| --- Day changed Tue Jun 23 2009 | ||
| ybit | s/cathode ray/electron gun from a crt | 00:10 |
|---|---|---|
| ybit | http://en.wikipedia.org/wiki/File:Scheme_TEM_en.svg | 00:11 |
| fenn | there's a lot more to it than just the electron gun | 00:19 |
| fenn | the TV choke coil is probably shaped all wrong for use in an SEM | 00:19 |
| fenn | it's part of the flyback converter (HV power supply) so you'd need to make a new coil, and once you've done that you might as well just make everything from scratch | 00:19 |
| ybit | http://itsyourexperiment08.wordpress.com/2008/10/24/diy-microscope-macgyver-does-leeuwenhoek/ | 00:20 |
| fenn | interesting how the black and white scan is preserved in the history of the SVG file | 00:21 |
| ybit | http://parkerlab.bio.uci.edu/microscopy_construction/build_your_own_twophoton_microscope.htm | 00:24 |
| ybit | time for sleep | 00:26 |
| fenn | damn chocolate | 01:15 |
| fenn | i'd be asleep now if it werent for you! | 01:16 |
| bkero | wootoff | 01:43 |
| fenn | wow 'dot' really sucks at drawing hierarchies | 02:49 |
| kanzure | ok. archived the twophoton microscope page, and the parkerlab documents. | 07:24 |
| kanzure | http://adl.serveftp.org/papers/parkerlab-UCI/ | 07:24 |
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| kanzure | apt-get install hwb | 07:37 |
| kanzure | http://reprapsource.com/ | 08:17 |
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| kanzure | todo: wget http://www.iop.org.ezproxy.lib.utexas.edu/EJ/article/0960-1317/19/1/015007/jmm9_1_015007.pdf -o "A low temperature surface modification assisted method for bonding plastic substrates | 10:44 |
| kanzure | " | 10:44 |
| kanzure | er.. | 10:44 |
| kanzure | ok, it's on adl.serveftp.org now | 10:46 |
| --- Log closed Tue Jun 23 10:50:31 2009 | ||
| --- Log opened Tue Jun 23 11:03:20 2009 | ||
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| -!- Irssi: #hplusroadmap: Total of 17 nicks [0 ops, 0 halfops, 0 voices, 17 normal] | 11:03 | |
| --- Log closed Tue Jun 23 11:10:48 2009 | ||
| --- Log opened Tue Jun 23 11:31:45 2009 | ||
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| -!- Irssi: #hplusroadmap: Total of 17 nicks [0 ops, 0 halfops, 0 voices, 17 normal] | 11:31 | |
| -!- Irssi: Join to #hplusroadmap was synced in 1 secs | 11:31 | |
| kanzure | bad programming joke of the day: http://imgur.com/nb9LO.jpg | 11:40 |
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| kanzure | genehacker: know of a differential equation that relates a gradient to an area, or something? | 12:07 |
| genehacker | no why? | 12:07 |
| kanzure | testing out skdb | 12:07 |
| genehacker | how? | 12:07 |
| kanzure | the submodule that deals with units in equations | 12:08 |
| genehacker | oh cool | 12:08 |
| genehacker | what are you trying to get it to do? | 12:08 |
| kanzure | integrate with respect to a unit | 12:09 |
| kanzure | (and other things) | 12:09 |
| genehacker | can't some programs already do that? | 12:09 |
| kanzure | like what? | 12:09 |
| genehacker | wolfram alpha, my calculator | 12:12 |
| kanzure | neither are open source | 12:12 |
| kanzure | I'm using sympy, the symbolic python library for equations | 12:12 |
| kanzure | http://sympy.org/ | 12:12 |
| kanzure | going to be submitting a patch to them soon I guess | 12:12 |
| kanzure | sympy.physics.units is somewhat of a joke :( | 12:13 |
| kanzure | a bad joke, that is | 12:13 |
| genehacker | http://arxiv.org/abs/physics/0703013 | 12:13 |
| genehacker | hey you don't think you could figure out how the toroidal form levitator in this paper works | 12:13 |
| genehacker | if it works | 12:13 |
| kanzure | not right now, I'm busy acting like I'm busy | 12:14 |
| genehacker | ok | 12:14 |
| genehacker | if the calculations are correct, it's possible to make a device for flying around in the air | 12:18 |
| genehacker | and all it takes is some sort of superconducting toroid | 12:18 |
| kanzure | like an airplane | 12:18 |
| genehacker | like superman | 12:18 |
