--- Log opened Sun Oct 30 00:00:19 2011
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08:00 < kanzure> michael nielsen on open science http://news.ycombinator.com/item?id=3174407
08:05 < klafka> i didn't realize he wrote a book on open access publishing
08:06 < klafka> oh because it came out this mont
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09:22 < kanzure> delinquentme: haha just saw your diybio email..
09:23 < kanzure> sorry you haven't got feedback heh
09:23 < delinquentme> i gotta post it more places as well
09:23 < delinquentme> and I really only need 1 lab to say " YES"
09:23 < delinquentme> and im in business
09:25 < klafka> i hate when you get distracted reading pizza blogs instead of working
09:25 < klafka> dammit
09:25 < kanzure> pizza blogs.. yeah that happens often for me??
09:26 < klafka> idk why
09:26 < klafka> i don't even eat pizza atm
09:26 < kanzure> delinquentme: you and fenn should meet up and sell robots to labs
09:27 < kanzure> have you met him yet? you've been in sf for at least two weeks now right?
09:27 < delinquentme> nah im back in PA
09:27 < kanzure> lame :/
09:27 < delinquentme> flew back yoostardah
09:27 < kanzure> oh well. he's probably better at interneting anyway.
09:27 < delinquentme> yeah i need to get out there
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09:30 < delinquentme> theres a few companies who are calling me n shit
09:30 < delinquentme> but like
09:30 < delinquentme> THEY NO SCIENCE
09:30 < delinquentme> Y U NO .. GOOD FOR HUMANITEH!?
09:30 < delinquentme> fenn, yuno?
09:30 < delinquentme> and kanzure what is fenn aboot?
09:30 < kanzure> fenn is the other skdb developer
09:31 < kanzure> http://fennetic.net/
09:31 < delinquentme> ohhhhh ic ic
09:34 < delinquentme> but you know what im saying about the 60 grand machine thing
09:34 < delinquentme> its like heres an open source version of your M3 .. which you can build for 10 grand
09:34 < delinquentme> maybs its just the build it and fucking make it all work
09:34 < kanzure> well think of it this way- how many diybio projects are using liquid handling machines? right now? none..
09:35 < kanzure> wait what? it cost you 10k?
09:35 < delinquentme> and like everything in science its gnashed and and cursed upon till its wholly apparent
09:35 < delinquentme> nah I havnt prototyped it yet
09:35 < delinquentme> and it can be made cheaper
09:35 < kanzure> oh this is 002
09:35 < kanzure> doh
09:36 < delinquentme> the current setup with a full 12 stack would be under 10g
09:36 < delinquentme> 12 blades
09:36 < klafka> what are you basing your design off of?
09:36 < kanzure> shit i thought this was 001
09:36 < delinquentme> klafka, im not sure I follow?
09:36 < kanzure> and that you were re-announcing it for some reason
09:37 < delinquentme> oh
09:37 < delinquentme> noted.
09:37 < kanzure> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_01.png
09:37 < kanzure> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_02.png
09:37 < kanzure> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_03.png
09:37 < kanzure> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_04.png
09:37 < kanzure> https://github.com/delinquentme/LH002/raw/master/images/LH002_full_05.png
09:37 < klafka> i mean are you basing your design off another pre-existing liquid handling machine
09:37 < klafka> like
09:37 < kanzure> https://github.com/delinquentme/LH001
09:37 < kanzure> https://github.com/delinquentme/LH002
09:37 < delinquentme> klafka, i guess i'd say that its based around a tecan evo .. but with less wasted space for the applications of biology
09:37 < klafka> if you're comparing it to a 60 grand machine
09:37 < delinquentme> yeahh thats what she looks like :D
09:37 < klafka> then you clearly have competition
09:38 < kanzure> delinquentme: quick suggestion.. dump the google docs file into the git repo
09:38 < delinquentme> and apparently github sucks for image hosting .. so i need to imgur it
09:38 < kanzure> eh
09:38 < delinquentme> klafka, yeah I definitely had the tecans in mind when designing it
09:39 < klafka> how  do you know btw, that your design will work?
