--- Day changed Tue Aug 25 2009
00:01 < genehacker> is it that heat on the brain thing
00:02 < genehacker> my airconditioning unit maintenance needs
00:08 < genehacker> errr... this is bad
00:08 < genehacker> I can see other people's file on the appserver
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11:07 < kanzure> this looks like an interesting journal: "journal of reducing space mission cost"
11:14 < kanzure> weird I found a campbell paper in one of these feeds
11:14 < kanzure> "An evaluation scheme for assessing the worth of automatically generated design alternatives"
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11:26 -!- Irssi: #hplusroadmap: Total of 30 nicks [0 ops, 0 halfops, 0 voices, 30 normal]
11:38 < ybit> http://c2.com/cybords/
11:38 < ybit> http://www.c2.com/cgi/wiki?ReciprocalityTheory
11:38 < ybit> mostly cybords
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12:42 < kanzure> xp_prg: can you please stop sending me two word emails?
12:49 < xp_prg> ok, like what?
12:52 < kanzure> like "Wow awesome!"
12:52 < kanzure> don't send me that.
12:52 < xp_prg> ok
12:53 < xp_prg> I have an initial lesson plan for biopython from someone who teached it!
12:54 < drazak_> I know a little biopython
12:54 < xp_prg> tell me how you use it and stuff
12:55 < drazak_> make primers
12:55 < drazak_> lulz
12:55 < drazak_> not that I ever got my script to work
12:56 < drazak_> but that's not because of biopython, it's because I don't know python
13:29 < xp_prg> what is a primer?
13:34 < kanzure> ..
13:34 < kanzure> didn't you say you were teaching a class on synthetic biology?
13:34 < xp_prg> is it the promoter region of a gene?
13:34 < xp_prg> I know the concepts but not all the lingo sometimes
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13:40 < ybit> kanzure: did you ever write a script to extract the title of a pdf and rename the file?
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14:00 < xp_prg> drazak_ is that right?
14:01 < xp_prg> I was right!
14:01 < drazak_> no
14:01 < drazak_> it isn't right
14:02 < xp_prg> it says it is the starting point of the transcription right?
14:02 < xp_prg> that is the promoter region
14:02 < drazak_> a primer is a oligonucleotide around 20nt long use as a starting point for a polymerase chain reaction
14:02 < drazak_> er, no
14:02 < drazak_> it's used as a template for PCR
14:03 < drazak_> you have a 5'-3' primer for the antisense start of PCR, and a 3'-5' for the sense start of pcr
14:03 < drazak_> A primer is a strand of nucleic acid that serves as a starting point for DNA replication.
14:03 < drazak_> from wikipedia
14:03 < xp_prg> what is the difference between a primer and a promoter region of a gene?
14:04 < drazak_> promoter reigons are for translation
14:04 < drazak_> this has nothing to do with translation
14:04 < xp_prg> how is that related to synthetic biology then?
14:05 < drazak_> I never said it was?
14:06 < drazak_> I was saying I used biopython to make primers
14:06 < drazak_> well, design primers
14:06 < xp_prg> oh ok
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14:08 < drazak_> please learn how to read
14:08 < xp_prg> I learned something very valuable just now thanks!
14:08 < drazak_> it makes communication over irc much easier if both parties can rad
14:08 < drazak_> er, read
14:08 < drazak_> typing helps too
14:08 < xp_prg> very true
14:09 < xp_prg> drazak_ tell me more stuff, help me to learn this better, my synthetic biology vocabulary needs help I think
14:09 < drazak_> er
14:09 < drazak_> synthetic biology is not a way to learn biology
14:09 < xp_prg> I am trying to change that
14:09 < xp_prg> I want it to be a starting point
14:09 < drazak_> that's a misconception spread by the DIY bio community, due to the fact that the starters are form IGEM members
14:09 < drazak_> but it's not
14:10 < drazak_> if you don't know shit about biology you're never going to learn watching other people do synbio
14:10 < xp_prg> it can be though
14:10 < xp_prg> drazak_ if your a programmer, synthetic biology is readily understandable
14:11 < drazak_> it isn't though
14:11 < drazak_> as kanzure posted
14:11 < xp_prg> why isn't it?
14:11 < xp_prg> are you a programmer?
14:11 < drazak_> the reality is that parts aren't black boxes
14:12 < xp_prg> but they are close enough that it can be a beginning point for entry into synthetic biology for programmers
14:12 < drazak_> so if it doesn't work
14:12 < drazak_> say you put some sort of plasmid into a cell
14:12 < drazak_> and you get no expression of the gene you wanted
14:12 < drazak_> what's it mean?
14:13 < xp_prg> well the gene never made it into the plasmid possibly
14:13 < xp_prg> the transcription factor was wrong
14:13 < xp_prg> the gene promoter region was wrong
14:13 < xp_prg> what else could it be?
14:15 < drazak_> er
14:15 < drazak_> what's wrong mean?
14:15 < drazak_> what would cause it not to go into the gene?
14:16 < drazak_> also: depending on how you made the plasmid, it may not be a plasmid without the gene
14:17 < xp_prg> well the cell membrane may not have the right receptor to allow the transcription factor in
14:18 < drazak_> er
14:18 < drazak_> not exactly
14:18 < xp_prg> the cell might need to be cold shocked to let the transcription factor in
14:18 < drazak_> you don't let transcription factors in, generally
14:18 < drazak_> they're produced by the cell
14:18 < drazak_> they're nuclear and/or cytosolic proteins
14:18 < xp_prg> what causes the inserted gene to get expressed then?
14:19 < drazak_> transcription factors from within the cell
14:19 < drazak_> you don't add them in the media or something
14:19 < drazak_> you can add an element to the media that causes the cells to produce transcription factors
14:19 < drazak_> but generally transcription factors can't penetrate the cell membrane
14:20 < xp_prg> I am confused by this, what is the elment tht tells the cell to make a transcription factor if it is not a transcription factor in itself?
