| --- Log opened Sat Jun 20 00:00:46 2015 | ||
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| fenn | wow, cryonics expert loses all data because of no backups, such irony | 01:39 |
|---|---|---|
| eleitl | Some people are not good with computers. | 02:02 |
| eleitl | Some people who are good with computers are just disorganized. | 02:03 |
| maaku | yeah, uh, that would describe me | 02:11 |
| * maaku looks at disorganized mess, silently shrieks in horror, and goes back to reading reddit | 02:11 | |
| eleitl | Heh. | 02:13 |
| eleitl | Right. /me goes to /r/collapse | 02:13 |
| eleitl | Hoster kicked out voat.co | 02:14 |
| eleitl | One of the reasons why I never got into Bitcoin is need for data discipline. | 02:15 |
| eleitl | Understanding wallets, keeping systems secure, having enough backup media around. And trust in an open source project in general. | 02:16 |
| eleitl | Trusting exchanges. Etc. | 02:16 |
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| fenn | the point is you're not supposed to trust an exchange | 04:01 |
| fenn | somehow nobody got the memo | 04:01 |
| fenn | parallella is now $99 | 04:19 |
| eleitl | yes, but I have got mine. | 04:30 |
| eleitl | not doing much with it, too limited on time. | 04:30 |
| kanzure | this whole planet is insufferable and crap; why do i have to be the only one that has backups. | 04:31 |
| eleitl | The point of trust in exchanges is that when you send money and buy bitcoin, and transfer it to your wallet the probability is sufficiently low that you get shafted. | 04:31 |
| eleitl | kanzure, let's each make an lg mirror, so that we don't need to RAID | 04:31 |
| eleitl | we'll be each other's redundancy | 04:32 |
| kanzure | way ahead of you | 04:32 |
| eleitl | see mail | 04:33 |
| eleitl | will be afk for a couple hours, kid needs to minecraft | 04:34 |
| fenn | those blocks don't mine themselves | 04:34 |
| eleitl | Network sync on 0.10.1.0 takes fucking forever | 04:35 |
| eleitl | 18 weeks behind, gimme a break | 04:35 |
| eleitl | allright, see you later | 04:35 |
| * fenn mumbles something about byzantine decentralized minecraft servers | 04:37 | |
| fenn | all these parallella demos are super unimpressive | 05:09 |
| kanzure | bitcoin-development mailing list is moving to bitcoin-dev at https://lists.linuxfoundation.org/mailman/listinfo/bitcoin-dev | 05:15 |
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| fenn | "The archive will be wiped on Tuesday, June 23rd, 2015 when the list is switched over" | 05:16 |
| fenn | wtf is the point of that | 05:17 |
| kanzure | to get the subscribers first | 05:17 |
| kanzure | since there's no good way to export from sourceforge | 05:17 |
| kanzure | also they are overriding the archives with a backup from sourceforge | 05:17 |
| fenn | there's no list of subscribers? | 05:19 |
| kanzure | dunno | 05:21 |
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| kanzure | so what were the conclusions from yesterday's oligonucleotide romp | 05:38 |
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| fenn | the machine needs a purpose to aim towards, error correction is hard, and we need a better understanding of the chemical reactions involved | 05:41 |
| kanzure | purpose should be at minimum primers, and it would be nice to have a few million bp | 05:46 |
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| eleitl | fenn, parallella fist gen is a toy/demo machine | 06:19 |
| eleitl | Next gen would have been more useful. And you need more embedded memory in each node. | 06:19 |
| eleitl | However, I don't expect they will get the money for second gen. | 06:20 |
| fenn | well it just seems like they aren't even trying... you could do better demos with a single core even | 06:20 |
| eleitl | Zero manpower. And the community never kindled. | 06:20 |
| eleitl | See me, for instance. Thing's been idling. | 06:21 |
| eleitl | Client "only" 11 weeks behind. | 06:21 |
| fenn | you can run a supercomputer.io image and let someone else utilize the spare cycles | 06:22 |
| eleitl | Synched 7 weeks in 3 hours. | 06:22 |
| eleitl | If I run that image I can't tinker with the system myself. It's exclusive. | 06:22 |
| fenn | i think you can just swap out the sd card | 06:23 |
| eleitl | Yes, but the system is not a reliable booter. | 06:24 |
| eleitl | It's rather flaky, actually. | 06:24 |
| fenn | oh that's too bad | 06:24 |
| fenn | often these sbc toys need a larger heavy duty power supply to run reliably | 06:25 |
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| eleitl | I have a heavy duty power supply. But even so, just checked, and the board was hanging at the two tuxes stage. I never rebooted it. | 06:26 |
| eleitl | It's well-ventilated, too. | 06:27 |
| eleitl | Now it is back up. For however long. | 06:27 |
| ThomasEgi | eleitl, have you checked the logfiles? maybe it's not the psu but some other weirdo thing. like waiting for networkinterfaces to get configured by dhcp etc. | 06:28 |
| fenn | i guess my programming efforts would be better devoted to figuring out the commodity "mali" GPU found in every cheap mobile phone processor | 06:28 |
| eleitl | No, the board has a static address. | 06:29 |
| eleitl | Maybe there was a power fluctuation in the last months, and it crashed. | 06:29 |
| eleitl | In any case Parallella is a single source vendor that has started smelling funny. | 06:32 |
| eleitl | But the stacked memory APU might become interesting, should Zen ever ship. | 06:32 |
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| eleitl | GPGPU always had memory bandwidth and access pattern issues. | 06:34 |
| fenn | it would be quite a trick for an open source chip design to start being sold by multiple companies | 06:34 |
| eleitl | Parallella isn't an open source design. | 06:34 |
| fenn | it's not? | 06:35 |
| fenn | i thought that was the whole point | 06:35 |
| eleitl | At least the chip isn't. Just the board and everything else. | 06:35 |
| eleitl | If the core was open we would have a chance. | 06:35 |
| fenn | bah. well what's the point then | 06:36 |
| eleitl | Olofsson hinted he *might* make it open eventually. | 06:36 |
| fenn | with so many open source cores available, why *wouldnt* you use one of them | 06:36 |
| eleitl | A toy system to prototype code on next-next gen supercomputers. | 06:36 |
| eleitl | Because it's a SHARCish DSP core. | 06:37 |
| fenn | ok, well i don't care about "supercomputers" | 06:37 |
| fenn | maybe that was cool in the 90's | 06:37 |
| eleitl | In general future computers will be all the same way. | 06:37 |
| fenn | right, we already are carrying around 8 core phone processors | 06:38 |
| eleitl | Small systems would be just smaller slices of bigger ones. Less nodes, but the same nodes. | 06:38 |
| eleitl | These are not cores, these are nodes on a mesh. It's a cluster on a chip. | 06:38 |
| fenn | i don't see what the difference is | 06:38 |
| eleitl | You can also buy a Xeon Phi, if you have the money, and want to burn 300 W. | 06:38 |
| eleitl | Very large difference. | 06:38 |
| eleitl | It has a signalling mesh with embedded memory, and no MMU. | 06:39 |
| eleitl | Parallella is being honest about physics. | 06:39 |
