--- Day changed Wed Sep 16 2009
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00:53 < flamoot> http://www.boners.com/grub/811686.html monster face
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02:08 < deviantlarva> hi, me, again^^
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02:58 < dira> http://www.youtube.com/watch?v=RB_l7SY_ngI&feature=fvst
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03:37 < deviantlarva> yeah, intersting
03:37 < deviantlarva> hi btw dira 
03:44 < dira> hey deviantlarva
06:36 < drazak> kanzure: doI mind if I link to one of your books on heybryan on the diybio list?
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08:35 < kanzure> drazak: no
08:36 < dira> kanzure , how is the 3D thing going ?
08:37 < kanzure> i don't know what you are asking about
08:38 < dira> collision detection to be exact
08:38 < kanzure> fenn rewrote it to use occ's bounding box methods, seems to work ok for now
08:39 < dira> so what is the next step ?automated engineering ?
08:42 < kanzure> a few different projects
08:42 < kanzure> one, to compute a number that represents the "compatibility" of a design using particular parts and components
08:42 < kanzure> two, an algorithm for converting from point clouds to boundary representations or bezier splines-- you can see the progress in skdb/import_tools/surf.py
08:43 < kanzure> three, some unit tests for graphsynth, and eventually integrating the graphsynth Node class into an assembly graph representation for parts in skdb. you can see the graphsynth progress over at: http://adl.serveftp.org/skdb/thirdparty/graphsynth.py
08:44 < kanzure> you can see the code for point clouds to breps over here: http://adl.serveftp.org/skdb/import_tools/surf.py
08:44 < dira> I see
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09:47 < dira> kanzure: I assume you've already seen this but just to make sure , http://ldd.lego.com/
09:48 < dira> + Microsoft robotic studio and Virtual Work Benches in general
09:52 < dira> including , virtual chemistry lab or even virtual medical training kits
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10:25 < fenn> dira: ldd is actually pretty sophisticated, i'm impressed
10:25 < dira> although such systems without proper HCI device are hard to work with
10:26 < fenn> oh i've seen much worse
10:27 < dira> :) don't tell me you are mechanical engineer ?
10:27 < fenn> meh
10:28 < fenn> i've done my fair share of 3d modeling
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10:29 < dira> the worst type of modeling systems are mechanical systems , then civil engineering systems and after that architecture 
10:29 < dira> I see
10:30 < fenn> dunno why you say they are the worst
10:32 < dira> based on details and oddness of particles , in modeling of building you rarely face particles inside each other , components are integrated and well defined , but in mechanical engineering , one particle might include hundreds of sub-particles with special materials and mechanical state
10:32 < fenn> that's just because architects don't care about details for some reason
10:33 < fenn> if i turned in a general idea of a sketch for an engine, you'd be pissed
10:33 < fenn> but for some reason that's okay with buildings
10:34 < dira> I'm talking about Civil engineering too, they don't need details too , at least as deep as mechanical sketches
10:34 < fenn> well that's just crap
10:37 < dira> I've been into modeling (more like simulation) of physical systems , applying Quantum mechanics  (simplified) to system of particles , since formula and situation is well defined that is easy too, so I guess , mechanical modeling is the worst case ;)
10:37 < dira> unless you give me an example...
10:39 < fenn> biological modeling is harder
10:39 < dira> ah , never thought of that, good example 
10:40 < dira> I've seen some medical training kit simulating surgery ! 
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10:41 < fenn> sure but i think they just start off with a data set
10:41 < fenn> they don't actually model the growth process
10:42 < dira> I cannot believe in their accuracy but even thinking about modeling hearth pumping and all those breathing effects is hard !
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10:42 < dira> *heart
10:46 < dira> I just get into an idea , is it possible to create HCI able to simulate resistance  or tension of  virtual items ? like when you reach wall in virtual world , it stops you from going further ?
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10:51 < dira> because that's critical in virtual engineering using HCI while working with particles ,  when you want to pickup a brick in real world , your fingers keep closing until they sense the resistance (touching surface of brick).
10:51 < fenn> yes that's called a haptic interface
10:52  * dira is googling the phrase
10:52 < fenn> there's even a consumer device, the novint falcon
10:52 < dira> useful link ?
10:53 < fenn> i don't know much about their use in CAD and 3d modeling
10:53 < fenn> it's mostly just "VR" whatever that meanss
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11:54 < fenn> genehacker: check this out http://adl.serveftp.org/lab/fenn/pngs/lego_digital_designer
11:59 < genehacker> cool
12:00 < genehacker> now get a robot to assemble them
12:00 < genehacker> http://adl.serveftp.org/lab/fenn/pngs/lego_digital_designer
12:00 < genehacker> oops
12:00 < genehacker> http://fora.tv/2009/05/30/Rodney_Brooks_Remaking_Manufacturing_With_Robotics
12:00 < fenn> too bad it's proprietary
12:00 < fenn> why do people keep linking to that?
12:02 < fenn> damn, worm gears don't work
12:07 < dira> that logo software even generates catalog indicating each action step by step  to create the total image
12:07 < dira> so it is easy to create one robot ;)
12:08 < genehacker> ????
12:09 < kanzure> there's something called 'parametric action representation' or something which could potentially be used for step-by-step task generation, however i'm not so sure yet
12:09 < dira> I'm sure it does the same job
12:10 < dira> they use it in their mindstorm website for robotic competitions
12:12 < dira> you just need to build robot to able to execute each operation like rotating , pushing and ... 
12:12 < dira> you can even use LDD to build that robot :p
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12:29 < dira> a little off topic : http://en.wikipedia.org/wiki/Microsoft_Robotics_Developer_Studio
12:29 < dira> support lego/NXT mindstorm too , beside its physix engine to support physical simulation based on defined models 
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12:32 < kanzure> so?
12:33 < kanzure> it's microsoft..