| genehacker | though he doesn't explain how the simpler form of the device works | 12:19 |
| genehacker | from the looks of it, it should only be capable of going east-west | 12:21 |
| genehacker | but he says that it can go north south and east west | 12:22 |
| ybit | this has become old, but can someone please upload a log of the channel for the past two days? i try to maintain a decent log file | 12:34 |
| kanzure | um. actually, no. I have had connection problems. | 12:36 |
| -!- kanzure- [i=bryan@dhcp-84-36.me.utexas.edu] has joined #hplusroadmap | 12:37 | |
| ybit | fenn told me the connection was 'fubared' yesterday, so i understand. but maybe fenn, genehacker, or any idlers could? | 12:39 |
| genehacker | ummmmm.... I don't have internet where I live | 12:39 |
| ybit | bkero, katsmeow-afk, and nsh are always in here | 12:39 |
| kanzure | ybit: fenn is on the same connection. | 12:39 |
| bkero | I'm always here. 8) | 12:40 |
| ybit | a little help then? :) | 12:40 |
| bkero | ybit: I'll upload my log for the channel for the last long while | 12:40 |
| ybit | ty | 12:41 |
| bkero | ybit: http://staff.osuosl.org/~bkero/#hplusroadmap.gz | 12:41 |
| genehacker | hmmm.... flexible superconducting tape | 12:44 |
| kanzure | I think you meant .log.gz, bkero | 12:45 |
| ybit | bkero: i was looking for logs from the past few days, i.e. this past weekend and yesterday :P | 12:50 |
| bkero | kanzure: You're right | 12:51 |
| bkero | ybit: Sorry, it's either you that has to tail -2000 it, or me | 12:51 |
| ybit | i'll do it | 12:55 |
| ybit | just need the log of last three days to do so though | 12:58 |
| kanzure | import sympy.physics.units as units | 12:58 |
| kanzure | import sympy | 12:58 |
| kanzure | type(units.m + units.m) == <class 'sympy.core.mul.Mul'> | 12:59 |
| kanzure | wtf? | 12:59 |
| ybit | #sympy ?? | 12:59 |
| kanzure | yeah but I still get to complain to you | 12:59 |
| ybit | :P | 12:59 |
| fenn | here's what i was working on last night.. it could probably use some graphviz tweaking: http://adl.serveftp.org/lab/fenn/taxonomy-neato.png | 12:59 |
| fenn | taxonomy of manufacturing processes | 13:00 |
| kanzure | so.. hierarchies? | 13:00 |
| ybit | fenn: do you have this in a svg? a lot easier to grep | 13:01 |
| fenn | better than that | 13:01 |
| genehacker | wow | 13:02 |
| genehacker | what about robotcasting? | 13:02 |
| genehacker | err robocasting | 13:04 |
| fenn | perhaps kanzure would like to get gitweb working so i dont have to do silly git commands on the server | 13:04 |
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| fenn | ybit: sorry i'm so slow http://adl.serveftp.org/skdb/taxonomy-graph.py http://adl.serveftp.org/skdb/taxonomy.yaml | 13:13 |
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| genehacker | hmmm... | 13:22 |
| ybit | i'm converting it to a svg | 13:31 |
| ybit | might take a day or two | 13:31 |
| ybit | oh nm | 13:33 |
| ybit | .yaml is just fine | 13:33 |
| fenn | dot does .svg output btw | 13:37 |
| fenn | http://adl.serveftp.org/lab/fenn/taxonomy-neato.svg | 13:40 |
| ybit | that's helpful | 13:47 |
| genehacker | could you spread it out so you can read everything? | 13:51 |
| fenn | i was trying to make something more like a cladogram though | 13:51 |
| genehacker | I think I've seen one of these before | 13:54 |
| kanzure | I have found it odd how almost every modern mother has a box of band-aids in the medicine cabinet, but I still don't have a dusty DNA synthesizer in my attic. | 13:54 |
| ybit | bkero: is it inconvenient for you to post a log of the last two days? | 13:55 |
| genehacker | well think about it kanzure | 13:57 |
| fenn | like this http://www.palaeos.com/Invertebrates/Molluscs/Bivalvia/cladogram.html or http://www.gavinrymill.com/dinosaurs/Cladogram/CladogramComplete.jpg | 13:57 |
| genehacker | why would you want a DNA synthesizer? | 13:57 |
| genehacker | you can just buy synthesized DNA from companies | 13:57 |
| genehacker | there's no need | 13:57 |
| genehacker | or that's what the companies that sell synthesized DNA say | 13:57 |