| fenn | is it just the size of the cache? | 06:39 |
| eleitl | There is no cache. | 06:39 |
| eleitl | That's the point, with embedded memory you don't need a cache. | 06:39 |
| fenn | uh, i have no idea what you're talking about | 06:40 |
| eleitl | It's a big waste eliminated, if you care about maximum crank from a given area of silicon real estate. | 06:40 |
| fenn | cache is just on-chip memory | 06:40 |
| eleitl | Why do you need a cache? Because your main core is so slow. | 06:40 |
| fenn | you need cache because memory accesses take so long, not because the CPU is slow. jeez | 06:41 |
| eleitl | Cache is not organized as RAM, it has access penalties, and what is in cache cannot be in RAM. | 06:41 |
| eleitl | Core, as in core memory. | 06:41 |
| eleitl | Olofsson did the right thing. | 06:42 |
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| eleitl | But people can't handle the truth. | 06:42 |
| eleitl | Your software development model prevents you from using hardware that is asymptotically approaching an optimal architecture. | 06:42 |
| eleitl | Of course, this means Parallella is dead. | 06:43 |
| fenn | well i agree about that, people are still running windows on x86 | 06:43 |
| eleitl | In another two decades, people will come to that understanding. | 06:43 |
| eleitl | Meanwhile, there's Xeon Phi, or DIY Beowulf. | 06:43 |
| eleitl | InfiniBand is cheap enough. | 06:44 |
| eleitl | But, you better have free power. | 06:44 |
| eleitl | If I fire up everything I have laying around I would be burning some kW. That's 2 kEUR/year. | 06:45 |
| eleitl | Uh, I don't think so. | 06:45 |
| fenn | most of that power is dissipated in copper "wires" in the chips. easily bypassed by using on-chip optical interconnects | 06:47 |
| kanzure | i think that for the oligonucleotide machine we should just copy existing protocols (posam or abi391) instead of fiddling at first | 06:47 |
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| kanzure | stepwise yield's gotta be high because even 80 bp tolerates almost no error | 06:47 |
| fenn | 80 was just an arbitrary number | 06:48 |
| kanzure | well, i think you want at least 20 bp wings on both ends | 06:48 |
| kanzure | .wa 4^20 | 06:48 |
| yoleaux | 4²⁰: 1099511627776; Scientific notation: 1.099511627776 × 10¹²; Number name: 1 trillion 99 billion 511 million 627 thousand 776; Number line: http://is.gd/S3hwXq; Number length: 13 decimal digits; Comparisons: ~0.055 × the number of red blood cells in the human body (~2×10¹³); ~3.7 × the number of stars in our galaxy (~3×10¹¹); ~10 × the number of people who have ever lived (~1.1×10¹¹) | 06:48 |
| eleitl | kanzure, I suggest using online server for data exchange | 06:49 |
| kanzure | i thought you said you had zero upload? | 06:49 |
| eleitl | shipping 3.5" will run into customs | 06:49 |
| kanzure | well i was thinking i'd just send you bitcoin, but whatever | 06:50 |
| eleitl | I have a 3 TByte box on GBit/s, but my home connection is 10+6/100+50. | 06:50 |
| kanzure | arghhh frank foran emails :-( | 06:50 |
| kanzure | *forman | 06:50 |
| eleitl | Customs don't like hard drives in the mail, and refuse to believe they're used, and just data carriers | 06:51 |
| kanzure | eleitl: well i have stuff to send (although not everything you seek) | 06:51 |
| kanzure | gimme ssh access and i can send | 06:51 |
| eleitl | Ok. Let's compare who has which parts. | 06:52 |
| kanzure | at the moment i can't send any of those parts | 06:52 |
| kanzure | i have other things though | 06:52 |
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| eleitl | Allright. Would a TByte would be enough? | 06:52 |
| kanzure | yes for now | 06:52 |
| eleitl | Great. Time to save up for these 6 TByte drives. | 06:53 |
| kanzure | http://diyhpl.us/~bryan/bryan.pub | 06:53 |
| eleitl | Thanks. Will set up a guest later today or tomorrow. | 06:54 |
| eleitl | Parallella board is still up. | 06:55 |
| eleitl | kanzure, I'm reasonably comfortable on FreeBSD as desktop now. | 06:56 |
| kanzure | and previously? | 06:56 |
| kanzure | what were you using? | 06:56 |
| eleitl | Was using Linux mostly, but you know where Linux has been goign in the last 10 years. | 06:56 |
| kanzure | i'm not sure i'm ready for the awesome responsibility of a stable system | 06:57 |
| kanzure | i'll stick with debian for now :-) | 06:57 |
| eleitl | I'm so getting tired of these updates I'll probably move to OpenBSD eventually. | 06:57 |
| kanzure | have you read libressl source code yet? | 06:58 |
| eleitl | I have an old Thinkpad with OpenBSD set up, but graphics isn't working yet, radeondrm issues. | 06:58 |
| kanzure | i mention libressl only because i have lately been pondering about https://github.com/bitcoin/secp256k1/blob/873a453d26b326cc71b3c5ff509058dfe0ce6884/src/tests.c | 06:58 |
| eleitl | No. I trust Theo & Co that they know what they're doing. | 06:59 |
| eleitl | At least more, than the ADHD teenagers do. | 06:59 |
| eleitl | Though *BSD is also somewhat crypto-tarded. | 06:59 |
| eleitl | kanzure, what do you think about running individual servers as ceph nodes across one ISP | 07:04 |
| kanzure | as opposed to what? | 07:05 |
| kanzure | instead of what, i mean | 07:05 |
| eleitl | Instead of having all nodes on one rented rack on the switch. Saves a lot of money and hassle. | 07:06 |
| kanzure | oh. i see. | 07:06 |
| kanzure | well, these days the way to run things is something like amazon glacier + some raid storage in jrayhawk's basement + some rack | 07:07 |
| eleitl | Never having to touch hardware. Never again driving a car full of heavy boxes. | 07:07 |
| kanzure | http://aws.amazon.com/glacier/ | 07:07 |
| eleitl | I don't trust my data to cloud vendors. | 07:08 |
| eleitl | Rented hardware and own installed OS is ok. | 07:08 |
| kanzure | i agree that only using cloud vendors is a dumb idea | 07:08 |
| kanzure | and i don't mind if people steal this data; i wish they would, so that it would be better replicated. | 07:08 |
| eleitl | At some point I will rent a rack in the local city, but that's far too expensive. | 07:08 |
| kanzure | jrayhawk would be very happy to host things for you | 07:09 |
| eleitl | He's a person known to you? | 07:10 |
| kanzure | he's a user in this channel | 07:10 |
| kanzure | probably sleeping at the moment | 07:11 |
| eleitl | why not onion lg from his place? | 07:11 |
| kanzure | things are in progress but not stabilized | 07:12 |
| eleitl | http://heybryan.org/shots/setups/jrayhawk/ <--?? | 07:13 |
| kanzure | haha yes http://heybryan.org/shots/setups/jrayhawk/IMG_0865.JPG | 07:13 |
| kanzure | (his brother is a singinst minion) | 07:14 |
| eleitl | Looks like a great place to have a fire. | 07:14 |
| kanzure | my understanding is that his hosting business is located elsewhere | 07:15 |
| eleitl | Whew. | 07:15 |
| kanzure | huh looks like greece is gonna implode | 07:19 |
| fenn | about time | 07:20 |
| eleitl | Took them their sweet while. | 07:24 |
| eleitl | Coming next: capital controls across Europe, and the war on cash. | 07:25 |
| eleitl | BTC: to the mooooon! | 07:25 |