12:33 < dira> eh , M$'s
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13:09 < any99506369> plausable deniability inherent in ordering cognitive inhancement pills online "sorry, i don't remember ordering those, and i never got them"
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14:50 < kanzure> here's the transcript from paredis' talk today at UT:
14:50 < kanzure> http://adl.serveftp.org/lab/talks/2009-09-16-paredis-utexas.html
14:56 < kanzure> fenn: http://www.modelica.org/libraries/Modelica/releases/3.1/ModelicaStandardLibrary_v3.1_build4.zip/at_download/downloadableFile/at_download/downloadableFile
14:58 < kanzure> line 2126 and onward show some equations for a linear spring damper
15:00 < kanzure> er sorry I guess you'd need to know which file I was looking at
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15:07 < kanzure> "PyMbs is a Python library for modelling holonomic multibody systems. It is able to generate simulation code for Python, Modelica and Matlab."
15:07 < kanzure> http://sourceforge.net/projects/pymbs/
15:11 < kanzure> simulink, scicos, ptolemy, modelica
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15:14 < jonathan__> ping
15:14 < kanzure> hello
15:14 < kanzure> jonathan__: 
15:14 < kanzure> http://adl.serveftp.org/lab/talks/2009-09-16-paredis-utexas.html
15:14 < kanzure> just got done with that talk today
15:14 < kanzure> hope you liked yesterday's rothemund transcript
15:16 < jonathan__> "The "diagram" is not a model."   well that's good
15:16 < kanzure> this is "buzzword soup"
15:16 < kanzure> our lab already implements most of this
15:17 < kanzure> just without the buzzword soup
15:19 < kanzure> also there was another talk yesterday from schlumberger .. http://adl.serveftp.org/lab/talks/2009-09-15-schlumberger.html
15:22 < kanzure> fenn: is it useful to have the components of simple linkages in skdb even though they don't actually correspond to anything physical other than basic chunks of materials?
15:26 < kanzure> jonathan__: what's up?
15:27 < jonathan__> workin on the robotics module to OO it
15:27 < kanzure> btw, yaml supports lists
15:28 < kanzure> or "sequences"
15:28 < kanzure> do you have any experience with modelica?
15:29 < jonathan__> never heard of it
15:29 < kanzure> i've been ignoring it for a while
15:29 < jonathan__> looks like vhdl kind of
15:30 < jonathan__> these days I dont want to use something unless 10,000 people are also using it.  otherwise it's too niche
15:31 < kanzure> unfortunately that's hard to tell on the net
15:31 < jonathan__> yaml has a lot of complex power
15:32 < jonathan__> I like the references the best
15:32 < kanzure> you mean pointers?
15:32 < jonathan__> whatever they call the &thing
15:32 < kanzure> ah yeah
15:32 < jonathan__> and the *thing
15:32 < kanzure> yes it's nice
15:32 < kanzure> i wish it would work across multiple documents though
15:32 < kanzure> that would absolutely blow my mind
15:33 < jonathan__> a bio guy sent me his java framework for a specific bio robot program.  He used xml.  totally unreadable and yucky
15:33 < kanzure> (at the moment it just crashes if it can't find what's being referenced)
15:33 < kanzure> yep
15:33 < kanzure> the other day I wrote an xml2yaml app thingy
15:33 < kanzure> however, it sucks
15:33 < kanzure> http://adl.serveftp.org/skdb/import_tools/del_repo/repo_to_yaml.py
15:34 < jonathan__> I dunno what's up with these CS guys, they always create these abnormally complex languages
15:34 < kanzure> it doesn't construct lists/sequences, doesn't use pointers, etc.
15:34 < kanzure> yes
15:34 < kanzure> UML seems to be a case of that
15:34 < kanzure> the guy who presented today is a big fan of UML, 
15:34 < kanzure> but he's doing the same thing that ADL is doing
15:34 < kanzure> except we're somehow doing it without as much bloat
15:34 < kanzure> although graphsynth, sadly, also uses bloatware/xml to represent graphs
15:34 < jonathan__> no one in industry uses UML.   bring it up in a design meeting and people will laugh or stare blankly.  it's useless
15:35 < kanzure> well that's what I thought
15:35 < kanzure> but apparently there are still people using it?
15:35 < kanzure> like, for code generation? wtf
15:35 < jonathan__> well, for meaningless code like widgets, ok
15:35 < kanzure> heh :)
15:35 < kanzure> i've almost always used code generation for gui stuff
15:35 < kanzure> but that's about it
15:35 < kanzure> except experimenting with SWIG once or twice. don't kill me :(
15:35 < jonathan__> or database query languages etc.  it is a pain to write that stuff by hand
15:36 < kanzure> check this out:
15:36 < kanzure> http://adl.serveftp.org/lab/sysml/
15:36 < kanzure> this was apparently at a conference that matt campbell (the lab pi) went to the other week in san diego
15:36 < kanzure> it's pretty bad
15:36 < jonathan__> uh
15:37 < jonathan__> basically the rule is, if you want people to use i, make it easy.   & thats not easy
15:37 < kanzure> apparently they use all these graphical diagram editors and don't like writing code any more
15:37 < kanzure> but anyway. i agree it's a terrible idea.
15:38 < jonathan__> plenty of academia is geared towards "invent super cryptic thing so that I can be the expert and publish it" etc
15:38 < kanzure> oh that's the trick is it? 
15:38 < kanzure> why didn't i think of that
15:38 < jonathan__> if they like graphical, why not use labview's language already
15:38 < kanzure> can you show me some of what your code is capable (or not capable) of?
15:38 < kanzure> you're doing it in perl, right?
15:39 < kanzure> if it was python i'd ask for a session demo
15:39 < jonathan__> right now it's all broken since I am moving to OO
15:39 < kanzure> camelpoop?
15:39 < jonathan__> I will post a video once it is done
15:40 < jonathan__> the manufacturer tech support isnt being quick about providing low level device commands either so right now I'm only doing movement
15:40 < kanzure> what's your connection interface?
15:41 < jonathan__> the commands are string commands for their s/w, or active-x for their newer s/w   - most people use visual basic to do similar things but only specific robot tasks
15:41 < jonathan__> thus none of their code is re-usable beyond a specific lab problem
15:42 < kanzure> isn't there something for windows called "hyperterminal" that can help you listen for the strings that are being sent?
