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| JayDugger | drethelin: "affordable" "rapid" for aerospace and governmental values of the adjectives | 02:30 |
|---|---|---|
| JayDugger | Notice all the authors work for NASA? | 02:43 |
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| archels | can anyone grab this paper? http://www.mitpressjournals.org/doi/abs/10.1162/NECO_a_00753 | 03:36 |
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| Betawolf | http://moscow.sci-hub.bz/f64e3b7d1361d9cec9a4fa4680331200/krunglevicius2015.pdf | 03:45 |
| Betawolf | archels: ^ | 03:46 |
| archels | cheers! | 03:49 |
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| archels | When analyzing data, scientists generally run a test for something called “statistical significance.” | 04:50 |
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| kanzure | .title http://www.mitpressjournals.org/doi/abs/10.1162/NECO_a_00753 | 08:52 |
| yoleaux | An Error Occurred Setting Your User Cookie | 08:52 |
| kanzure | bah | 08:52 |
| kanzure | worthless | 08:52 |
| kanzure | http://techcrunch.com/2015/07/23/ginkgo-bioworks-takes-on-zymergen-with-45-million-in-series-b-funding/ | 08:59 |
| kanzure | welp our mole probably got $50k of that and it probably vests over 1 bajillion years | 09:01 |
| kanzure | "Rose fragrance is a scarce commodity, with a major looming global shortage. However, Ginkgo was able to recreate a synthetic and genetically identical rose oil in mass quantities using Bioworks1" | 09:01 |
| kanzure | there's a shortage of smelling like shit? | 09:02 |
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| kanzure | bloop | 09:56 |
| kanzure | .title http://worldbuilding.stackexchange.com/questions/14442/how-to-eat-the-moon | 10:05 |
| yoleaux | space - How To Eat the Moon - Worldbuilding Stack Exchange | 10:05 |
| kanzure | .title http://www.phys.unsw.edu.au/~jw/cryoblurb.html | 10:05 |
| yoleaux | Cryobiology and anhydrobiology - physical stresses in cells at low temperature and/or low hydration | 10:05 |
| kanzure | https://www.reddit.com/r/space/comments/2f8ln3/dyson_spheres_seem_easier_than_people_think/ | 10:06 |
| kanzure | ugh? https://www.reddit.com/r/rational | 10:07 |
| eudoxia | good christ | 10:08 |
| kanzure | eudoxia: report? | 10:10 |
| eudoxia | what | 10:10 |
| kanzure | it's a more formal way of saying "sup" | 10:11 |
| kanzure | have you been replaced by a can of red bull yet? | 10:12 |
| eudoxia | oh, right. nothing. i got exams coming up. | 10:12 |
| eudoxia | you know i've never actually tried red bull | 10:12 |
| eudoxia | what's up on your end kanzure | 10:14 |
| kanzure | still bitcoin stuff | 10:14 |
| eudoxia | what sort of bitcoin stuff | 10:15 |
| kanzure | see pm | 10:16 |
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| CaptHindsight | kanzure: the wash step is after the coupling so the oligo strands don't wash away, sorry it's taken 12 hrs+ to get back to you | 10:45 |
| CaptHindsight | step 1) bond the first base to a silane coated slide or a glass bead | 10:47 |
| CaptHindsight | that base is going to be stuck there until you cleave it | 10:50 |
| CaptHindsight | you can add as many bases as you wish to it in a linear fashion | 10:51 |
| CaptHindsight | lets just say 20 for the example | 10:51 |
| CaptHindsight | you leave the oligo bonded to the slide or tray that you want to build on... | 10:52 |
| CaptHindsight | lets call this oligo the "foundation", I haven't found a coined term yet for this yet | 10:54 |
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| CaptHindsight | the oligo that you wish to be bonded to the foundation is cleaved from the tray or bead and coupled together | 10:55 |
| kanzure | the was hstep is after the coupling, yes, but if you want to get two oligos together and then have a wash step, you're going to wash away those oligos :-( | 10:55 |
| CaptHindsight | now you have a oligo 20 bases long | 10:55 |
| CaptHindsight | kanzure: nope, since the first oligo is still bonded to the tray or bead | 10:56 |