09:39 < kanzure> sorry gitduino or other git-based hardware hosting isn't up yet
09:39 < kanzure> klafka: he built LH001
09:39 < klafka> oh you did?
09:39 < klafka> nice
09:39 < kanzure> http://www.youtube.com/watch?v=ZY5IY5CZ1es
09:39 < klafka> so are you trying to turn this into like os hardware?
09:40 < klafka> or trying to get a company to take your design and sell it and market it
09:40 < klafka> like george church did
09:40 < delinquentme> klafka, yeah it currently is up on github
09:40 < delinquentme> like all the files you need to print the parts
09:40 < delinquentme> oh never thought about that...
09:40 < delinquentme> this was with his MAGE machine?
09:41 < klafka> polonator
09:42 < delinquentme> wow
09:42 < delinquentme> haha so much to do
09:42 < delinquentme> klafka, thanks for the heads up on that
09:42 < klafka> indeed
09:42 < klafka> np
09:43 < delinquentme> thermo said they were interested but i didnt know companies operate like that
09:43 < delinquentme> SO
09:43 < delinquentme> its like always FINISH IT!!!!
09:43 < kanzure> did thermo understand that it's about open hardware?
09:44 < delinquentme> yeah
09:44 < kanzure> reaallly how fascinating..
09:44 < delinquentme> the specific branch is just interested in stitching together stuff for labs
09:44 < delinquentme> like its the common
09:44 < delinquentme> " we need it all for 10 grand"
09:45 < kanzure> they do one-off consulting projects?
09:45 < kanzure> ok
09:45 < kanzure> hey i forget is there an open source syringe pump yet? or is that still in the pipeline
09:46 < klafka> syringe pump?
09:46 < klafka> also is there an oss micropippetter
09:46 < kanzure> ah yep http://blog.reprap.org/2005_03_01_archive.html
09:46 < kanzure> http://staff.bath.ac.uk/ensab/replicator/Pix/syringe-pump-h.jpg
09:47 < kanzure> "The RP syringe pump. The only non-RP parts are the syringe (which only costs a few pence), a length of M5 studding plus an M5 nut, four M3 screws, and the motor (245-6089; available from RS Components - click the link). We have a later versions with an optical counter on the motor shaft for precise metering, with heating jackets, and a whole range of different capacity syringes."
09:47 < kanzure> well fuck all this other shit
09:47 < kanzure> that's the primary component you need for diybio-style microfluidics
09:49 < kanzure> http://www.youtube.com/watch?v=pNdARr_t1dQ
09:50 < delinquentme> very nice!
09:50 < delinquentme> who is working on this??
09:50 < kanzure> i wrote some crummy software to generate svg-based designs for lab on a chip stuff, but it never went anywhere
09:50 < kanzure> i got a laser cutter and did test prints
09:51 < klafka> what is diybio actually doing that's interesting
09:51 < kanzure> but it was just surface tension stuff
09:51 < klafka> frankly it seems to me the cost of biotech hasn't really reached the hacker level
09:51 < klafka> we're in pre-altair days
09:52 < kanzure> klafka: the LA group is doing some pretty cool projects
09:52 < klafka> oh?
09:52 < kanzure> like their neural tissue culture, directed evolution/selection of an extremophile and genome sequencing thereof..
