| --- Day changed Tue Aug 04 2009 | ||
| -!- wrldpc2 [n=benny@pool-173-48-253-182.bstnma.fios.verizon.net] has joined #hplusroadmap | 00:00 | |
| embraceunity | http://www.felicifia.org/viewtopic.php?f=23&t=176#p1160 | 00:17 |
|---|---|---|
| embraceunity | check out that troll | 00:17 |
| -!- splicer [n=patrik@h189n3c1o261.bredband.skanova.com] has quit ["Ex-Chat"] | 00:34 | |
| -!- genehackerclone [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has quit [Read error: 110 (Connection timed out)] | 00:35 | |
| -!- embraceunity [n=quassel@74.94.105.238] has quit [Remote closed the connection] | 01:05 | |
| -!- Phreedom [n=freedom@195.216.211.175] has joined #hplusroadmap | 01:32 | |
| -!- freedom_ [n=freedom@195.216.211.175] has joined #hplusroadmap | 02:42 | |
| -!- Phreedom [n=freedom@195.216.211.175] has quit [Read error: 104 (Connection reset by peer)] | 02:42 | |
| -!- freedom_ is now known as Phreedom | 02:49 | |
| kanzure | never use "oh maybe jata sent some plane tickets" as an excuse to get out of bed in the morning | 04:33 |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero | 06:09 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: chizu, kardan|, boogles | 06:10 | |
| -!- Netsplit over, joins: kardan|, bkero, boogles, chizu | 06:11 | |
| -!- qgqg [n=qg@rtfm.insomnia.org] has joined #hplusroadmap | 06:16 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: QuantumG | 06:17 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: fenn | 06:25 | |
| -!- Netsplit over, joins: fenn | 06:26 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero | 06:26 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: chizu, kardan|, boogles | 06:27 | |
| -!- Netsplit over, joins: kardan|, bkero, chizu, boogles | 06:28 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: CIA-43, draz|exhausted | 07:03 | |
| -!- Netsplit over, joins: draz|exhausted, CIA-43 | 07:04 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: CIA-43, draz|exhausted | 07:11 | |
| -!- Netsplit over, joins: draz|exhausted, CIA-43 | 07:12 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero | 07:15 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: CIA-43, draz|exhausted | 07:15 | |
| -!- Netsplit over, joins: draz|exhausted, CIA-43 | 07:16 | |
| -!- bkero [n=bkero@osuosl/staff/bkero] has joined #hplusroadmap | 07:18 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: CIA-43, draz|exhausted | 07:18 | |
| -!- Netsplit over, joins: draz|exhausted | 07:18 | |
| -!- CIA-38 [n=CIA@208.69.182.149] has joined #hplusroadmap | 07:20 | |
| kanzure | old but I was looking at it again this morning anyway: http://topographica.org/Home/index.html | 07:30 |
| ybit | i hadn't seen it, thanks for sharing | 07:33 |
| ybit | or maybe i did and had forgot *shrugs* | 07:37 |
| kanzure | how to make MEAs via wire EDM: http://heybryan.org/~bbishop/docs/neuro/A%20highly%20flexible%20manufacturing%20technique%20for%20microelectrode%20array%20fabrication%20-%20Fofonoff2002preprint.pdf.txt | 07:56 |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero | 08:11 | |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: draz|exhausted, chizu, kardan|, boogles | 08:11 | |
| -!- bkero [n=bkero@osuosl/staff/bkero] has joined #hplusroadmap | 08:21 | |
| -!- boogles [n=boogles@osuosl/staff/Boogles] has joined #hplusroadmap | 08:24 | |
| -!- chizu [n=chizu@osuosl/staff/chizu] has joined #hplusroadmap | 08:24 | |
| -!- draz|exhausted [n=drazak@drazak.net] has joined #hplusroadmap | 08:31 | |
| -!- kardan| [n=kardan@p54BE4D9D.dip.t-dialin.net] has joined #hplusroadmap | 08:31 | |
| -!- draz|exhausted is now known as draz|lab | 08:54 | |
| draz|lab | kanzure: is the method for creating oligio-strands of rna the same as for dna? | 08:59 |
| -!- ybit-scanning [i=4894195a@gateway/web/freenode/x-aawztakmlfhnhasp] has joined #hplusroadmap | 09:15 | |
| ybit-scanning | guess it would be helpful if i'm going to ssh into my computer to write down my ip address | 09:16 |
| draz|lab | lol | 09:18 |
| CIA-38 | skdb: kanzure * r2026799ee45d / (4 files in 3 dirs): make tag_hack work and make package loading with templates in | 09:36 |
| kanzure | draz|lab: no, but once you have DNA, why not just do a reverse transcriptase? | 09:36 |
| kanzure | er, wait, a non-reverse | 09:36 |
| kanzure | gah I suck | 09:36 |
| fenn | small strands of RNA won't last very long in most environments | 09:41 |
| draz|lab | basically I'm asking how they make commercial RNA that you can buy | 09:42 |
| fenn | due to RNAse everywhere and just plain chemical instability | 09:42 |
| fenn | what do you use RNA for? | 09:42 |
| kanzure | ribosome display | 09:51 |
| kanzure | in vitro protein synthesis (transcription and translation, although sometimes only translation) | 09:52 |
| kanzure | sometimes miRNA for transient gene expression hacks | 09:53 |
| -!- kardan_ [n=kardan@p54BE6D15.dip.t-dialin.net] has joined #hplusroadmap | 09:54 | |
| draz|lab | siRNA for silencing genes | 10:03 |
| -!- kardan| [n=kardan@p54BE4D9D.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] | 10:10 | |
| * ybit-scanning awaits joseph jackson's faq on post-scarcity, maybe it will be worth a read | 10:29 | |