15:42 < jonathan__> i.e. spend months creating s/w framework and all it does is 1 experiment
15:42 < kanzure> it's been so long since i last used windows. is it hyperterminal that i'm thinking of?
15:42 < jonathan__> hyperterminal doesnt do that, but it's not so much a question of getting the commands, more like decoding them
15:42 < kanzure> it comes pre-installed on windows98 or something
15:42 < kanzure> i see
15:43 < kanzure> well i'd hope that they have this plaintext stream
15:43 < kanzure> but that's unlikely i guess
15:43 < jonathan__> D1,OV420P30M0R
15:43 < kanzure> hah
15:43 < jonathan__> means, aspirate to well #7
15:43 < kanzure> well that sucks
15:44 < jonathan__> ha, I sent a very simple email to the tech support and they replied:  "what's perl?  I have not come across that before"
15:44 < kanzure> you should make them pay you the privledge of letting them give you answers to your questions that they counterquestion.
15:44 < kanzure> er, wait
15:44 < kanzure> there's a joke somewhere in there.. sorry.
15:47 < jonathan__> yea
15:47 < jonathan__> except, they hold the proprietary docs, so got to be nice
15:48 < jonathan__> I did reply something like "surprising since it is the #1 language in bioinformatics" or something, ha
15:49 < kanzure> true that
15:49 < jonathan__> it's been going back & forth for about 2 mos. now.   tech support is always this way.  first ask, then they say "do it the simple way".  then tell them that isnt powerful enough, then they say "try it the simple way again".. etc....  until finally they break
15:49 < kanzure> tech support actually talks to you?
15:49 < kanzure> are they under some sort of legal obligation?
15:49 < kanzure> how does this work
15:51 < jonathan__> ha
15:51 < jonathan__> the customer (ut lab) pays a lot of $$$ for support contract
15:51 < jonathan__> support contract says stuff like:  "must respond to all email within 72 hours" etc
15:52 < jonathan__> which means, they can reply "Got your email will discuss with the internal team" or etc of course
15:52 < kanzure> hah! "learn perl regular expressions within 72 hours, go!"
15:52 < kanzure> bwahah
15:52 < jonathan__> then they assign a tracking ID to the issue for reference, it goes in their database, and on their side if they have ID's open too long, their managers complain to them
15:52 < jonathan__> etc
15:53 < jonathan__> i.e. support issue that is open >2 weeks will send automatic email to the regional boss who will hammer the support team "why isnt this resolved???" etc
15:54 < jonathan__> which of course leads to the habit of support personell who artificially close the support ticket with stuff like, "this should help you, let me know if it doesnt, I am closing this ticket now" etc
15:54 < jonathan__> kind of dismissive
15:54 < jonathan__> it depends on the company
15:54 < jonathan__> I think all undergrads should do at least 6 mos as tech support somewhere.  great problem solving skills.
15:55 < kanzure> hm, that would depend actually
15:55 < jonathan__> "IT" is the worst of course.   IT guys never give support tickets or follow up.  lame.
15:55 < kanzure> i bet in many cases they would lose brain cells
15:55 < kanzure> because a lot of tech support call centers just have a knowledge management system
15:55 < fenn> i learned regex in << 72 hours
15:55 < kanzure> and you go through the routines
15:55 < kanzure> fenn: wtf?
15:55 < jonathan__> there's a lot of levels to tech support
15:56 < jonathan__> front line, sure, follow the internal databse
15:56 < jonathan__> closer to the tier1 customers, each problem gets more unique and there is skill involved
15:56 < kanzure> i hope so. that would renew some faith in commercial tech support.
15:57 < jonathan__> forces the basics...    too many postdocs go for these crazy solutions to problems like "I know!  We can use UML and XML and a graphical blah blah blah"...    ugh, just get it to work command line first
15:57 < jonathan__> the question is:  "which regex".   sysv ok simple.  gnu, more stuff & more annoying.  perl, uhhh I doubt i
15:58 < fenn> i actually liked the whole SysML idea once it was explained properly
15:58 < jonathan__> perl re is ridiculously powerful/complex
15:58 < kanzure> the implementation is totally wrong
15:58 < fenn> i still don't think it _needs_ to be graphical as the UML people seem to think
15:58 < kanzure> a lot of it is very similar to matt's work
15:58 < jonathan__> it needs a graphical paperclip guy like microsoft word
15:59 < fenn> kanzure: do you know how to run a different python with bpython? 2.5 vs 2.6
15:59 < kanzure> #bpython will
15:59 < kanzure> i don't
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16:18 < drazak> I swear to god the next person that emails me to start a pissing contest, I'm going to smite
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16:48 < jonathan__> I think I'm going to refactor the diybio faq
16:48 < jonathan__> split up into smaller sections
16:55 < jonathan__> ha, see the biosci spam?  "MicroRNA Clunkers Program. Economic Crisis affecting your microRNA research?   Exiqon is here to help.  Trade in your clunker. "
17:13 < kanzure> jonathan__: that's ok but last time you totally mangled it :)
17:13 < kanzure> http://openwetware.org/wiki/DIYbio/FAQ
17:14 < kanzure> ok new sections seem fine to me
17:24 < jonathan__> considering everyone seems to want to "do stuff" its funny there is a lack of faq on "doing stuff"
17:24 < kanzure> yeah :(
17:25 < jonathan__> even simple stuff like computational i.e. blast
17:25 < kanzure> bioperl and biopython are really, really easy to use
17:29 < kanzure> hm i wish i had more time to explore the parametric action representation research
17:29 < kanzure> they have these methods of automatically generating service manuals for different machines
17:29 < kanzure> apparently the airforce has funded much of this research
17:29 < kanzure> in particular for the maintenance of jets
17:30 < kanzure> which is pretty much what skdb is going towards
17:30 < kanzure> lemme grab some pretty diagrams
17:31 < kanzure> hm this is taking a while to upload
17:49 < kanzure> http://adl.serveftp.org/papers/instructions.zip
17:51 < kanzure> ok added the images
17:51 < kanzure> adl.serveftp.org/papers/instructions/
17:51 < kanzure> er, http://adl.serveftp.org/papers/instructions/
17:52 < kanzure> for instance: http://adl.serveftp.org/papers/instructions/Virtual%20humans%20for%20validating%20maintenance%20procedures.pdf.1.png
17:53 < kanzure> of course, 3D isn't that important to me
17:53 < jonathan__> looks like ikea
17:53 < kanzure> but in skdb you already have the models so it's not a big deal
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17:54 < kanzure> jonathan__: isn't ikea a car company?