| kanzure | so what if that's what they say? | 13:58 |
| kanzure | "why would you need a brain when you can just buy one" | 13:58 |
| kanzure | "why would you need a brain when you can just buy thinktime from Google?" | 13:58 |
| genehacker | yeah | 13:59 |
| fenn | i wish i could buy thinktime from google | 13:59 |
| fenn | but the bastards give it away for free! | 13:59 |
| genehacker | synthetic DNA chemicals are fairly hard to come by | 13:59 |
| kanzure | what is this analysis based off of, genehacker? | 14:00 |
| kanzure | have you figured out how to synthesize GNA yet? | 14:00 |
| genehacker | no | 14:00 |
| genehacker | hmmm... | 14:00 |
| genehacker | maybe not | 14:00 |
| kanzure | fenn: if you bought thinktime from google, then you would have to use that thinktime in order to get some return on investment otherwise you'll run out of thinktimes on google | 14:01 |
| genehacker | I might have found a website that sells cheap( ~$25) photolabile? phosphoramidite | 14:01 |
| genehacker | s | 14:01 |
| genehacker | the thing about synthesizing GNA is that we have to make photolabile GNA phosphoramidites | 14:02 |
| bkero | ybit: It would be just as inconvenient for me as it is you | 14:04 |
| genehacker | I don't think anyone's done that yet | 14:04 |
| kanzure | why not make the photolabile phosphoramidites? | 14:04 |
| ybit | bkero: why is that? | 14:04 |
| ybit | i don't have the log file | 14:05 |
| fenn | didnt he just post the link? | 14:05 |
| ybit | yeah, but it ends on friday | 14:05 |
| ybit | i was looking for one of the past 2 days | 14:05 |
| genehacker | why? | 14:05 |
| genehacker | I don't know how | 14:06 |
| bkero | ybit: What would you do to cut it down to 2 days? | 14:06 |
| ybit | you could tail or manually copy and paste to a pastebin | 14:06 |
| ybit | or copy/paste to a .txt file on the server | 14:07 |
| bkero | Any reason you couldn't do that? I'm actually in class | 14:07 |
| ybit | because i don't have the log file | 14:07 |
| fenn | seems the log ends on may 15 | 14:07 |
| fenn | the one bkero linked to | 14:07 |
| ybit | right | 14:07 |
| bkero | Damn irc logging, guess I don't have it then | 14:08 |
| ybit | bkero: alright, and i don't need to bother you right now anyway | 14:08 |
| ybit | fenn, you were on for most of the time i was... | 14:08 |
| genehacker | but GNA synthesis is pretty simple | 14:09 |
| fenn | fine fine | 14:09 |
| ybit | :) | 14:09 |
| fenn | it's not like you missed anything | 14:09 |
| genehacker | it's only 3 steps | 14:09 |
| kanzure | genehacker: ammonia kinase | 14:10 |
| genehacker | ??? | 14:11 |
| genehacker | what's that? | 14:11 |
| fenn | ybit: http://adl.serveftp.org/last-two-days.log | 14:11 |
| genehacker | interesting | 14:11 |
| kanzure | http://en.wikipedia.org/wiki/Ammonia_kinase | 14:12 |
| ybit | ty fenn | 14:12 |
| kanzure | "Thus, the two substrates of this enzyme are ATP and NH3, whereas its two products are ADP and phosphoramide." | 14:12 |
| genehacker | ok now how do we make photolabile phosphoramidites from that? | 14:12 |
| ybit | fenn: what irc client do you use? that would be great to have a client or plugin which presents the conversation from all rooms like that | 14:14 |
| fenn | irssi | 14:14 |
| fenn | i actually wasnt trying to do that, i just messed up the logging settings somehow | 14:15 |
| bkero | ybit: http://staff.osuosl.org/~bkero/hplus.log.gz | 14:15 |
| ybit | thanks bkero, was retrieved | 14:24 |
| kanzure | phosphoramidate = H2NO3P-2 | 14:29 |
| kanzure | phosphoramide = H6N3OP | 14:29 |
| kanzure | genehacker: this is a basic chemistry problem, btw. aminos and estrifications are quite common. | 14:31 |
| kanzure | for instance, | 14:31 |
| kanzure | an ester of H3PO3 would be formed by condensation of an alcohol and an acid, plus subsequent elimination of water | 14:31 |
| genehacker | oh cool | 14:31 |
| genehacker | guess I need to learn ochem | 14:31 |
| genehacker | got any books on it? | 14:31 |
| kanzure | stacks of them | 14:31 |