| kanzure | eleitl: did you get a good chuckle out of http://greece.greekreporter.com/2015/04/01/yanis-varoufakis-greece-will-adopt-the-bitcoin-if-eurogroup-doesnt-give-us-a-deal/ | 07:25 |
| eleitl | Heh. | 07:28 |
| eleitl | You might remember the BTC national currency plan some people we know had. | 07:28 |
| kanzure | dooms day https://github.com/gavinandresen/bitcoinxt/commit/821e223ccc4c8ab967399371761718f1015c766b | 07:29 |
| eleitl | Has it gone nuclear yet? | 07:29 |
| kanzure | went nuclear weeks ago | 07:29 |
| eleitl | No, I mean is this the actual fork that is being deployed now? | 07:30 |
| eleitl | Talk is cheap, but code isn't. | 07:30 |
| kanzure | he has threatened to campaign companies to deploy this fork (or he claims they have already agreed to) | 07:30 |
| fenn | 1TB blocks in 2035 eh | 07:30 |
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| kanzure | " ... doubling every two years (so 16MB in 2018)" | 07:30 |
| kanzure | this guy is insane | 07:30 |
| eleitl | Is there a way to fire him? | 07:30 |
| fenn | oh wait it's 1GB in 2035 nm | 07:30 |
| kanzure | eleitl: well he has no position, really | 07:31 |
| kanzure | eleitl: all of his power is because people believe him when he claims he was blessed by satoshi forever | 07:31 |
| midnightmagic | sigh | 07:34 |
| midnightmagic | No. No, it hasn't gone nuclear yet. | 07:34 |
| kanzure | his threats were the nukes | 07:34 |
| midnightmagic | Somebody's waiting for a good time I guess. | 07:34 |
| kanzure | this is going nuclear: http://sourceforge.net/p/bitcoin/mailman/message/34155307/ | 07:35 |
| kanzure | that's the very definition | 07:35 |
| kanzure | society is not yet accustomed to a decentralized system, so companies are far more likely to say "yep okay let's go with it" without thinking about whether the changes are likely to cause a catastrophic partial hard-fork | 07:36 |
| midnightmagic | No it's not. That's just bluster. | 07:36 |
| kanzure | when you become more popular, you have to weigh your own popularity against what you say, so that you don't cause anyone to think that trusting you is a substitute for running rule validation or something | 07:36 |
| kanzure | neutrality has to be emphasized above all else, because otherwise you risk accidentally hard-forking the network into oblivion by accidentally convincing people that you have any authority whatsoever | 07:36 |
| kanzure | see also http://www.reddit.com/r/Bitcoin/comments/3aeow8/blockstream_has_a_very_serious_conflict_of/csca13a | 07:37 |
| midnightmagic | He's said a few times now that users don't matter. Like.. you. And you, and whoever reading this. You are users, and you don't matter. | 07:37 |
| kanzure | and http://www.reddit.com/r/Bitcoin/comments/37vg8y/is_the_blockstream_company_the_reason_why_4_core/crqnnni | 07:37 |
| kanzure | i don't mind that he thinks that users don't matter, what i care about is whether he's abusing his position to force anything (even if it's a good idea) | 07:38 |
| fenn | "blockstream has a conflict of interest because they want to implement their ideas" | 07:38 |
| fenn | yeah that makes sense, sure | 07:38 |
| eleitl | It seems I'll update my node to the latest sane position, and will wait a long time after that. | 07:39 |
| kanzure | that thread started because the cia.vc person started throwing back accusations on the mailing list or something | 07:39 |
| kanzure | eleitl: waiting is a wise decision | 07:39 |
| kanzure | fenn: in that thread, i posted a comment where i explained that blockstream is not the origin of engineering constraints, and people went absolutely nuts when i posted that :-) | 07:41 |
| eleitl | Is that a sane version still: 213.239.218.20:8333 /Satoshi:0.10.0/ ? | 07:41 |
| kanzure | there's a better version out, but that's probably fine | 07:41 |
| kanzure | as far as i know there's no way to get the wrong blockchain at the moment by running the defaults that come with bitcoin-core | 07:42 |
| fenn | all this insinuation about "conflicts of interest" and "so-and-so is a government agent" looks pretty childish from the outside | 07:43 |
| eleitl | kanzure, how quickly does the client catch up to the latest transactions? | 07:43 |
| fenn | yeah so what, it doesn't matter. only the ideas matter | 07:43 |
| eleitl | I thought that part was supposed to be fixed now, but it's still dead slow. | 07:43 |
| kanzure | eleitl: 0.11 has a faster initial sync, takes maybe 2 hours? | 07:44 |
| kanzure | fenn: yes it's childish; if the nsa wants to suggest good ideas, they are welcome to. but they shouldn't be butthurt when everyone rejects their idea. | 07:44 |
| eleitl | Ok, so 0.10.1.0 in FreeBSD is still not quite fresh. | 07:44 |
| kanzure | fenn: part of what's going on is that there was a media campaign- so what you're seeing is a bunch of programmers trying to respond to user concerns and complaints; and they are upset that these technical wackos have different ideas or explanations. | 07:45 |
| eleitl | This might become a good idea in the coming time, if you have physical gold: http://www.npr.org/sections/krulwich/2011/10/03/140815154/dissolve-my-nobel-prize-fast-a-true-story | 07:47 |
| fenn | my point is it's not "the NSA" it's just an individual who has a past that is vaguely associated with some intelligence agency, which is not at all surprising for a cryptographer | 07:48 |
| fenn | likewise, it's not at all surprising that some libertarian programmers started a company to advance their ideas | 07:49 |
| eleitl | bbl | 07:53 |
| kanzure | he isn't a cryptographer, and so far nobody has been able to identify his motivations for proposing the ideas that he has (usually ideas that break decentralization) and certain other motivations are a better explanation | 07:53 |
| kanzure | additionally, his argument tactics are the lousy dirty fighting type where he never replies to specific concerns and just makes up accusations to shift the spotlight etc | 07:54 |
| kanzure | even if those allegations you have made were true, his ideas should still be evaluated on their merits and lack of merits | 07:55 |
| fenn | yes i am pretty disappointed with his lack of response to direct questions | 07:56 |
| kanzure | or what about his conflation of forking a git repository and forking the blockchain, heh | 07:56 |
| kanzure | also he likes to claim that bitcoin-core has no process, even though he is repeatedly linked to https://github.com/bitcoin/bips/blob/master/bip-0001.mediawiki | 07:57 |
| fenn | that's just whiny "there's no decisionmaking because you haven't agreed to my decision!" non-logic | 07:58 |
| kanzure | blah http://www.reddit.com/r/Bitcoin/comments/3aieuj/gavin_andresens_block_size_increase_code_8mb_cap/ | 08:00 |
| kanzure | wat "Doubling every two years is conservative compared to historical bandwidth increases " | 08:00 |
| fenn | that's totally wrong | 08:00 |
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| midnightmagic | In Canada, ISPs are actually *reducing* bandwidth, and *charging more* for the same bandwidth plans if you want to stay with your original plans. | 08:02 |
| fenn | oh hmm maybe it does fit nielsen's law | 08:03 |
| fenn | .c 1.5^20 | 08:03 |
| yoleaux | 1.5²⁰ = 3325.25673007965087890625 | 08:03 |
