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| ParahSailin | i got two mouse chips from affy | 06:25 |
|---|---|---|
| ParahSailin | next time i go on site i need to go upstairs and grab a bunch of human ones | 06:25 |
| ParahSailin | genechip mouse genome 430 2.0 array if anyone's curious | 06:26 |
| ParahSailin | not sure if this is scrap or viable | 06:26 |
| ParahSailin | hm, i gotta have them genotype my family as a fringe benefit | 06:30 |
| kanzure | ParahSailin: can you possibly claim that you have a very very large extended family | 06:31 |
| ParahSailin | they should have known that before they gave a guy with an irish name a job | 06:32 |
| ParahSailin | their problem for not catching that sooner | 06:32 |
| ParahSailin | i actually have no idea how a microarray is actually run | 06:33 |
| ParahSailin | so what i need looks like the genome wide human 6.0 array | 06:34 |
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| ParahSailin | kanzure: you ever worked with svitla in the ukraine? | 06:38 |
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| kanzure | ParahSailin: i don't think so | 06:41 |
| kanzure | "the flow of blood (heartbeats) are visible in brain tissue" | 06:42 |
| kanzure | ""In Self/Less, a science-fiction thriller to be released in the U.S. today, July 10, 2015, Damian Hale, an extremely wealthy aristocrat (Ben Kingsley) dying from cancer, undergoes a $250 million radical medical procedure at a lab called Phoenix Biogenic in Manhattan to have his consciousness transferred into the body of a healthy young man"" | 06:46 |
| kanzure | eh i'll probably skip that | 06:46 |
| ParahSailin | wow lame, our human chip has less than a million snps? no wonder illumina eating our lunch | 06:46 |
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| kanzure | maybe there are patent problems? | 06:49 |
| ParahSailin | nah, they just got lazy | 06:49 |
| ParahSailin | over ten years of no competition | 06:52 |
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| ParahSailin | damn, they have no goat panel | 07:02 |
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| eleitl | kanzure, trying to get latest LG sources | 07:25 |
| eleitl | requires manual intervention, everything online is stone old | 07:25 |
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| JayDugger | Good luck, eleitl. | 08:02 |
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| eleitl | Got the sources. | 09:32 |
| eleitl | Thanks, JayDugger. | 09:32 |
| eleitl | Shoveling manure and source code. | 09:33 |
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| eleitl | I think LG could use the loving attention of a good dev. | 09:35 |
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| kanzure | their source code has always been bad | 09:56 |
| kanzure | i am also not completely convinced that they are keeping good metadata | 10:06 |
| kanzure | also, i wonder if set builders are faster than carpenters or machinists | 10:06 |
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| CaptHindsight | plenty of room in the FPGA on the MESA card for inkjet control | 10:43 |
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| archels | potential here for cognitive enhancement? http://www.newscientist.com/article/dn27877-burst-of-light-speeds-up-healing-by-turbocharging-our-cells.html | 11:11 |
| knobuddy | try shining a flaslight in ur ear | 11:13 |
| yoleaux | 3 Jul 2015 03:41Z <nmz787_> knobuddy: I think this is the closest thing to that far-side comic that I guess (and hope) is a joke http://www.theallium.com/policy/taylor-swift-announces-she-will-no-longer-review-for-nature/ | 11:13 |
| knobuddy | i guess that's an offline msg relay via bot | 11:14 |
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| nmz787_i | CaptHindsight: might check into the brand-name septum-seal called SureSeal | 12:08 |
| CaptHindsight | nmz787: well the suppliers would have to adopt it or we'd have to repackage it | 12:10 |
| CaptHindsight | http://blog.chembark.com/2013/08/04/hacks-for-septa/ | 12:12 |
| CaptHindsight | http://www.chemglass.com/product_view.asp?pnr=AF-0522 | 12:17 |
| CaptHindsight | the HP TIJ cartridges use a bladder to hold the ink | 12:17 |
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| CaptHindsight | if you don't push the needles through the seals in the reagent bottles until the printer enclosure is flooded with Argon that should also solve the problem | 12:20 |
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| CaptHindsight | http://www.opentrons.com/ any automation engineer could have made this | 13:00 |
| CaptHindsight | do workers in Bio labs not talk to engineers in other tech? | 13:01 |
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| juri_ | no, the communication methods seem to be radically different. | 13:15 |
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| juri_ | I have been trying to help whe baltimore underground science space, but they don't use a mailing list, or IRC. | 13:16 |
| CaptHindsight | I bet that they reinvented G-code as well | 13:18 |
