| --- Log opened Fri Jul 10 00:00:06 2015 | ||
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| justanotheruser | Is there a lot of redundancy in this database? | 02:32 |
|---|---|---|
| justanotheruser | It seems bacterias gonna be about 600Gb | 02:32 |
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| kanzure | redundancy but also slight variation | 04:35 |
| justanotheruser | yeah, doesn't look like it would be cost efficient to do my own compression | 05:03 |
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| kanzure | .tell delinquentme https://www.youtube.com/watch?v=JiyxPae4h5A&t=17m30s | 05:18 |
| yoleaux | kanzure: I'll pass your message to delinquentme. | 05:18 |
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| 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. | 06:33 |
| 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." | 06:34 |
| 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 | 07:05 |
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| eudoxia | well this is underwhelming | 08:10 |
| Adlai | "underwhelming" is underinformative | 08:11 |
| 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 | 08:14 |
| eleitl | Do you think the magnets will work for the corpus? | 08:15 |
| kanzure | get it from usenet | 08:15 |
| eleitl | http://libgen.education/repository_nzb/ ? | 08:16 |
| 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? | 08:17 |
| kanzure | looking | 08:19 |
| kanzure | it's mentioned on their forum somewhere | 08:19 |
| eleitl | Yes, found it. Thanks. | 08:20 |
| kanzure | ah faster than me, weird | 08:20 |
| eleitl | I had forum open already. | 08:22 |
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| eleitl | nzb health is questionable | 08:26 |
| eleitl | kanzure, how many TB at the moment? | 08:26 |
| kanzure | i delegated this and the person is sleeping at the moment | 08:27 |
| eleitl | Allright. | 08:27 |
| 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 | 08:28 |
| eleitl | Great. Get ready for some phone bills. | 08:29 |
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| 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) | 09:38 |
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| 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. | 09:39 |
| 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 | 09:42 |
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| 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 | 09:50 |
| CaptHindsight | tjtr33 have you seen these at Keiling yet? | 09:51 |
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| CaptHindsight | http://www.cs-lab.eu/en/produkt-31,3-simDriveAC_Servo_400W_325V_Model_M4H040K.html anyone ever heard of/used them? | 10:01 |
| nmz787_i | CaptHindsight: they look OK for some applications | 10:03 |
| nmz787_i | I have not used or heard of them specifically | 10:04 |
| CaptHindsight | heh, posted to the wrong channel | 10:04 |
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| CaptHindsight | nmz787: looks like a low budget brand of servo drives and motors | 10:06 |
| 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 | 10:10 |
| CaptHindsight | in equivalent power specs | 10:11 |
| nmz787_i | ah | 10:11 |
| 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 | 10:12 |
| CaptHindsight | yeah for sub micron | 10:13 |
| CaptHindsight | even for <5um over temp | 10:13 |
| 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? | 10:28 |
| 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 | 10:30 |
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| 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. | 11:01 |
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| 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 | 11:24 |
| CaptHindsight | looks like they spent ~$18K on drives, motors and positioners | 11:26 |
| 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 | 11:27 |
| CaptHindsight | there are equivalent stages for less | 11:28 |
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| CaptHindsight | even now from parker | 11:28 |
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| juri_ | I'm in the process of building a robot on an optical table. | 11:29 |
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| juri_ | it's been a long process. tight budget. AKA, what i can beg, borrow, and steal. | 11:30 |
| 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 | 11:31 |
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| juri_ | as long as i stay in the free hardware/software world, limited budgets and tools are a thing. | 11:40 |
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| 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 | 11:47 |
| kanzure | yes, the posam people overspent on their actuation equipment | 11:51 |
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| justanot1eruser | sooo much Escherichia_coli | 11:59 |
| justanot1eruser | I need a server setup so I can use all their bandwidth | 12:00 |
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| 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) | 12:12 |
| kanzure | justanot1eruser: whatcha up to anyway | 12:14 |
| kanzure | http://i.imgur.com/7mD6sEb.jpg | 12:19 |
| kanzure | https://i.imgur.com/DLkxFj1.jpg | 12:19 |
| 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) | 12:20 |
| kanzure | justanot1eruser: well it's a thursday/friday, you can't expect them to work on a thursday/friday | 12:21 |
| justanot1eruser | right, that probably is against union rules | 12:25 |
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| 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 | 12:56 |
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| CaptHindsight | easy for since me I find bargains on things like linear servos, air bearings, drivers etc and have a CNC shop | 12:58 |
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| 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 | 13:00 |
| CaptHindsight | there should be plenty of room to squeeze the printhead control into the Mesa FPGA | 13:09 |
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| kanzure | CaptHindsight: how easy to copy... hmm. well, very. | 13:23 |
| CaptHindsight | kanzure: so no real machining involved | 13:28 |
| CaptHindsight | just assembly | 13:28 |
| kanzure | hmm. that is a good question. | 13:28 |
| kanzure | it depends on how advantageous the machined part would be | 13:29 |
| CaptHindsight | that means a pre-drilled surface plate, brackets etc | 13:29 |
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| kanzure | hmmm well those aren't very difficult to machine | 13:30 |
| CaptHindsight | depends on your tools | 13:30 |
| 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. | 13:31 |