| ybit-scanning | fenn, nice idea about using links to find experts in a field... | 10:30 |
| * ybit-scanning is too tired to do anything but cheerlead atm | 10:35 | |
| ybit-scanning | and scan books | 10:36 |
| flazmot__ | 08:34 < pleiades> i wonder if there's a standard conversational ratio of masculine to feminine nouns in languages that have 'em | 10:36 |
| flazmot__ | 08:34 < pleiades> like in INTERCAL, you must start a line with "PLEASE" at least 1/3 and not more than 1/2 of the time | 10:37 |
| flazmot__ | 08:34 < pleiades> or the compiler gets uncomfortable | 10:37 |
| flazmot__ | 08:34 < pleiades> like that | 10:37 |
| flazmot__ | 08:34 < pleiades> o_o | 10:37 |
| -!- kardan_ [n=kardan@p54BE6D15.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] | 10:57 | |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has joined #hplusroadmap | 11:00 | |
| ybit-scanning | it's a huge waste of time to not be tunneled into the comp right now :| | 11:07 |
| ybit-scanning | qgqg, and you are? | 11:07 |
| ybit-scanning | ah, quantumg | 11:07 |
| ybit-scanning | goonie is new | 11:07 |
| ybit-scanning | and brandon high, aka boogles.. haven't seen you around | 11:08 |
| ybit-scanning | osuosl staff, gotcha | 11:09 |
| ybit-scanning | goonie is from portland state uni | 11:11 |
| ybit-scanning | and now i'm going home to be productive since i was an idiot and didn't write down the i.p. address | 11:11 |
| -!- embraceunity [n=quassel@74.94.105.238] has joined #hplusroadmap | 11:11 | |
| -!- ybit-scanning [i=4894195a@gateway/web/freenode/x-aawztakmlfhnhasp] has quit ["Page closed"] | 11:13 | |
| flazmot__ | ... | 11:21 |
| -!- flazmot__ is now known as flazmot | 11:35 | |
| -!- any86288028 [n=someone@99-194-249-199.dyn.centurytel.net] has joined #hplusroadmap | 11:39 | |
| * ybit remembered that gmail keeps a log of ip addresses | 11:41 | |
| ybit | unfortunately, it was the incorrect address which i was looking for | 11:48 |
| -!- katsmeow-afk [n=someone@99-195-185-221.dyn.centurytel.net] has quit [Read error: 110 (Connection timed out)] | 11:56 | |
| kanzure | ybit: dyndns (ddclient on debian) is handy for these ip problems. | 12:07 |
| draz|lab | you know | 12:12 |
| draz|lab | there's no sofa's on our floor of the lab | 12:12 |
| draz|lab | I dunno about the otehr floors, but it seems to me that there's osmethigns eriously wrong with the fact that there are no sofas on this floor of the lab | 12:13 |
| kanzure | fenn: called jata a few minutes ago. gave her the option of scheduling the trip for after the 12th as long as the tickets are in my inbox before the 12th | 12:23 |
| kanzure | there's a #pcb | 12:25 |
| kanzure | there's also #kicad | 12:26 |
| kanzure | hm | 12:26 |
| CIA-38 | skdb: kanzure * reb23d5f58d04 /core/template.py: forgot to add the template | 12:31 |
| CIA-38 | skdb: kanzure * r21c1e1b9a766 /core/skdb.py: make it so that you do not need to use itertools on the package | 12:32 |
| CIA-38 | skdb: kanzure * r2b062096d75a /core/yamlcrap.py: fix yamlcrap.py print statements (remove them) | 12:34 |
| kanzure | fenn: sys.stderr.write() | 12:34 |
| kanzure | raise TypeError, str(blah)."hah" | 12:35 |
| -!- grummund [n=grummund@unaffiliated/grummund] has joined #hplusroadmap | 12:47 | |
| CIA-38 | skdb: kanzure * r2fb35bacaddc /unittests/test_yamlcrap.py: added some unit tests for yamlcrap | 12:56 |
| kanzure | hello grummund | 12:56 |
| -!- embraceunity [n=quassel@74.94.105.238] has quit [Remote closed the connection] | 12:56 | |
| fenn | hey i'm writing unit tests for yamlcrap | 12:56 |
| fenn | tag_hack in particular | 12:56 |
| kanzure | well. there you go. | 12:56 |
| fenn | fucker | 12:57 |
| kanzure | they pass. | 12:57 |
| grummund | kanzure: hi | 12:58 |
| kanzure | anything interesting? | 12:58 |
| grummund | so... wtf is this place ;P | 12:58 |
| kanzure | we're building "apt-get but for hardware" | 12:58 |
| grummund | umm ok ;-} is that anything to do with reprap? | 13:00 |
| -!- Ian_Dani1er [n=it@69.61.230.246] has joined #hplusroadmap | 13:02 | |
| kanzure | grummund: yes, actually | 13:03 |
| grummund | oh... neat | 13:03 |
| kanzure | ideally this program will spit out instructions for building a reprap, for instance | 13:03 |
| kanzure | but that's just one potential application | 13:03 |
| grummund | i just watched the video of that | 13:03 |
| kanzure | but a lot of people are interested in the reprap designs | 13:03 |
| CIA-38 | skdb: kanzure * r9bac434e54de / (4 files in 3 dirs): switch screw metadata over to the new format, clean up comments in lego metadata | 13:11 |
| draz|lab | how is this yaml thing gonna work anyway? | 13:13 |
| kanzure | anything in particular you're wondering about? | 13:13 |
| draz|lab | I mean, the end purpose, what will it be used for? | 13:13 |
| kanzure | two main things | 13:13 |
| kanzure | (1) people typing out specific data from catalogs for various parts | 13:14 |
| draz|lab | also: I have 31 genes that I need to design primers for | 13:14 |
| kanzure | (2) metadata for a package that includes classes that use that specific data, etc. | 13:14 |
| kanzure | draz|lab: try something in bioperl/biopython.. I think there's a primer generator method | 13:14 |