14:20 < drazak_> so, lets use one I know
14:21 < drazak_> so there's this protein, called VEGF
14:21 < drazak_> vascular endothelial growth facotr
14:21 < drazak_> there are receptors on the outside of cells called VEGFR1 and VEGFR2
14:21 < drazak_> depending on the receptor, VEGF in the media can cause a cell to produce many different transcription factors for endothelial related genes
14:21 < xp_prg> ok
14:22 < xp_prg> well VEGF enters the cell and binds to a gene promoter region does it not?
14:22 < xp_prg> causing the gene to be expressed?
14:22 < drazak_> o
14:22 < drazak_> er, no
14:22 < drazak_> vegf binds to a membrane protein
14:22 < xp_prg> right the receptor right?
14:22 < drazak_> it never enters the cell
14:23 < drazak_> it binds to the receptor, which sends a signal to the nucleus
14:23 < xp_prg> oh wow, I did not know that!
14:23 < drazak_> this is why you need to learn basic biology first
14:24 < xp_prg> but can't a protein enter a cell via endocytosis and bind to a promoter region of a gene?
14:25 < parolang>  /j #php
14:28 < kanzure> ybit: look around for renamepdf.py
14:32 < xp_prg> drazak_ ?
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15:12 < novaxian> hello
15:13 -!- novaxian is now known as Xirdal
15:13 < drazak_> xp_prg: well, yes, but that happens less often than people tellyou
15:13 < parolang> Xirdal: Hi :)
15:14 < Xirdal> hi
15:14 < Xirdal> hmm
15:14 -!- Xirdal is now known as novaxian
15:14 < xp_prg> how does a cell know what receptors to have?
15:14 < novaxian> seems xirdals already taken
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15:21 < novaxian> hello
15:21 < novaxian> anyone here work with thermophilc bacteria?
15:23 < drazak_> xp_prg: the lineage of the cell usually determines that
15:23 < drazak_> xp_prg: sorry, I'm at the lab, so I'm in and out
15:26 < kanzure> hello novaxian 
15:27 < drazak_> novaxian: like the bacteria taq polymerase is from?
15:29 < novaxian> drazak ill look into that
15:29 < novaxian> afk
15:29 < drazak_> it's like thermophilus aquarius
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15:33 < genehacker> did somebody say thermophilic bacteria?
15:33 < parolang> <novaxian> anyone here work with thermophilc bacteria?
15:35 < genehacker> yeah I know
15:36 < genehacker> kanzure can heekscad make a curve through a given set of points
15:37  * ybit doesn't have renamepdf.py anywhere, btw.. kanzure, do you mind me fetching at certain hours or do you want me to send you the hdd?
15:38 < kanzure> you will get more if you send the hdd
15:38 < kanzure> ybit: try searching for "rename pdf zotero py"
15:39 < kanzure> genehacker: yes especially with the heekspython plugin
15:39 < kanzure> genehacker: do you have the parametric gear generator script yet?
15:39 < genehacker> yeah
15:39 < genehacker> in matlab...
15:39 < kanzure> were you going to send it or commit it?
15:40 < genehacker> oh sure
15:40 < genehacker> it makes a picture of a gear
15:40 < genehacker> input gear teeth number
15:40 < kanzure> is that all?
15:40 < genehacker> need to iron out kinks so one can make gears that actually mesh
15:41 < genehacker> you can adjust base radius
15:42 < genehacker> I need to make it so one can make gears of different teeth numbers that mesh
15:42 < genehacker> and figure out how to export matlab drawing data to something useful
15:43 < genehacker> but it makes pretty gear pictures for now
15:46 < genehacker> how do Iadd a website to ubuntu's sudo repository thing? 
15:47 < kanzure> do you know what you want to add?
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15:47 < kanzure> sudo vim /etc/apt/sources.list
15:47 < genehacker> deb http://www.opennovation.org/ubuntu hardy main contrib non-free  
15:47 < genehacker> how do I add that?
15:48 < kanzure> sudo vim /etc/apt/sources.list
15:48 < kanzure> do you know how to use vim?
15:48 < kanzure> if not, do this:
15:48 < kanzure> echo "deb http://www.opennovation.org/ubuntu hardy main contrib non-free " >> /etc/apt/sources.list
15:50 < kanzure> http://brlcad.org/~erik/glassbearing.png
15:50 < genehacker> permission denied
15:50 < kanzure> sudo it
15:50 < kanzure> don't forget both >>
15:51 < genehacker> not working
15:52 < kanzure> ok then just use vim
15:52 < kanzure> vim /etc/apt/sources.list
15:52 < kanzure> press i, then go to the bottom of the file and add that text you pasted
15:52 < kanzure> then press escape, then type ":wq<enter>"
15:54 < kanzure> since when is maradydd on lifeboat.com?
15:56 -!- OSGuido [n=chatzill@190.168.64.22] has joined #hplusroadmap
15:56 < kanzure> hey guido
15:57 < OSGuido> hey there, Bryan
15:57 < kanzure> joseph was around yesterday.
15:57 < OSGuido> yes, he was the one who told to hang around here
15:57 < OSGuido> he said I'd like it
15:58 < ybit> aside from space exploration, what are some other projects for diyers to increase our understanding of nature?
15:58 < genehacker> what does :wq<enter> do?
15:58 < kanzure> ybit: sounds ridiculously vague.
15:58 < OSGuido> a newbie question. Is it bad manner to capitalize your SN here? pretty much everybody seems to go lowercase
15:58 < kanzure> genehacker: w for write, q for quit.
15:58 < ybit> kanzure: it is vague, please answer vaguely :)
15:58 < genehacker> add a # in front of it right?
15:59 < kanzure> OSGuido: no, but it's easier on those of us who use the tab button a lot. we can type y<tab> and get ybit, without typing it entirely
15:59 < ybit> OSGuido: it doesn't matter
15:59 < kanzure> genehacker: not a # but a :
15:59 < kanzure> genehacker: so press escape, then :, then w, then q, then enter
15:59 < kanzure> later you might want to run "vimtutor" when you have nothing to do
15:59 < OSGuido> oh, I see. like the CLI
16:00 < OSGuido> thanks
16:00 < ybit> vi
16:00 < ybit> whoops
16:00 < ybit> hmm
16:00 < kanzure> actually tab completion works with uppercase letters even when you use lowercase letters
16:00 < kanzure> so, nevermind. my bad.
