S. Department of Energy. Cetus responded, explaining the differences between PCR and the atomic bomb. | 21:52 |
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| fenn | it would be funny if the fate of the entire planet weren't in their hands | 21:52 |
| catern | [citation needed] | 22:03 |
| catern | http://en.wikipedia.org/wiki/History_of_polymerase_chain_reaction | 22:03 |
| fenn | go cite yourself | 22:03 |
| fenn | .title https://xkcd.com/978/ | 22:03 |
| yoleaux | xkcd: Citogenesis | 22:03 |
| ebowden | Heh, didn't the guy who developed PCR end up becoming an aids denialist or something like that? | 22:17 |
| fenn | if you read what he actually says, no | 22:18 |
| fenn | if you believe fox news or whatever, yes | 22:18 |
| fenn | basically he's upset that the CDC spends so much money on aids treatment because in the process they end up supporting "the aids establishment" and label things as aids that are really just diseases of the third world | 22:19 |
| fenn | opportunistic infections resulting from weakened immune systems due to aids look mighty similar to opportunistic infections from weakened immune systems due to malnutrition | 22:19 |
| fenn | i'm actually trying to find the book "dancing in the mind fields" if anyone has it | 22:20 |
| fenn | field* | 22:21 |
| fenn | lol "Duesberg proposed his hypothesis that AIDS is caused by long-term consumption of recreational drugs and/or antiretroviral drugs, and that HIV is a harmless passenger virus." | 22:34 |
| fenn | so aids is caused by anti-aids drugs, problem solved | 22:34 |
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| fenn | "although Duesberg and the AIDS denialist movement have garnered support from some prominent scientists, including Nobel Prize winner Kary Mullis, most of this support is related to Duesberg’s right to hold a dissenting opinion, rather than support of his specific claim that HIV does not cause AIDS." | 22:40 |
| sheena | how bout i send you some samples, fenn and you make me a tester machine? :D | 22:42 |
| fenn | wah | 22:42 |
| fenn | i've been trying to get away from biology since 2003 | 22:43 |
| fenn | i thought for sure there would be a $50 diybio lab in a box kit by now | 22:46 |
| sheena | make ittttttt | 22:52 |
| sheena | what do you want to do instead of bio? | 22:53 |
| fenn | tech-nomadism and wearable enhancements | 22:54 |
| fenn | sheena: here's a list of documents related to things i'm interested in; it may or may not make any sense http://fennetic.net/irc/stuff | 23:10 |
| sheena | those both sound like biology to me | 23:11 |
| sheena | foam puzzle mats.gnumeric? | 23:11 |
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| fenn | trying to find the cheapest play mat tiles per square foot | 23:14 |
| fenn | i'd rather have the gray ones but it seems colorful alphabet is 20% less, and more widely available | 23:14 |
| sheena | heh we have this same issue | 23:17 |
| sheena | but i suspect not for the same reason | 23:17 |
| sheena | what are you using it for? | 23:17 |
| fenn | floor covering | 23:18 |
| fenn | i've used blue EPS board but it tends to get dinged up | 23:18 |
| fenn | polyurethane foam is tougher and interlocks | 23:19 |
| fenn | basically i hate carpet | 23:19 |
| fenn | it's hard to know if something is a book or a paper, or if this categorization even matters anymore | 23:22 |
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| sheena | carpet hate is reasonable. you want soft/insulating? | 23:26 |
| fenn | right | 23:26 |
| sheena | https://www.facebook.com/5stardogs/photos/pb.221290505558.-2207520000.1415172437./10152679346915559/?type=3&theater | 23:27 |
| sheena | this is what we do with them | 23:27 |
| fenn | i figured it was something to do with dogs :) | 23:27 |
| sheena | there are some INCREDIBLE floors out there | 23:27 |
| sheena | depending what your needs are re insulation, cushion, traction, impact.... | 23:28 |
| sheena | cost.. heh | 23:28 |
| fenn | EPS or polyisocyanurate with radiant barrier can provide a good deal of insulation and and impact absorption, if you use it underneath the foam mat | 23:29 |
| fenn | i started using EPS for lost foam metal casting, and started finding lots of other uses for it | 23:30 |
| fenn | there's a white bead board version that's even cheaper and squishier | 23:30 |
| fenn | what's the pole slalom course called? and why isn't it a human sport? | 23:31 |
| sheena | http://dinoflex.com/index.php/product/walk_soft | 23:31 |
| sheena | agility? | 23:32 |
| sheena | pole slalom being the weave poles? | 23:32 |
| fenn | right | 23:32 |
| fenn | http://www.armynavydeals.ca/asp/products_details.asp?SKU=b0923200 | 23:41 |
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| fenn | oh sorry here's the spreadsheet http://fennetic.net/irc/foam_puzzle_mats.gnumeric | 23:42 |
| fenn | the background maybe is black so select all | 23:42 |
| fenn | http://n55.dk/MANUALS/BED_MODULES/BED.html | 23:49 |
| fenn | 60 cm triangles, polyethylene foam density 40 kg / m3, 20 mm and 10 mm | 23:49 |
| fenn | Velcro tape 20 mm | 23:49 |
| fenn | seems the velcro would get expensive | 23:49 |
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| --- Log closed Wed Nov 05 00:00:41 2014 | ||
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