--- Day changed Tue Aug 04 2009
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00:17 < embraceunity> http://www.felicifia.org/viewtopic.php?f=23&t=176#p1160
00:17 < embraceunity> check out that troll
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04:33 < kanzure> never use "oh maybe jata sent some plane tickets" as an excuse to get out of bed in the morning
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07:30 < kanzure> old but I was looking at it again this morning anyway: http://topographica.org/Home/index.html
07:33 < ybit> i hadn't seen it, thanks for sharing
07:37 < ybit> or maybe i did and had forgot *shrugs*
07:56 < 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
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08:59 < draz|lab> kanzure: is the method for creating oligio-strands of rna the same as for dna?
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09:16 < ybit-scanning> guess it would be helpful if i'm going to ssh into my computer to write down my ip address
09:18 < draz|lab> lol
09:36 < 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
09:41 < fenn> small strands of RNA won't last very long in most environments
09:42 < 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?
09:51 < kanzure> ribosome display
09:52 < kanzure> in vitro protein synthesis (transcription and translation, although sometimes only translation)
09:53 < kanzure> sometimes miRNA for transient gene expression hacks
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10:03 < draz|lab> siRNA for silencing genes
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10:29  * ybit-scanning awaits joseph jackson's faq on post-scarcity, maybe it will be worth a read
10:30 < ybit-scanning> fenn, nice idea about using links to find experts in a field...
10:35  * ybit-scanning is too tired to do anything but cheerlead atm
10:36 < 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
10:37 < 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
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11:07 < 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
11:08 < ybit-scanning> and brandon high, aka boogles.. haven't seen you around
11:09 < ybit-scanning> osuosl staff, gotcha
11:11 < 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
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11:21 < flazmot__> ...
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11:41  * ybit remembered that gmail keeps a log of ip addresses
11:48 < ybit> unfortunately, it was the incorrect address which i was looking for
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12:07 < kanzure> ybit: dyndns (ddclient on debian) is handy for these ip problems.
12:12 < draz|lab> you know
12:12 < draz|lab> there's no sofa's on our floor of the lab
12:13 < 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
12:23 < 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
12:25 < kanzure> there's a #pcb
12:26 < kanzure> there's also #kicad
12:26 < kanzure> hm
12:31 < CIA-38> skdb: kanzure * reb23d5f58d04 /core/template.py: forgot to add the template
12:32 < CIA-38> skdb: kanzure * r21c1e1b9a766 /core/skdb.py: make it so that you do not need to use itertools on the package
12:34 < CIA-38> skdb: kanzure * r2b062096d75a /core/yamlcrap.py: fix yamlcrap.py print statements (remove them)
12:34 < kanzure> fenn: sys.stderr.write()
12:35 < kanzure> raise TypeError, str(blah)."hah"
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12:56 < CIA-38> skdb: kanzure * r2fb35bacaddc /unittests/test_yamlcrap.py: added some unit tests for yamlcrap
12:56 < kanzure> hello grummund 
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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.
12:57 < fenn> fucker
12:57 < kanzure> they pass.
12:58 < 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"
13:00 < grummund> umm ok ;-} is that anything to do with reprap?
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13:03 < 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
13:11 < CIA-38> skdb: kanzure * r9bac434e54de / (4 files in 3 dirs): switch screw metadata over to the new format, clean up comments in lego metadata
13:13 < 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
13:14 < 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.
13:17 < 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
13:24 < 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?
13:32 < draz|lab> pure fucking magic
13:47 < 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
13:48 < fenn> i dont get your unit test; can i please delete it?
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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?
13:50 < 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
13:51 < 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
13:52 < 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.
13:53 < 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
13:59 < 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
14:00 < fenn> no
14:02 < 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
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14:02 < kanzure> lego_package.make("lego") ?
14:02 < kanzure> there's a Lego object defined in packages/lego/lego.py
14:03 < 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?
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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()
14:05 < 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?
14:06 < 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
14:07 < 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?)
14:08 < 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'?
14:14 < 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
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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
14:25 < kanzure> some_pack.list_parts()
14:25 < kanzure> some_pack.options(something something something)
14:33 < kanzure> something about loading up parts from data.yaml
14:42 < 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
14:43 < kanzure> it did an automerge, so there's no telling wtf might have been fudged
15:01 < 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
15:02 < 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
15:04 < fenn> on loading, do some sort of class magic so that lego_package.Lego = lego.Lego
15:05 < fenn> it's not exactly an instance
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15:09 < kanzure> hello embraceunity 
15:09 < kanzure> anything new?
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15:18 < 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
15:19 < kanzure> why did you delete my updates to open_package()
15:20 < 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()
15:21 < 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
15:22 < 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
15:23 < kanzure> fine
15:23 < fenn> why are you using yaml.load_all?
15:23 < kanzure> fixed
15:25 < 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
15:26 < 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
15:27 < fenn> sure about that?
15:27 < kanzure> have you done that?
15:28 < fenn> no
15:30 < 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?
15:31 < fenn> ok
15:35 < 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
15:36 < kanzure> did you run the tests?
15:37 < CIA-38> skdb:  * r58d6e46bcc00 /packages/ (lego/metadata.yaml screw/metadata.yaml): tag_hack syntax changed
15:38 < fenn> why do i get "NameError: global name 'skdb' is not defined"
15:39 < fenn> "unit unit test test" isnt funny if it's not testing skdb.Unit
15:40 < 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
15:41 < 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
15:43 < fenn> it's just a list of interfaces and what they are compatible with
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16:07 < 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
16:14 -!- draz|lab is now known as drazak
16:19 -!- qgqg is now known as QuantumG
16:32 < 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
16:37 -!- ybit [n=ybit@unaffiliated/ybit] has quit ["leaving"]
16:37 -!- ybit [n=ybit@unaffiliated/ybit] has joined #hplusroadmap
16:51 < ybit> would you guys/gals be interested in a mumble chat server for this room?
