2009-02-08.log

--- Day changed Sun Feb 08 2009
-!- wrldpc [n=ben@c-98-217-190-207.hsd1.ma.comcast.net] has joined #hplusroadmap00:03
-!- PeerInfinity [n=someone@216.36.180.162] has quit []00:12
-!- wrldpc [n=ben@c-98-217-190-207.hsd1.ma.comcast.net] has quit []00:26
-!- gene [n=chatzill@wireless-128-62-93-215.public.utexas.edu] has quit [Read error: 104 (Connection reset by peer)]00:31
-!- wrldpc [n=ben@173.48.207.37] has joined #hplusroadmap01:25
-!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has joined #hplusroadmap10:13
fenni think we've got ourselves a cad program: http://fennetic.net/pub/irc/heekscad_fillets.jpg10:49
-!- PeerInfinity [n=someone@216.36.180.162] has joined #hplusroadmap11:09
-!- wrldpc [n=ben@173.48.207.37] has quit []11:10
-!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has quit [Remote closed the connection]11:47
kanzurehm, I wonder if it is worth the effort to get people to convert protocol-online.org into the clinical protocol XML format that I mentioned in the "recipe representation" thread12:07
-!- elias` [n=me@unaffiliated/elias/x-342423] has quit [Read error: 110 (Connection timed out)]12:43
kanzure3_So how am I supposed to know whether or not a "buffer" is a 'reagent' or a 'specimen' in the protocol?13:00
kanzure3_http://www.mcb.uct.ac.za/pcrcond.htm for PCR.13:00
kanzure3_I guess specimen is supposedly coming from 'patients', whereas reagents are required to make the protocol-magic happen.13:01
kanzure3_(seeing as how CLP-ML comes from a clinical environment.)13:02
fennspecimen changes whereas reagent stays the same?13:02
fennacross different experiments13:02
kanzure3_in the initiation? ok. I can go with that.13:02
kanzure3_also, why publish a DTD, write up a paper about how awesome it is, and then fail to include a complete example XML file13:03
kanzure3_haven't we come across this before in some other areas? at least the PSL people had an example (though a weird one)13:04
fennyeah you'd expect them to come up with hundreds of examples and test cases in the process of developing the standard, so why not include them13:04
fenni think the claimed reason is so they dont introduce "bugs" or test cases that dont mean what they ought to13:05
fennbut that's lame13:05
kanzure3_hrm, then there's another element - materials - which is at the same level as reagents, and the same level as specimenRequirements13:14
kanzure3_the DTD: http://www.clinchem.org/content/vol0/issue2006/images/data/clinchem.2006.071449/DC1/clinchem.2006.071449-2.txt13:15
kanzure3_so materials != instruments != specimens != reagents13:15
kanzure3_what would count as a material? a test tube? or is that an instrument?13:15
kanzure3_is water a material, or a reagent?13:15
kanzure3_reagent = any chemical used in a laboratory test or experiment.13:16
kanzure3_specimens: dna that you want to amplify, primers, ..13:19
kanzure3_reagents: taq, DMSO, nucleotides13:19
kanzure3_materials: buffer? test tubes?13:19
kanzure3_instruments: open source gel box, thermocycler, straw :p13:20
kanzure3_(this, kiddies, is why ontology sucks)13:20
kanzure3_does buffer come in pcr kits these days? if so, that would imply that in this system, buffer should be a reagent, even though it seems more like a material.13:52
kanzure3_(reagent has a subsection for 'kit' actually, but that's kinda cheating methinks)13:53
-!- elias` [n=me@unaffiliated/elias/x-342423] has joined #hplusroadmap14:15
kanzure3_http://heybryan.org/~bbishop/docs/protocols/pcr.xml15:16
kanzure3_this does more damage than it does good.15:16
fenni dont get why buffer is one reagent15:20
fenn"1.5mM Mg2+, usually some detergent, perhaps some gelatin or BSA"15:20
fennshould be separate reagents no?15:20
kanzure3_this ontology sucks. yes. /me fixes15:21
fenncan you nest reagents?15:21
kanzure3_<!ELEMENT reagent ((include | identity), description?, value?, prep*,  stability*, storage*, (p | figure)*)>15:22
kanzure3_doesn't look like it.15:22
fennmaybe that's what <kit> is for15:22
fennbut i really think it should be nestable15:23
fennnext point; is there a way to describe temperature changes in units?15:23
kanzure3_even if there was, this would be something about the input/output to the thermocycler, no?15:24
fennno?15:24
kanzure3_then what for?15:24
fenndoes a protocol describe the tools you use or just the process that 'stuff' goes through?15:24
kanzure3_the process.15:24
fenni'd argue that they should be separate15:24