17:54 < kanzure> oh you mean for furniture
17:55 < kanzure> dunno what's going on with the skeletons though
17:56 < kanzure> kind of gruesome if you ask me
17:58 < jonathan__> omg
17:58 < genehacker> ikea a car company?
17:58 < jonathan__> the dissertation in that directory even includes an ikea as a case study
17:58 < genehacker> huh?
17:59 < genehacker> what did I mis?
17:59 < kanzure> genehacker: http://adl.serveftp.org/papers/instructions/
17:59 < jonathan__> the premise of using pictures is what, do avoid translation?
18:00 < kanzure> i don't want to use pictures
18:00 < kanzure> i like text instructions too
18:00 < jonathan__> I dont really find the pictures too useful, I prefer a recipe
18:00 < kanzure> i think text, video and pictorial are all useful
18:00 < kanzure> but "only pictorial" is totally useless
18:00 < jonathan__> the pictures can be generated from a good recipe
18:00 < kanzure> yes
18:00 < kanzure> i agree
18:00 < kanzure> the best paper by far in that directory was Automating maintenance instructions study
18:01 < genehacker> yup it's to avoid translation
18:01 < kanzure> well they suck.
18:01 < kanzure> jonathan is right.
18:01 < genehacker> true
18:01 < genehacker> but it sucks not having a robot to assemble stuff too
18:01 < kanzure> i don't think you know what we are talking about
18:03 < genehacker> I know what you are talking about
18:03 < jonathan__> the robot is useless unless it can operate on something.  so it is chicken and egg
18:03 < genehacker> automatic insturction generation right
18:03 < jonathan__> robot can be replaced by an undergrad
18:04 < kanzure> you mean me? :(
18:04 < genehacker> I'm an undergrad
18:08 < genehacker> so have you been able to generate instructions?
18:08 < kanzure> yes but fenn hates it
18:09 < drazak> I just posted the most ghetto gel electrophoresis chamber idea, ever
18:10 < genehacker> let me guess, it uses gello?
18:10 < drazak> no, tupperwear
18:10 < drazak> and you can use agarose or whatever
18:10 < genehacker> ok
18:10 < genehacker> hahaha
18:10 < drazak> oops, I forgot to say that you have to remove the tape after casting
18:10 < drazak> or well
18:11 < drazak> er, oh well
18:11 < drazak> I'm stuffed full of sushi
18:11 < jonathan__> who here is a mech eng
18:11 < genehacker> I am
18:11 < kanzure> me
18:11 < drazak> I've taken mech eng
18:11 < jonathan__> if so why tupperware.  pls post how to pour a mold which results in a nice chamber
18:12 < drazak> jonathan__: you use the tupperwear as your mold
18:12 < jonathan__> I want a 1-piece chamber poured into some cheap disposable (clay or something) mold
18:12 < fenn> lego
18:12 < genehacker> http://reprap.erikdebruijn.nl/files/research/NASA%20as%20user%20innovator%20-%20WPMicrogravityFDM.pdf
18:12 < jonathan__> bu hao lego
18:12 < fenn> i used to make casting boxes out of lego for plaster and wax molds
18:12 < genehacker> nasa put a stratasys in vomit comet and it worked
18:13 < genehacker> what did you cast?
18:13 < drazak> jonathan__: cut rectangles off each end, cover with tape, pour gel, let it set, take off tape, put gel in tupperwear in bigger tupperwear, in larger tupperwear attach electrodes, add buffer, add voltage, boom
18:13 < genehacker> jonathan cline right?
18:13 < jonathan__> the material for the cast is not important
18:13 < genehacker> I could just machine one for you
18:13 < jonathan__> finding the pourable acrylic is the important part
18:14 < genehacker> polyester resin might work too
18:14 < genehacker> a gel box mold is a fairly simple structure
18:14 < jonathan__> exactly, simple
18:15 < drazak> jonathan__: I'm not saying to make a gel box, I'm saying use the tupperware as the gel box
18:15 < drazak> :D
18:15 < drazak> it's ghetto
18:15 < jonathan__> yes, I know 
18:16 < jonathan__> if you need a really simple 220v power source let me know
18:17 < genehacker> are there any standard gel box sizes?
18:18 < genehacker> also what could we use a gel electrophoresis setup for?
18:20 < genehacker> besides gene "finger printing"
18:21 < jonathan__> it is used for everryyyyything
18:21 < genehacker> I really thing we need to do something more advanced than gel boxes if we want to do true diybio
18:22 < jonathan__> define "true diybio"
18:22 < drazak> sure
18:22 < jonathan__> you mean genetic engineering?
18:22 < drazak> which is why I proposed the simplest way
18:22 < drazak> takes 10 minutes to build
18:22 < genehacker> give me an example of everything first
18:23 < jonathan__> nothing in biology can be measured except by amplifying (pcr) or by running on gel if already amplified
18:23 < genehacker> measuring what?
18:23 < jonathan__> everything in the lab here eventually hits a gel to verify "it is what it is"
18:23 < jonathan__> genes of course
18:23 < jonathan__> or proteins
18:24 < fenn> so you don't like fluorescent labeling?
18:24 < genehacker> what about the chemicals to run the gel aren't those going to be hard to obtain
18:24 < fenn> or radioisotope uptake
18:24 < drazak> jonathan__: proteins you do on a PAGE, and those are verticle
18:24 < jonathan__> too expensive for common stuff
18:24 < drazak> genehacker: nah, the only hard thing might be EtBr, but eh
18:24 < jonathan__> page is still a matrix run on high voltage
18:24 < jonathan__> and they are vertical only for convenience
18:24 < genehacker> so can you seperate out proteins?