| kanzure | that ester (er, the phosphite) is useful in making phosphoramidite | 14:31 |
| kanzure | which isn't the same thing as making a phosphoramide | 14:32 |
| genehacker | virtual books | 14:32 |
| kanzure | yes | 14:32 |
| genehacker | link | 14:33 |
| kanzure | server is currently inaccessible to pesky outsiders, sorry | 14:33 |
| kanzure | maybe I'll copy some files to a thumb drive for you and get them on the lab server by tomorrow | 14:34 |
| fenn | you should get rauchwerk to toss you some fluffy clouds | 14:34 |
| kanzure | he's too busy trying to find actual data | 14:34 |
| kanzure | pentaerythritol synthesis setup: http://www.orgsyn.org/orgsyn/orgsyn/prepContent.asp?prep=CV1P0425 | 15:05 |
| kanzure | http://asmeurersympy.wordpress.com/2009/06/22/how-to-permanently-lose-data-with-git-and-then-retrieve-it-again/ | 15:07 |
| kanzure | (colored prompt?) | 15:07 |
| kanzure | genehacker: I am less interested in how to synthesize phosphoramidites as I am interested in figuring out how in the hell you plan to do protecting groups | 15:10 |
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| kanzure | NPPOC chloride sounds like the easiest to make. | 15:42 |
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| fenn | ok the latest rendering looks a lot better: http://adl.serveftp.org/lab/fenn/taxonomy-small.png | 16:31 |
| kanzure | 1 g of NPPOC-dC(ib) Amidite from Sigma-Aldrich: $480 | 16:32 |
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| fenn | and here's one for you ybit: http://adl.serveftp.org/lab/fenn/taxonomy.svg | 16:32 |
| fenn | but the coloring's different since it's random | 16:32 |
| fenn | i suppose i could hash the node name and use that as the random seed or something | 16:33 |
| kanzure | or just save the seed | 16:33 |
| kanzure | (er, that you used in the first place) | 16:34 |
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| kanzure | genehacker: do you know how to synthesize photolabile protecting groups? | 16:44 |
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| kanzure | wonder why genehacker got all uppity about having to make nucleobases | 18:04 |
| kanzure | nucleotidases do it for you .. | 18:04 |
| kanzure | http://en.wikipedia.org/wiki/Nucleotidase | 18:04 |
| kanzure | er, besides the sorting problem | 18:06 |
| kanzure | which I guess could be solved by gel electrophoresis and isolating different strands of DNA with mainly one of the four bases each | 18:06 |
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| kanzure | ybit: did you take my keys? | 19:01 |
| kanzure | blah = pq.Quantity([1],'J*s') | 20:07 |
| kanzure | blah.simplified --> kg*m**2/s | 20:07 |
| kanzure | [1] s*J | 20:08 |
| kanzure | print q.dimensionality -> s*J | 20:08 |
| kanzure | print q.simplified -> [ 1.] kg·m²/s | 20:09 |
| kanzure | hm. 'J*s^2' is apparently the same as 'J*s**2' | 20:10 |
| kanzure | inspect.getargspec() looks useful | 20:24 |
| kanzure | but I'm not sure how much this is going to help to figure out which methods of a package compute various units, like Screw.breaking_force() for instance | 20:25 |
| fenn | one way is to make a conversion table/tree with references to the functions | 20:31 |
| fenn | the other way is to put some string(?) "look at me i convert torque to force" in the functions | 20:31 |
| fenn | but breaking_force() isn't even a conversion really (is it?) | 20:31 |
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| kanzure | genehacker: you do not add anything to protecting groups. | 20:49 |
| kanzure | protecting groups exist so that when you shine light at them, they cleave and everything is unprotected | 20:49 |
| kanzure | then the chemical reactions are able to proceed | 20:49 |
| kanzure | thus, synthesis. | 20:49 |
| genehacker | not even nitrogenous bases? | 20:50 |
| kanzure | what? | 20:50 |
| kanzure | what are you asking? | 20:50 |
| genehacker | the photolabile phosphoramidites I read about have protecting groups that cleave off in the presence of light so the next nucleotide can be add | 20:51 |