| kanzure | IIRC. don't kill me if there isn't. | 13:14 |
| draz|lab | nah | 13:17 |
| draz|lab | I'm not going to do that | 13:17 |
| draz|lab | also I need to do other stuff before I start designing primers | 13:17 |
| draz|lab | I'm doing so PFM with excel | 13:17 |
| kanzure | " | 13:24 |
| kanzure | "So let me pose the counterquestion: do I have a right to | 13:24 |
| kanzure | "compensation" that requires restricting you from configuring your own | 13:24 |
| kanzure | material property in a design of my invention?" | 13:24 |
| kanzure | PFM? | 13:24 |
| draz|lab | pure fucking magic | 13:32 |
| fenn | hey is there a reason you put test_* files in the same dir as the file they're testing? | 13:47 |
| kanzure | in pymates? | 13:47 |
| kanzure | no | 13:47 |
| fenn | i dont get your unit test; can i please delete it? | 13:48 |
| -!- strages [n=strages@c-68-62-216-5.hsd1.al.comcast.net] has quit [Read error: 113 (No route to host)] | 13:49 | |
| kanzure | what do you not get about it | 13:49 |
| kanzure | the problem is that you'll get a tag error if it's broken | 13:49 |
| fenn | what is testing for StopIteration supposed to do? | 13:49 |
| fenn | and does this actually do something? self.assertFalse(True, message="hello") | 13:50 |
| kanzure | no | 13:50 |
| kanzure | that fails completely | 13:50 |
| kanzure | that line can definitely be thrown away | 13:50 |
| kanzure | anyway, testing for StopIteration isn't important | 13:51 |
| fenn | well i'm getting rid of it since i dont see the point | 13:51 |
| kanzure | you don't see the point of testing tag_hack? | 13:51 |
| fenn | no, i mean, i dont see the point of the tests you did | 13:51 |
| kanzure | loader.next() will fail badly if yaml doesn't like its input | 13:51 |
| kanzure | very very badly | 13:52 |
| fenn | but that doesnt have anything to do with tag_hack | 13:52 |
| kanzure | if tag_hack is broken, then the tests will fail | 13:52 |
| kanzure | the two lines I mean | 13:52 |
| fenn | wah. | 13:52 |
| kanzure | there's no history on that file btw | 13:53 |
| kanzure | so if you want to just copy and paste the four lines or something that's fine | 13:53 |
| kanzure | hm writing some unit tests for packages, I'm wondering whether or not we should have a generic way to load up an object or not | 13:59 |
| kanzure | should lego_package.Lego() work? | 13:59 |
| kanzure | should lego_package.Part() wokr? | 13:59 |
| kanzure | *work | 13:59 |
| fenn | no | 14:00 |
| kanzure | lego_package.load_part() ? but then how does it know from metadata.yaml which one the "part" is? i.e., in lego/metadata.yaml there is lego.Lego, lego.Peg, and lego.Hole, which one is the "part"? The only way to figure that out would be to load them all up and look .. but what if there are multiple parts in a package? | 14:02 |
| kanzure | so that method doesn't work | 14:02 |
| -!- genehacker2 [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has joined #hplusroadmap | 14:02 | |
| kanzure | lego_package.make("lego") ? | 14:02 |
| kanzure | there's a Lego object defined in packages/lego/lego.py | 14:02 |
| kanzure | I want it, but I'm not sure what the API should be for the Package class and its access to that information | 14:03 |
| fenn | if you can do lego_package.Part() that'd be cool | 14:03 |
| kanzure | what if there's multiple parts in the package? | 14:03 |
| -!- strages [n=strages@c-68-62-216-5.hsd1.al.comcast.net] has joined #hplusroadmap | 14:04 | |
| fenn | um, lego_package.Brick(2,4,flat=True, color="Red") etc | 14:04 |
| kanzure | then why not lego_package.lego() instead of .Part() ? | 14:04 |
| fenn | actually there are specific lego colors so probably lego_package.red | 14:04 |
| kanzure | er, .Lego() | 14:04 |
| fenn | what is Lego() supposed to do? | 14:05 |
| kanzure | if you are going to do .Brick() | 14:05 |
| kanzure | oh | 14:05 |
| kanzure | okay | 14:05 |
| kanzure | so what I'm really asking is any_package.Part() <- should that always return something? | 14:05 |
| fenn | what would Part() return? | 14:06 |
| kanzure | in the case of packages that have only a single part, I would expect it to return me an instance of the part it defines and packages. | 14:06 |
| kanzure | push? | 14:06 |
| fenn | wouldnt that be lego_package.part? | 14:06 |
| fenn | or someotherpackagewithonlyonepart.part | 14:06 |
| CIA-38 | skdb: * r40bc0f882574 /core/yamlcrap.py: actually pass a list of tags to tag_hack; also yaml_type is only needed for loading. since Dummy never gets loaded therefore it shouldnt have one? | 14:07 |
| CIA-38 | skdb: * rb640e4a85a5b / (5 files in 3 dirs): is it just me or is git really stupid | 14:07 |
| CIA-38 | skdb: * r1c57e9f57185 /unittests/test_yamlcrap.py: Revert "added some unit tests for yamlcrap" | 14:07 |
| CIA-38 | skdb: * rea54c375a7d4 /core/skdb.py: skdb.load now automatically detects tag_hack for dummy tags | 14:07 |
| CIA-38 | skdb: * r7833261f5df2 /unittests/test_yamlcrap.py: lots of tests for tag_hack; test_bad_tag still fails :( | 14:07 |
| kanzure | er where is that "part" attr defined? | 14:07 |
| kanzure | is that in the metadata, or what? | 14:07 |
| fenn | in metadata | 14:07 |
| fenn | otherwise how do you know what the part is? | 14:07 |