18:25 < genehacker> using gel eletrophoresis?
18:25 < drazak> genehacker: any time you want to seperate something by size you run a gel
18:25 < drazak> genehacker: or my charge
18:25 < drazak> genehacker: or by shape
18:26 < drazak> or by shape and charge if you do a 2d gel
18:26 < genehacker> awesome
18:26 < jonathan__> capillary electrophoresis is out of reach of diy for the long term I think
18:26 < drazak> yeah
18:27 < genehacker> could we seperate Taq polymerase out?
18:27 < jonathan__> "gel" = agar
18:27 < jonathan__> agar is too thick for proteins, the proteins dont move
18:27 < genehacker> so what do we use?
18:28 < drazak> polyacrylmide
18:28 < drazak> 2-20%
18:28 < genehacker> oh cool
18:28 < jonathan__> that's the point of all the different reagents...
18:28 < genehacker> that's availale at home depot
18:28 < genehacker> plant section
18:29 < genehacker> comes in granules though, so it might be hard to use
18:29 < genehacker> I think that's what they are
18:30 < genehacker> yup
18:31 < drazak> yeah, it was mentioned on the group that you can use agar instead of purified agarose
18:31 < drazak> if you're worried about DNAase or RNAase contamination, you can treet them with DETC
18:33 < genehacker> so could we use gel electrophoresis to somehow test  for diseases?
18:33 < drazak> it's done all the time :)
18:34 < drazak> well I guess they use qrt-pcr more than GE now, but you can do GE, pcr some samples, run them on the gel, if you get a band the right size then you have a gene, if it's a viral gene then you had a virus
18:34 < genehacker> how? and how do we get the chemicals?
18:35 < genehacker> the problem is getting the chemicals
18:36 < drazak> 99% of this stuff you can buy as a private citizen from invitorgen or sigmalaldritch
18:36 < genehacker> and delivered to my house?
18:36 < genehacker> how much?
18:37 < drazak> it depends on what you're buying
18:37 < genehacker> isn't this stuff expensive(bad for stuff that is expended)?
18:39 < drazak> you can buy primers for 12 bucks a primer, and primers are good for atleast a couple hundred pcrs, taq polymerase, you only need a little, it's maybe 100 bucks for 200 reactions, primermix is cheap, DETC is cheapish, and you can get agar at the hardware store
18:39 < drazak> you need a thermocycler or to use hot water baths
18:40 < genehacker> wow primers are cheaper than I though
18:40 < drazak> yeah
18:40 < drazak> it's 6$ for the forward, 6$ for the reverse
18:40 < drazak> it's more at sigma, but I'll get you the name of the palce that we order from that's so cheap
18:41 < genehacker> so taq or any use ful polymerase is going to be expensive
18:42 < drazak> think about how many reactions you get out of it though
18:43 < drazak> it's only a couple bucks per reaction
18:43 < genehacker> so just as an example, I want to determine if I have a certain virus
18:43 < genehacker> how would I do that?
18:44 < genehacker> that's comparable to the cost of pharmaceuticals
18:45 -!- jonathan__ [n=jonathan@dhcp-146-6-214-4.icmb.utexas.edu] has quit []
18:46 < genehacker> you mentioned that this could be done with gel electrophoresis
18:46 < drazak> ok, so you need a sample from blood, if it's an rna virus you isolate rna, dna virus isolate dna, if you isolated rna you need to do reverse transcriptase, so then you have your dna, determine your concentration of dna, and then mix 80ng of dna (2 microlitres if you had 40ng/ul), .5ul taq, 2ul primer, 7.5ul primer mix, 13ul water, do the pcr, then take 15ul of your sample and mix it with 3ul of loading dye on some parafilm, then load it into the gel (whic
18:46 < drazak> where'd I get cut off?
18:47 < genehacker> (whic
18:47 < drazak> h you made and put in the gel box and covered with buffer) and then run the  gel for an hour
18:47 < genehacker> so how do you isolate DNA?
18:48 < drazak> use a dna isolation kit, it's usually chaper than buying the reagents
18:48 < drazak> or rna isolation kit
18:48 < genehacker> and how is concentration determined
18:48 < drazak> nanodrop or EtBr dilutions
18:49 < genehacker> how do DNA and RNA isolation kits work?
18:49 < drazak> generally they have a salt spin column
18:49 < genehacker> which is?
18:50 < drazak> so you take your sample homogenize it, put it in the spin column and spin for whatever time it says, then your run some buffers through to clean it up, do dnase digestion if you're isolating rna, then run some more buffers, then elute into water
18:50 < drazak> you need a microfuge
18:50 < drazak> all dna isolation methods need one though
18:51 < drazak> or a highspeed centrifuge
18:52 < genehacker> not all
18:52 < genehacker> there is microfluidic dna isolation
18:54 < genehacker> http://research.ncku.edu.tw/re/news/e/20090109/images/090105065937DihqBc.jpg
18:54 < genehacker> check that out
18:54 < drazak> all traditional methods
18:55 < genehacker> we need not be traditionalists
18:55 < drazak> listen
18:55 < drazak> for getting started
18:55 < drazak> diybio needs to get it's head out of it's ass and stop trying to reinvent the wheel
18:57 < genehacker> how so?
18:58 < drazak> microfluidics=out of our reach
18:58 < genehacker> not so
18:58 < drazak> synbio=we don't have the infrastructure for it
18:58 < genehacker> I wouldn't call it trying to reinvent the wheel
18:59 < drazak> it is
18:59 < genehacker> I'd call it trying to do something we can't
18:59 < drazak> if we can't do the traditional methods we certainly can't manage to do the enw methods that 2 labs in the whole world are using
18:59 < genehacker> we can do shrinky dink microfluidics
18:59 < genehacker> what infrastructure is needed for synbio?