| kanzure | yes, but if you want to assemble two oligos together, they have to be free-floating | 10:56 |
| CaptHindsight | only one end has to be from the foundation | 10:57 |
| CaptHindsight | one is anchored at one end with the other end free for coupling, the second oligo may be free floating | 10:58 |
| kanzure | it's not clear whether the dna ligase enzyme is compatible with that scheme | 10:59 |
| CaptHindsight | there are | 10:59 |
| CaptHindsight | I've been looking into the different agents for capping, coupling, cleaving etc | 10:59 |
| CaptHindsight | it looks to me that most authors don't really know how to put the steps together in writing or they are purposely obfuscating this | 11:01 |
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| CaptHindsight | they read like most textbooks, explanations designed to be memorized vs understood | 11:02 |
| kanzure | ok so you want to do on-bead gene assembly | 11:02 |
| kanzure | or solid-support gene assembly | 11:02 |
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| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-1-rationale-tools-method/ | 11:04 |
| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-2-xilinx-ise-suite-register-file-testing/ | 11:04 |
| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-3-instruction-set-decoder-ram/ | 11:04 |
| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-4-alu-comparisons-branching/ | 11:04 |
| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-5-pipeline-and-control-unit/ | 11:04 |
| kanzure | http://labs.domipheus.com/blog/designing-a-cpu-in-vhdl-part-6-program-counter-instruction-fetch-branching/ | 11:04 |
| CaptHindsight | with inkjet printing on a slide you can make thousands of short oligos | 11:05 |
| CaptHindsight | that slide can anchor the "foundations" | 11:06 |
| CaptHindsight | the next oligos can be cleaved off the slide and moved to the foundations using light or electrostatic charge | 11:08 |
| CaptHindsight | so they are still all on the same slide or tray | 11:08 |
| CaptHindsight | this may be done in parallel | 11:08 |
| CaptHindsight | so you can have 10, 100 etc foundations that remain bonded to the slide | 11:09 |
| CaptHindsight | and then cleave the next oligos and direct them to the foundations for coupling | 11:10 |
| CaptHindsight | cleaving may be selective with a laser | 11:13 |
| kanzure | not sure how to do it with light- we haven't figured that out yet | 11:15 |
| CaptHindsight | I saw some photocleavable couplings that when activated leave the ends free to be bonded | 11:15 |
| kanzure | all of the light-based actuation methods work for only very small surface areas, and don't work for very tiny droplets. | 11:15 |
| kanzure | or rather, they work for tiny droplets if you have lots of optics | 11:15 |
| kanzure | or if you fabricate a microelectrode array | 11:15 |
| CaptHindsight | either and the array would be the same slide that you inkjet the drop onto | 11:16 |
| kanzure | if you have a large microelectrode array that can move tiny droplets, then you don't need an inkjet printhead i think | 11:16 |
| kanzure | well, nevermind, i take that back, it's more convenient to use an inkjet head | 11:17 |
| CaptHindsight | true, but the inkjet builds lots of drops faster | 11:17 |
| kanzure | ok. so now we need to fabricate a microelectrode array that can move 100k spots simultaneously or whatever. | 11:17 |
| CaptHindsight | not all at the same time | 11:17 |
| kanzure | and which method are you talking about for re-linking an oligo? | 11:18 |
| CaptHindsight | say you have a 100 x 100 array | 11:18 |
| kanzure | if you don't do it all at the same time, then you might as well just use slow pipettes | 11:18 |
| CaptHindsight | the first row of 100 could be the foundations | 11:18 |
| CaptHindsight | then row 2 is cleaved drop by drop and moved to combine with the foundation in its same column | 11:19 |
| CaptHindsight | to link a foundation to the next free floating oligo we have to decide which method | 11:21 |
| CaptHindsight | there are a few to choose from | 11:21 |