fennok good15:24
fennso you talk about temperature, not about thermocycler settings15:25
kanzure3_there should be a BOM, bill of technologies, and then some other things15:25
kanzure3_hrm.15:25
fennof course there should be an explanation of how to set your thermocycler as well, but it shouldnt be the only way15:26
fennthere's lots of human readable text explaining things that could be in code15:27
fennwhat's the purpose of this, btw15:27
kanzure3_cat blah.bom > /dev/checkout15:28
fennso its just a list of materials? then why all the process stuff15:28
kanzure3_instructions.15:28
kanzure3_theoretically this should be a data format for protocol-online.org15:29
kanzure3_instead of having all of those protocols written up in varying details15:29
kanzure3_*varying detail15:29
fennhow would protocol-online benefit from having semantic metadata?15:29
kanzure3_well, this would be more for diybio people to use this information to see that they need to go get a certain kit, or whatever15:29
kanzure3_codifying the information rather than just leaving it out in the mailing list, all raw and dead-like15:30
kanzure3_*poke*15:30
fennhey is protocol-online.org just a bunch of links to other webpages?15:30
kanzure3_yes :(15:30
fennfuck that15:30
kanzure3_sucks huh15:31
fennthey could at least periodically check to make sure the link isn't dead15:31
kanzure3_most of the links are dead now15:31
fennwell duh, that's what happens15:31
kanzure3_internet archive favors .edu's or so it seems, so it's not entirely a lost cause15:31
kanzure3_right15:31
fennhow come you and me have to do this stuff..15:32
fenntired of fixing this broken planet15:32
fennreagents should link to a dedicated page or xml file for that reagent15:34
fennunless it matters which supplier it comes from15:34
kanzure3_ideally it shouldn't, but in practice I've heard it does.15:35
fennoh, and <specimen> ng isnt a volume :)15:36
kanzure3_maybe a better way to represent this information would be some way of separating reusable and one-time tools, materials, items, etc.15:36
kanzure3_ng nanograms?15:36
fennya15:36
kanzure3_oh wait :)15:36
kanzure3_blah15:36
fennwhat, you mean you dont reuse your pipette tips?!15:37
kanzure3_http://www.mcb.uct.ac.za/pcrcond.htm <-- really I was just copying and pasting through this15:37
kanzure3_heh15:37
kanzure3_so, there's instructions and notes; list of reusable materials, tools, etc.; list of one-time use materials, tools, instruments15:38
kanzure3_anything else?15:38
kanzure3_(I'm effectively coming up with a brand new ontology, which is probably a bad idea, but it's not like anyone else has grown the balls to do things right the first time anyway.)15:39
fennhow many turtles do you want?15:39
kanzure3_turtles get their own files :)15:40
fenngood15:40
kanzure3_heh, that might be a fun python script to write. "please input an integer from 1 to 1000 for the number of turtles in this specification."15:40
fennmicrosoft ontology creation wizard15:40
kanzure3_"I see you are writing a suicide note. Would you like assistance?"15:40
fenni think the most important part is the <step> section, which seems to be rather neglected15:43
fennthere should at least be some <temperature> and <time> for each step15:43
fennbut then i start thinking about it and it could be a generic <unit> tag15:43
kanzure3_sounds like those two elements should go inside of a "before" and "after" element15:43
fennyes15:43
kanzure3_or, rather, a "stop here" element15:43
fennhuh?15:44
kanzure3_well, before/after is what they should observe, whereas "stop at this point" would tell them when to stop.15:44
fenni just mean <step> <unit gamma-radiation='56rem'> </step>15:44
kanzure3_just a difference in the names. means same thing15:44
kanzure3_oh15:44
fenni forgot xml always has closing tags15:45
kanzure3_or, <unit blah />15:45
fenn<unit blah />?15:45
kanzure3_instead of <unit></unit>15:45
kanzure3_just saying, it's not always a closing tag.15:46
fennis that how you put it in one tag?15:46
kanzure3_yes15:46
kanzure3_http://users.comcen.com.au/~journals/mipeabs2005.htm "MIPE -- an XML-format to facilitate the storage and exchange of PCR-related data"16:08
kanzure3_hrm, ignore.16:08
kanzure3_http://mipe.sourceforge.net/16:08
kanzure3_mipe2pcroverview.pl: Prints high level data on each or selected PCR product.16:10
kanzure3_mipe2pcrprimers.pl: Prints data on fw and rev PCR primers for PCR products.16:10