16:00 -!- Joseph [n=chatzill@adsl-157-138-244.cae.bellsouth.net] has joined #hplusroadmap
16:00 < kanzure> hey Joseph.
16:00 < Joseph> Ok I have to do a call in a little bit
16:00 < ybit> vim is nice, but emacs is essentially an OS within itself
16:00 < Joseph> Basically guido wants to talk specifics a bit
16:00 < kanzure> ybit needs to stop trying to start flamewars
16:01 < ybit> :)
16:01 < genehacker> dang it's not quiting
16:01 < Joseph> I still have to get a breakdown of costs and labor time from Carlson
16:01 < kanzure> genehacker: what are you pressing?
16:01 < ybit> genehacker: :q!
16:01 < kanzure> Joseph: I think that's a first step.
16:01 < genehacker> I shall read vim tutor
16:01 < ybit> esc -> :q!
16:01 < kanzure> ybit: he doesn't want to lose his changes.
16:01 < Joseph> Then we can hash back and forth about whether it is totally unreasonable
16:01 < ybit> oh
16:01 < ybit> wq!
16:01 < ybit> or just wq
16:01 < novaxian> ybit i would say mycology is very important, potentials in bioremediation
16:01 < kanzure> why do you need to q! when you wq?
16:02 < ybit> i corrected myself
16:02 < ybit> ty novaxian 
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16:02 < ybit> should have been using emacs, poor fella
16:02 < kanzure> well that can't be good
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16:02 < kanzure> all he was trying to do was save a file in vim,
16:02 < ybit> :P
16:02 < kanzure> and he ended up killing his irc client?
16:02 < novaxian> i read somewhere recently that there is research going on over at OSU on generating electricity from cyanobacteria
16:03 < novaxian> ie living solarpanels
16:03 < kanzure> novaxian: search around for "microbial fuel cells"
16:03  * ybit is curious how expensive and feasible it is to build a particle accelerator
16:03  * ybit needs to grab a few papers on creating artificial black holes
16:03 < kanzure> ybit: there's a few ways to do it with crystals at home, but in general most people are going to tell you something about billions of dollars
16:03 < ybit> kanzure: did you read this in a paper or on some site?
16:04 < kanzure> paper
16:04 < ybit> if you have citations, i'm all eyes
16:05 < ybit> "An ordinary CRT television set is a simple form of accelerator. There are two basic types: linear accelerators and circular accelerators." i never thought about it like so
16:05 < ybit> minus the second sentence
16:07 < kanzure> http://heybryan.org/books/papers/pyroelectric-ion-acceleration/
16:07 < kanzure> Electron acceleration for X-ray production using paired pyroelectric crystals
16:07  * ybit yippies
16:07 < kanzure> Ferroelectric lithium tantalate thin film derived from peroxide
16:11 < OSGuido> so, 
16:12 < OSGuido> you all were discussing yesterday if ou can replicate the Lava Amp prototype, right?
16:12 < kanzure> among other things
16:12 < kanzure> there are some ways to make a better/easier device
16:15 < OSGuido> I agree. The prototype is not going to be the final version. But what we need now is to replicate the proof of concept, a dirty, cheap, quick hack
16:15 < OSGuido> for us to show 
16:15 < kanzure> it's possible to do a dirty, quick cheap hack that does not use thermal convective flows
16:15 < OSGuido> explain
16:16 < kanzure> lightbulb + fan
16:16 < kanzure> spiral
16:16 < OSGuido> It's not obvious to me
16:16 < OSGuido> remember I am not an engineer 
16:17 < kanzure> lightbulbs generate heat
16:17 < OSGuido> yes
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16:17 < fenn> the goal is to raise and lower the temperature about 20 times
16:18 < fenn> the lava amp does this by circulating fluid around in a circle using convection
16:18 < OSGuido> yes
16:18 < fenn> the problem is you don't really have any way of knowing if the fluid is actually moving or not
16:18 < fenn> however you can simply raise and lower the temperature instead
16:19 < ybit> OSGuido: here: http://web.bryant.edu/~bblais/projects/cycler/
16:19 < OSGuido> the point with the Lava Amp is exactly that, constant temperature
16:19 < ybit> it's not difficult, i have the components here, but i was distracted when i realized that purifying proteins was a little more important
16:20 < kanzure> ybit: these guys are thinking of spending $100k on us
16:20 < kanzure> er, on Rob/Rik
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16:20 < ybit> o.O
16:20 < genehacker_> lava amp?
16:20 < genehacker_> link to convection based thermocycler?
16:20 < genehacker_> do you need a way to tell if it's moving?
16:20 < kanzure> genehacker_: http://heybryan.org/~bbishop/docs/thermocycler.pdf
16:20 < ybit> well, okay, sure.. give fenn and kanzure 100k, that might speed up dev of skdb :)
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16:20 < kanzure> genehacker_: no.
16:21 < kanzure> genehacker_: we can just use another design.
16:21 -!- genehacker_ is now known as genehacker
16:21 < fenn> genehacker_: this is probably quicker for you http://adl.serveftp.org/papers/unsorted/A%20Pocket-Sezied%20Convective%20PCR%20Thermocycler.pdf
16:21 < genehacker> if you do, I have some Ideas
16:21 < kanzure> we don't have to
16:21 < kanzure> just use a good design instead
16:21 < fenn> supposedly they used fluorescent tracer beads
16:22  * kanzure doesn't have any 10micron beads laying around
16:22 < genehacker> that means they had to have a camera or something to track the beads
16:22 < fenn> well you don't have any Taq polymerase and NTP's laying around either
16:22 < OSGuido> not reallyisn't this device slow compared to the Lava Amp?
16:22 < genehacker> correct?
16:22 < OSGuido> you actually have to wait until temp drops
16:22 < fenn> OSGuido: i think it needs a fan
16:23 < OSGuido> if I am understanding this well
16:23 < OSGuido> but you go ON-OFF
16:23 < OSGuido> right?