| CaptHindsight | heh, they are need the original makerbot startup space | 13:19 |
| CaptHindsight | need/near | 13:19 |
| streety | mailing lists seem quite common in bio labs | 13:19 |
| streety | perhaps a last resort beyond a certain scale though | 13:20 |
| streety | the DC diybio group only has a meetup page as yet | 13:21 |
| CaptHindsight | I was just looking through a list of diybio groups | 13:21 |
| CaptHindsight | most don't look active | 13:22 |
| CaptHindsight | just a webpage, facebook etc | 13:22 |
| juri_ | streety: do i know you? ;) | 13:23 |
| streety | I'm not sure | 13:24 |
| streety | this is me -> https://github.com/streety/ | 13:24 |
| juri_ | have you dropped by hacDC for a 3d thursdays? | 13:24 |
| streety | no, not yet | 13:25 |
| streety | I keep meaning to make the trip, but other things keep cropping up | 13:25 |
| kanzure | CaptHindsight: yes, generally biologists are quite isolated from the engineering and computation people | 13:26 |
| juri_ | ah. i'm the instructor there, and was a member of the meat hacking group. | 13:26 |
| kanzure | additionally, many of the community labs tend to take most of their activity in person instead of online, thus why there's no content (sadly) | 13:26 |
| kanzure | CaptHindsight: yes, we should talk to the suppliers about sureseal and see what they say | 13:27 |
| kanzure | also might be a good question to post to the diybio mailing list | 13:29 |
| CaptHindsight | maybe write a biologist friendly front end for Linuxcnc | 13:31 |
| CaptHindsight | seems what they might be up to at opentrons | 13:31 |
| CaptHindsight | turn lab work into G-code | 13:32 |
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| kanzure | "speedup intersection code" https://github.com/pboyer/verb/commit/1a3853e2c1beb6b5f81547ff3378a41080adcf9c | 14:23 |
| kanzure | "A practical algorithm for surface-surface intersection" http://www.cs.berkeley.edu/~hling/research/paper/intersection.htm | 14:28 |
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| juri_ | CaptHindsight: I maintain a 3d modelling system that spits out 2D gcode for laser cutting. | 14:56 |
| CaptHindsight | juri_: I've built all sorts of lab robots using Linuxcnc for the controller | 15:04 |
| CaptHindsight | what is missing is an easy to use G-code generator to create programs | 15:05 |
| CaptHindsight | program routines where it's just pick-n-place or dispense from a nozzle or syringe | 15:06 |
| kanzure | have you seen the octoprint tool? | 15:08 |
| CaptHindsight | or a gantry that moves from spot to spot raising and lowering something to set locations and intervals | 15:08 |
| kanzure | this has a simple web interface for planning 3d prints http://octoprint.org/ | 15:09 |
| CaptHindsight | kanzure: I've only seen the website. I didn't see any tools | 15:09 |
| kanzure | there's some screenshots here https://www.youtube.com/watch?v=TQzGQN440Ns | 15:09 |
| CaptHindsight | oh .org vs .com | 15:09 |
| kanzure | around 1m 40sec i guess | 15:10 |
| CaptHindsight | oh great, they went weenie and built if for repraps | 15:11 |
| kanzure | yeah... | 15:11 |
| CaptHindsight | toys vs machines | 15:11 |
| CaptHindsight | I use this a great example of a horrible UI for multi axis machines http://reprap.org/mediawiki/images/1/12/Pronterface.png | 15:15 |
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| CaptHindsight | https://fedoraproject.org/w/uploads/4/4b/RepetierHost.png Repetier knew what to do | 15:16 |
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| kanzure | superkuh: mike darwin does something similar to your "constant audio playback of scientific documents" technique. | 16:02 |
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| kanzure | biopreservation inc. documents http://www.cryocare.org/index.cgi?subdir=bpi&url=bpi.html | 16:14 |
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| juri_ | I like the pronterface UI. what don't you like about it? | 16:20 |
| kanzure | http://cryoeuro.eu:8080/download/attachments/1441801/Darwin_Michael_+G_+Biography_v4.3.pdf | 16:22 |
| CaptHindsight | juri_: you can't see what the tool is doing | 16:22 |
| kanzure | "As a child, Darwin initially experimented with halting decomposition in small dead animals by | 16:22 |
| kanzure | immersing them in 70% isopropyl alcohol." | 16:22 |
| juri_ | it's pretty intuitive to me. | 16:23 |
| CaptHindsight | juri_: for comparison look at Axis, Gmoccapy in Linuxcnc or Repetier | 16:24 |
| juri_ | ugh. repetier. non-free #(%$. | 16:24 |
| juri_ | haven't looked at the others. | 16:25 |
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| streety | I've observed someone using an interface similar to the Pronterface UI, even with regular use they still needed to stop and think about which direction they wanted to move . . . every time they wanted to move | 16:46 |
| kanzure | eh just use a joystick | 16:47 |
| kanzure | wait do they still make joysticks anymore | 16:48 |
| streety | not sure that solves the issue. you could still match up movements either looking down from above or up from beneath, etc | 16:55 |
