--- Log opened Fri Jul 10 00:00:06 2015
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02:32 < justanotheruser> Is there a lot of redundancy in this database?
02:32 < justanotheruser> It seems bacterias gonna be about 600Gb
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04:35 < kanzure> redundancy but also slight variation
05:03 < justanotheruser> yeah, doesn't look like it would be cost efficient to do my own compression
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05:18 < kanzure> .tell delinquentme https://www.youtube.com/watch?v=JiyxPae4h5A&t=17m30s
05:18 < yoleaux> kanzure: I'll pass your message to delinquentme.
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06:33 < kanzure> .title http://pubs.rsc.org/en/content/articlelanding/2015/lc/c5lc00297d
06:33 < yoleaux> Reagent pencils: a new technique for solvent-free deposition of reagents onto paper-based microfluidic devices - Lab on a Chip (RSC Publishing)
06:33 < kanzure> weird.
06:34 < kanzure> .tilte http://infoscience.epfl.ch/record/207509
06:34 < kanzure> .title http://infoscience.epfl.ch/record/207509
06:34 < yoleaux> Long-term culture and high-resolution imaging of C. elegans using an automated microfluidic platform
06:34 < kanzure> "We describe a microfluidic platform for the automated culture, treatment and long-term high-resolution imaging of C. elegans. Our device features: (i) a microfluidic design tailored for the isolation of L4 larvae from a mixed larval population and for their successive culture and treatment; (ii) a worm immobilization method, based on the thermoreversible sol-gel transition of the biocompatible triblock copolymer Pluronic F127 inside the ...
06:34 < kanzure> ... microfluidic chip, thereby enabling high-resolution imaging; (iii) an integrated temperature control system, both to ensure viable environmental conditions for C. elegans culture and to steer the worm immobilization/release process. We apply this device to observe mitochondrial dynamics in muscle cells during aging at single worm resolution."
07:05 < eudoxia> second trubrain shipment's arrived
07:05 < eudoxia> i took a boost one this time
07:05 < eudoxia> if i don't push to github in 2 days call an ambulance
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08:10 < eudoxia> well this is underwhelming
08:11 < Adlai> "underwhelming" is underinformative
08:14 < eleitl> kanzure, do you have a working link for LG source code?
08:14 < eleitl> The usual one 404s.
08:14 < kanzure> don't think so
08:15 < eleitl> Do you think the magnets will work for the corpus?
08:15 < kanzure> get it from usenet
08:16 < eleitl> http://libgen.education/repository_nzb/ ?
08:17 < kanzure> doesn't work for me
08:17 < kanzure> so far magnets have not been reliable for me
08:17 < kanzure> usenet
08:17 < eleitl> might be geoblocked
08:17 < eleitl> usenet where?
08:19 < kanzure> looking
08:19 < kanzure> it's mentioned on their forum somewhere
08:20 < eleitl> Yes, found it. Thanks.
08:20 < kanzure> ah faster than me, weird
08:22 < eleitl> I had forum open already.
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08:26 < eleitl> nzb health is questionable
08:26 < eleitl> kanzure, how many TB at the moment?
08:27 < kanzure> i delegated this and the person is sleeping at the moment
08:27 < eleitl> Allright.
08:28 < kanzure> what a slacker, right? sleeping and such
08:28 < eleitl> What next, eating? Breathing, perhaps?
08:28 < kanzure> mike gave me his phone number, says to call whenever
08:29 < eleitl> Great. Get ready for some phone bills.
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09:38 < nmz787_i> oh man, HackBnB is a great idea (give somone your place to stay while you're out of town, in exchange for hacking progress)
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09:39 < kanzure> er... that implies that the value of hacking is less than or equal to the value of a place to stay? that's weird.
09:42 < nmz787_i> guess you just need to rent to less-experienced hackers?
09:42 < nmz787_i> also, you don't necessarily need to run the hacker ragged
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09:50 < CaptHindsight> anyone try these yet?  http://www.automationtechnologiesinc.com/products-page/ac-servo-motors/the-ac-servo-driver-ac-servo-motor-400w-set
09:50 < TMA> maybe the expected depreciation of the place to stay (say 10% chance of the apartement being razed) is factored in
09:50 < CaptHindsight> http://www.automationtechnologiesinc.com/products-page/ac-servo-motors/servo-driversimdrive-servo-motor-750w-set
09:51 < CaptHindsight> tjtr33  have you seen these at Keiling yet?