16:23 < fenn> also it's too large
16:23 < genehacker> aren't you guys going to sell this as a kit or something?
16:23 < OSGuido> yes, too large too
16:23 < ybit> yeah, it's slower than a commercial unit
16:23 < genehacker> if you're sell it as a kit you don't need to worry about speed
16:23 < genehacker> if this is for the military you do 
16:23 < OSGuido> then the Lava Amp is better, the paper says it can amplify in 20-30 min, depending on amp. size
16:23 < fenn> OSGuido: the light bulb turns on and off to maintain a constant temperature, but it also switches between different temperatures throughout the cycle
16:24 < fenn> 20-30min is fast?
16:24 < OSGuido> and it's mnot like the Lava Amp is expensive
16:24 < fenn> you're throwing tens of thousands of dollars at it
16:25 < OSGuido> in my lab, a commercial, peltier based device can take  up to 3 hours
16:25 < fenn> that's just stupid
16:25 < OSGuido> most of the time is going up and down
16:25 < OSGuido> so, I guess this means you cannot/won't help us
16:25 < kanzure> not at all..
16:26 < OSGuido> Ok
16:26 < kanzure> honestly 20-30 minutes is not fast
16:26 < OSGuido> compared to what?
16:26 < OSGuido> the bulb device is much slower
16:27 < OSGuido> commercial devices (or at least the ones I have worked with) can take up to 2-3 hours
16:27 < OSGuido> that was one of the reasons I liked the Lava Amp
16:28 < fenn> the machine i used (basically a light bulb with capillary tubes) "1605 ATC, Air Thermocycler This first of it's kind machine held 48 sample tubes, four cycle programs and was able to complete 30 cycles in less than 20 minutes"
16:28 < OSGuido> how big is it?
16:28 < fenn> shoe box sized
16:28 < OSGuido> too big
16:29 < fenn> you're just being contrary
16:29 < OSGuido> have you seen how big was the Lava Amp?
16:29 < OSGuido> I am not being contrarian, please stop assuming stuff
16:30 < fenn> how do you load samples into the lava amp tube?
16:30 < OSGuido> that's a problem that we have to solve
16:31 < kanzure> what's wrong with making a smaller Air Thermocycler?
16:31 < OSGuido> I was thinking special shaped pipette tips
16:31 < OSGuido> do you have a pic of the working device? can it be as small as a Lava Amp?
16:32 < OSGuido> let me tell you what I have in mind, my ideal device
16:32 < OSGuido> so tiny that you can connect it to a USB port, and it will let you know when the amplification is done
16:33 < OSGuido> no moving parts
16:33 < OSGuido> Lava Amp is small enough for that, and, IIRC, you can draw enough power from an USB port to fuel the thing
16:33 -!- nchaimov [n=cowtown@c-24-21-45-17.hsd1.wa.comcast.net] has quit [Read error: 104 (Connection reset by peer)]
16:34 < fenn> you will need a microcontroller to negotiate 500mA from the port
16:34 -!- nchaimov [n=cowtown@c-24-21-45-17.hsd1.wa.comcast.net] has joined #hplusroadmap
16:34  * ybit is curious why 16:30 <genehacker> kanzure really needs to do this in a private channel
16:34 < fenn> since you need a microcontroller anyway, might as well use it to do real temperature control of the aluminum bars
16:34 < ybit> er, whoops
16:35 < ybit> um, anyway, i was curious why tenth value thickness isn't on wikipedia
16:35 < fenn> instead of the hacky "insert screws with different thermal conductivities"
16:35 < OSGuido> sure, for the final device we need that
16:35 < OSGuido> but now we want the prototype
16:36 < OSGuido> I was thinking (and, again, I am not an engineer, so please understand)
16:37 < OSGuido> maybe two or three other heaters, so the machine is programmable from your laptop, or even from your cellphone
16:37 < OSGuido> if you connect batteries to it
16:37 < fenn> kanzure: do you remember the nasa study on energy per kilogram removed vs precision?
16:38 < kanzure> no :(
16:38 < OSGuido> temp 1= 95, temp 2= 65 temp 3= 72
16:38 < OSGuido> whatever
16:39 < OSGuido> is this feasible? possible? could you do it with the Air Amp?
16:41 < kanzure> fenn: thermodynamic analysis of manufacturing processes
16:42 < fenn> OSGuido: the lightbulb would use too much power to run on batteries i think
16:42 < OSGuido> yes
16:42 < OSGuido> that's another reason I prefer the Lava Amp, not a lot of power
16:42 < fenn> OSGuido: have you seen the microfluidic spiral thermocycler?
16:43 < OSGuido> no, I'd like to see it please
16:43 < fenn> it's basically the same idea but instead of a circle around a bar, it's a spiral on a flat plate
16:43 < fenn> there are 3 temperature controlled zones
16:44 < OSGuido> OK
16:44 < OSGuido> is there any major difference?
16:44 < drazak_> xp_prg: still want a biology lesson?>
16:45 < drazak_> xp_prg: also I suggest taht you get a biochem book from kanzure
16:45 < fenn> OSGuido: it doesn't rely on convection flow, teflon tubing, and bypasses the whole sample loading issue
16:45 < drazak_> xp_prg: or a molecular biology book, since that's more what you're looking at doing, but most biochemistry books cover molecular biology in some form or another, even if they don't call it that
16:45 < drazak_> kanzure: do you know if you have any actual molecular biology books?
16:46 < kanzure> yes
16:46 < OSGuido> so, how do you move the sample through the zones?
16:46 < drazak_> kanzure: could you email me some or put someon adl.serveftp.org or somewhere else I can get them at more than 10kb/s?