kanzure3_mipe2snps.pl: Prints data on each SNP for PCR products.16:10
kanzure3_mipe2sbeprimers.pl: Prints data on SBE primers for each SNP in each PCR product.16:10
kanzure3_mipe2putativesbeprimers.pl: For each SNP, prints flanking regions for SBE primer design.16:10
kanzure3_mipe2genotypes.pl: Prints genotypes for all samples for all SNPs.16:10
-!- ferrouswheel [n=jp@121-73-144-159.cable.telstraclear.net] has joined #hplusroadmap16:36
kanzure3_fenn: re: http://fennetic.net/pub/captainslog/beeping try rmmod sndspkr.17:50
fennmy way doesnt require root access17:53
fennand works over ssh connections etc17:53
fennand you can still make it beep if  you want by doing `echo -e '\007' | sudo tee /dev/tty10` (or something like that)17:55
fennreally i just hate how it beeps when you press tab17:56
fenni guess the right way is echo 'set bell-style none' >> ~/.inputrc17:57
fenn"Thanks a lot, you saved my life" " Were you going to take suicide because of the system bell? "17:59
fennperhaps he was being stalked by rabid wolves while using his wearable computer18:00
kanzureyou know, that happened to me just the other day too18:00
kanzurestalked by rabid wolves club.18:00
kanzurebut in general, what do I need the system beep for? I know when I'm doing something wrong.18:00
kanzureexcept maybe for my own \007's18:01
kanzure3_aha, found it - http://www.aber.ac.uk/compsci/Research/bio/robotsci/video/ - I was talking with Talli the other day and my memory farted out on me.18:01
fenndunno, its not like computers do anything important enough to warrant a beep18:02
kanzure"the machine that goes ping"18:02
fennmaybe if your battery is about to die18:02
fennmy god an academic website with videos that are under 10MB18:03
fennwhat is the world coming to!18:03
-!- gene [n=chatzill@wireless-128-62-93-215.public.utexas.edu] has joined #hplusroadmap18:09
kanzurelike?18:11
kanzure3_http://www.gnu.org/software/gengetopt/gengetopt.html#Basic-Usage18:14
kanzure3_rawr18:15
kanzure3_I'm furious.18:15
kanzure3_I've never ever seen a .ggo file..18:15
fennlol18:18
fennapt-file search .ggo18:18
fenngengetopt: /usr/share/doc/gengetopt/examples/sample1.ggo18:18
fenngengetopt: /usr/share/doc/gengetopt/examples/sample2.ggo18:18
fennbecause it doesnt exist18:18
kanzurehrm. so why isn't .ggo included in .deb's top level root tree dir?18:20
kanzureit's more used to generate the getopt-related sourcecode in a project's sources, but still.18:21
geneis unpatent up?18:23
kanzure3_no18:24
fennwhy would someone use gengetopt instead of getopt?18:33
kanzure3_(found gengetopt from http://autogen.sourceforge.net/compare.html )18:33
kanzure3_"18:34
kanzure3_wyg uses flex and bison to generate a configuration file parser, but uses getopt_long to parse the command line options."18:34
kanzure3_http://autogen.sourceforge.net/autoopts.html18:35
kanzure3_"nearly eliminates the hassle of parsing and documenting command line options. This package allows you to specify several program attributes, up to 100 option types and many attributes for each option."18:35
kanzure3_with autoopt, you feed in some C structs and it generates it, which is less parseable IMHO unless I want to deal with some grammars18:39
kanzure3_whereas gengetopt seems to have that text-based file format (sort of)18:39
kanzure3_http://www.google.com/search?client=opera&rls=en&q=filetype:ggo&sourceid=opera&ie=utf-8&oe=utf-8 18:40
kanzure3_ Results 1 - 26 of 26 for filetype:ggo18:40
fennperhaps you could write a backend hack to python-getopt or perl-getopt instead18:42
fennfor maximum assimilation-to-effort ratio18:42
fennand c-getopt of course18:43
* kanzure3_ personstalks the maintainer, http://www.lorenzobettini.it/18:43
fennit would be awesome if everyone had a .ggo file, but since that's not the case, are you really going to rewrite every piece of software in existence?18:43
fenni actually wrote about the futility of assimilating software in my gingery wiki a long time ago18:44
kanzure3_what sort of work with python-getopt are you talking about?18:44
fenn"We have an advantage, since one man can understand foundry, bench work, machining, engineering, and electronics, and know most every nook and cranny of each subject. One person cannot hardly hope to understand and be up to date on the latest versions of the kernel, X, GCC, and Gnome, and proficient at coding for all of them."18:44
fenni mean intercepting the calls to getopt and siphoning them off into some metadata database that describes the usage18:45