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10:01 < CaptHindsight> http://www.cs-lab.eu/en/produkt-31,3-simDriveAC_Servo_400W_325V_Model_M4H040K.html  anyone ever heard of/used them?
10:03 < nmz787_i> CaptHindsight: they look OK for some applications
10:04 < nmz787_i> I have not used or heard of them specifically
10:04 < CaptHindsight> heh, posted to the wrong channel
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10:06 < CaptHindsight> nmz787: looks like a low budget brand of servo drives and motors
10:10 < nmz787_i> yeah, there are certainly lower budget ones too
10:10 < nmz787_i> those seem pretty high power compared to what you can get on the lower end
10:10 < CaptHindsight> AC servo motor and drives for less than the price of closed loop 0.36 deg steppers and drives
10:11 < CaptHindsight> in equivalent power specs
10:11 < nmz787_i> ah
10:12 < CaptHindsight> http://catalog.orientalmotor.com/item/category-3001281/r-series-closed-loop-stepping-motors/ar46aa-3?&plpver=11&origin=keyword&by=prod&filter=0
10:12 < nmz787_i> most stuff I'm interested in needs interferometry, linear-slides, or some sort of optical (visual or computer vision) feedback to close the loop
10:13 < CaptHindsight> yeah for sub micron
10:13 < CaptHindsight> even for <5um over temp
10:28 < nmz787_i> CaptHindsight: so do you want that synthesizer shipped over to you?
10:28 < nmz787_i> the almost-posam-minus-the-inkjet-head-and-open-'air'-wells?
10:30 < nmz787_i> with closed source controls that would need to be hacked on, and the pretty inefficient synthesis method it can perform... it would be a decent undertaking just to get it turned on and running like it used to
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11:01 < juri_> kanzure: as a free software/hardware hacker, i find the price of living in my preferred location is greater than the value placed on my 24/7 hacking activities.
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11:24 < CaptHindsight> nmz787: they used Parker Ballscrew positioners and parker sevro dives, I use those all the time
11:24 < CaptHindsight> those were expensive 15 years ago
11:26 < CaptHindsight> looks like they spent ~$18K on drives, motors and positioners
11:27 < CaptHindsight> ouch, they even bough Parker cables, thats >$1500 right there
11:27 < CaptHindsight> $23K on the stage and optical table
11:27 < nmz787_i> bbl
11:27 < nmz787_i> i'd spend that too if i had it, and wanted things to be turn-key
11:28 < CaptHindsight> there are equivalent stages for less
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11:28 < CaptHindsight> even now from parker
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11:29 < juri_> I'm in the process of building a robot on an optical table.
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11:30 < juri_> it's been a long process. tight budget. AKA, what i can beg, borrow, and steal.
11:31 < CaptHindsight> yeah, I've seen your other machines
11:31 < CaptHindsight> nice job with limited budget and tools
11:31 < CaptHindsight> I have a complete cnc shop so it makes it easier
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11:40 < juri_> as long as i stay in the free hardware/software world, limited budgets and tools are a thing.