16:46 < ybit> drazak_: http://adl.serveftp.org/papers/unsorted/Molecular%20Biology%20and%20Genomics%20(Elsevier,%202007).pdf
16:46 < fenn> OSGuido: either gravity or a pump of some sort
16:46 < ybit> i grabbed that from bioxplorere.com
16:46 < kanzure> drazak_: http://heybryan.org/books/Biology/
16:46 < ybit> bioxplorer*
16:47 < fenn> OSGuido: there are a lot of ways to generate fluid motion.. i'm not an expert in microfluidics
16:47 < drazak_> kanzure: is heybryan not being raped and/or on faster internet
16:47 < kanzure> no :(
16:47 < OSGuido> I'd think that it's easier with no pumps
16:47 < drazak_> kanzure: :(
16:48 < fenn> one possibility is a valvular conduit and a laser to induce rapid boiling
16:48 < OSGuido> but I don't know a lot of microfludis, just thinking from the point of view of my prejudice: As little moving parts as possible
16:48 < OSGuido> too complex, I'd say
16:48 < fenn> bah
16:48 < fenn> you dont even know what i just said
16:48 < fenn> that doesn't mean it's complex
16:49 < OSGuido> Lava Amp has no laser
16:49 < fenn> lava amp is a pain in the ass
16:49 < OSGuido> so, why do we need to add one?
16:49 < OSGuido> OK, I guess we are not really going anywhere here
16:49 < drazak_> kanzure: you need to find a solution to that, as having all that shit publicly availible is useless if it takes 48 hours to download a single book
16:49 < kanzure> guido: a laser is a good idea
16:49 < kanzure> guido: it's a light-emitting diode in many cases
16:49 < OSGuido> so thanks for your time, anyway
16:49 < kanzure> this is one of the cheapest OEM components out there
16:50 < OSGuido> I didn't know you could emit coherent light with such a small thing
16:50 < OSGuido> cool
16:50 < fenn> argh
16:50 < fenn> OSGuido: how old are you, just curious
16:50 < OSGuido> but I still fail to see why would we want that, if we have a proven device that works
16:51 < fenn> from what i've heard nobody has replicated it
16:51 < fenn> i.e. you don't have any device anyway
16:51 < OSGuido> that's what we are trying to do
16:51 < OSGuido> and we need help, obviously
16:51  * fenn wonders if he should be getting paid for providing valuable strategic business advice
16:51 < drazak_> kanzure: you have a couple books that I almost bought
16:51 < drazak_> fenn: :P
16:52 < OSGuido> well, I talked to Bryan in private and we offered to do just that
16:52 < OSGuido> and that's why I am here
16:52 < kanzure> yes but we have some better ideas
16:53 < OSGuido> on what criteria are they better?
16:53 < OSGuido> faster, cheaper, smaller, simpler, sturdier, all of that at the same time?
16:53 < fenn> OSGuido: ok, i just don't like the lava amp because it's hard to load, not obvious how to manufacture in quantity, poor temperature and process control in general..
16:53 < drazak_> OSGuido: listen man, it seems like someone had an idea, did it, it worked, and then no more thought was put into it
16:54 < Joseph> Well Nitin 
16:54 < OSGuido> Cool, fenn. 
16:54 < fenn> OSGuido: "faster, cheaper, smaller, simpler, sturdier, all of that at the same time?" yes i'd say so
16:54 < Joseph> did have lots of thoughts to improve
16:54 < Joseph> but he graduated and left
16:54 < Joseph> haha
16:54 < Joseph> We've got him involved to address all this
16:54 < fenn> maybe you don't feel like switching gears at this point though
16:54 < drazak_> kanzure: 1 day 7 hours to download 10 files from heybryan :(
16:54 < kanzure> drazak_: yeah I suck
16:55 < OSGuido> The bulb is not better, based on that. And I fail to see why the spiral is better, other than the loading
16:55 < fenn> lots of emotional and financial investment to be overcome :P
16:55 < fenn> the spiral has a fixed number of cycles
16:55 < OSGuido> no emotional, I did not invent the thing. To me it is all the same, I just want it to work and be cheap enough for a poor kid in my country
16:55 < drazak_> kanzure: you do :(
16:56 < kanzure> maybe if you'd all stop raping my server for a few minutes..
16:56 < fenn> kanzure: the only thing raping your server is a robot with tentacles
16:56 < drazak_> kanzure: I'm only slightly raping it, a grand total of 10kb/s is not rape
16:56 < fenn> no offence drazak
16:56 < drazak_> OSGuido: have you actually done pcr?
16:57 < OSGuido> yes, I have, years of it
16:57 < drazak_> OSGuido: so how much lab experience do you really have?
16:57 < OSGuido> several years. I have a degree in biology
16:58 < OSGuido> and we have undergrad theses here
16:58 < drazak_> could you be more specific? for example, 2 years in a such and such lab, a year in a such and such lab, and 3 years in a such and such lab
16:58 < drazak_> 4 years of biology as an undergrad means you've done pcr like 10 times
17:00 < OSGuido> You do not know the kind of lab experience we have here, or how long I have worked on my current lab., so, again, please, stop assuming things
17:00 < drazak_> which is why I asked you to be more specifc
17:00 < OSGuido> as I said, we have undergrad theses here
17:01 < drazak_> what the hell does that mean?
17:01 < kanzure> fenn and I were just wondering that
17:01 < fenn> i think this is a language issue
17:01 < OSGuido> I am here since 2002, having worked in PCR, ELISA, western blots, restriction enzymes
17:01 < OSGuido> during the years
17:01 < drazak_> how much of everything have you done?
17:01 < OSGuido> my lab has produced plenty of papers in our field
17:01 < kanzure> drazak_: why are you asking?
17:02 < drazak_> kanzure: just curious
17:02 < drazak_> OSGuido: well then what lab are you in, I'll pubmed you?
17:02 < OSGuido> And I have done plenty of SDS_PAGE, agarose gels, DNA purification, mostly from bacteria
17:03 < OSGuido> I have no papers yet. My adviser is Concepción JL
17:03 < OSGuido> Parasite ENzymology Lab.