16:53 < ybit> it might be awhile before it's setup since i'm compiling qt4 atm for it
17:02 < fenn> VoIRC?
17:02 < kanzure> I wouldn't expect a voice-to-voice system to require qt4, especially a "chat server"
17:05 < kanzure> `"I am sovereign" isn't a political statement, it's a physics statement.`
17:05 < fenn> sounds deeply philosophical
17:06 < 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
17:07 < fenn> derrr. what?
17:07 < fenn> philosophical(possible(x)) != possible(x) ?
17:08 < fenn> or is is more like Person.can_do(x) vs Person().can_do(x)
17:12 < ybit> kanzure: that was for for mumble, found out i need murmur, thought mumble did the serving as well
17:20 -!- embraceunity [n=quassel@74.94.105.238] has quit [Remote closed the connection]
17:37 < 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
17:46 < CIA-38> skdb: fenn * rea5aef02ad2e /core/interface.py: silly double-quotes
17:49 < kanzure> ok I could have done that :p
17:53 < 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
17:54 < 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?
17:55 < 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
17:56 < 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?
17:57 < 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
17:58 < 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
17:59 < 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
18:00 < 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
18:01 < 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
18:02  * ybit needs to create an ir reciever now that therehave a bed in the computer room
18:02 < ybit> s/therehave/there's
18:29 < fenn> "Yarg is a semi-hard cow's milk cheese made in Cornwall"
18:29 < fenn> aww. '"Yarg" is simply "Gray" spelled backwards'
18:35 < kanzure> hm I wonder if anyone has studied rTMS and pregnant women
18:35 < kanzure> in particular rTMS of the fetus
18:36 < kanzure> "Repetitive transcranial magnetic stimulation (rTMS) can induce short-term
18:36 < kanzure> reorganization of human motor cortex."
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18:59 < drazak> fenn: see diybio post
19:01 < drazak> hm, apparently hasn't been updated yet
19:04 < 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
19:05 < 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
19:09 < fenn> yeah pcr is more of a digital thing; i guess i was rambling at that point
19:10 < 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
19:11 < 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
19:12 < 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
19:13 < drazak> are googlegroups slow or something?>
19:13 < drazak> I emailed my reply like 20 minutes ago
19:14 < drazak> that's a hell of a long time
19:14 < drazak> for a google page not to have loaded yet
19:17 < 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]."
19:19 < drazak> fenn: so describe for me the pcr technique that you'd uise to determine what kind of cheese you're eating?
19:21 -!- 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
19:22 < drazak> how do you define regular old pcr
19:22 < drazak> do you do gel electrophoresis after?
19:23 < 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
19:24 < drazak> "pcr" though, it's "pcr then gel then sequencing"
19:24 < drazak> but yes it is pretty standard
19:25 < 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
19:26 < 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
19:27 < 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
19:28 < drazak> http://en.wikipedia.org/wiki/Housekeeping_gene
19:35 < 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
19:36 < 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
19:41 < drazak> fenn: ^
19:42 < fenn> yep
19:42 < drazak> :)
19:42 < drazak> sorry for spoiling your fun though :(
19:43 < 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
19:44 < 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
19:45 < 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
19:46 < drazak> and then you do whatever next step you want
19:46 < drazak> is the diy bio google group slow for you guys too?
19:47 < 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
19:48  * ybit has wasted so much time today trying to find an im client which supports otr 
19:49 < 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
19:50 < 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
19:51 < ybit> center-im, still messing with it. may just give into weechat-otr/bitlbee
19:53 < 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
19:54 < 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
19:55 < 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/
19:56 < ybit> someone try connecting to my mumble server please
19:56 < ybit> 192.168.1.149:64738
19:57 < drazak> that isn't gonna work
19:57 < drazak> that's an internal private ip address
19:57 < ybit> argh
19:59 < ybit> 71.207.247.209:64738
20:00 < 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?
20:01 < 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?
20:02 < 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
20:03 < 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?
20:04 < drazak> doesn't explain why it's not showing on the site
20:04 < ybit> anyone want to try connecting to the mumble server?
20:05 < 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
20:06 < 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)
20:07 < 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?
20:08 < 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
20:09 < 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
20:10 < 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
20:13 < ybit> drazak: or you could just check groups.google.com/whattheaddresssistodiybiomailing
20:14 < 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>
20:23 -!- Ian_Daniher [n=it@69.61.230.246] has joined #hplusroadmap
20:25 < kanzure> hey Ian_Daniher 
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20:42 < drazak> are any of you part of the molecular biology online google group?
20:51 < kanzure> link?
20:52 < drazak> http://groups.google.com/group/molecularbio?hl=en&lnk=
20:54 < fenn> wow 1146 members
20:55 < drazak> yeah
20:55 < drazak> that's why I joined
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21:26 -!- any86288028 is now known as katsmeow
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21:52 -!- fenn changed the topic of #hplusroadmap to: "Questionnably high levels of techno-determinism"
21:53 -!- fenn changed the topic of #hplusroadmap to: "a totally unbridled techno-anarchy. Questionnably high levels of techno-determinism too."
23:10 < ybit> lastlog daemon