| CaptHindsight | http://www.genelink.com/newsite/products/mod_detail.asp?modid=133 photocleavable linker | 11:23 |
| CaptHindsight | kanzure: 100um spots are easy to achieve with a laser for triggering a cleave | 11:29 |
| CaptHindsight | http://imagebin.ca/v/29eLd1TYvEx9 summary of DNA microarrays | 11:37 |
| CaptHindsight | inkjet has the cheap chemistry to build the oligos what did we say 50-100 bases long | 11:40 |
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| CaptHindsight | we can also fabricate an electrode array cheaply that is also the slide/tray | 11:41 |
| CaptHindsight | the change in the first step to the inkjet might be printing a photocleavable bond | 11:43 |
| CaptHindsight | then the rest of the 50-100 bases are done as they did with POSaM | 11:44 |
| CaptHindsight | and since the photocleaveble bonding agent is a bit more expensive we only use it once per 50 to 100 bases, so we use 1/50 to 1/100 as much as if it is used for every base | 11:45 |
| CaptHindsight | they are sensitive to 300nm - 350nm | 11:48 |
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| CaptHindsight | they don't have a graph so I don't know where exactly the sensitivity drops off but... | 11:49 |
| CaptHindsight | it;s mist likely well under 400nm so we could use a UV laser to cleave and use visible spectrum for light guided/activated | 11:50 |
| CaptHindsight | mist/most | 11:50 |
| kanzure | hmm. | 11:52 |
| kanzure | so we would be using a single laser to move >100k droplets? | 11:52 |
| CaptHindsight | laser to cleave | 11:52 |
| CaptHindsight | light or electrostatic to move drops | 11:52 |
| CaptHindsight | visible light | 11:52 |
| CaptHindsight | UV laser to cleave | 11:53 |
| kanzure | "the photocleaveble bonding agent is a bit more expensive we only use it once per 50 to 100 bases" | 11:53 |
| kanzure | what does this mean? reconnecting an oligo to the surface? | 11:53 |
| CaptHindsight | I can clarify | 11:53 |
| CaptHindsight | they are only anchored once to the tray/slide using the photocleaveble | 11:55 |
| kanzure | and your plan is to see if dna ligase can combine a free-floater oligo with a surface-immobilized oligo? | 11:55 |
| CaptHindsight | for the first base or each drop by inkjet to the slide/tray/electrostatic array | 11:55 |
| kanzure | i think there should be a writeup | 11:56 |
| CaptHindsight | thats how it's done | 11:56 |
| kanzure | (and also, i'm distracted writing bitcoin software at the moment...) | 11:56 |
| CaptHindsight | yeah, no problem | 11:56 |
| CaptHindsight | many papers and website that offer this info also mention how these steps or products are used in patented DNA synthesizers | 11:57 |
| kanzure | there's no dna synthesizer on the market that uses dna ligase | 11:58 |
| kanzure | (or the previous markets for that matter) | 11:58 |
| CaptHindsight | I think this is semantics at work here, let me clarify | 11:58 |
| CaptHindsight | you can use the same chemistry to bond an anchored oligo to a free floating oligo as it used to build each oligo | 11:59 |
| CaptHindsight | it/is | 11:59 |
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| kanzure | is that true? i think you have only one 5' end. | 12:03 |
| CaptHindsight | you can choose what stays capped and what gets deprotected | 12:11 |
| CaptHindsight | all the chems are there I bet it's patents that keep all the lowest cost tech from ending up in the same machine | 12:12 |
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| kanzure | yes but what's the mechanism? which chemistry and which reactions? | 12:17 |
| kanzure | these are things that we need to know in order to implement this | 12:17 |
| CaptHindsight | http://www.genelink.com/newsite/products/modoligosENDMODIFIERS.asp for example | 12:20 |
| CaptHindsight | inkjet to build the oligos from 1 - 100 bases long | 12:22 |
| kanzure | i don't think any of those linkers allow other oligos to be attached | 12:23 |
| kanzure | not sure | 12:23 |
| CaptHindsight | electrostatic to move the oligos for bonding to each other | 12:23 |