17:04 < fenn> http://adl.serveftp.org/papers/unsorted/Continuous_Flow_Thermal_Cycler_Microchip_for_DNA_Cycle_Sequencing.pdf
17:04  * fenn actually looks at the paper now
17:05 < fenn> uh, so i guess that wasn't the paper i was thinking of
17:07 < OSGuido> OK, these devices coupled to pumps, actually have an advantage
17:08 < OSGuido> you could couple the thing to a detector, and perform multiple PCR pretty much like a flow chart, based on the results of the PCR
17:08 < kanzure> gkm389
17:08 < kanzure> it's somewhere on: http://heybryan.org/books/papers/microfluidics/
17:09 < OSGuido> great for barcoding with no sequencing
17:09 < QuantumG> http://tiltedtwister.com/sudokusolver.html
17:09 < kanzure> aha
17:09 < kanzure> http://heybryan.org/books/papers/microfluidics/gkm389%20Miniaturized%20PCR%20chips%20for%20nucleic%20acid%20amplification%20and%20analysislatest%20advances%20and%20future%20trends.pdf
17:09 < kanzure> there you go
17:10 < OSGuido> but, I wonder if we could not do the same with Lava Amp, and pumps, as the DNA would have to be from the original sample, not extracted from the loops
17:14 < xp_prg> what is the stuff that is used to plate petri dishes so the cells grow?
17:15 < drazak_> xp_prg: what stuff?
17:15 < xp_prg> you like auto clave it then poor it into a petri dish then use a write to spread the cells on it
17:16 -!- superkuh [n=hukrepus@unaffiliated/superkuh] has quit [Connection timed out]
17:16 < xp_prg> write = wire
17:16 < drazak_> xp_prg: LB broth
17:16 < xp_prg> I think it is powdered agar
17:17 < kanzure> there are many types of growth media
17:17 < drazak_> xp_prg: oh, yeah, you can use agar
17:17 < drazak_> xp_prg: that's for plates
17:17 < drazak_> xp_prg: ie. solid cultures, lb broth is for liquid culture, those are both media for bacteria, IE. e.coli
17:18 < genehacker> superkuh was here?
17:18 < xp_prg> ok right we used plates
17:19 < genehacker> pumps present a problem
17:19 < genehacker> but only really if we need precise flow control
17:20 < OSGuido> what's the problem? I am not sure how precise it'd had to be, I just think it's possible, but no details
17:21 < genehacker> the problem with pumps is that you need one in the first place
17:21 < drazak_> OSGuido: very precise
17:21 < OSGuido> you put the sample on a central well, pump it from there to other wells, where it is amplifed/not amplified, you get a color, and based on that, the sample from the central well is pumped to otehr wells
17:22 < OSGuido> you could use it to identify bacteria, like you use differential media now
17:23 < OSGuido> amplify the genes that code for metabolic pathways, the flow chart would be the same
17:23 < genehacker> hold on a second
17:23 < genehacker> that sounds complicated
17:23 < OSGuido> I am sure it is not easy, but the first step is having ultra small, not so slow pCR
17:23 < fenn> genehacker: the reason we use a laser is so we dont need a pump
17:23 < drazak_> it would be nice if there was a machine that you could put dna samples into, close the lid, and it has all the reagents inside, that it could transfer accurately
17:24 < genehacker> what sort of laser?
17:24 < fenn> the laser creates a tiny bubble of water vapor, like in an inkjet print cartridge
17:24 < drazak_> ultimately, if I had my own perfect lab, I'd want that
17:24 < fenn> genehacker: you can actually use the lasers from cd-r drives
17:24 < genehacker> infrared?
17:24 < fenn> ya
17:24 < drazak_> fenn: how do you cool the laser?
17:24 < genehacker> no need drazak
17:24 < drazak_> fenn: er, cool the sample with the laser?
17:24 < drazak_> just air cool the sample?
17:24 < drazak_> seems like a slow way to do it
17:24 < fenn> drazak_: the total energy going in is miniscule
17:25 < fenn> it's actually quite efficient
17:25 < OSGuido> If you'd use trehalose based reagents, it solves the problem of reagetns and storage
17:25 < genehacker> is this droplet microfluidics or channel microfluidics?
17:25 < OSGuido> just add the sample in a pproper dilution, but trehalose is expensive
17:25 < fenn> either i guess
17:25 < fenn> i'm sort of concerned about contamination when reusing microfluidics
17:25 < OSGuido> that's a big concern, yes
17:26 < fenn> but water-in-oil emulsion would reduce contamination i think
17:26 < OSGuido> even more given that PCR is so sensitive
17:26 < drazak_> fenn: ok, so you get your sample up to 94C for denaturing, then you wait for it to cool to 60C, and then how do you hold it at 60C with the laser?
17:26 < genehacker> fenn there are many approaches to avoiding contamination
17:27 < fenn> the laser doesn't heat the sample, it's just for pumping it around
17:27 < drazak_> ah
17:27 < drazak_> I missed that part
17:27 < genehacker> wouldn't it be better to use heating elements in the channel?
17:27 < genehacker> lasers need optics
17:27 < OSGuido> you use it to move the sample through temperature zones
17:27 < OSGuido> at a fixed temp, 
17:27 < fenn> the heating would probably be done by a resistor pressed against the glass (polycarbonate)
17:28 < fenn> OSGuido: right
17:28 < genehacker> then why not uses the resistors to move the fluid around?
17:28 < OSGuido> that's what Lava Amp does
17:28 < genehacker> ok
17:28 < fenn> the laser advances material by a certain amount each time so you can control the speed of movement
17:29 < OSGuido> has anyone here based with trehalose-nbased PCR reagents?
17:29 < genehacker> anyway why not use a serpentine channel with heat at one end of the serpentine and cold at the other like one professor here is doing?
17:29 < xp_prg> is it even possible to purchase a microfluidics chip anywhere at all?
17:30 < genehacker> yes
17:30 < genehacker> xp_prg you can purchase microfluidic lego blocks
17:30 < genehacker> as they are called
17:31 < genehacker> I don't understand what you want to acomplish
17:31 < xp_prg> synthetic biology on a microfluidic basis
17:33 < genehacker> do you want to amplify a sample or sample from a central well and do tests on the sample?