| kanzure | no that's the template you're thinking of | 14:07 |
| fenn | um. | 14:07 |
| kanzure | there is no part attr currently in metadata.yaml (anywhere) | 14:07 |
| fenn | so in a package with only one part, the template is the data? | 14:07 |
| kanzure | right? | 14:07 |
| kanzure | no, the template is not the data | 14:07 |
| kanzure | data.yaml has the data | 14:07 |
| kanzure | (right?) | 14:07 |
| fenn | right | 14:08 |
| fenn | wouldnt it be package.parts[0] | 14:08 |
| kanzure | I see metadata.yaml has a "classes" attr, but not a part attr | 14:08 |
| kanzure | or a parts attr | 14:08 |
| fenn | what are 'parts'? | 14:08 |
| kanzure | in pymates there was this ability to say pymates.Part() | 14:14 |
| kanzure | and this would make a Part object to some particular specification | 14:14 |
| kanzure | like with a particular name | 14:14 |
| kanzure | but now I'm porting this over to the package-based system | 14:14 |
| kanzure | and saying Part() doesn't really make sense because there's not just .. "one part" | 14:14 |
| kanzure | there might be multiple types of screws, and other parts other than a screw in the screw package | 14:14 |
| -!- wrldpc2 [n=benny@pool-173-48-253-182.bstnma.fios.verizon.net] has quit [] | 14:15 | |
| kanzure | er in the screw package there isn't multiple other parts of course so that's a bad example | 14:15 |
| kanzure | but in a chair package there might be (?) | 14:15 |
| kanzure | I don't actually have an example of a package that has multiple parts in it | 14:15 |
| kanzure | some_pack.list_parts() | 14:25 |
| kanzure | some_pack.options(something something something) | 14:25 |
| kanzure | something about loading up parts from data.yaml | 14:33 |
| CIA-38 | skdb: kanzure * r5e871558eafe / (core/skdb.py packages/lego/lego.py unittests/test_package.py): added unit tests for packages (not working yet), added a setup method for the lego package | 14:42 |
| CIA-38 | skdb: kanzure * r69ae57f4a6bb / (core/skdb.py core/yamlcrap.py unittests/test_yamlcrap.py): Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb | 14:42 |
| kanzure | er I should have checked that merge before pushing | 14:42 |
| kanzure | it did an automerge, so there's no telling wtf might have been fudged | 14:43 |
| fenn | block = lego_package.classes.select("Lego")() | 15:01 |
| fenn | what is select for? | 15:01 |
| kanzure | just trying to pick an object from data.yaml | 15:01 |
| kanzure | er wait | 15:02 |
| kanzure | no | 15:02 |
| kanzure | that's for picking which of the "classes" to instantiate | 15:02 |
| kanzure | I guess you could do lego_package.classes["Lego"]() | 15:02 |
| kanzure | but this still looks like shit | 15:02 |
| fenn | on loading, do some sort of class magic so that lego_package.Lego = lego.Lego | 15:04 |
| fenn | it's not exactly an instance | 15:05 |
| -!- embraceunity [n=quassel@74.94.105.238] has joined #hplusroadmap | 15:07 | |
| kanzure | hello embraceunity | 15:09 |
| kanzure | anything new? | 15:09 |
| -!- grummund [n=grummund@unaffiliated/grummund] has left #hplusroadmap [] | 15:14 | |
| fenn | skdb.load is supposed to parse a string, like yaml.load | 15:18 |
| fenn | skdb.load("lego") is just a string, not a package | 15:18 |
| kanzure | fixed | 15:18 |
| kanzure | why did you delete my updates to open_package() | 15:19 |
| CIA-38 | skdb: * r7cbb7b0174a8 /core/skdb.py: keep track of implcit resolvers instead of just trusting yaml; this should speed up loading a bit too | 15:20 |
| CIA-38 | skdb: * r03a67fca9e8e /unittests/test_yamlcrap.py: make sure tag_hack doesn't kill all the other custom tags | 15:20 |
| CIA-38 | skdb: * r2e0fe30a262a /core/skdb.py: not sure why this was commented out | 15:20 |
| CIA-38 | skdb: * rcfdf106ba3a1 / (core/skdb.py packages/lego/lego.py unittests/test_package.py): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb | 15:20 |
| CIA-38 | skdb: * r7a024c606c64 /unittests/test_package.py: somehow i get the feeling you didnt actually run this | 15:20 |
| fenn | too slow! | 15:20 |
| kanzure | why did you delete my updates to open_package() | 15:20 |
| fenn | er, which commit did i do that? | 15:21 |
| fenn | i dont remember doing anything to open_package; i probably overwrote the changes because kate didnt realize the file had changed | 15:21 |
| kanzure | you deleted something.next() | 15:21 |
| kanzure | you were complaining about it earlier | 15:21 |
| kanzure | but it's kind of important for the tests to pass, you see | 15:22 |
| fenn | oh. i added that into skdb.load | 15:22 |
| kanzure | but skdb.load loads a string | 15:22 |
| kanzure | skdb.open_package does not | 15:22 |
| fenn | if it gets a tag_hack document first it returns the next document instead | 15:22 |
| fenn | it = skdb.load | 15:22 |
| kanzure | fine | 15:23 |
| fenn | why are you using yaml.load_all? | 15:23 |
| kanzure | fixed | 15:23 |
| CIA-38 | skdb: kanzure * r186b6dcc2ca3 /core/skdb.py: fix open_package | 15:25 |
| CIA-38 | skdb: kanzure * r58fe0d191d8d /unittests/test_package.py: work on test_package | 15:25 |
| CIA-38 | skdb: kanzure * raedfd1128472 / (core/skdb.py unittests/test_yamlcrap.py): merged | 15:25 |