| kanzure | well, it makes sense to think before moving a machine, perhaps a simulation mode would be useful | 16:59 |
| streety | To a certain extent you are correct. I would suggest thinking about the movement you want to make is sensible, but being forced to think about how to execute a movement is just bad design | 17:17 |
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| CaptHindsight | https://www.youtube.com/watch?v=4Mz7tzVSsYk here the AXIS GUI in Linuxcnc you can preflight the program and also watch the position in real time | 18:10 |
| CaptHindsight | https://www.youtube.com/watch?v=fWKYQUj5AOs or using the SIM | 18:16 |
| kanzure | he is suggesting that i sleep in DMSO i am not sure i trust him | 18:19 |
| CaptHindsight | the DNA inkjet can simulate it's program before execution to see if you programmed something goofy | 18:22 |
| CaptHindsight | the worst thing is crash the head into something | 18:23 |
| CaptHindsight | we sometimes add a laser to set a ZERO for Z so you don't crash the head while scanning | 18:24 |
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| kanzure | brian wowk made some molecules that act like antifreeze proteins except better | 18:41 |
| kanzure | tree frogs can survive freezing up to -20 celsius | 18:42 |
| kanzure | mammalian brains can survive being 60% frozen, no memory loss | 18:43 |
| kanzure | the tree frogs make a cryoprotectant with glucose. then they move all their water from their organs to various body cavities, like between their lungs or their cerebrospinal fluid cavities. | 18:46 |
| kanzure | he has frozen his abdomen before.... | 18:47 |
| kanzure | apparently the way to survive frostbite is to not bend the appendage at all, and warming it up in a sane way. otherwise you irreversibly damage it. | 18:49 |
| drethelin | good to know | 18:51 |
| kanzure | also he says you need to use microwave/rf reheating to avoid ice nucleation, which is a problem fahy has run into | 19:00 |
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| kanzure | he was using fluorocarbon to perfuse dogs after vitrifying and after perfusing with cryoprotectant, to get dogs down 5 degrees celsius/minute (this is much faster than normal) | 19:03 |
| kanzure | "you can perfuse a person at 1000 liters/minute with gas" | 19:04 |
| kanzure | "use a hyperbaric chamber to increase the heat transfer capacity, and move 10x more the heat with the same volume of gas" (well duh?) | 19:06 |
| kanzure | "the human body will tolerate 500 psi just fine, but not 2000 psi" | 19:07 |
| drethelin | wouldn't want to kersplode | 19:09 |
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| CaptHindsight | ooh, I can get Epson 1430 printheads from China in bulk | 19:55 |
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| kanzure | hmm why aren't we using gas sterilization instead of autoclaves | 20:04 |
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| kanzure | intranasal insulin apparently helps with alzheimers | 20:21 |
| drethelin | aren't autoclaves more general | 20:25 |
| kanzure | something about a japanese anime about racoons... and then japan started to import racoons? wtf | 20:27 |
| drethelin | japan already had raccoon dogs | 20:28 |
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| kanzure | "biological effects of freezing and super cooling" | 20:37 |
| kanzure | "the shallows" (meh) | 20:37 |
| kanzure | he works at a gas station | 20:42 |
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| CaptHindsight | kanzure: sent updated specs, I'll finish it tomorrow | 21:01 |
| kanzure | awesome; i'm still on the phone but will look. | 21:05 |
| kanzure | yes i think we need to focus on the interface with the chemicals eventually, but this is an excellent start to the electromechanical components | 21:07 |
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| kanzure | .title https://www.youtube.com/watch?v=Fjr3A_kfspM | 22:19 |
| yoleaux | Freezing North American Wood Frogs - YouTube | 22:19 |
| kanzure | .wik rana sylvatica | 22:22 |
| yoleaux | "The wood frog (Lithobates sylvaticus) has a broad distribution over North America, extending from the southern Appalachians to the boreal forest with several notable disjunct populations including lowland eastern North Carolina." — https://en.wikipedia.org/wiki/Rana_sylvatica | 22:22 |
| kanzure | "... wood frogs can tolerate the freezing of their blood and other tissues.[6][7] Urea is accumulated in tissues in preparation for overwintering, and liver glycogen is converted in large quantities to glucose in response to internal ice formation. Both urea and glucose act as cryoprotectants to limit the amount of ice that forms and to reduce osmotic shrinkage of cells.[8][9] Frogs can survive many freeze/thaw events during winter if no ... | 22:24 |
| kanzure | ... more than about 65% of the total body water freezes." | 22:24 |
| kanzure | "Biochemical adaption for freezing tolerance in the wood frog,Rana sylvatica" http://link.springer.com/article/10.1007/BF00688788 | 22:25 |