| fenn | .c 2^10 | 08:04 |
| yoleaux | 2¹⁰ = 1024 | 08:04 |
| midnightmagic | that's not a superscript zero. | 08:04 |
| midnightmagic | ôoh | 08:04 |
| midnightmagic | maybe it is. nevermind. sorry. | 08:04 |
| kanzure | eternal vigilance | 08:04 |
| kanzure | .wa deoxyribonucleic acid | 08:11 |
| yoleaux | deoxyribonucleic acid bases: Members: adenine: guanine: thymine: cytosine; NFPA label: http://is.gd/ChaI4a | 08:11 |
| kanzure | pfft | 08:11 |
| kanzure | i really hate visualizations of dna like https://upload.wikimedia.org/wikipedia/commons/8/81/ADN_animation.gif | 08:12 |
| kanzure | this is far better https://upload.wikimedia.org/wikipedia/commons/8/8b/DNA-ligand-by-Abalone.png | 08:12 |
| fenn | i really hate visualizations of dna like http://images.google.com/search?tbm=isch&q=dna | 08:15 |
| fenn | at least put some molecules in there ffs | 08:15 |
| kanzure | aaaa you just gave me cancer | 08:15 |
| kanzure | what's worse is that there does not seem to be any good name for the real deal | 08:19 |
| kanzure | "realistic dna" does not produce the results i want | 08:19 |
| kanzure | "dna electrostatic potential" also does not help | 08:19 |
| fenn | space filling model? | 08:23 |
| kanzure | that's a good start, although all the coloration looks wrong | 08:24 |
| kanzure | also i think the individual atoms (i think they are actually the electron orbitals?) should be made translucent | 08:24 |
| fenn | something something molecular orbitals | 08:25 |
| fenn | honestly i'm surprised i don't find this image | 08:25 |
| kanzure | heh surely someone has done a visualization of dna plus orbitals | 08:26 |
| fenn | like this is only one base pair rendered as orbitals https://chemistry.osu.edu/~herbert/images/DNA_orbs.gif | 08:26 |
| kanzure | definitely needs to be transparent. and rotating. | 08:26 |
| fenn | they would look slightly different in a full molecule | 08:26 |
| fenn | because the base pairs interact with each other etc | 08:27 |
| kanzure | "A portion of a DNA-protein complex 1D66 (Marmorstein, 1992) with the DNA van der Waals surface colored by relative orientation of bases" http://www.stolaf.edu/people/hansonr/jmol/jac/jmol/data/straightness.png | 08:28 |
| kanzure | ugh this is what happens when you don't make accurate scientific illustrations https://thinkerbelleblog.files.wordpress.com/2014/03/dna-telepathy.jpg?w=620 | 08:30 |
| fenn | awesome | 08:31 |
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| fenn | actual image of dna for reference http://people.ucalgary.ca/~zleonenk/Image8.gif | 08:33 |
| fenn | heraclitus thought all was fire, but now we know better - all is made of string | 08:35 |
| fenn | woah i'm not sure i believe this image is real http://bio.gsi.de/RESEARCH/rastermicro.html | 08:38 |
| fenn | hrm. http://cdn.theatlantic.com/static/mt/assets/science/1-dna-imaged-with-electron-microscope-for-the-first-time.jpeg | 08:42 |
| kanzure | "This is a view of knotted DNA as viewed through an electron microscope. (From Wasserman, Dungan, and Cozzarelli, 1985)" http://media.web.britannica.com/eb-media/54/109254-004-A1C93A7D.jpg | 08:42 |
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| fenn | a zoomed in view of http://cdn.theatlantic.com/static/mt/assets/science/dn22545-dna-imaged-with-electron-microscope-for-the-first-time.jpeg | 08:43 |
| fenn | the knotted thing is supertwisted around chromatin i think | 08:43 |
| kanzure | that is not zoomed >:( | 08:43 |
| fenn | i hate how they don't actually give a scale on the scale bar | 08:44 |
| fenn | like what is the point of a scale bar then | 08:44 |
| fenn | "the method only works with "cords" of DNA made up of six molecules wrapped around an seventh acting as a core. That's because the electron energies are high enough to break up a single DNA molecule." | 08:45 |
| kanzure | ah.... | 08:45 |
| fenn | fuck you ACS | 08:45 |
| fenn | i don't want your stinking cookies | 08:46 |
| kanzure | "Controlling a Single DNA Molecule in an Electric Field by Means of In Situ Atomic Force Microscopy" http://infoscience.epfl.ch/record/184694/files/2012_Jeong_J.%20Electrochem.%20Soc.pdf | 08:46 |
| kanzure | aren't we supposed to have single-atom resolution afm stuff | 08:47 |
| fenn | .title http://onlinelibrary.wiley.com/doi/10.1002/smll.201400265/full | 08:48 |
| yoleaux | Single-Molecule Reconstruction of Oligonucleotide Secondary Structure by Atomic Force Microscopy - Pyne - 2014 - Small - Wiley Online Library | 08:48 |
| fenn | figure 3 is not bad | 08:48 |
| kanzure | pdf http://www.researchgate.net/profile/BW_Hoogenboom/publication/261752009_Single-Molecule_Reconstruction_of_Oligonucleotide_Secondary_Structure_by_Atomic_Force_Microscopy/links/547320000cf24bc8ea19b4b7.pdf | 08:48 |
| kanzure | https://www.london-nano.com/news-and-events/news/lcn-researcher-awarded-2015-wiley-journal-of-molecular-recognition-young | 08:51 |
| kanzure | .title https://www.youtube.com/watch?v=KH3B0JTzLHE | 08:54 |
| yoleaux | Getting Started with AFM in Biology -- It's Easier Than You Think - YouTube | 08:54 |
| kanzure | various other videos https://www.asylumresearch.com/Webinars/ | 08:54 |
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| eleitl | Whew. Just imported my wallet on FreeBSD, and it worked. | 09:37 |
| kanzure | you may be interested in looking up shamir secret sharding and multisig | 09:37 |
| eleitl | New features? | 09:38 |
| kanzure | multisig was released ~2012 (a feature called pay-to-scripthash or p2sh) | 09:38 |
| kanzure | shamir secret sharding is just a cryptographic magic trick for splitting up a secret into multiple parts, such that you can safely give different shards to people and as long as they don't all collude they wont know the full secret | 09:39 |
| kanzure | (so you would keep a shard for yourself or something) | 09:39 |
| eleitl | So you pay, and publish on the blockchain? | 09:39 |
| kanzure | your wallet is probably using p2pkh outputs (pay-to-pubkeyhash) and for multisig you would just make a transaction to pay to your multisig/p2sh address(es) instead | 09:40 |
| kanzure | anyway, it depends on your security requirements for your wallet file | 09:40 |
| eleitl | Is LibreSSL standard for Bitcoin Core client, or is that a FreeBSD speciality? | 09:41 |
| kanzure | bitcoin-core only works with openssl | 09:43 |
| kanzure | libressl has differences that make it incompatible with bitcoin | 09:43 |
| kanzure | bitcoin-core is attempting to transition to libsecp256k1 (actually i don't know the status; the transition may have already been made?) | 09:43 |
| kanzure | unfortunately bitcoin-core originally came with some consensus-critical code that was depending on openssl | 09:44 |
| kanzure | and openssl on different platforms has different behavior for those function calls :-( | 09:44 |
| kanzure | thus why they are trying to move to libsecp256k1 | 09:44 |
| eleitl | Client version: v0.10.1.0-gd8ac901 using LibreSSL 2.1.6 | 09:44 |
| eleitl | That's what the client tells me. | 09:45 |
| kanzure | i believe that 0.11 or maybe the bitcoin-core master branch will produce very loud warnings if you are using libressl | 09:46 |
| kanzure | https://github.com/bitcoin/bitcoin/pull/6244 | 09:46 |