09:52 < klafka> interesting
09:52 < klafka> that's gotta be a _lot_ of cash still
09:52 < klafka> well if they're doing full genome sequencing
09:53 < delinquentme> i need learning hacks
09:53 < kanzure> they also pcr'd out a copy of gfp from squid or whatever
09:53 < delinquentme> learning fucking takes too long
09:53 < klafka> that's interesting
09:53 < kanzure> klafka: nope they are collaborating with beijing genome institute for that
09:53 < kanzure> klafka: http://diyhpl.us/wiki/transcripts/open-science-summit-2011/joyce-peng-beijing-genomics-institute.txt
09:53 < klafka> oh god bgi
09:53 < klafka> lol
09:53 < klafka> bgi scares me
09:53 < klafka> anyway
09:53 < klafka> time for hair cut
09:53 < kanzure> yep :)
09:53 < delinquentme> yeah that was nothing more than a commercial
09:53 < delinquentme> for bgi
09:53 < kanzure> delinquentme: sure.. but maybe klafka didn't know about them
09:54 < delinquentme> re hev sequencers and gov money
09:54 < kanzure> delinquentme: i'm surprised how a lot of the audience didn't know about their 140+ sequencers
09:54 < delinquentme> well thats why you advertise!
09:54 < delinquentme> *grumbles*
09:54 < kanzure> haha but it was huge news a few years back
09:54 < kanzure> so that presentation
09:54 < kanzure> said that they were using github
09:54 < delinquentme> oh ps i was mentioned on derek lowes blog :D
09:54 < kanzure> they had a screenshot and i tried to get the url
09:54 < kanzure> https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis
09:54 < kanzure> but they deleted the actual repo or something..
09:54 < kanzure> so this is just the 1/100th-ly-sized repo
09:55 < klafka> dude they ordered like 30 or something pacbio sequencers too
09:56 < kanzure> ncbi will be crushed
09:56 < kanzure> demolished. raped.
09:56 < delinquentme> the NCBI data is safe
09:56 < kanzure> i mean in terms of data input :)
09:56 < delinquentme> nexus and google collabo assured that
09:56 < kanzure> where are you going to put all those hundreds of petabytes hmm
09:56 < delinquentme> if you didnt hear about that
09:57 < delinquentme> so should I move to the bay and work at random company
09:57 < delinquentme> or stay in pitt and work @ cmu and do collaboratings
09:57 < delinquentme> I think cmu is where its going to be at
09:57 < kanzure> you will probably not find a job that intersects everything you want.
09:58 < kanzure> so you could either do random collaborations that probably won't pay
09:58 < kanzure> or you can do a startup with fenn or on your own
09:58 < kanzure> but even then it's not a guarantee that any money will come of it
09:59 < delinquentme> kanzure, who was the designer on the syringe pump
09:59 < kanzure> dunno.. adrian bowyer would know
10:00 < kanzure> adrian bowyer <a.bower@bath.ac.uk>
10:00 < kanzure> oops
10:00 < kanzure> adrian bowyer <a.bowyer@bath.ac.uk>
10:02 < kanzure> huh, http://people.bath.ac.uk/ensab/G_mod/Svlis/
10:02 < kanzure> i didn't know about that geometric kernel. it seems to be based on subdivision of surfaces.
10:51 < Technicus> Hello . . . I am planning a building project and I want to keep track of the materials, budget, hours, process, documents, etc...  Does anyone here have a suggestion for an opens source project management suite?
10:51 < Technicus> Hopefully my question is not too off topic . . .
10:52 < ybit> Technicus: github
10:53 < ybit> github and your favorite text editor?
10:53 < ybit> rather
10:53 < ybit> your favorite vcs and text editor
10:54 < ybit> org-mode is great for tracking time spent on a project
10:54 < ybit> Github can handle org files
10:54 < ybit> the display of them
10:55 < ybit> If you need to export to other formats, C-x-e-g then choose to export into other formats like html, markdown, etc.
10:56 < ybit> this isn't off-topic at all, btw :)
10:57 < Technicus> ybit: I should maybe be a little more specific . . . I am rebuilding an RV and I want to do cost analysis of parts and materials.  Another thing is that I intend to replace the drive train and suspension with components from a M939 series truck.
10:58 < ybit> Maybe you want a spreadsheet editor then?
10:58 < ybit> org-mode has this too, but i'll be quiet about it now :)
10:59 < kanzure> i don't think org-mode is a good suggestion here
10:59 < Technicus> Perhaps that would be appropriate.  I do also want to clock the time I put into research, development and build.