| fenn | is there some reason for putting individual classes in their own file that i'm not aware of? | 15:25 |
| fenn | i just do it so i dont have to scroll as much | 15:25 |
| kanzure | history | 15:25 |
| fenn | history of what? | 15:25 |
| kanzure | the code | 15:25 |
| kanzure | pre-rendered response: not if you move it out of the super-mega-file | 15:26 |
| fenn | what was i supposed to ask? | 15:26 |
| kanzure | "git already tracks history" or something obvious like that | 15:26 |
| fenn | oh. well it does | 15:26 |
| kanzure | that's true | 15:26 |
| kanzure | but not if you move code out of a file | 15:26 |
| fenn | sure about that? | 15:27 |
| kanzure | have you done that? | 15:27 |
| fenn | no | 15:28 |
| kanzure | fenn: if you're going to update the tag_hack standard then I think you should also fix the metadata to conform to the new standards | 15:30 |
| kanzure | so could you do that? | 15:30 |
| fenn | ok | 15:31 |
| CIA-38 | skdb: * r87c9bb8aa097 / (4 files in 2 dirs): get rid of yaml_type as it can be resolved automatically | 15:35 |
| CIA-38 | skdb: * r5260f448362c / (core/skdb.py unittests/test_package.py): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb | 15:35 |
| kanzure | did you run the tests? | 15:36 |
| CIA-38 | skdb: * r58d6e46bcc00 /packages/ (lego/metadata.yaml screw/metadata.yaml): tag_hack syntax changed | 15:37 |
| fenn | why do i get "NameError: global name 'skdb' is not defined" | 15:38 |
| fenn | "unit unit test test" isnt funny if it's not testing skdb.Unit | 15:39 |
| CIA-38 | skdb: kanzure * r85ab608d9cea /core/skdb.py: fix global name error | 15:40 |
| CIA-38 | skdb: kanzure * r5284008f19a8 / (6 files in 3 dirs): Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb | 15:40 |
| fenn | so i've been trying to add a lego grammar to packages/lego/interfaces.py | 15:41 |
| fenn | meanwhile i got distracted with yaml | 15:41 |
| fenn | er, so please don't mess with lego too much | 15:41 |
| kanzure | please don't call it a grammar, campbell will want to see it in .grxml format | 15:41 |
| kanzure | okay | 15:41 |
| fenn | it's just a list of interfaces and what they are compatible with | 15:43 |
| -!- Ian_Dani1er [n=it@69.61.230.246] has quit [Client Quit] | 16:02 | |
| CIA-38 | skdb: * rf7df34fc4e67 /doc/proposals/legos.py: see packages/lego/lego.py | 16:07 |
| CIA-38 | skdb: * r0415d2ef2ca3 /core/interface.py: change to orientation vector; removing unused stuff | 16:07 |
| CIA-38 | skdb: * rda8102d33c42 / (packages/lego/interfaces.py pymates/tests.py): halfway done | 16:07 |
| CIA-38 | skdb: * rf5ded4d4b3b3 /core/skdb.py: Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb | 16:07 |
| -!- draz|lab is now known as drazak | 16:14 | |
| -!- qgqg is now known as QuantumG | 16:19 | |
| drazak | so, I have a 10cm dish of MSCs | 16:32 |
| drazak | gonna serial passage them into a t-75 then a t-150 if we have them at the lab | 16:32 |
| drazak | I haven't checked out the TC room much | 16:32 |
| -!- ybit [n=ybit@unaffiliated/ybit] has quit ["leaving"] | 16:37 | |
| -!- ybit [n=ybit@unaffiliated/ybit] has joined #hplusroadmap | 16:37 | |
| ybit | would you guys/gals be interested in a mumble chat server for this room? | 16:51 |
| ybit | it might be awhile before it's setup since i'm compiling qt4 atm for it | 16:53 |
| fenn | VoIRC? | 17:02 |
| kanzure | I wouldn't expect a voice-to-voice system to require qt4, especially a "chat server" | 17:02 |
| kanzure | `"I am sovereign" isn't a political statement, it's a physics statement.` | 17:05 |
| fenn | sounds deeply philosophical | 17:05 |
| kanzure | it's hard to explain to people the difference between the philosophical issue of whether or not you can do X versus whether or not you can actually do X | 17:06 |
| fenn | derrr. what? | 17:07 |
| fenn | philosophical(possible(x)) != possible(x) ? | 17:07 |
| fenn | or is is more like Person.can_do(x) vs Person().can_do(x) | 17:08 |
| ybit | kanzure: that was for for mumble, found out i need murmur, thought mumble did the serving as well | 17:12 |
| -!- embraceunity [n=quassel@74.94.105.238] has quit [Remote closed the connection] | 17:20 | |
| kanzure | fenn: have you fixed skdb/core/interface.py line 40 yet? the one that causes skdb/unittests/test_yamlcrap.py to fail at the moment | 17:37 |
| CIA-38 | skdb: fenn * rea5aef02ad2e /core/interface.py: silly double-quotes | 17:46 |
| kanzure | ok I could have done that :p | 17:49 |
| kanzure | fenn: don't you get "ConstructorError: expected a mapping node, but found scalar | 17:53 |
| kanzure | " ? | 17:53 |
| fenn | yes | 17:53 |
| fenn | i can't figure it out | 17:53 |
| kanzure | gee seems like my code kinda fixed that earlier today huh | 17:53 |
| fenn | no actually i dont think it's the same problem | 17:54 |
| kanzure | "foo" is a mapping | 17:54 |
| kanzure | but you give it a scalar value in the yaml | 17:54 |
| fenn | which "foo" | 17:54 |
| kanzure | !foo | 17:54 |
| fenn | you mean Foo() is a mapping? | 17:54 |
| fenn | anyway it doesnt matter if i give it a scalar value or a mapping value | 17:55 |
| kanzure | well it expects a mapping | 17:55 |
| fenn | !foo bar: 123 fails also | 17:55 |
| kanzure | yes it does matter because it seems to complain in one way but not the other | 17:55 |