| genehacker | you expose where you want the A's to go | 20:51 |
| genehacker | put down the A's and they stick | 20:52 |
| kanzure | what does that have to do with nitrogenous bases | 20:52 |
| kanzure | or, rather, what does that have to do with your question | 20:52 |
| genehacker | we need NPPOC -deoxyadenosine and what not | 20:52 |
| genehacker | how do we get the deoxyadenosine? | 20:53 |
| kanzure | NPOCC-Cl means NPOCC chloride | 20:53 |
| genehacker | yeah | 20:53 |
| kanzure | not deoxyadenosine | 20:53 |
| genehacker | I know | 20:53 |
| kanzure | then why did you say NPOCC-deoxyadenosine | 20:53 |
| kanzure | anyway, here are some notes | 20:54 |
| kanzure | http://adl.serveftp.org/papers/phosphoramidites/notes.txt | 20:54 |
| genehacker | the next step is to make the stuff you remove the protecting group from during DNA synthesis | 20:54 |
| kanzure | ok. | 20:54 |
| genehacker | understand now? | 20:54 |
| kanzure | no | 20:54 |
| genehacker | you can't do dna synthesis with protecting groups alone correct? | 20:57 |
| kanzure | that's correct | 20:57 |
| kanzure | although someone did DNA synthesis on this four-branched dendrimer via condensation of acetaldehyde and formaldehyde | 20:58 |
| kanzure | but it was a branched oligonucleotide in the end, not a double helix or single strand | 20:58 |
| genehacker | so how do we use these protecting groups? | 20:59 |
| genehacker | in your notes it says they can be used for peptide synthesis? | 21:00 |
| drazak_ | genehacker: think of a protecting group like this, it's like the paper on doublesided tape, you have to take it off before they can stick together | 21:00 |
| genehacker | yeah I know that | 21:00 |
| kanzure | you add them to the byproducts of the nucleotidases | 21:00 |
| genehacker | what's the paper and what's the tape? | 21:00 |
| kanzure | what? | 21:00 |
| kanzure | there is no paper | 21:00 |
| kanzure | you use nucleotidases to convert your nucleotides to nucleosides | 21:01 |
| kanzure | you add your protecting groups to the nucleosides | 21:01 |
| genehacker | ok | 21:01 |
| kanzure | you shine light at your nucleosides+protecting-groups to unprotect it | 21:01 |
| kanzure | you separate your nucleotides by gel electrophoresis | 21:01 |
| kanzure | (er, that step was out of order) | 21:02 |
| kanzure | um, and that "-" in "nucleosides+protecting-groups" should be removed (except that it's harder to read) | 21:02 |
| genehacker | that's it? | 21:02 |
| genehacker | I thought they modified the nucleosides a bit more than just protecting groups | 21:03 |
| kanzure | where? | 21:03 |
| genehacker | removing the protecting group turns the nucleoside into a nucleotide? | 21:04 |
| kanzure | a nucleoside is a nucleotide without a phosphate. | 21:05 |
| genehacker | yeah I know | 21:05 |
| kanzure | removing the protecting group means that the nucleoside is able to react with the strand that you are synthesizing | 21:05 |
| genehacker | how? | 21:05 |
| kanzure | the protecting group isn't there to .. er, protect it | 21:06 |
| kanzure | there's also some other steps in between each cycle of addition of course | 21:07 |
| kanzure | otherwise ddNTPs would just combine into long chains when in storage in their little bottles :p | 21:07 |
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| kanzure | I think I killed him. | 21:07 |
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| genehacker | ugh why am I still using firefox for browsing? | 21:14 |
| genehacker | so here's the deal photolabile phosphoramidites don't have steps in between | 21:14 |
| kanzure | according to who? | 21:15 |
| genehacker | according to the people who did maskless array gene synthesis | 21:15 |
| kanzure | that's not helpful because I don't know the name of those people off the top of my head | 21:16 |
| kanzure | apparently I am now admining abundancestudies.org | 21:17 |
| kanzure | bah, no ssh access | 21:17 |
| genehacker | I don't know who | 21:20 |
| genehacker | so how do we get NPPOC-d-adenosine [N6-tac] β-cyanoethylphosphoramidite | 21:22 |