19:00 < drazak> everything
19:00 < drazak> we don't have the reagents, we don't have the equipment, and most people don't have the knowledge
19:01 < genehacker> we don't have the reagents?
19:01 < drazak> maybe kay aull does
19:01 < genehacker> we don't have the reagents for much of this diybio stuff
19:01 < drazak> but 90% of diybio people are all theoretical
19:01 < drazak> 95% of diybio have no wetwork experience
19:02 < genehacker> correct
19:02 < genehacker> hell I hardly have any
19:02 < drazak> it kinda pisses me off when people think it's so easy just to do everything
19:02 < drazak> "oh yeah you just pippete stuff into tubes"
19:02 < drazak> well pippetting .5uL isn't the most easy thing in the world, thanks
19:03 < genehacker> oh wow
19:03 < genehacker> I found a bunch of sources for pyrex wafers
19:23 < fenn> 0.5ul with a p2 is pretty easy
19:27 < drazak> fenn: well yeah, but theres a technique to it, you can't put it on the side, you need to get it in the bottom of the tube with the rest of it, you need to make sure you don't pick up extra on the outside of the tip
19:28 < drazak> with that small ammount having extra on the outside of your tip will mess up your ratio easily
19:28 < fenn> yeah it's not like dumping in a liter into a swimming pool
19:28 < drazak> exactly
19:28 < drazak> most people pippetting for the first time are just like
19:28 < drazak> SPRAY
19:28 < drazak> not gently getting the liquid with the rest
19:29 < drazak> of course if you're doing 600ul, you can just screw around with it :P
19:31 < drazak> but there is a technique to it
19:31 < drazak> pippeting is a skill
19:31 < kanzure> like not forgetting what you just pippetted
19:31 < fenn> that's a tough one
19:32 < drazak> definitely
19:32 < drazak> that's what we need a smartbench for
19:32 < drazak> :)
19:32 < kanzure> how hard could it be to turn on a webcam?
19:33 < kanzure> they haven't done anything with that project in a year
19:33 < drazak> that was always my thought
19:33 < kanzure> http://diybio.org/projects/
19:33 < drazak> camera+computer
19:33 < kanzure> there's also this weird ass shot of mackenzie
19:33 < drazak> there's programs to add tags to objects
19:33 < kanzure> never understood that either
19:33 < drazak> mac is lulzy
19:33 < kanzure> opencv or other image process library stuff comes later.. just use a webcam for starters.
19:34 -!- genehacker [i=genehack@wireless-128-62-43-62.public.utexas.edu] has quit [Read error: 110 (Connection timed out)]
19:34 < kanzure> also, voltage sensors would be neat
19:34 < kanzure> like playing "operation"
19:34 < fenn> heh AR augmented pipettor
19:34 < fenn> don't make me PCR reaction you
19:34 -!- any99506369 is now known as katsmeow
19:37 < drazak> rofl
19:40 < fenn> but seriously i'd love to have protocol instructions overlaid on stuff on the lab bench
19:41 < kanzure> overlaid?
19:41 < kanzure> oh, AR/VR
19:41 < fenn> literally arrows going from one tube to another
19:41 < fenn> "pipette 5ul from here to here"
19:41 < kanzure> it wouldn't be too hard to get "color coded object labeling" going on
19:41 < kanzure> where you have it know the identity of an object by a color
19:41 < fenn> pinouts for breadboarding too.. i'm always looking back and forth at the datasheet
19:41 < kanzure> counting tiny pins?
19:42 < fenn> seems i can only remember one pin at a time
19:42 < fenn> electronics chips
19:42 < kanzure> yes i know
19:42 < kanzure> i too have spent many hours counting pins
19:42 < fenn> i think you could train a computer to recognize a chip just by its shape
19:43 < fenn> then add some fiducial code (what are they called again?)
19:43 < drazak> nah, too many share the same package
19:43 < fenn> the square barcode thingies
19:43 < drazak> if it has resolution to read those
19:44 < fenn> actually i dont think you need that, you could just say "this chips is this number"
19:44 < drazak> yeah
19:46 < fenn> actually you just need to know the orientation of the breadboard
19:48 < kanzure> openmodelica tutorial: http://www.ida.liu.se/labs/pelab/modelica/OpenModelica/Documents/ModelicaTutorialFritzson.pdf
20:03 < kanzure> why is this a language?
20:04 < kanzure> "keyword 'flow' indicates that (in this case) currents of connected pins sum to zero, example: flow Current i;" (pg 36)
20:05 < kanzure> "Connections between connectors (ports) are realized as equations in modelica" (pg 37) 
20:05 < kanzure> ah
20:05 < kanzure> connect(pin1,pin2) corresponds to "pin1.i + pin2.i = 0" 
20:06 < kanzure> so it's just setting up the constraints of the problem
20:08 < kanzure> openmodelica notebook seems to be their gui: http://images.google.com/images?q=openmodelica%20notebook&oe=utf-8&rls=org.debian:en-US:unofficial&client=iceweasel-a&um=1&ie=UTF-8&sa=N&hl=en&tab=wi
20:10 < kanzure> on pg 44 they show a simple dc model.. they connect the "p" variable of an inductor to the "n" variable of an electromotive force (emf). any ideas as to what that might mean?
20:10 < drazak> what is openmodelica?
20:10 < kanzure> what is the "n" variable? 
20:10 < kanzure> drazak: modelica is a modeling language apparently. openmodelica is an open source library and compiler for the language.
20:10 < kanzure> but again i'm not sure why this is a language
20:11 < drazak> 'modeling language' like, 3d modeling?
20:11 < kanzure> what does "compiling" it do?
20:11 < kanzure> no, this is for parts and components being connected together
20:11 < kanzure> kind of like in skdb
20:11 < fenn> i think p and n are like "effort" and "flow" (not necessarily p=effort but you get the idea)
20:11 < drazak> oh right
20:11 < fenn> there are 4 variables
20:11 < fenn> (this i remember from the paredis slides)
20:12 < kanzure> there was a page in here before pg 40 that had a nice, more extensive diagram that slightly matches matt's usual "efforts and flows" lookup table
20:12 < fenn> oh, duh. "previous" and "next"
20:12 < fenn> or maybe positive/negative
20:13 < fenn> i don't really like that :(
20:13 < fenn> polarity only matters for diodes
20:13 < fenn> and what do you do with a transistor
20:14 < fenn> kanzure: shouldn't you be reading about quantum mechanics?