| kanzure | however, if the blockchain is getting synced and you see no problems, then *shrug* no harm i guess | 09:47 |
| kanzure | but the moment that you want to start making decisions about what's canonical, whether you have been paid, or whether you have paid others, you should make sure you're using consensus-compatible software | 09:47 |
| kanzure | oh there might be some harm i guess, like "you might be more likely to relay wrong data to other nodes on the network"... hmm. | 09:48 |
| eleitl | I guess I have to start building deterministic builds of my own. | 09:48 |
| kanzure | up to you, at the moment i am not doing deterministic builds for myself | 09:48 |
| eleitl | Haven't used KDE in so many years. It still sucks, but in new ways. | 10:07 |
| kanzure | hmm | 10:51 |
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| kanzure | https://placesjournal.org/article/library-as-infrastructure/ | 12:20 |
| kanzure | gah, nothing about how they should be participating in file sharing | 12:20 |
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| CaptHindsight | kanzure: how long are the fragments that you wish to synthesize? | 13:24 |
| kanzure | 1 to 100 million (anything in this range would be great) | 13:27 |
| CaptHindsight | yes, the goal is the whole length in seconds | 13:27 |
| kanzure | amount of time doesn't matter to me | 13:27 |
| kanzure | well it sort of matters | 13:27 |
| CaptHindsight | yeah | 13:27 |
| kanzure | if it takes a week but it works, i don't care | 13:27 |
| kanzure | if it takes a year.. i care somewhat more. | 13:28 |
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| ParahSailin | hows that cambrian company doing | 13:28 |
| kanzure | might be closing down | 13:29 |
| ParahSailin | they didnt even ship the faintly luminescing plant? | 13:29 |
| kanzure | ceo is dead | 13:29 |
| ParahSailin | oh wu | 13:29 |
| ParahSailin | im pretty out of all loops | 13:30 |
| kanzure | https://www.facebook.com/huffmantm/posts/10105111442071011 | 13:30 |
| kanzure | http://igem.org/In_Memory_Of_Austen | 13:30 |
| ParahSailin | they really need to make bike lanes | 13:30 |
| ParahSailin | our peeps are dropping like flies | 13:30 |
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| -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church | 13:36 | |
| -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] | 13:36 | |
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| -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 | 13:36 | |
| CaptHindsight | sure | 13:36 |
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| CaptHindsight | linker = points of attachment | 13:37 |
| kanzure | in biology land this is often called "solid support" | 13:37 |
| CaptHindsight | I didn't realize how crudely this is being done | 13:37 |
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| CaptHindsight | I'm picking up the vernacular :) | 13:38 |
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| CaptHindsight | we need a fast single molecule printer | 13:42 |
| kanzure | single molecule manipulation is not easy to implement | 13:43 |
| CaptHindsight | easy and hard is relative | 13:43 |
| CaptHindsight | my kids used to ask me if something was hard or easy to do.... | 13:44 |
| kanzure | i believe we have been able to isolate single proteins with lasers (optical traps) | 13:44 |
| kanzure | so what's your plan then? | 13:44 |
| CaptHindsight | my answer was generally for me of for you | 13:44 |
| kanzure | your answer should have been, "you're an idiot and should stop assessing problems like that" | 13:44 |
| kanzure | "instead your assessment method should be x" | 13:45 |
| CaptHindsight | it got the same point across | 13:45 |
| kanzure | CaptHindsight: have you seen https://github.com/kanzure/nanoengineer | 13:45 |
| CaptHindsight | nice | 13:46 |
| CaptHindsight | I recall the animations | 13:46 |
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| CaptHindsight | kanzure: maybe we'll have to build/write the post processor for nano-G-code | 13:48 |
| CaptHindsight | who is working on this and are they making anything public? (single molecule manipulators and printers) | 13:49 |
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| kanzure | the enzymaticsynthesis mailing list also spent some time talking about "single-nucleotide guns" to blast nucleotides towards dna molecules (well not dna but various oligo types) | 13:51 |
| kanzure | (i believe nzm787 was the one who came up with the "nucleotide gun" terminology) | 13:51 |
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| kanzure | i have also often wanted some sort of circular rotaring disk with atomically-sharp tips that would be able to rotate the right components into place. however, constructing the correct tips is an extremely hard task. | 13:51 |
| kanzure | http://diyhpl.us/~bryan/papers2/nanotech/Optimal%20Tooltip%20Trajectories%20in%20a%20Hydrogen%20Abstraction%20Tool%20Recharge%20Reaction%20Sequence%20for%20Positionally%20Controlled%20Diamond%20Mechanosynthesis.pdf | 13:51 |
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| CaptHindsight | DNA glue gun | 13:52 |
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| CaptHindsight | kanzure: as far as an inkjet printer goes, Epson has some models that hold a cd tray | 14:00 |
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| CaptHindsight | we could hack the controller for multipass printing | 14:01 |
| kanzure | there are enzymes that essentially do that already | 14:01 |
| kanzure | at least the gluing part | 14:01 |
| kanzure | really what we need is an optically or electrically responsive polymerase that chooses nucleotides based on whatever signal it is given | 14:01 |
| kanzure | but so far nobody knows how to do rational engineering of proteins to that extent, and directed evolution of that sort of enzyme requires a lot of intermediate work a few million times over (so would probably require microfluidic chips etc etc... lots and lots of equipment) | 14:01 |
| kanzure | i am far more optimistic about oligonucleotide and phosphoramidite chemistry | 14:01 |
| kanzure | couldn't we just get one with an sdk instead | 14:02 |
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| CaptHindsight | Epson Stylus Photo 1400 for example | 14:02 |
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| CaptHindsight | the next step above that is to make a stage with an Epson head similar to the Posam only with Linuxcnc for control | 14:03 |
| kanzure | head should probably stay put, move stage under | 14:04 |
| kanzure | (but i don't care) | 14:04 |
| CaptHindsight | if someone wants to use a *duino or poopieboard for control they can knock themselves out doing so | 14:04 |
| kanzure | no thanks | 14:04 |
| kanzure | i'd take linuxcnc over poopduino | 14:04 |
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| CaptHindsight | PC with LPT and stepper drivers | 14:05 |
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| CaptHindsight | my other concern is how the fluid behaves in the printheads, does it settle, how often do they need to be flushed etc | 14:06 |