kanzure3_so, just to make sure I understand,18:46
kanzure3_there would be some options that are never called and thus never put into that database18:46
kanzure3_(if that database was only seeded by calls from python-getopt hacks that I have yet to implement)18:46
fennwell.. maybe it'd make more sense to just download the code and grep for getopt calls18:53
fennblah18:53
kanzure3_I wouldn't mind a .ggo creation wizard though.18:54
kanzure3_actually, it would still suck since options and what they conflict with (etc.) are only known by the authors18:54
kanzure3_but on the other hand, many people quickly complain about undocumented switches, so I guess we can assume the man pages are current18:54
genewhoa, my computer is acting very strangely18:57
geneit's been plugged in, but the battery charge stays at 15%18:57
kanzure3_the power adapters sometimes fail.18:57
kanzure3_that's what's presently wrong with my laptop (or, rather, the brick)18:58
genehmmm... or perhaps do I need some more isotopes...18:59
genethough they aren't supposed fail until about 5 years from now19:00
genehttp://www.boingboing.net/2009/02/08/russian-heavy-indust.html19:00
geneb2b to the max19:00
fennmy laptop was stuck at 10% when i bought it and went downhill from there19:20
genethis is a fairly new laptop fenn19:20
fennmy condolences19:20
geneI think something has gone horribly wrong19:20
genehuh? is that smoke?19:20
fennquick throw it in the bathtub!19:21
geneI don't have one!19:21
genejk19:21
fennum, kitty litter box?19:21
geneno, I don't have a cat19:21
fennsome sort of non-flammable container?19:21
genethere is none to be found19:21
geneit's not on fire19:21
fennyou call yourself a hacker?19:21
geneI need a multimeter19:22
genetest the powersupply19:22
geneok I think the power supply  might have failed19:24
geneit isn't as hot19:24
kanzureyou know your civilization sucks when you know a power supply fails when it stops being hot.19:25
kanzureit shouldn't be hot to begin with..19:25
fennbut heat is a universal indicator!19:25
fenneven people who are blind deaf and american can tell when something is hot19:25
genebut the cool blue LED light in the  connector is still on19:26
fennthen it probably is still working19:26
kanzuregene: that hardly matters.19:26
kanzurepfft19:26
kanzurethe green light on my adapters were still going off19:26
fennif your comp isnt drawing any power then it wont make the brick hot?19:26
* kanzure has a drawer full of them19:26
geneI know19:26
fennmaybe the wire between the connector and the brick failed somewhere19:27
genethis baby probably sucking all the power it can19:27
geneit shows it's plugged in19:27
fennok then19:27
fennget a multimeter, cut the wire, measure current flow19:27
fennwhat have you got to lose19:27
geneI don't have one19:27
fenn^^ get one19:27
kanzuremake one. get a resistor and five packs of gum.19:28
genewell dell will replace it for free so you might be right19:28
fennthey replace it but dont want the old unit?19:28
geneyeah19:28
gene"my keyboard broke" "Ok here, have a new one"19:29
genedidn't even own the laptop19:29
fennwell its just a few more chinese slaves after all19:29
genestill sent me a new one19:29
geneteachers didn't even find out about it being broken19:29
kanzuregene: you don't own your laptop?19:30
genewell at my old school19:30
genethey gave us laptops19:30
geneI own my laptop now19:30
kanzurefenn: [[foo]] might be an ok link to mention to les.19:40
fennyes i was thinking about that19:48
fenngene did you see that there's now a usable open source cad program? http://fennetic.net/pub/irc/random-screenshot8.png19:52
genedoes it have smart dimensions?19:53
fennno parametric dimensions yet, but i think its coming soon (for real, not BRL-CAD "soon")19:53
fenni mentioned fillets and chamfers yesterday and it was included today19:54
fennnow that's fairly easy with opencascade but still..19:54
genedoes it do extrude hole?19:54
genedo you have to make things with primitives?19:54
fenni dont know how to draw on surfaces yet (or if it's possible)19:55
gene....19:55
fennbut you can extrude sketches19:55
gene亞__亞19:56
gene⎲__⎲19:57
genewell hope it improves19:57
fenndont predator-face me19:58
genejust having fun with unicode20:02
genebest unicode symbol ever: ㊷20:02
fennby "extrude hole" you mean something like sketch-up right?20:03
geneyou sketch something on a surface then extrude a hole in the shape of it20:03