| genehacker | http://genome.cshlp.org/content/12/11/1749.full | 21:22 |
| genehacker | here | 21:22 |
| genehacker | so we can make NPPOC-Cl | 21:24 |
| genehacker | how do we get from that to d-adenosine [N6-tac] β-cyanoethylphosphoramidite | 21:24 |
| genehacker | so I see | 21:27 |
| kanzure | already told you how to make it | 21:27 |
| kanzure | in the email | 21:27 |
| kanzure | also in the link to the notes | 21:27 |
| genehacker | just add a protecting group to a nucleoside? | 21:28 |
| kanzure | http://adl.serveftp.org/papers/phosphoramidites/notes.txt | 21:28 |
| ybit | what is abundancestudies.org? | 21:28 |
| genehacker | well we need to try this out | 21:28 |
| kanzure | no, NPPOC-Cl is a bit more complicated | 21:28 |
| kanzure | ybit: it's joseph jackson's website | 21:28 |
| kanzure | joseph is trying to make a Journal of Abundance | 21:28 |
| ybit | about? | 21:28 |
| ybit | oh | 21:28 |
| kanzure | "Abundance" | 21:28 |
| ybit | yeah, gl with that | 21:29 |
| fenn | here is your git snack for the day: | 21:29 |
| kanzure | sarcasm? | 21:29 |
| fenn | git log --pretty=oneline --abbrev-commit | 21:29 |
| ybit | kind of | 21:29 |
| kanzure | now we need a catchy name for that | 21:29 |
| fenn | alias gl='... | 21:29 |
| kanzure | heh | 21:29 |
| fenn | gl~~!! | 21:30 |
| genehacker | what's the structure of NPPOC-Cl? | 21:30 |
| ybit | sarcasm due to frustration of not recieving the workbench tonight | 21:30 |
| kanzure | genehacker: I think you should read the notes. | 21:31 |
| kanzure | NPPOC is basically 2-(2-Nitrophenyl) propoxycarbonyl | 21:31 |
| fenn | sarcasm is just one more service i offer. chaos, panic, and disorder... my work here is done. | 21:31 |
| ybit | and because "abundance" is highly general at this moment, not saying the journal won't have any substance, it's just hard to say much about something when there isn't a clear definition of what he's after | 21:32 |
| genehacker | ok I think I get it now | 21:32 |
| ybit | afk for a few | 21:32 |
| genehacker | so we need to make some of it | 21:32 |
| genehacker | why did you say it is hard? | 21:32 |
| kanzure | who said that? | 21:32 |
| genehacker | making NPPOC-Cl? | 21:33 |
| kanzure | I don't think I did. | 21:33 |
| kanzure | ybit: joseph actually has more thoughts about abundance than he actually bothers writing about. over the phone he's much more thorough. I heard him live on some blog-by-phone thingy. | 21:33 |
| genehacker | no, NPPOC-Cl is a bit more complicated | 21:34 |
| kanzure | what? | 21:34 |
| kanzure | more complicated than what? | 21:34 |
| genehacker | you said that | 21:34 |
| kanzure | oh | 21:35 |
| kanzure | more complicated than adding it to a nucleotide | 21:35 |
| kanzure | yes, that's what I said. | 21:35 |
| kanzure | there's a few apparati that you're going to have to build | 21:35 |
| kanzure | like a distillation column | 21:35 |
| genehacker | and I'm sure we need reagent grade stuff | 21:36 |
| kanzure | fenn: are you just reading off of the coasters over there? | 21:36 |
| kanzure | genehacker: not really | 21:36 |
| kanzure | genehacker: the reaction yields are fairly high for the majority of these reactions | 21:36 |
| genehacker | hmmmm | 21:36 |
| genehacker | reagent grade means that what you have is very pure | 21:37 |
| fenn | yield and purity are different things.. | 21:37 |
| fenn | who is 'newell' named after? | 21:37 |
| genehacker | exactly fenn | 21:37 |
| kanzure | he should still look over the method before giving up | 21:37 |
| fenn | i agree high purity reagents are not necessary for starters | 21:38 |
| genehacker | good point | 21:38 |
| genehacker | so how do we 1. get adequate quantities of DNA to digest 2. seperate out different nucleosides | 21:40 |
| kanzure | are you seriously asking #1 ? | 21:40 |
| kanzure | #2 would be some sort of super gel | 21:41 |
| genehacker | not so sure a gel would seperate out different nucleotides | 21:42 |