| kanzure | what about !foo\nbar: 123 | 17:55 |
| fenn | same | 17:55 |
| fenn | hm | 17:56 |
| genehacker2 | kanzure did you put that stuff on the server? | 17:56 |
| kanzure | what stuff? | 17:56 |
| fenn | ok !foo\nbar: 123 works | 17:56 |
| fenn | wtf | 17:56 |
| * kanzure grins | 17:56 | |
| kanzure | do I get cookie | 17:56 |
| genehacker2 | the microfluidics stuff | 17:56 |
| kanzure | genehacker2: did you give it to me? | 17:56 |
| genehacker2 | yes | 17:57 |
| genehacker2 | last night | 17:57 |
| fenn | you want some unidentified cheese? | 17:57 |
| kanzure | huh? | 17:57 |
| genehacker2 | embraceunity even seeded it | 17:57 |
| kanzure | I was asleep last night | 17:57 |
| kanzure | he did? | 17:57 |
| kanzure | oh | 17:57 |
| kanzure | on filebin | 17:57 |
| kanzure | okay yeah I didn't get that | 17:57 |
| genehacker2 | okay have it again | 17:57 |
| genehacker2 | http://filebin.ca/ayxuh | 17:58 |
| genehacker2 | http://filebin.ca/ordqrh | 17:58 |
| kanzure | which one is it? | 17:58 |
| fenn | i wish the marker on that foo error would point at the scalar value, not the tag | 17:58 |
| kanzure | ok it's on the server now | 17:59 |
| genehacker2 | read it sometime | 17:59 |
| kanzure | http://adl.serveftp.org/papers/ordqrh.zip | 17:59 |
| kanzure | http://adl.serveftp.org/papers/ayxuh.zip | 17:59 |
| kanzure | now what the hell is in these files | 17:59 |
| kanzure | these are terrible filenames | 17:59 |
| genehacker2 | what are? | 18:00 |
| kanzure | ayxuh.zip | 18:00 |
| kanzure | it doesn't tell me what's in there | 18:00 |
| genehacker2 | oh let me fix that | 18:00 |
| kanzure | no you should just tell me the title of the files or something | 18:00 |
| kanzure | and I'll rename them | 18:00 |
| genehacker2 | http://filebin.ca/ordqrh/MicrofluidicsHistoryTheoryandApplications.zip | 18:00 |
| kanzure | ok | 18:00 |
| kanzure | http://adl.serveftp.org/papers/MicrofluidicsHistoryTheoryandApplications.zip | 18:01 |
| CIA-38 | skdb: fenn * rc57f725dcba2 /unittests/test_yamlcrap.py: fixed testcase; yaml.YAMLObject expects mapping and error marker points at wrong place | 18:01 |
| * ybit needs to create an ir reciever now that therehave a bed in the computer room | 18:02 | |
| ybit | s/therehave/there's | 18:02 |
| fenn | "Yarg is a semi-hard cow's milk cheese made in Cornwall" | 18:29 |
| fenn | aww. '"Yarg" is simply "Gray" spelled backwards' | 18:29 |
| kanzure | hm I wonder if anyone has studied rTMS and pregnant women | 18:35 |
| kanzure | in particular rTMS of the fetus | 18:35 |
| kanzure | "Repetitive transcranial magnetic stimulation (rTMS) can induce short-term | 18:36 |
| kanzure | reorganization of human motor cortex." | 18:36 |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has quit [Read error: 60 (Operation timed out)] | 18:41 | |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has joined #hplusroadmap | 18:49 | |
| drazak | fenn: see diybio post | 18:59 |
| drazak | hm, apparently hasn't been updated yet | 19:01 |
| drazak | fenn: anyway, as my email says, I'm not aware of any singular PCR technique that could be used to identify the type of cheese | 19:04 |
| drazak | fenn: also I'm not awere of PCR machines that need calibration, other than RT-PCR machines, but that's laser or LED calibration | 19:05 |
| fenn | yeah pcr is more of a digital thing; i guess i was rambling at that point | 19:09 |
| drazak | pcr is an amplification thing | 19:10 |
| drazak | rt-pcr is used to measure the ammount of a specific segment of dna | 19:10 |
| fenn | it's either there or not there though | 19:10 |
| drazak | not really | 19:10 |
| drazak | you may still find it at a ct of 39 or something | 19:10 |
| drazak | even if it wasn't there | 19:10 |
| fenn | non-specific amplification is pretty easy to detect | 19:11 |
| drazak | that's like a magnification of 2^39 | 19:11 |
| drazak | yup, at a Ct of 30some | 19:11 |
| drazak | past 35 it's backround and irrelevant | 19:11 |
| drazak | also you can't detect no specific, unless it falls within your primers | 19:11 |
| drazak | with RT-PCR your primers are flourescently labeled | 19:12 |
| drazak | creating a map is impossible, however creating primers that you can detect against a housekeeping gene, aka GAPDH | 19:12 |
| drazak | taht's pretty easy | 19:12 |
| drazak | are googlegroups slow or something?> | 19:13 |
| drazak | I emailed my reply like 20 minutes ago | 19:13 |
| drazak | that's a hell of a long time | 19:14 |
| drazak | for a google page not to have loaded yet | 19:14 |
| kanzure | "The late myelination of the dlPFC can partly explain why adolescents' behavior is characterized by motivational difficulties, impulsivity and addiction (also in the context of video games and virtual scenes) [18]." | 19:17 |
| drazak | fenn: so describe for me the pcr technique that you'd uise to determine what kind of cheese you're eating? | 19:19 |
| -!- splicer [n=patrik@h189n3c1o261.bredband.skanova.com] has joined #hplusroadmap | 19:21 | |
| fenn | just regular old pcr | 19:21 |
| fenn | find the 16S sequence | 19:21 |
| fenn | add that to the cheese map | 19:21 |
| fenn | repeat a bazillion times | 19:21 |