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11:47 < CaptHindsight> I find lots of bargains on very high end components since they are typically outside the range of hobbyists budget and skill
11:47 < CaptHindsight> lots of people have trouble tuning servos and shy away from them
11:51 < kanzure> yes, the posam people overspent on their actuation equipment
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11:59 < justanot1eruser> sooo much Escherichia_coli
12:00 < justanot1eruser> I need a server setup so I can use all their bandwidth
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12:12 < kanzure> CaptHindsight: perhaps we could do a deal with a mail-order dna synthesis company (e.g. they sponsor parts/labor or some other aspect)
12:14 < kanzure> justanot1eruser: whatcha up to anyway
12:19 < kanzure> http://i.imgur.com/7mD6sEb.jpg
12:19 < kanzure> https://i.imgur.com/DLkxFj1.jpg
12:20 < justanot1eruser> trying to download refseq from Virginia Tech since apparently they're more competent than the National Institute of Health (who never replied to my email btw)
12:20 < justanot1eruser> googles new thing? Forget what it's called
12:20 < kanzure> (from http://googleresearch.blogspot.co.uk/2015/06/inceptionism-going-deeper-into-neural.html ) (apparently these algorithms like eyeballs)
12:21 < kanzure> justanot1eruser: well it's a thursday/friday, you can't expect them to work on a thursday/friday
12:25 < justanot1eruser> right, that probably is against union rules
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12:56 < CaptHindsight> kanzure: the big questions are how easy should a new POSaM be to copy? Budget, skill, resourcefulness etc
12:56 < CaptHindsight> also how fast and how accurate do you want the drops
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12:58 < CaptHindsight> easy for since me I find bargains on things like linear servos, air bearings, drivers etc and have a CNC shop
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13:00 < CaptHindsight> the surface tension of the drops is going to pull them onto the layer below so 20um repeatability is low cost, fast and easy to reproduce without NASA level skills
13:09 < CaptHindsight> there should be plenty of room to squeeze the printhead control into the Mesa FPGA
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13:23 < kanzure> CaptHindsight: how easy to copy... hmm. well, very.
13:28 < CaptHindsight> kanzure: so no real machining involved
13:28 < CaptHindsight> just assembly
13:28 < kanzure> hmm. that is a good question.
13:29 < kanzure> it depends on how advantageous the machined part would be
13:29 < CaptHindsight> that means a pre-drilled surface plate, brackets etc
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13:30 < kanzure> hmmm well those aren't very difficult to machine
13:30 < CaptHindsight> depends on your tools
13:31 < CaptHindsight> what you have available
13:31 < CaptHindsight> do you have a mill?
13:31 < kanzure> nah not at the moment
13:31 < CaptHindsight> well will others?
13:31 < kanzure> well.... let's pick a target audience. there's a bunch of options.
13:32 < kanzure> if we want something that a stereotypical "biohacker" can throw together, then no machining- most biohackers don't have cnc equipment
13:32 < CaptHindsight> I can design with all off the shelf or full custom and anywhere in between
13:32 < kanzure> are any of the off-the-shelf particularly tricky to machne on your own if someone wants to?
13:32 < CaptHindsight> for me I see it all as legos
13:33 < CaptHindsight> well I could machine custom brackets and make them available
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13:34 < CaptHindsight> the printhead and the valves need a custom bracket no matter what
13:34 < kanzure> ah interesting point
13:35 < CaptHindsight> also the CNC control and printing software allow for flexibility
13:35 < CaptHindsight> it's easy to have a 20 x 30cm XY or 30 x 35cm XY but just changing positioners available to you
13:36 < CaptHindsight> then you just need different mounting locations for the surface plate
13:36 < kanzure> yep, agreed
13:37 < CaptHindsight> do we make one standard design that it is easy enough to modify based on what you can scrounge?
13:37 < kanzure> further note: if we expect "biohackers" to machine their own parts, then we should anticipate them to have approximately zero cnc experience and should not expect them to be bevel masters or something
13:38 < CaptHindsight> I see CNC hobbyists even screw up simple things like how to mount something square
13:38 < CaptHindsight> or choosing something rigid enough
13:39 < CaptHindsight> most people like the comfort of plans that they can follow
13:39 < kanzure> as long as cad files and schematics are available, it doesn't matter if someone has to buy the parts from you or some other vendor
13:39 < CaptHindsight> like Ikea only if you have a wood shop you can further customize
13:39 < CaptHindsight> ok
13:39 < kanzure> another detail you should consider is if you want to be shipping out plates, brackets and doohickeys to biohackers for a while :-)
13:40 < CaptHindsight> with CAD files they can even hire a local shop to fab something
13:40 < CaptHindsight> but people often get lost with things like how to mount a positioner square and level
13:41 < CaptHindsight> so maybe a standard design that people can follow to the letter and if they have the skills and tools they can easily make changes
13:41 < CaptHindsight> it's just becomes a support nightmare if you want to help them with something custom
13:42 < CaptHindsight> we see it with CNC machines all the time
13:42 < CaptHindsight> and this is a bit more precise than a reprap that you have to massage to get working just right temporarily
13:43 < CaptHindsight> this is an order of magnitude more precise
13:45 < CaptHindsight> the custom PCB will have schematics and PCB files (gerbers)
13:45 < CaptHindsight> and a BOM, I doubt that they will change that
13:46 < CaptHindsight> the stage has to be aligned square and level
13:46 < CaptHindsight> premade parts will bolt together and have pins for alignment
13:46 < CaptHindsight> ^^mechanical parts
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13:56 < kanzure> CaptHindsight: https://azcobiotech.com/reagents-for-oligonucleotide-synthesis/liquid-reagents/
13:57 < kanzure> CaptHindsight: https://azcobiotech.com/reagents-for-oligonucleotide-synthesis/phosphoramidites/
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14:10 < CaptHindsight> kanzure: it would be nice to have those in a proper bottle and connector
14:12 < kanzure> i don't know the names of the necessary connectors
14:13 < CaptHindsight> they look like they might have a septum or membrane on the 1g bottle
14:13 < CaptHindsight> 4g bottle
14:13 < CaptHindsight> the 1g looks like a screw cap
14:18 < CaptHindsight>  The tubing connects to the needle inlets with 1.6 mm I.D. PharMed® tubing and to the vials with 20 gauge non-coring stainless steel needles, 5 cm in length.