| kanzure | "A procedure for the rapid estimation of sulfated nucleotides has been developed in this laboratory using polyacrylamide gel electrophoresis for separation ..." | 21:42 |
| kanzure | this doesn't sound like a super big problem | 21:43 |
| genehacker | oh we can do TLC | 21:43 |
| genehacker | and we can make our own TLC plates according to instructables | 21:43 |
| genehacker | well | 21:43 |
| genehacker | now this is starting to get interesting | 21:43 |
| fenn | i'm really wary of any plan relying on 'according to instructables' | 21:43 |
| kanzure | TCL? | 21:43 |
| fenn | TLC is basically a glass microscope slide with a thin layer of alumina sintered on it | 21:43 |
| fenn | it's like paper chromatography but more uniform and more inert | 21:44 |
| genehacker | ok | 21:44 |
| fenn | and not terribly useful for bulk quantities | 21:44 |
| kanzure | "paper electrophoresis" huh | 21:44 |
| fenn | also i'm not convinced you'd have enough separation between such similar molecules as the different bases | 21:44 |
| genehacker | I don't think we need bulk quantities | 21:44 |
| fenn | it's not electro- anything, the solvent moves along by capillary action | 21:45 |
| genehacker | instructables has an article about making TLC plates from glass slides and silica gel packets | 21:45 |
| fenn | genehacker: why are you considering making your own TLC plates? | 21:45 |
| fenn | they also had an article about making a clean room by removing the carpet | 21:46 |
| genehacker | why not? | 21:46 |
| fenn | "if you're really serious" | 21:46 |
| fenn | i think you do need bulk quantities | 21:46 |
| kanzure | how much is bulk | 21:47 |
| fenn | because you have to wash the plate off between every base synthesized | 21:47 |
| genehacker | cool only one chemical is on the DEA's list II | 21:48 |
| fenn | genehacker: kanzure says you claim you dont have to wash off the plate, but how could that possibly work? | 21:48 |
| genehacker | and that's the one we can make if we modify some bacteria to make it | 21:48 |
| * fenn regrets asking already | 21:48 | |
| genehacker | I don't know, I have to go change my router's mac address so I can hopefully use the internet at my place | 21:49 |
| fenn | genehacker: you owe me a cookie | 21:49 |
| genehacker | sure you can have one | 21:50 |
| genehacker | hmmm... I also have to figure out the password for it if the previous owner changed it | 21:51 |
| fenn | push the button | 21:53 |
| genehacker | that's all? | 21:54 |
| kanzure | push the reset button | 21:58 |
| genehacker | ok | 21:59 |
| kanzure | fenn: did you ever bother to look over the data in these files? | 22:01 |
| kanzure | http://adl.serveftp.org/papers/adesign/adesign-libraryEM.zip | 22:01 |
| kanzure | (might be a tarbomb) | 22:01 |
| kanzure | http://adl.serveftp.org/papers/adesign/adesign-edited.zip | 22:01 |
| kanzure | ^ that one is definitely not a tarbomb, although larger | 22:01 |
| genehacker | kanzure I'd recommend posting that stuff to diybio | 22:02 |
| kanzure | what stuff | 22:02 |
| fenn | look over the data? you mean the 3 or 4 columns of unlabeled numbers? (with two or three entries each) | 22:02 |
| kanzure | yes | 22:03 |
| genehacker | the stuff about making protecting groups and nucleosides | 22:03 |
| fenn | yeah i looked at it | 22:03 |
| fenn | irssi nickcolor.pl title.pl | 22:09 |
| -!- kanzure changed the topic of #hplusroadmap to: there is a disturbance in the cookie matrix | 22:09 | |
| fenn | in irssi-scripts | 22:11 |
| fenn | move to .irssi/scripts/autorun/ | 22:11 |
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| -!- Netsplit niven.freenode.net <-> irc.freenode.net quits: tarbo2, kanzure-, bkero, xp_prg | 22:37 | |
| -!- Netsplit over, joins: xp_prg | 22:37 | |
| -!- Netsplit over, joins: kanzure-, tarbo2, bkero | 22:37 | |
| ybit | kanzure: what extropy mailing list did the "world’s first brain prosthesis" come from? | 23:21 |
| -!- PeerInfinity [n=someone@216.36.180.162] has quit [Read error: 110 (Connection timed out)] | 23:58 | |
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