20:15 -!- genehacker [i=genehack@wireless-128-62-43-62.public.utexas.edu] has joined #hplusroadmap
20:15 < kanzure> it's okay, i took some drugs so i'll be up forever
20:16 < drazak> need that adderall
20:17 < kanzure> fenn: it wouldn't be a stretch to go fetch openmodelica's model of a screw and dump it into the skdb screw package
20:18 < fenn> there are a lot of things about screws that they won't be concerned with
20:18 < kanzure> these do seem to be simplified models, yes
20:18 < fenn> i'm all for a "generate openmodelica" of course
20:18 < kanzure> how about import openmodelica?
20:18 < fenn> eh?
20:18 < kanzure> well there seems to be some connectivity information that is recoverable, although it may not be useful
20:18 < fenn> there's a mapping from each skdb class to modelica class
20:19 < kanzure> sure.
20:19 < fenn> i need a better way to integrate packages that may not necessarily be installed
20:19 < kanzure> to integrate? what?
20:20 < fenn> like try: import openmodelica; except ImportError: blah
20:20 < fenn> but less sucky
20:20 < kanzure> i actually like that
20:20 < kanzure> i mean, it's worked so far
20:20 < fenn> i don't. it screws up the flow of the code
20:21 < fenn> if i didn't have to worry about it, things would be in different places (much more logically arranged)
20:21 < fenn> i shouldn't have to turn everything inside out because of a package dependency
20:21 < kanzure> oh you mean when debugging something?
20:21 < fenn> no i mean the structure of the code, the order words appear on the screen
20:22 < kanzure> the import statements seem to be at the top usually
20:23 < fenn> yeah but if i'm doing try: import then i have to put all the code for that plugin inside the try statement
20:23 < fenn> unless i can do "if using_modelica:"
20:23 < fenn> but i dont think that always works
20:23 < kanzure> when does it not work?
20:24 < kanzure> that's the "c preprocessor" way :p
20:24 < fenn> hmm
20:24 < fenn> well it turned out to be a bit more involved with OCC
20:25 < kanzure> skdb.geom should fail with the "occ" issues on your box
20:25 < fenn> and then again with igraph, python-graph
20:25 < kanzure> on your laptop i mean
20:25 < fenn> right, that's how i've been testing (halfassedly)
20:26 < fenn> you could also do something like OCC.py: raise ImportError
20:26 < genehacker> kanzure have you tried modafinil?
20:26 < fenn> i don't get why modelica doesn't use icons
20:26 < fenn> what's the point of graphical programming without icons?
20:26 < kanzure> genehacker: i forget. i can check my medical records if you want.
20:27 < kanzure> there's such a long list it's ridiculous.
20:27 < fenn> oh, nevermind, i guess they do use icons
20:27 < kanzure> fenn: yeah the "notebook" thingy.
20:27 < fenn> it's sysml that doesn't use icons
20:27 < kanzure> but they use diagrams instead?
20:27 < fenn> there's this labview-ish thing on p. 15/16
20:31 < fenn> mujahideen
20:33 -!- katsmeow is now known as katsmeow-afk
20:36  * ybit needs adrafanil
20:36  * ybit is sleepy
20:37  * ybit prefers jobs which don't suck the life out of you
20:37 < fenn> kanzure: http://www.flickr.com/photos/oddwick/3016657700/in/set-72157608736702937/
20:37 < ybit> i have quite a few comments on the pythonocc install that i'm looking at
20:37 < ybit> first off, make sure the person has python2.5-dev
20:38 < ybit> took me forever to figure out why gcc test was failing and thus scons wouldn't compile (still won't compile, getting there...)
20:38 < ybit>  wrapper/SWIG/linux_darwin/BRep*
20:38 < fenn> does it have to be 2.5?
20:38 < ybit> that's the dir
20:38 < ybit> doubt it, i'm using 2.5 though
20:39 < fenn> so just python-dev then
20:39 < ybit> yeah
20:39 < ybit> wrapper/SWIG/win32/LocOpe*
20:40 < ybit> take note of the directory, it's different than the dir structure which you were using when the install notes were written
20:40 < fenn> are you following compile_pythonocc?
20:40 < kanzure> which version did you checkout?
20:40  * fenn loses track of how many mangled copies kanzure has littered around the internets
20:40 < ybit> python-gccxml doesn't exist
20:40 < fenn> you shouldn't need it
20:41 < fenn> that's for rebuilding the swig files
20:41 < ybit> http://pastebin.com/f64b005dc
20:42 < ybit> that's where i'm at currently, but i'm so flippin tired right now, not even sure if i'm going to bother fixing it tonight
20:43 < fenn> well i updated the file that's being displayed on the wiki (why isn't it under version control hmm)
20:43 < fenn> ybit: first of all, you shouldn't even bother with scons
20:43 < fenn> use setup.py
20:44 < fenn> it seems to me like scons is a half finished project (and maybe setup.py is 7/8's finished)
20:44 < ybit> spent the entire afternoon going over business details with my grandfather and other family members, looks like it will be pushed to the side for the time being and i'll continue learning welding and whatever metal work my dad and job teaches me + ev @ work
20:44 < fenn> who is ev?
20:44 < ybit> oh, electric vehicles
20:45 < ybit> guess i will have to refer to Phreedom as evgeny now 
20:45 < fenn> huh?