| kanzure | ParahSailin: do people just use micropipettors to get samples out of each well? like on a picotiter plate. | 14:06 |
| kanzure | CaptHindsight: well there's a flush/wash step after each chemical i think | 14:06 |
| CaptHindsight | can the ACTG ink hold up to thermal inkjet? | 14:09 |
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| kanzure | these things are quite finikey; i wouldn't want to vary from the protocol that posam used. | 14:10 |
| kanzure | even slight variations in equipment, temperature, chemistry, or other variables might cause complete catastrophic failure in the whole thing | 14:11 |
| kanzure | (so getting good at debugging is quite helpful, heh) | 14:11 |
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| kanzure | btw i think we're going to need a micropipettor on a stage as well | 14:12 |
| kanzure | to collect each bead from each well :-/ | 14:12 |
| CaptHindsight | it can be on the same stage | 14:13 |
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| kanzure | sure | 14:13 |
| kanzure | i think that the church lab had to use some cameras to help guide their micropipettor into each well for some reason? i can't remember why. maybe it was related to detecting whether the bead was collected or not. | 14:14 |
| CaptHindsight | next to the head or the head can be swapped | 14:14 |
| kanzure | yea should be next to it | 14:14 |
| CaptHindsight | not a problem | 14:14 |
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| kanzure | if you don't care about contamination between pores, you don't have to switch out pipette tips either | 14:15 |
| CaptHindsight | openCV for all the imaging | 14:15 |
| kanzure | otherwise you have to replace pipette tips after every step or something https://www.youtube.com/watch?v=_uXtQLaaYsc&t=10s | 14:15 |
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| CaptHindsight | I've even used the 0.5um I.D. orifice pipette tips for deposition | 14:16 |
| CaptHindsight | cheap and consistent | 14:16 |
| kanzure | .title https://www.youtube.com/watch?v=pC-FonGglEM | 14:17 |
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| * kanzure glares at yoleaux | 14:18 | |
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| midnightmagic | and by a simple glare, did the Deep One cause a rending in IRC reality. | 14:19 |
| CaptHindsight | it's easy enough to make an automated pipette tip changer, but manual change is probably enough | 14:19 |
| kanzure | "The Epson™ F057020 print head (available from Agson Electronics, Cherry Hill, NJ) print head is uniquely suited to inkjet microarraying. It contains six fluid channels that can hold the four standard monomers, the catalyst, and still accept a modified monomer, monomer mixture, or preformed linker. It contains 192 total nozzles. The droplet size quoted by the manufacturer is a mere 6 pL. Droplet size varies with viscosity and surface ... | 14:20 |
| kanzure | ... tension, and consequently temperature, but based on solvent consumption for the work described here, our droplet sizes are closer to 10 pL. The newer Epson print heads actually have more nozzles that squirt smaller volumes (4 pL). More nozzles can result in faster synthesis. These tiny droplet volumes (4-10 pL) enable high spot densities and make consumption of reagents hard to measure, but that keeps the costs down. " | 14:20 |
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| yoleaux | Opentrons : Pick & Place - YouTube | 14:20 |
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| kanzure | CaptHindsight: some use of pipette tips require manual change after each transportation task (e.g., load liquid, move, dispense liquid, get new tip) | 14:20 |
| CaptHindsight | ok, then it should be automated | 14:21 |
| kanzure | thermal print head can't be used here according to the documentation | 14:21 |
| kanzure | ( http://bioinformatics.org/pogo/POSAM_Man_Ch1_Assembly_v1-2_040601.pdf ) | 14:21 |
| kanzure | (page 6) | 14:21 |
| CaptHindsight | what is the solvent used for the AGTC vehicles? | 14:23 |
| CaptHindsight | have a link to the supplier? | 14:24 |
| CaptHindsight | must be water free | 14:25 |
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| kanzure_ | ah there is an update, http://techdev.systemsbiology.net/posam/POSAM_Man_Ch1_Assembly_v1-4_050511.pdf | 14:32 |
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| kanzure_ | 192 nozzles. hm. | 14:34 |
| CaptHindsight | wow some of the drawing are 15 years old | 14:34 |
| CaptHindsight | just think how much of this tech would be farther along if more people were working on this | 14:34 |
| kanzure_ | hm that group also does microfluidics foundry stuff http://corefacilities.systemsbiology.net/fabrication | 14:36 |
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| CaptHindsight | the DNA "laser printer" is an intermediate step, the molecular printer is what we really need | 14:56 |
| CaptHindsight | metals are easy | 14:56 |
| kanzure | can you describe your implementation idea? | 14:56 |
| CaptHindsight | I'm pondering | 14:57 |
| CaptHindsight | still looking at what is already out there | 14:57 |
| CaptHindsight | it would cross over into building a replicator or transporter | 15:00 |
| CaptHindsight | so pretty widespread applications | 15:00 |
| CaptHindsight | but the inkjet is straightforward and simple | 15:01 |
| CaptHindsight | I wonder if anyone made an open Epson head controller yet | 15:02 |
| CaptHindsight | we could use a Mesa FPGA card for that with some additional analog for driving the head | 15:03 |
| CaptHindsight | http://store.mesanet.com/index.php?route=product/product&path=83_85&product_id=67 | 15:05 |
| CaptHindsight | or their ethernet FPGA card | 15:05 |
| CaptHindsight | http://store.mesanet.com/index.php?route=product/product&path=83_85&product_id=291 | 15:06 |
| CaptHindsight | Price: US$59.00 | 15:06 |
| kanzure | i'm not worried about motion control, mesa cards are fine everyone has worked with them before | 15:07 |
| CaptHindsight | the FPGA would also drive the printhead | 15:09 |
| CaptHindsight | along with some additional analog circuitry | 15:10 |
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| kanzure | CaptHindsight: yep | 15:30 |
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| CaptHindsight | http://www.glenresearch.com/Catalog/ultramild.php#p20 they don't mention the vehicle | 15:50 |
| CaptHindsight | http://www.glenresearch.com/Catalog/abi.php#p6 | 15:51 |
| kanzure | .title | 15:52 |
| yoleaux | ABI DNA Synthesizer | Monomers | Supports | Columns | Glen Research | 15:52 |
| kanzure | i think if we purchase anything it should be from azco biotech | 15:52 |
| kanzure | first reason is because azco biotech does lots of dna synthesizer equipment stuff plus reagents | 15:52 |
| kanzure | another reason is that they have been friendly on the diybio mailing list before- so they are at least okay with talking with people who aren't employed by an academic institution | 15:52 |
| kanzure | and finally, the dude i bought the abi 391 from, apparently had been working with azco biotech to get his phosphoramidites etc | 15:53 |
| CaptHindsight | heh | 15:53 |