17:33 < OSGuido> genehacker: me? portable barcoding without sequencing
17:33 < genehacker> ok
17:33 < genehacker> that clarifies things
17:33 < fenn> OSGuido: here's the laser pump i'm talking about http://www.fluimedix.com/gfx/LASER DRIVEN MICROPUMP.pdf
17:33 < OSGuido> let's assume you have a totally unknown sample
17:34 < OSGuido> you do not even know if it's bacteria or eucariotic 
17:34 < xp_prg> I want to implement chemical pathways using cells to achieve novel goals
17:34 < xp_prg> I also want to transform cells
17:34 < OSGuido> you make a PCR for let's say hystones. No amp? Bacteria. Amplification? well, many things are possible
17:35 < genehacker> so figure out what's making you sick basically?
17:35 < OSGuido> then if hystone positive, you perform PCR for Rubisco
17:35 < OSGuido> negative? not a plant
17:36 < OSGuido> genehacker: That's a potential use, but many others are possible, educational devices are possible 
17:36 -!- embraceunity [n=quassel@74.94.105.238] has joined #hplusroadmap
17:36 < genehacker> so do you want a device that does everything or one thing?
17:36 < kanzure> hey embraceunity 
17:36 < embraceunity> yo
17:37 < OSGuido> hey there!
17:38 < OSGuido> well, that's a bit far away. For now, I want small, fast, cheap PCR. Open and hackable. Then, many devices will be possible
17:38 < OSGuido> my main concern is detection
17:38 < OSGuido> but you could use a reaction that with inorganic phosphate in the medium, turns of a certain colort
17:38 < xp_prg> what about transforming cells and chemical pathways?
17:39 < OSGuido> so, no amplification, no color
17:39 < OSGuido> xp_prg: I do not understand
17:39 < genehacker> so a simple device that's small and preforms PCR? so small that it's on or off a chip?
17:40 < OSGuido> something like that
17:40 -!- superkuh [n=hukrepus@unaffiliated/superkuh] has joined #hplusroadmap
17:40 < genehacker> hello superkuh
17:40 < genehacker> microfluidics isn't very hackable
17:40 < superkuh> Hello.
17:41 < genehacker> so that might be out of the question
17:41 < OSGuido> not yet
17:41 < genehacker> well no one has a way to make GOOD microfluidics in their own home
17:41 < OSGuido> first step towards it: PCR in a device small enough to hook it up directly to an USB port
17:42 < OSGuido> you could have generic devices, you could load primers
17:42 < fenn> genehacker: what's wrong with laser printer on overhead sheets, then fed through a laminator?
17:43 < OSGuido> different primers, on different wells, and program the thing to tell the PCR order
17:43 < genehacker> the problem with good microfluidics is that they are made from EXPENSIVE chromium coated borosilicate glass used to make masks for microchips
17:43 < fenn> oh poo poo
17:43 < genehacker> can't make something from borosilicate that way
17:43 < fenn> it's just photographic reduction
17:44 < OSGuido> so, you buy the thing, blank, load the primers and program it, load a pre made program and run it
17:44 < genehacker> well if we could get the borosilicate, etchants, and photoresist we could try that maskless lithography thing
17:44 < genehacker> ok
17:45 < OSGuido> modify the program to your needs, if you have different primers or so
17:45 < genehacker> so first off list the tasks that need to be preformed 
17:45 < fenn> borosilicate is used because it tolerates heat shock better.. we won't be doing any heat shock
17:46 < OSGuido> 1 PCR; 2 Amp. detection; 3 Moving the sample to different wells; 4 programmable
17:47 < genehacker> what chemicals are needed needed?
17:47 < drazak_> OSGuido: so you want a qrt-pcr microfluidics machine
17:48 < genehacker> the problem is that most microfluidic devices are one-shot deals
17:48 < genehacker> its hard to clean microfluidics channels
17:49 < OSGuido> PCR reaction mix. And some substance that react with phosphate and gets coloured
17:49 < kanzure> that's only if you're using a bad surface material
17:49 < fenn> kanzure: even for PCR?
17:49 < genehacker> amp. detection
17:49 < genehacker> what is that?
17:49 < kanzure> I'd check to see if they were using special materials in the spiral PCR paper
17:49 < fenn> originally i thought the lava amp was a tube wrapped around some heaters 20 times, in a spiral
17:50 < fenn> that's not such a terrible idea is it?
17:50 < genehacker> just hot embossed PC?
17:50 < genehacker> remove question mark
17:50 < OSGuido> amplification detection
17:50 < genehacker> any solvents?
17:50 < OSGuido> no, not a tube wrapped in spiral 20 times
17:51 < genehacker> do any processes involve solvents?
17:51 < OSGuido> just a simple loop around a heater with different temperatures
17:52 < OSGuido> genehacker: I do not think so, but again, my idea is not very specific, I haven't thogut a lot about details
17:53 < OSGuido> just the general process
17:53 < fenn> how do you make sure that it spends enough time at each temperature, with convection?
17:53 < genehacker> It would be nice if you could give me the reagents that need to go in each process that would be nice
17:54 < OSGuido> I don't know. That's a really good question. some reactions need more time on the annealing part
17:54 < genehacker> give me the reagents necessary for 1, 2, and 3
17:55 < OSGuido> but I thought that baybe a loop with one of the sides wrapped on itself, like a heater, would allow the sample to be at one temp for longer time
17:56 < genehacker> the reagents don't matter so much as the number of reagents and contamination problems
17:56 < genehacker> that could occur if they got in at a different step
17:57 < genehacker> but for now just need the max number at each step
17:58 < OSGuido> 1: taq, dNTPs, target DNA, ATP, primers and Mg+2
17:58 < genehacker> number of reagents determines the number of reagent inputs from there we can start designing the thing
17:58 < OSGuido> 2: a moecule that reacts with the phosphate that is produced by 1 and has a different color when it reacts
17:58 < OSGuido> no, no
17:59 < OSGuido> there is a technique where you solidify all the reagents in trehalose, and you just add the sample in enough buffer to thaw it
17:59 < genehacker> did you just say solidify?