| drazak | how do you define regular old pcr | 19:22 |
| drazak | do you do gel electrophoresis after? | 19:22 |
| ybit | drazak: after? | 19:23 |
| fenn | hm. ok i guess i was thinking you'd sequence the bands | 19:23 |
| drazak | I mean, if you think PCR is like what yous ee in regenesis, then you don't know that you have to do gel electrophoresis on the results | 19:23 |
| drazak | you'd have to sequence bands? | 19:23 |
| drazak | how do you get bands? | 19:23 |
| drazak | gel electrophoresis? | 19:23 |
| fenn | yeah | 19:23 |
| drazak | exactly | 19:23 |
| drazak | it's not PCR | 19:23 |
| drazak | :) | 19:23 |
| fenn | pcr->gel->sequencing is pretty standard procedure | 19:23 |
| drazak | "pcr" though, it's "pcr then gel then sequencing" | 19:24 |
| drazak | but yes it is pretty standard | 19:24 |
| fenn | well, eventually once you have a bunch of sequences you could do PCR on the highly variable regions of 16S | 19:25 |
| fenn | to test for existence | 19:25 |
| drazak | what housekeeping gene would you use? | 19:25 |
| fenn | what's a housekeeping gene? | 19:25 |
| drazak | what is "existence" <35? | 19:25 |
| fenn | whether the sequence is there or not | 19:25 |
| drazak | you can't test that | 19:26 |
| drazak | lol | 19:26 |
| drazak | you'll still get some response probably | 19:26 |
| fenn | bah | 19:26 |
| drazak | a housekeeping gene is a gene that you compare your results to see how much of it there is | 19:26 |
| drazak | however you have to isolate DNA from cheese | 19:27 |
| drazak | whether or not it's cow DNA or bacterial DNA is important too, how do you determine which one you have? | 19:27 |
| drazak | a common housekeeping gene is GAPDH | 19:27 |
| drazak | http://en.wikipedia.org/wiki/Housekeeping_gene | 19:28 |
| drazak | fenn: make sense? | 19:35 |
| drazak | it's not as easy as it sounds :P | 19:35 |
| drazak | you could do it with electrophoresis if you knew the sequences of all of the 16S genese found in every cheese | 19:35 |
| drazak | assuming that no two are the same | 19:35 |
| drazak | you'd want to test some other genese too | 19:35 |
| drazak | as one gene isn't very reliable | 19:35 |
| drazak | you could also do pcr and then electrophoresis if you don't have restriction enzymes | 19:36 |
| drazak | but you'd need to have an ever better map of the gene in every different strain of bacteria that you wished to look for | 19:36 |
| drazak | fenn: ^ | 19:41 |
| fenn | yep | 19:42 |
| drazak | :) | 19:42 |
| drazak | sorry for spoiling your fun though :( | 19:42 |
| fenn | now that i think about it, you'd have to splice the 16s sequence into a plasmid and clone it; otherwise how do you know the bacteria will grow in your culture? | 19:43 |
| drazak | what do you mean? why are we growing bacteria? | 19:43 |
| drazak | you could get a dna sample from the cheese like you would from a tissue sample | 19:43 |
| drazak | homogenize it, do a nanodrop for dna, and then pcr it | 19:44 |
| fenn | right | 19:44 |
| fenn | nanodrop doesn't lyse cells | 19:44 |
| drazak | well | 19:44 |
| drazak | I oversimplified, like you | 19:44 |
| fenn | i think you can just cook them, or add distilled water | 19:44 |
| fenn | anyway, yes you should try to quantify the free DNA in the sample | 19:45 |
| drazak | you homogenize the cheese into something called RLT buffer, and then you do a midi or mini prep to get the purified dna, and then you do a nanodrop to determine the concentration of dna, and then you do a pcr with the total concentration of dna the same across all of the different kinds of cheeses you're testing | 19:45 |
| drazak | the standard is .5ug | 19:45 |
| drazak | and then you do whatever next step you want | 19:46 |
| drazak | is the diy bio google group slow for you guys too? | 19:46 |
| drazak | so now you have a bunch of dna that starts with whatever forward primer you use and ends with the sense version of whatever reverse primer you use, and you're going to do something with it, you could send it out to be sequenced, clone it into a plasmid and grow it in e. coli like you said, but then you have to do everything all over again (-pcr) to use the plasmid | 19:47 |
| * ybit has wasted so much time today trying to find an im client which supports otr | 19:48 | |
| ybit | a cli im client | 19:49 |
| ybit | so far the options are: bitlbee-otr, weechat-otr, center-im, or finch | 19:49 |
| ybit | finch only supports xterm, no urxvt and its ui is just plain silly | 19:49 |
| ybit | having to go through bitlbee server is an inconvenience but works | 19:50 |
| ybit | and having all irc in weechat is nice | 19:50 |
| ybit | s/irc/im | 19:50 |
| ybit | center-im, still messing with it. may just give into weechat-otr/bitlbee | 19:51 |
| ybit | and i give up, TODO tonight: murmurd, uzbl cookies, history, ad-block, and xmonad tabs | 19:53 |
| ybit | TODO tomorrow: back to postfix, dovecot, and offlineimap finally | 19:53 |
| ybit | and hopefully gnus+bbdb by the end of the night if i'm not wasted with friends celebrating croking age | 19:54 |
| fenn | drazak: the cheese is a mixed culture so you have to clone it if you want to sequence | 19:54 |
| drazak | fenn: right | 19:55 |