| CaptHindsight | apparently the printheads last for a few months | 15:54 |
| CaptHindsight | 3 month swap for preventative maintenance | 15:55 |
| CaptHindsight | not sure if they used it 24/7 | 15:55 |
| CaptHindsight | " When acetonitrile is used as the solvent, 200 ppm water will reduce coupling efficiency 50% (Brown and Brown, | 15:56 |
| CaptHindsight | 1991). Enclosing the working area just above the microarray slides with the smallest possible volume would greatly improve the purity during the coupling step. " | 15:56 |
| kanzure | i doubt they used it 24/7--- at minimum they have to do all that pumping before/after use to replace the atmosphere, and can't be used during that | 15:57 |
| kanzure | perhaps there's a way to avoid losing atmosphere when replacing the slides with fresh slides? | 15:58 |
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| kanzure | you could have a retractable cover that goes over the bottom of the enclosure, then you remove the slides underneath, maximum gas loss is from much smaller volume | 15:58 |
| jrayhawk_ | eleitl: if you have a particularly good usecase for a system with multiple xeon phis, let me know. i built one for the local university but there's been near-zero pressure to actually get it deployed. | 16:04 |
| kanzure | how sad | 16:05 |
| jrayhawk_ | they would, in principle, like to run interesting research projects on it | 16:05 |
| CaptHindsight | the entire printhead needs to be in the chamber since the printhead relies on a slight negative pressure to operate | 16:08 |
| CaptHindsight | or the fluid won't jet or just run out of the nozzles | 16:09 |
| CaptHindsight | the slides could go through an airlock | 16:10 |
| kanzure | airlock would probably be faster | 16:11 |
| kanzure | would be interesting to have that automated too (if it's cheap/easy/not a catastrophe) | 16:11 |
| kanzure | probably a stack of slides that slide off inside | 16:11 |
| kanzure | or a slide pick-n-placer | 16:11 |
| CaptHindsight | just some valves, actuator and another drive system | 16:11 |
| CaptHindsight | that to | 16:11 |
| kanzure | well anyway-- it might speed things up, as long as they can be stored efficiently | 16:11 |
| CaptHindsight | stack of slides for the day/hours | 16:12 |
| kanzure | right | 16:12 |
| kanzure | or not slides, i guess it's the pore things | 16:12 |
| CaptHindsight | sample tray | 16:12 |
| CaptHindsight | build tray | 16:12 |
| kanzure | nah just use ambiguous terminology like everyone else, "the workpiece" | 16:13 |
| kanzure | :-/ | 16:13 |
| CaptHindsight | nucleotide collector array | 16:14 |
| kanzure | nah, your trays are fine | 16:14 |
| CaptHindsight | stack of trays or a big rotary table with multiple trays? | 16:19 |
| CaptHindsight | https://youtu.be/WKCSVIGmlFo?t=17s | 16:20 |
| kanzure | i think that only depends on ohw much room is available, and how the trays get stored | 16:20 |
| CaptHindsight | or belt drive for samples and airlock | 16:21 |
| kanzure | yea but where do they go once out of the airlock | 16:21 |
| CaptHindsight | verification and sorting good/bad | 16:22 |
| kanzure | if it requires human intervention then that's a bottleneck and you might as well not have multiple slides inside plus the airlock; you'll never be able to use the automatic slide placer because slides are going to be still in the airlock. | 16:23 |
| CaptHindsight | nitrogen filled slide cassette | 16:24 |
| CaptHindsight | what is the next device that the trays are off to? | 16:25 |
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| kanzure | well, the beads need to be collected and some of them are placed into the same reaction chamber (some other pore, usually larger) for polymerase chain reaction (pcr) or gibson assembly | 16:26 |
| CaptHindsight | well you have to plan out the entire production line and see what makes sense | 16:27 |
| kanzure | .wik gibson assembly | 16:28 |
| yoleaux | "Gibson assembly is a DNA assembly method which allows for the joining of multiple DNA fragments in a single, isothermal reaction. It was invented in 2009 by Daniel Gibson while he was at the J. Craig Venter Institute (JCVI)." — https://en.wikipedia.org/wiki/Gibson_assembly | 16:28 |
| kanzure | this was originally used for >100 kbp molecule synthesis | 16:29 |
| kanzure | most interesting proteins are 1 kbp to 50 kbp, the extra space is useful for specifying other proteins at the same time | 16:29 |
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| kanzure | i think the median or average protein dna length is ~1.5 kbp | 16:30 |
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| kanzure | green fluorescent protein (gfp) is about ~700 bp | 16:32 |
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| CaptHindsight | kanzure: I saw the chart. That machine must have pipettes that transfer oligos from the printer sample tray to the gibson tray | 16:46 |
| CaptHindsight | cnc eyedropper and enzyme dispenser with heater | 16:47 |
| kanzure | maybe not- perhaps you could flip the tray fast enough to transfer it by gravity. | 16:47 |
| kanzure | or surface tension could keep the beads inside each pore | 16:47 |
| CaptHindsight | for parallel assembly | 16:47 |
| CaptHindsight | we were doing similar with 1 liter bags of fragments | 16:48 |
| kanzure | describe? | 16:48 |
| CaptHindsight | a gantry robot that would place bags of oligos in different temp baths | 16:49 |
| kanzure | oh, what for? | 16:49 |
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| CaptHindsight | break down DNA strands... | 16:51 |
| CaptHindsight | or for combining strands | 16:52 |
| kanzure | was this something we discussed? | 16:52 |
| kanzure | bags? | 16:52 |
| CaptHindsight | no, I'm under NDA for the exact application | 16:52 |
| CaptHindsight | but it's not rocket science | 16:52 |
| CaptHindsight | i just built the machines | 16:52 |
| CaptHindsight | they would also perform manual operations between automated steps | 16:53 |
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| CaptHindsight | they aren't fully automated yet | 16:53 |
| CaptHindsight | if all the trays have the same oligos then yeah you could just dump the whole tray | 16:54 |
| CaptHindsight | I was thinking that a single tray would have multiple different oligos | 16:54 |
| CaptHindsight | and you might want to combine different oligos at different times | 16:55 |
| CaptHindsight | don't we have to QC each oligo before assembling? | 16:56 |
| CaptHindsight | only combine known good oligos and strands? | 16:56 |
| kanzure | ah didn't understand that you mean previous work you did | 16:56 |
| kanzure | when i said dump i mean if you flip it fast enough i think you could line up the pores (upside down) to where you want gravity to take the payload | 16:57 |
| CaptHindsight | how about sending me a flow chart of the whole operation | 16:57 |
| kanzure | does it have to be visual? i'm really not good at that, i am better with text | 16:58 |
| CaptHindsight | I follow you, we are just looking at the sample tray differently | 16:58 |
| kanzure | flipping/spinning was just a silly idea heh (only because if it works, it would be far faster than pipetting to get it to the gibson tray) | 16:59 |