20:45 < ybit> i called Phreedom ev for short for quite awhile
20:45 < katsmeow-afk> ybit : 1960's early 70's Ford had a hydraulic boost cylinder on the end of the pitman arm rather than a hydraulic boost steering gearbox , let me put in an order for 2 now
20:46 < fenn> well, you could try calling him Phreedom
20:46 < ybit> katsmeow-afk: i'll keep an eye out if the business goes back into business :|
20:46 < katsmeow-afk> k :-)
20:46 < fenn> shockingly brilliant idea, i know
20:46 < katsmeow-afk> off to postoffice, bbl
20:46 < ybit> i could, but then that's a brilliant idea left alone
20:47 < ybit> setup.py, here we come, and then bedtime
20:47  * fenn cries himself into chocolate induced insomnia
20:47 < ybit> btw, nobody told me about steel toe boots
20:47 < ybit> i have to buy me a pair if i'm going to do some welding
20:47 < fenn> you don't need steel toed boots to weld
20:47 < fenn> just not sandals or running shoes
20:47 < ybit> i just kind of figured that's what i would need and i asked a few guys today who have welded and they all suggested it
20:48 < ybit> i only have running shoes and cheap dress-up boots
20:48 < fenn> they probably wear carhart overalls too
20:48 < ybit> i've yet to be meet anyone in a long time that's worn those :P
20:49 < ybit> s/that's worn/that wears/ (for katsmeow-afk's sanity)
20:49 < fenn> that's is posessive
20:49 < ybit> oh right
20:50 < fenn> no, wait
20:50 < ybit> i'm sleepy?
20:50 < ybit> i think you're right
20:50 < ybit> i'm going to say you are
20:50 < fenn> you is -> you'se
20:51 < ybit> oh right, so did you look at the pastebin fenn, do i need some of that stuff? it looks like a bunch occ libs are missing
20:52 < fenn> the "checking ... no"  stuff is fine, but you have to fix the environment paths to find the .i files
20:52 < fenn> they moved them into src/wrapper/ i think
20:53 < fenn> i updated this page, you have to hit reload to see changes http://adl.serveftp.org/dokuwiki/pythonocc
20:53 < fenn> anyway it's for setup.py instead of scons
20:53 < fenn> seems to work a lot better
20:54 < fenn> sorry it's not totally checked and polished etc
20:54 < kanzure> Chlorophyll derivatives as visual pigments for super vision in the red
20:54 < kanzure> http://adl.serveftp.org/papers/Chlorophyll%20derivatives%20as%20visual%20pigments%20for%20super%20vision%20in%20the%20red.pdf
20:55 < fenn> kanzure: that's ridiculous
20:55 < genehacker> no this is:
20:56 < genehacker> http://www.physorg.com/news172225206.html
20:57 < fenn> yeah
20:58 < ybit> i'm almost certain this will break your system fenn 
20:58 < ybit> sudo apt-get install libopencascade-visualization-dev libopencascade-dev
20:58 < ybit> sudo apt-get install libopencascade-dev scons python-psyco swig checkinstall x11proto-core-dev libx11-dev
20:58 < fenn> well, the second line isn't really necessary
20:58 < ybit> because visualization-dev depends on the foundation-dev which can't be installed at the same libopencascade-dev is installed
20:59 < fenn> yar
20:59 < ybit> and if libopencascade-dev is install, libopencascade-wok is removed
20:59 < ybit> opencascade-wok
20:59 < ybit> not lib*
20:59 < fenn> guh
20:59 < fenn> first off, remove *opencascade*
20:59 < ybit> it's almost better to just manually install occ
21:00 < fenn> then enable opennovation repo's and install libopencascade-visualization-dev
21:00 < fenn> libopencascade* should all be 6.3.0
21:00 < fenn> you need 6.3.0 for pythonocc (don't ask me why)
21:01 < kanzure> probably because the wrappers were generated on 6.3.0
21:01 < kanzure> the wrappers/headers
21:01 < fenn> i would really like to figure out how this whole thing works some day
21:02 < kanzure> here's how it works:
21:02 < kanzure> you give ".h" files to swig
21:02 < fenn> i get the general idea
21:02 < kanzure> swig takes these and..
21:02 < kanzure> oh.
21:02 < fenn> it's the specific bits that don't really add up
21:02 < fenn> like where are all the .i files hiding?
21:02 < fenn> and where are the transformations described?
21:02 < kanzure> i think they may have created those by hand
21:02 < fenn> no
21:03 < ybit> guess i should also edit /etc/preference to prefer the jaunty mirror over the unstable for occlibs
21:04 < fenn> i think you should forget about /etc/apt/preference
21:04 < ybit> s
21:04 < fenn> when you meddle too much it tends not to work as desired
21:04 < fenn> or you could learn the hard way, whatever
21:05 < fenn> i thought you were using debian?
21:10 < ybit> fenn: i am
21:24 < ybit> python-gccxml is still nowhere to be found if you want to go ahead and remove that from the instructions
21:27 < ybit> will have to fix the following tomorrow
21:27 < ybit> /home/heath/builds/pythonOCC/src/wrapper/SWIG/linux_darwin/Standard_wrap.cpp:1: warning: The C++ parser does not support -dy, option ignored
21:28 < ybit> /home/heath/builds/pythonOCC/src/wrapper/SWIG/linux_darwin/Standard_wrap.cpp:3037:32: error: Standard_Failure.hxx: No such file or directory
21:29 < ybit> /usr/include/opencascade/Standard_Failure.hxx
21:29 < ybit> the libs aren't linked correctly as you mentioned
21:29 < ybit> off to bed
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21:52 < fenn> it's really unfortunate that compiling stuff is procedural knowledge and not declarative knowledge
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22:42 < genehacker> kanzure don't you have some papers on microcontact printing
22:42 < kanzure> probably?
22:43 < kanzure> do you mean imprinting?
22:44 < genehacker> yeah or stamp lithography
22:48 < kanzure> yeah somewhere
22:49 < genehacker> ok
22:52 < genehacker> http://www.rsc.org/Publishing/ChemTech/Volume/2007/03/hot_wax_and_peel.asp
22:52 < genehacker> excellent
22:52 < genehacker> a way to purify dna 
22:59 -!- genehacker2 [i=genehack@wireless-128-62-43-62.public.utexas.edu] has joined #hplusroadmap
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23:58 < genehacker2> WTF?
23:59 < genehacker2> nvm