fenneven a curved surface?20:04
fennwhat happens when you sketch on a sphere20:04
kanzurein solidworks, if you draw on a sphere, the proper trig is not applied to make it stretch around the sphere and be all properlike20:05
geneI don't think you can20:05
kanzureinstead, you just extrude that shape through/down and it eventually intersects with the sphere.20:05
fennok so it's just a convenience thing20:06
fenn"syntactic sugar"20:06
fenni.e. same thing as extruding a sketch and doing CSG subtraction20:06
kanzureyes20:07
genehey kanzure want to see the parts list for the filter?20:13
kanzure3_why do we have a parts list and why wasn't I informed of it?20:13
fennheh20:13
genebecause you left early20:13
kanzure3_left what early?20:13
genethe meeting20:13
kanzure3_it was over.20:14
geneI'll just send it to you20:14
genejust bolts and stuff for my design20:14
kanzure3_pulled from a catalog?20:14
geneno20:15
genenot from a catalog20:15
genefrom home depot20:16
geneit's just a generalized part list20:16
kanzure3_http://heybryan.org/bioreactor/membraneless_filtration/parts_list.txt20:16
kanzure3_hrm.20:16
kanzure3_why are you using his yahoo account?20:17
genegood point20:17
genethat's the only one google knows20:18
kanzure3_all staff members have mail.utexas.edu addresses.20:18
geneok20:19
kanzure3_but anyway, ok.20:19
genehmmm...20:20
geneI bet we might have all we need except nuts n' bolts in the green house20:20
genewill try to meet with the machine shop guy tomorrow?20:21
genewhen did you meet with him?20:21
kanzurelast last Friday20:21
geneok20:21
kanzureI still have the paperwork, if you want to grab it from me that's fine.20:22
genewhat did he say the files had to be in to be machined?20:22
kanzureand then we'll email the designs to Travis (ENS machine shop)20:22
kanzurewell, I tried asking him that, but he seemed very confused20:22
kanzureI think STL and DXF are safe bets here20:22
genesend me the information on what to do20:22
kanzurewhat information?20:22
geneok just travis?20:23
kanzureyes20:23
genelast name?20:23
kanzurecrooks20:23
geneok20:23
genedamn, how do I put that the hole needs to be threaded?20:23
kanzurethere's an area for notes on the paperwork20:24
geneOk let me see the paperwork tomorrow20:24
fennhave you guys actually built one of these yet?20:24
genethat's what we're going to do20:25
kanzureno, I was supposed to get the designs in to the machine shop last week, but somehow time vanished in between max more, lebkowsky, mom, rauchwerk, les, ..20:25
fenn"We have prepared a 3D pdf of the machine which allows you to rotate it, zoom in on it and turn individual components on and off to allow easy identification of all parts."20:33
fenncookie for whoever figures out wtf they were thinking20:34
kanzure3_http://www.geocities.com/foetsch/mfgraph/automake.htm GNU automake by example21:02
kanzure3_"In 1991 people started to write shell scripts to guess these settings21:05
kanzure3_for some GNU packages.21:05
kanzure3_"21:05
kanzure3_http://www.lrde.epita.fr/~adl/dl/autotools.pdf21:06
kanzureodd, a guy makes an iphone app for $2.99 and gets 200 users, and then gets on the news21:11
kanzurewhat a load of crap.21:11
kanzure3_http://lists.gnu.org/archive/html/help-gengetopt/2000-10/msg00002.html  gengetopt & XML (2000)21:21
kanzure3_http://lists.gnu.org/archive/html/help-gengetopt/2000-10/msg00009.html 21:34
kanzure3_"I'll try to have [a DTD] drawn up in the next 48 hours. Unless someone beats me to it."21:34
kanzure3_nine years later..21:34
kanzure3_yay gnu hackers.21:35
kanzure3_I think Jason Morrison got it kinda wrong http://twitter.com/jayunit - "CNC graffiti http://www.hektor.ch/"21:37
kanzure3_http://heybryan.org/off-the-wall.html is probably what he's thinking of21:38
kanzure3_woah, what's with the explosion in registrations? http://groups.google.com/group/diybio/members?&sort=date&order=rev21:43
kanzure3_it was at 540 yesterday or something21:53
kanzure3_$50/seat for 2nd balcony tickets for Jerry Seinfeld, Friday April 3rd 7 pm. 22:35
kanzureles mentioned some book series that was published as an enhancement to gingery, but with data tables, schematics and better figures, written by an engineer23:02
kanzureany idea on the ref?23:02
genehttp://www.acoustics.org/press/132nd/2aaa8.html23:21
genekosher sound amplification23:21
-!- PeerInfinity [n=someone@216.36.180.162] has quit []23:32

Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!