14:20 < CaptHindsight> http://i00.i.aliimg.com/photo/v1/715061888/r290_print_head_Epson_Stylus_Photo_P50.jpg  the tubing slips over those posts on the printhead
14:23 < CaptHindsight> http://imagebin.ca/v/28BvcTBHB1Fz  and needles on the other end as shown here
14:25 < CaptHindsight> better shown here  http://imagebin.ca/v/28BwOYErioQv
14:44 < kanzure> exposing the contents of those bottles to normla atmosphere is very very bad
14:44 < kanzure> *normal
14:44 < CaptHindsight> yes, why it would be nice to have a sealed system
14:44 < CaptHindsight> no needles
14:44 < kanzure> brb lunch
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15:04 < kanzure> back
15:06 < CaptHindsight> kanzure: I didn't notice that the POSaM printhead parking it self between prints
15:07 < CaptHindsight> so an inert atmosphere is assumed when printing
15:08 < CaptHindsight> having to purge everything is kind of a pain as well
15:09 < kanzure> yup, it's argon
15:09 < kanzure> or er... the abi 391 uses argon. dunno what posam used.
15:09 < CaptHindsight> someone mentioned it's the water that really needs to be kept out
15:10 < kanzure> oxygen also tends to be reactive
15:10 < CaptHindsight> I'd think
15:12 < kanzure> "okay so now for the REAL plan, let's ignite the oxygen atmosphere inside of the enclosure and just burn all the gas out" er....
15:12 < CaptHindsight> any idea how long the reagents can sit in the heads?
15:12 < CaptHindsight> welding gas is cheap and easy to get
15:12 < kanzure> no clue, i think we're going to have to test that sort of thing
15:13 < CaptHindsight> is there a fluid we can use as a flush that can stay in the heads?
15:13 < kanzure> quite likely
15:13 < CaptHindsight> there is a little bit of mixing that goes on inside the area behind the nozzles
15:14 < CaptHindsight> the volume is ~25uL
15:14 < CaptHindsight> it would be nice to not lose any reagent, or at least minimize loss and and contact with 02 and water
15:15 < CaptHindsight> - 1 and
15:15 < kanzure> maybe you could pull some plastic wrap over the inkjet head, for when you want to expose the rest of the enclosure to normal atmosphere
15:15 < CaptHindsight> with inkjet fluids you just waste purge
15:15 < kanzure> (the posam enclosure had human-sized gloves to work with the contents inside)
15:16 < CaptHindsight> we can make a condom for the printhead
15:16 < kanzure> yep
15:16 < kanzure> actually a condom might work fine :P
15:17 < CaptHindsight> and actual inkjet industry term
15:18 < kanzure> oh
15:18 < CaptHindsight> some fluids have high vapor pressures so you don't want them drying in the nozzles
15:18 < CaptHindsight> so you park and cap the nozzles
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15:44 < CaptHindsight> most desktop inkjet printers do this over a waste tank or sponge to be sure enough ink gets wasted daily
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15:53 < kanzure> .title https://www.youtube.com/watch?v=CVFscjOsPRA
15:53 < yoleaux> Carbon Based Lifeforms - Interloper [2010] . HQ - YouTube
15:53 < CaptHindsight> kanzure: if we make the print area smaller it will also become more affordable
15:55 < CaptHindsight> the vacuum check for the slides in the POSaM is ~12" x 12"
15:55 < CaptHindsight> check/chuck
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15:56 < CaptHindsight> what's our slide/tray size?