| 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 | 13:32 |
| CaptHindsight | well I could machine custom brackets and make them available | 13:33 |
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| CaptHindsight | the printhead and the valves need a custom bracket no matter what | 13:34 |
| kanzure | ah interesting point | 13:34 |
| 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 | 13:35 |
| CaptHindsight | then you just need different mounting locations for the surface plate | 13:36 |
| kanzure | yep, agreed | 13:36 |
| 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 | 13:37 |
| CaptHindsight | I see CNC hobbyists even screw up simple things like how to mount something square | 13:38 |
| CaptHindsight | or choosing something rigid enough | 13:38 |
| 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 :-) | 13:39 |
| 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 | 13:40 |
| 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 | 13:41 |
| 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 | 13:42 |
| CaptHindsight | this is an order of magnitude more precise | 13:43 |
| CaptHindsight | the custom PCB will have schematics and PCB files (gerbers) | 13:45 |
| CaptHindsight | and a BOM, I doubt that they will change that | 13:45 |
| 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 | 13:46 |
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| kanzure | CaptHindsight: https://azcobiotech.com/reagents-for-oligonucleotide-synthesis/liquid-reagents/ | 13:56 |
| kanzure | CaptHindsight: https://azcobiotech.com/reagents-for-oligonucleotide-synthesis/phosphoramidites/ | 13:57 |
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| CaptHindsight | kanzure: it would be nice to have those in a proper bottle and connector | 14:10 |
| kanzure | i don't know the names of the necessary connectors | 14:12 |
| 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 | 14:13 |
| 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. | 14:18 |
| 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 | 14:20 |
| CaptHindsight | http://imagebin.ca/v/28BvcTBHB1Fz and needles on the other end as shown here | 14:23 |
| CaptHindsight | better shown here http://imagebin.ca/v/28BwOYErioQv | 14:25 |
| 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 | 14:44 |
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| kanzure | back | 15:04 |
| CaptHindsight | kanzure: I didn't notice that the POSaM printhead parking it self between prints | 15:06 |
| CaptHindsight | so an inert atmosphere is assumed when printing | 15:07 |
| CaptHindsight | having to purge everything is kind of a pain as well | 15:08 |
| 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 | 15:09 |
| kanzure | oxygen also tends to be reactive | 15:10 |
| CaptHindsight | I'd think | 15:10 |
| 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 | 15:12 |
| 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 | 15:13 |
| 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 | 15:14 |
| 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) | 15:15 |
| CaptHindsight | we can make a condom for the printhead | 15:16 |
| kanzure | yep | 15:16 |
| kanzure | actually a condom might work fine :P | 15:16 |
| CaptHindsight | and actual inkjet industry term | 15:17 |
| 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 | 15:18 |
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| CaptHindsight | most desktop inkjet printers do this over a waste tank or sponge to be sure enough ink gets wasted daily | 15:44 |
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| 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 | 15:53 |
| CaptHindsight | the vacuum check for the slides in the POSaM is ~12" x 12" | 15:55 |
| CaptHindsight | check/chuck | 15:55 |
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| CaptHindsight | what's our slide/tray size? | 15:56 |
| kanzure | larger means more spots, so it's a tradeoff | 15:57 |
| CaptHindsight | plus they have an oversized work volume | 15:57 |
| CaptHindsight | 20" x 24" x 4" for only a 12" x 12" slide area | 15:58 |
| CaptHindsight | we can downsize to 14" x 14" travel | 15:59 |
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| juri_ | CaptHindsight: why the mesa FPGA? I've got a spartan 6 here... | 16:14 |
| CaptHindsight | juri_: Mesa is the board maker | 16:15 |
| CaptHindsight | it uses a Xilinx | 16:15 |
| 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 | 16:16 |
| juri_ | (supported by FPGATOOLS) | 16:17 |
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| CaptHindsight | http://www.mesanet.com/fpgacardinfo.html | 16:17 |
| CaptHindsight | The 6I24 use a Xilinx Spartan6 X16 or X25 FPGA in a 256 ball BGA package: XC6SLX16FTG256 or XC6SLX25FTG256 depending on 6I24 model. | 16:19 |
| juri_ | nice. | 16:20 |
| CaptHindsight | I'll be using the Xilinx tools but you are free to use whatever you wish | 16:20 |
| juri_ | sounds like a plan. | 16:22 |
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| CaptHindsight | kanzure: http://imagebin.ca/v/28D3LRO00bQ8 DNA inkjet block diagram | 18:14 |
| 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 | 18:16 |
| kanzure | what about the actuation for replacing the atmosphere in the enclosure? | 18:17 |
| CaptHindsight | solenoid valves | 18:18 |
| CaptHindsight | kanzure: rev 0.1 specs sent | 18:24 |
| kanzure | CaptHindsight: could you be more specific about the things you are hoping i will edit? sorry about being clueless here. | 18:27 |
| 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 | 18:29 |
| kanzure | (brb) | 18:30 |
| CaptHindsight | don't worry | 18:30 |
| CaptHindsight | we can finish the spec over the weekend | 18:32 |
| 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 | 18:35 |
| 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 | 18:36 |
| 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? | 18:37 |
| CaptHindsight | we'll focus on all the long lead time parts first | 18:38 |
| CaptHindsight | printhead controller, linear positioners | 18:38 |
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| kanzure | you might need -80 or -20 celsius freezers | 18:53 |
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| kanzure | nature.com seems to be down | 20:26 |
| kanzure | "Recording action potentials from the surface of the brain" http://www.buzsakilab.org/content/PDFs/Khodagholy2014.pdf | 20:29 |
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| JayDugger | Good morning, everyone. | 22:34 |
| FourFire | good morning | 22:48 |
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| --- Log closed Sat Jul 11 00:00:07 2015 | ||
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