| kanzure | "Hatchling turtles survive freezing during winter hibernation" http://www.pnas.org/content/85/21/8350.full.pdf | 22:25 |
| kanzure | "Hypometabolic homeostasis in overwintering aquatic amphibians" http://jeb.biologists.org/content/200/2/387.full.pdf | 22:26 |
| kanzure | "Strategies for exploration of freeze responsive gene expression: advances in vertebrate freeze tolerance" http://www.researchgate.net/profile/Kenneth_Storey/publication/8609790_Strategies_for_exploration_of_freeze_responsive_gene_expression_advances_in_vertebrate_freeze_tolerance/links/0deec51f7e22fbe53d000000.pdf | 22:26 |
| kanzure | "Glucose concentration regulates freeze tolerance in the wood frog Rana sylvatica" http://jeb.biologists.org/content/181/1/245.full.pdf | 22:26 |
| kanzure | "Cold ischemic organ preservation: lessons from natural systems" http://www.researchgate.net/profile/Kenneth_Storey/publication/8174973_Cold_ischemic_organ_preservation_Lessons_from_natural_systems/links/0deec51f7e23188749000000.pdf | 22:27 |
| kanzure | "Forever young: mechanisms of natural anoxia tolerance and potential links to longevity" http://downloads.hindawi.com/journals/omcl/2010/306209.pdf | 22:28 |
| kanzure | "Genetic and epigenetic regulation in hypometabolism" http://trnres.com/ebook/uploads/nowakowska/T_13334498848%20Nowakowska.pdf | 22:31 |
| kanzure | ah primate torpor is apparently a thing, http://www.sciencedirect.com/science/article/pii/S1672022915000467 | 22:32 |
| kanzure | "Primate Torpor: Regulation of Stress-activated Protein Kinases During Daily Torpor in the Gray Mouse Lemur, Microcebus murinus" | 22:32 |
| kanzure | "Very few selected species of primates are known to be capable of entering torpor. This exciting discovery means that the ability to enter a natural state of dormancy is an ancestral trait among primates and, in phylogenetic terms, is very close to the human lineage. To explore the regulatory mechanisms that underlie primate torpor, we analyzed signal transduction cascades to discover those involved in coordinating tissue responses ... | 22:33 |
| kanzure | ... during torpor. The responses of mitogen-activated protein kinase (MAPK) family members to primate torpor were compared in six organs of control (aroused) versus torpid gray mouse lemurs, Microcebus murinus. The proteins examined include extracellular signal-regulated kinases (ERKs), c-jun NH2-terminal kinases (JNKs), MAPK kinase (MEK), and p38, in addition to stress-related proteins p53 and heat shock protein 27 (HSP27)." | 22:33 |
| kanzure | "Importantly, both adipose tissues possess specialized functions that are critical for torpor, with brown adipose required for non-shivering thermogenesis and white adipose utilized as the primary source of lipid fuel for torpor. Overall, these data indicate crucial roles of MAPKs in the regulation of primate organs during torpor." | 22:33 |
| kanzure | an interesting variation (that mike did not suggest..) is that you could do directed evolution and selective breeding for organs that better survive freezing, and in particular you could select the ones that seem to make gross anatomical changes during the freezing process (or in preparation for freezing- perhaps with some signaling method that you pick). these changes might not confer any survival benefit whatsoever, except that we ... | 22:35 |
| kanzure | ... suspect that the changes might confer survival benefits. so we can just select the organs that seem to be more likely to survive, even if they aren't actually surviving yet. | 22:35 |
| kanzure | (however, since organs seem to already be surviving at some rate, it seems like that sort of technique will not be required) | 22:35 |
| kanzure | and for the purposes of recovery, you could do the reverse- something like, take an organ down to low temperature but not freezing, and then check whether the changes you want are happening, and select the organisms for the ones that perform appropriate cleanup and resuscitation, and uhh then figure out some way to ensure that those genetic expression networks are triggered when thawing 4realz | 22:39 |
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| drethelin | hmm | 22:50 |
| drethelin | I'm confused by what the goal is here | 22:50 |
| drethelin | to figure out how to adapt humans to cryogenics? | 22:50 |
| drethelin | also torpor is really interesting, especially hibernation | 22:50 |
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| drethelin | if we can figure out how it works we can cure something like obesity like THAT | 22:51 |
| drethelin | with few if any long-term side efefcts | 22:51 |
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| drethelin | if we can duplicate the fat deposition and burning switches | 22:51 |
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| kanzure | drethelin: i just want adaptation of any animal to cryonics (including cryoresuscitation), not necessarily human yet | 23:26 |
| kanzure | thus my selective breeding and directed evolution project description from earlier this year | 23:26 |
| drethelin | ah | 23:27 |
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