15:57 < kanzure> larger means more spots, so it's a tradeoff
15:57 < CaptHindsight> plus they have an oversized work volume
15:58 < CaptHindsight> 20" x 24" x 4" for only a 12" x 12" slide area
15:59 < CaptHindsight> we can downsize to 14" x 14" travel
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16:14 < juri_> CaptHindsight: why the mesa FPGA? I've got a spartan 6 here...
16:15 < CaptHindsight> juri_: Mesa is the board maker
16:15 < CaptHindsight> it uses a Xilinx
16:16 < juri_> is it a spartan 6 lx9 or lx45?
16:16 < CaptHindsight> depends on the board we choose
16:16 < juri_> those are the only two FPGAs i'll support, here. ;)
16:16 < CaptHindsight> and if we also squeeze the printhead controller into it along with motion control
16:17 < juri_> (supported by FPGATOOLS)
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16:17 < CaptHindsight> http://www.mesanet.com/fpgacardinfo.html
16:19 < CaptHindsight> The 6I24 use a Xilinx Spartan6 X16 or X25 FPGA in a 256 ball BGA package: XC6SLX16FTG256 or XC6SLX25FTG256 depending on 6I24 model.
16:20 < juri_> nice.
16:20 < CaptHindsight> I'll be using the Xilinx tools but you are free to use whatever you wish
16:22 < juri_> sounds like a plan.
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18:14 < CaptHindsight> kanzure: http://imagebin.ca/v/28D3LRO00bQ8  DNA inkjet block diagram
18:16 < kanzure> CaptHindsight: needs moar sensors, like humidity, temperature, vibration (just kidding), maybe something else
18:16 < CaptHindsight> heh, all part of the IO we decide
18:17 < kanzure> what about the actuation for replacing the atmosphere in the enclosure?
18:18 < CaptHindsight> solenoid valves
18:24 < CaptHindsight> kanzure: rev 0.1 specs sent
18:27 < kanzure> CaptHindsight: could you be more specific about the things you are hoping i will edit? sorry about being clueless here.
18:29 < CaptHindsight> kanzure: I'll fill in much more
18:29 < kanzure> it would be very helpful if you have a set of docs for another older project (i could even sign an nda) for a sample of what sort of things you'd like me to help work with you towards
18:30 < kanzure> (brb)
18:30 < CaptHindsight> don't worry
18:32 < CaptHindsight> we can finish the spec over the weekend
18:35 < nmz787_i> get some of these for temp and humidity... good to saturation and will keep working, and all compensated and digital-out https://learn.adafruit.com/dht
18:35 < nmz787_i> the sht series are the cheaper chinese ripoffs
18:36 < nmz787_i> and these for CO2, if you were to need that (I don't think so) http://www.co2meter.com/products/k-30-co2-sensor-module
18:37 < nmz787_i> (in general though, that last one is a NIR monochromatic spectrometer
18:37 < CaptHindsight> well those would nice to have to know that you are at ZERO O2
18:37 < CaptHindsight> in case there's something wrong
18:37 < nmz787_i> or, well, since it's a monochromatic system, maybe it would be called a chromameter?
18:38 < CaptHindsight> we'll focus on all the long lead time parts first
18:38 < CaptHindsight> printhead controller, linear positioners
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18:53 < kanzure> you might need -80 or -20 celsius freezers
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20:26 < kanzure> nature.com seems to be down
20:29 < kanzure> "Recording action potentials from the surface of the brain" http://www.buzsakilab.org/content/PDFs/Khodagholy2014.pdf
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22:34 < JayDugger> Good morning, everyone.
22:48 < FourFire> good morning
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--- Log closed Sat Jul 11 00:00:07 2015