| kanzure | "The end modifiers add a reactive functional group which can be used for conjugation" conjugation with what | 12:24 |
| CaptHindsight | where did the biochemists go in here? | 12:26 |
| CaptHindsight | looks like I'm the only one plowing through this | 12:26 |
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| CaptHindsight | kanzure: there are several chem suppliers | 12:28 |
| CaptHindsight | I'd suggest creating a side by side comparison of costs and flow chart for each step of each process available | 12:29 |
| CaptHindsight | then you can easily see which ones are more desired based on price and tech available for moving chems and oligos around | 12:29 |
| kanzure | i just need the chemistry right now. no handwaving- just something that will work. | 12:31 |
| CaptHindsight | looks like a combo of photoreactive and Phosphoramidite | 12:32 |
| CaptHindsight | http://www.jnanobiotechnology.com/content/9/1/57/figure/F1 but rather than use light deprotection in every cycle... | 12:33 |
| CaptHindsight | light deprotection is only used for every 50 or 100 cycles | 12:34 |
| CaptHindsight | they dry with helium btw | 12:35 |
| CaptHindsight | wow, no expense spared | 12:35 |
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| CaptHindsight | kanzure: is there a wiki for this channel? | 13:40 |
| chris_99 | http://diyhpl.us/wiki | 13:41 |
| kanzure | CaptHindsight: http://diyhpl.us/wiki/dna/synthesis/notes/ | 13:50 |
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| kanzure | .title https://news.ycombinator.com/item?id=9937372 | 16:57 |
| yoleaux | Optimizing CRISPR: Sub-second searches on a 3 billion base genome | Hacker News | 16:57 |
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| kanzure | cluckj: welcome back | 18:21 |
| cluckj | thanks | 18:21 |
| cluckj | what's up? | 18:26 |
| mgin | hey | 18:28 |
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| kanzure | http://i.imgur.com/k8FKq6H.jpg | 19:31 |
| mgin | disgusting | 19:33 |
| mgin | i really don't like you | 19:33 |
| yashgaroth | ok mgin you have finally proven yourself to be enough of a dick, I shall now reveal to you the secrets of eternal life | 19:34 |
| mgin | ban? | 19:34 |
| yashgaroth | if you like | 19:35 |
| mgin | no | 19:35 |
| kanzure | mgin: please continue | 19:38 |
| mgin | that was an offensive image | 19:40 |
| mgin | and you refuse to answer any questions in a straight manner | 19:40 |
| mgin | that's all. | 19:40 |
| kanzure | can you give me an example of what you would consider a straight answer? | 19:40 |
| mgin | yes, this response to your question that I am making right now. | 19:41 |
| mgin | would be an example of a straight answer | 19:41 |
| kanzure | and "look at our plans" is not a straight answer to your question "what are you doing"? | 19:41 |
| mgin | see how i responded directly to the question asked of me, in english? | 19:41 |
| mgin | i didn't link you to anything or ignore you at all | 19:41 |
| mgin | i just wrote out a coherent, direct response | 19:41 |
| kanzure | perhaps you hate hyperlinks? | 19:42 |
| mgin | that's all. | 19:42 |
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| ParahSailin_ | kanzure: yeah its like they hadnt heard of reference alignment and made their own crappy crap from scratch | 19:56 |
| ParahSailin_ | bwa would have been orders of magnitude faster if they had bothered to do a simple literature search on a not-new-at-all subject | 19:56 |
| ParahSailin_ | points for trying i guess | 19:57 |
| cluckj | what the fuck did I come back to? | 20:00 |
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| kanzure | cluckj: things that are up, http://diyhpl.us/wiki/dna/synthesis/notes/ | 20:08 |
| cluckj | sweet | 20:13 |
| cluckj | I am still writing...should be done with a first draft soon | 20:29 |
| cluckj | for varying values of "soon" | 20:33 |
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| justanotheruser | erasmus: is there something you wanted? | 23:44 |
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| --- Log closed Fri Jul 24 00:00:20 2015 | ||
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