| fenn | only once you have a sequence can you use species-specific primers | 19:55 |
| drazak | fenn: you can do other parts of the process prt-cloning | 19:55 |
| drazak | s/prt/pre/ | 19:55 |
| ybit | someone try connecting to my mumble server please | 19:56 |
| ybit | 192.168.1.149:64738 | 19:56 |
| drazak | that isn't gonna work | 19:57 |
| drazak | that's an internal private ip address | 19:57 |
| ybit | argh | 19:57 |
| ybit | 71.207.247.209:64738 | 19:59 |
| drazak | do posts need to be ok'd before they go to the main page on diybio? | 20:00 |
| ybit | no | 20:00 |
| ybit | wait, main page? | 20:00 |
| ybit | are you referring to the mailing list or diybio.org? | 20:01 |
| drazak | mailing list | 20:01 |
| drazak | sorry | 20:01 |
| ybit | oh, no | 20:01 |
| drazak | I emailed diybio@groups.google.com or whatever the hell the reply email is, and it still hasn't shown up on the website | 20:01 |
| drazak | that was like an hour and ten minutes ago | 20:01 |
| ybit | drazak: what's your name? | 20:01 |
| drazak | Ben Gadoua | 20:02 |
| kanzure | drazak: did you register on the mailing list? | 20:02 |
| drazak | kanzure: yeah, like a year ago | 20:02 |
| kanzure | huh | 20:02 |
| ybit | drazak: topic post? | 20:02 |
| ybit | post topic* | 20:02 |
| drazak | fenns cheese thing | 20:02 |
| ybit | ah | 20:03 |
| ybit | yeah, not there. maybe you saved it in your drafts or something instead of sending it | 20:03 |
| drazak | maybe it's showed up as drazak? | 20:03 |
| drazak | doesn't explain why it's not showing on the site | 20:04 |
| ybit | anyone want to try connecting to the mumble server? | 20:04 |
| ybit | so.. this is an idea... it's a server for the community.. you can idle there but if you need to talk to someone quickly you can PM them to chat with you in mumble | 20:05 |
| kanzure | why | 20:05 |
| drazak | why not just chat here in pm | 20:06 |
| drazak | or via email | 20:06 |
| drazak | or w/e | 20:06 |
| kanzure | technical stuff doesn't work well by voice | 20:06 |
| kanzure | fenn and I have been rediscovering this :/ | 20:06 |
| drazak | I emailed some fucker in cornell and he still hasn't emailed me back | 20:06 |
| fenn | i already knew | 20:06 |
| kanzure | rediscovering | 20:06 |
| drazak | I wanted to know what isoform of vegf they used | 20:06 |
| drazak | so basically | 20:06 |
| ybit | i'm caught up on voice communications.. guess i'm distracted again | 20:06 |
| fenn | this guy who talks really fast tried to explain virtual pointers to me over the phone (after not having touched C++ for 5 years) | 20:06 |
| drazak | this growth factor, vascular endothelial growth factor A, comes in 6 slice variants | 20:07 |
| ybit | oh well, it's an alt to skype i suppose | 20:07 |
| drazak | the most common is 165, that means 165 amino acids, the next most common are 121 and 189 | 20:07 |
| drazak | but not necessarily in that order | 20:07 |
| kanzure | 165? not 16S? | 20:07 |
| kanzure | sorry misread | 20:08 |
| drazak | no worries | 20:08 |
| drazak | and then he wrote a paper saying that he cultured mesenchymal stem cells in the presence of vegf | 20:08 |
| drazak | and failed to mention which type of vegf he cultured it in the presence of | 20:08 |
| kanzure | okay | 20:08 |
| kanzure | thanks | 20:08 |
| drazak | it has to be 121 or 165 as 189 and larger versions are stronlg heparin binding due to splices of the 6th and 7th exon | 20:09 |
| ybit | voice communications/friendship | 20:10 |
| drazak | email kind of sucks in the respect that you don';t kmnow whether or not they have received the email or if they have decided to just ignore you | 20:10 |
| ybit | kind of odd. guess i will quit with that stuff now | 20:10 |
| ybit | drazak: or you could just check groups.google.com/whattheaddresssistodiybiomailing | 20:13 |
| ybit | anyone have otr encryption and willing to test my setup? | 20:14 |
| drazak | that's what I have been checking | 20:14 |
| ybit | IM h2i@jabber.org if ya want | 20:14 |
| ybit | </spam> | 20:14 |
| -!- Ian_Daniher [n=it@69.61.230.246] has joined #hplusroadmap | 20:23 | |
| kanzure | hey Ian_Daniher | 20:25 |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] | 20:28 | |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has joined #hplusroadmap | 20:33 | |
| drazak | are any of you part of the molecular biology online google group? | 20:42 |
| kanzure | link? | 20:51 |
| drazak | http://groups.google.com/group/molecularbio?hl=en&lnk= | 20:52 |
| fenn | wow 1146 members | 20:54 |
| drazak | yeah | 20:55 |
| drazak | that's why I joined | 20:55 |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] | 21:14 | |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has joined #hplusroadmap | 21:21 | |
| -!- any86288028 is now known as katsmeow | 21:26 | |
| -!- kardan| [n=kardan@p54BE6D15.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] | 21:40 | |
| -!- fenn changed the topic of #hplusroadmap to: "Questionnably high levels of techno-determinism" | 21:52 | |
| -!- fenn changed the topic of #hplusroadmap to: "a totally unbridled techno-anarchy. Questionnably high levels of techno-determinism too." | 21:53 | |
| ybit | lastlog daemon | 23:10 |
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!