10:59 < kanzure> it sounds like you need a lot of separate tools
10:59 < kanzure> there's no way a tool will do all of that for you :)
10:59 < kanzure> "oh and it would also cook my breakfast"
11:00 < Technicus> Yeah . . . I thought that would be the case, because I also want to develop some schematics.
11:01 < ybit> apt-cache search time | grep track
11:01 < ybit> wmwork
11:01 < ybit> worklog
11:01 < ybit> gtimelog
11:01 < kanzure> there's some commercial PDM (product data management) tools that will cost you many 100s of grands
11:01 < Technicus> Mostly looking for ways to keep track of what I am trying to do, so I don't get lost, repeat things, and can demonstrate progress.
11:02 < ybit> (oooorrrrrrg-mode)
11:05 < delinquentme> syncrobid
11:05 < Technicus> kanzure: I'll employ LibreOffice Calc before I shell out a penny for any commercical product data management software. :)
11:05 < delinquentme> but i dont think its open source Technicus
11:06 < Technicus> kanzure: . . . or write my own.
11:40 < drazak> kanzure: latest Nature mentions the DIYBio mailing list
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16:11 < klafka> reading people on arstechnica talk about the jstor/schwartz thing is really painful
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16:36 < kanzure> lunar space elevator stuff.. http://www.lpi.usra.edu/meetings/leag2011/pdf/2043.pdf
16:36 < kanzure> klafka: why's that?
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16:40 < klafka> this one comment about how people who work in journal publishing put in a lot of work and the cost of journals basically covers the expenses
16:40 < klafka> when elsevier made 1.3 billion net profit last year
16:40 < klafka> basically anti-michael nielsen
16:40 < klafka> hey kanzure  are you familiar w/ bitbucket
16:40 < klafka> ?
16:40 < klafka> if I pushed a change from one computer, and i want another computer which already has a repo on it updated with those changes what would be thje command
16:40 < klafka> it seems like it's a pull request
16:41 < klafka> but i can't find how to actually request one
16:50 < klafka> nvm
16:51 < kanzure> yes i'm familiar with bitbucket
16:51 < kanzure> hg pull right?
16:52 < kanzure> oh, you meant social features
16:52 < klafka> oh no
16:52 < klafka> i figured it out
16:52 < klafka> it wasn't a bitbucket feature
16:52 < klafka> it was a git feature
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20:11 < kanzure> http://www.youtube.com/watch?v=V6sFw4_GlhY
20:11 < kanzure> he takes the monkey bars to go upstairs?
20:11 < kanzure> this guy is ok in my book
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22:37 < kanzure> toilet paper microfluidics http://www.youtube.com/watch?v=kcdKxuYC8V8
22:39 < Stee|> kanz, do you keep up with Lab Chip?
22:40 < kanzure> nope
22:40 < Stee|> good paper on how to achieve mixing in microfluidic systems, which is pretty difficult
22:40 < Stee|> I'm trying to predict loss of energy due to dipole mixing (hill's spherical vortex) so I ran across the paper
22:41 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/Mixing-induced%20activity%20in%20open%20flows.pdf
22:41 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/Patterning%20of%20flow%20and%20mixing%20in%20rotating%20radial%20microchannels.pdf
22:41 < kanzure> might help..
22:41 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/Review%20-%20Micromixers.pdf
22:41 < Stee|> yeah, the issues is I'm mostly dealing with a synthetic jet ejecting into its own residual
22:41 < Stee|> which...hasn't ever been addressed.
22:41 < Stee|> ever.
22:41 < Stee|> bleagh
22:54  * kanzure sleeps
22:57 < superkuh> I found another use for toilet paper the other day, in high voltage pulsed autotransformers soaked with copper sulfate: http://superkuh.com/library/Electronics/vector-inversion_autotransformers_design_%20JC%20Martin_%20I%20Smith.pdf
--- Log closed Mon Oct 31 00:00:20 2011