| CaptHindsight | if the samples are arranged on the tray with a mirror of what they will get dumped into then you could flip the tray | 16:59 |
| kanzure | well i think the destination has larger pores, but they align correctly or something (you would choose pore assignments based on this) | 16:59 |
| kanzure | (has larger pores because you are combining multiple strands) | 17:00 |
| kanzure | but yes you're right that dna sequencing (reading) or quality control should be some step in this, in an ideal world | 17:00 |
| CaptHindsight | so to decide on how the printer should operate also depends on what machine the samples go to next | 17:00 |
| kanzure | nmz787 had some method based on shining a light on the sample to determine whether the strand is near the correct mass... i forget the details of his technique. | 17:00 |
| CaptHindsight | so a flow chart is probably the next step | 17:01 |
| kanzure | do you have an example flow chart you have done work from in the past? possibly one you could share privately with me | 17:01 |
| CaptHindsight | the sample trays can be designed to make this easy | 17:02 |
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| CaptHindsight | so far we have inkjet printer ---> Gibson assembler | 17:03 |
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| CaptHindsight | but it looks like all the steps haven't been all thought out | 17:03 |
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| CaptHindsight | printer ---> QC with light measurement ---> Gibson assembler | 17:05 |
| kanzure | no, i also mentioned pcr (polymerase chain reaction) | 17:05 |
| kanzure | quality control might have to be dna sequencing or mass spec or spectrophotometry | 17:05 |
| kanzure | after gibson assembly you'd probably want to do polymerase chain reaction again | 17:06 |
| CaptHindsight | try to standardize the trays to work at each step | 17:06 |
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| CaptHindsight | sounds like we have an assembly line to design | 17:07 |
| kanzure | eventually you need to get an ecoli culture going where you insert the plasmid or gene into the cells, then visually identify whether gfp has been expressed | 17:07 |
| kanzure | well, it depends on which parts you want to automate | 17:07 |
| kanzure | dna synthesis is the most important | 17:07 |
| kanzure | i think the posam people were only using their machine for dna hybridization reasons.. so they didn't have much for downstream processing.. | 17:08 |
| CaptHindsight | looks like you can build the whole assembly line for <$10k | 17:09 |
| kanzure | probably | 17:09 |
| CaptHindsight | they spent $20k on motion components | 17:11 |
| CaptHindsight | but it was off the shelf and plug and play | 17:12 |
| kanzure | hehe | 17:12 |
| CaptHindsight | parker positioners, servos and drives | 17:13 |
| CaptHindsight | nice but pricey new | 17:13 |
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| CaptHindsight | I find them on ebay for 1/4 the price in great condition | 17:14 |
| kanzure | that makes repeatability really hard- how are others going to make the same equipment in the future? just hope and pray that someone puts up similar equipment on ebay? | 17:14 |
| kanzure | besides, i can afford $20k if necessary | 17:15 |
| CaptHindsight | we can design our own | 17:15 |
| kanzure | motion controllers? good point | 17:15 |
| CaptHindsight | the electronics are all off the shelf, Mesa FPGA, a PC etc LPT port card, stepper drivers | 17:16 |
| CaptHindsight | the analog to the printheads needs to be built | 17:16 |
| kanzure | some of the valve switches looked pricey. haven't thought about making those. | 17:16 |
| CaptHindsight | the stages can be timing belts, steppers and linear bearings | 17:17 |
| CaptHindsight | those might have been chosen based on what catalog their procurement manager had | 17:18 |
| CaptHindsight | but we can shop around | 17:18 |
| kanzure | have you seen transcriptic's molecular biology assembly line? | 17:18 |
| kanzure | http://avideos.5min.com/134/5187134/518713362_4.mp4 | 17:18 |
| kanzure | it's just a long linear assembly line basically | 17:19 |
| kanzure | and the actuation slides along the length of the enclosure | 17:19 |
| CaptHindsight | <-- watching video | 17:21 |
| CaptHindsight | yeah line and you can put loops in it | 17:22 |
| CaptHindsight | for recursive operations | 17:22 |
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| CaptHindsight | heh systemd malware issue, back | 17:33 |
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| kanzure | i have uploaded that video to youtube for safekeeping https://www.youtube.com/watch?v=49X7nDBgaPc | 17:41 |
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| delinquentme | +1 kanzure | 17:50 |
| delinquentme | https://github.com/transcriptic | 17:50 |
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| kanzure | CaptHindsight: if you can send me an example flowchart, that would help. ideally one that you have actually found useful in the past. | 17:53 |
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| maaku_ | wow they've come quite a way | 17:59 |
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| kanzure | greetings maaku | 18:01 |
| maaku | cheers | 18:01 |
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| kanzure | https://medium.com/bitcoin-think/killing-the-dragon-named-bitcoin-is-money-b6dce5b86535 | 18:46 |
| kanzure | CaptHindsight: hmm so if you are synthesizing 10,000 different variations of a 10 kbp gene (say for some protein), you may not want to introduce all strands simultaneously into cells in the same petri dish. so if cell culture automation is included in the design scope (which i think is a mistake- scope should be kept small), then it should be decided upfront whether the projects should be restricted to only those that are suitable for ... | 19:10 |
| kanzure | ... inserting all dna variations into the same petri dish (same batch of cells). | 19:10 |
| kanzure | otherwise if you need 10k different cell cultures then your only practical option is bubble-based containment of cells in a microfluidic device. unless you have lots and lots of lab/facility space. | 19:12 |
| kanzure | and if you are making microfluidic devices then you might as well instead do some variation of http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf | 19:13 |
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| kanzure | actually that's not true. large-scale petri dish management may not be so bad..... | 19:15 |
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| CaptHindsight | kanzure: you just make a modular system | 20:19 |
| CaptHindsight | similar to whats in the video | 20:19 |
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| CaptHindsight | and try to standardize the size of whatever makes sense | 20:20 |
| CaptHindsight | sample trays, dishes, whatever travels from station to station | 20:20 |
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| kanzure | yep | 21:05 |
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| --- Log closed Sun Jun 21 00:00:28 2015 | ||
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