17:59 < OSGuido> let me look for it
17:59 < genehacker> as in something turns to solid
18:00 < genehacker> that presents a problem
18:00 < genehacker> especially if we want something reusable
18:01 < OSGuido> wait a second, please
18:02 < OSGuido> http://www.google.co.ve/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.apczech.cz%2Fpdf%2FpuReTaq_RTG.pdf&ei=EW2USpeiJoOZlAfPr4CsDA&usg=AFQjCNGBr3LnFb3gdCVxNOdomha5kKBbig&sig2=iLqNbI6NLhIVrMggtSyDCA
18:02 < OSGuido> why a problem?
18:02 < genehacker> it makes jams possible
18:02 < genehacker> jams are bad
18:02 < genehacker> it might be hard to remove a jam
18:03 < OSGuido> well, the bead would be waiting at the well
18:03 < OSGuido> you'd just pump the sample with enough buffer
18:03 < genehacker> ok
18:03 < OSGuido> it arrives to the well, where the bead is
18:03 < genehacker> we need to know things like that to design this device
18:03 < OSGuido> it melts, you rise temp, and PCR begins
18:04 < OSGuido> does it makes any sense?
18:04 < genehacker> yeah 
18:05 < OSGuido> good
18:05 < OSGuido> but I think such a device is still far away
18:06 < OSGuido> now, my interest is the PCR, but we do not seem to agree on how to do it
18:06 < genehacker> ok so get step 1 working then move on to the other stuff later
18:07 < genehacker> but  If we are going to make a reusable MF device we should really make it out of something with rigid channels not silicone
18:07 < OSGuido> OK
18:08 < genehacker> some heat resistant would be good too
18:08 < genehacker> so we can autoclave it
18:08 < OSGuido> could you just pump some solution on it and clean it?
18:08 < OSGuido> yes!
18:08 < genehacker> there is one thing you need to remember when you work with microfluidics
18:08 < OSGuido> but I'd be curious to see a programmable device that can stand an autoclave
18:08 < genehacker> low reynolds number
18:09 < OSGuido> no turbulence
18:09 < genehacker> yeah
18:09 < genehacker> because fluid starts to behave like syrup on that scale
18:09 < OSGuido> yes, 
18:10 < genehacker> definately needs testing
18:10 < genehacker> well I have to leave
18:10 < OSGuido> thanks a lot for your help
18:10 < genehacker> hey anytime
18:11 < genehacker> I'd really like to see stuff like this take off
18:11 < OSGuido> talk to you later
18:14 < xp_prg> genehacker I am going to teach a class on synthetic biology, got any pointers on the content of such a class?
18:15 < drazak_> xp_prg: explain to me concisely what synthetic biology is
18:16 < drazak_> xp_prg: if you can't do that you can't teach synthetic biology
18:17 < xp_prg> synthetic biology is the novel use of synthetic dna to solve problems via abstraction, reusability, formal methods, and synthetic design using cells
18:20 < drazak_> do you even know what the means?
18:20 < xp_prg> drazak_ yes I do
18:20 < drazak_> then explain it
18:23 < xp_prg> abstraction:  dna into parts, and standards based connectability, no longer configuring/programming via cagt but actuals parts
18:23 < drazak_> so using codons?
18:25 < xp_prg> resusability:  parts can be used again and in different orders and possibly in different cells
18:25 < xp_prg> drazak_ in how they connect together and codons yes
18:25 < drazak_> er
18:25 < drazak_> you don't even know what you're talking about
18:25 < drazak_> you aren't qualified to teach a class on synthetic biology
18:26 < xp_prg> formal methods:  like biomodels.net, sbml, a formal way of describing reactions, chemical signaling networks
18:27 < xp_prg> synthetic design:  cell designer, modeling and simulation before raw experimentation
18:28 < xp_prg> what is it you think I don't know?
18:30 < drazak_> you're using terms wrong/out of context
18:30 < drazak_> as if you heard them and then diced it sounded smart, and then decided to use it because it sounded smart
18:30 < xp_prg> drazak_ I understand these concepts well
18:30 < xp_prg> its weird to me you think I am just making this stuff up
18:31 < genehacker> xp_prg are you a professor?
18:31 < drazak_> genehacker: he's a programmer
18:31 < xp_prg> yes I have taught advanced computer science for years
18:31 < genehacker> you aren't a biologist
18:31 < xp_prg> I know
18:31 < genehacker> I'm not a big fan of classes on developing fields
18:31 < xp_prg> wow why not genehacker?
18:32 < drazak_> because people make shit up
18:33 < genehacker> because it's a developing field, the techniques you may be teaching could become obsolete and useless within the next few years as the field develops
18:34 < genehacker> learned that from the guy who heads up zyvex
18:38 < xp_prg> but you have to start somewhere
18:38 < xp_prg> its an exciting field, get used to this approach as cutting edge technologies are not the exception anymore but the rule
18:38 < genehacker> yeah
18:38 < genehacker> the best place to start would be in biology
18:38 < xp_prg> I don't mind being partially wrong as long as I am "mostly" right
18:39 < xp_prg> which I believe I am 
18:39 < drazak_> xp_prg: you're not mostly right though
18:39 < drazak_> xp_prg: you need to learn some biology
18:39 < xp_prg> where have you seen me be mostly wrong?
18:39 < genehacker> I don't believe I'm right
18:39 < genehacker> I believe I need to go eat dinner
18:40 < xp_prg> drazak_ ?
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18:45 < drazak_> xp_prg: because I said codon you started using it, you don't know shit about the bench work part of this, reusing plasmids is very hard to do, you'd never be able to purify them(unless it's from e.coli, and the plasmid has a gene for antibiotic resistence), you didn't know about primers for pcr, and you don't know about the mechanism by which transcription happens, designing a cell with current tools is impossible
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18:48 < genehacker> I don't know either
18:48 < xp_prg> a codon is the section of a gene that is used as a primer or a stop
18:48 < xp_prg> commonly called start/stop codon
18:48 < xp_prg> I do know what that is!
18:48 < genehacker> how long is a codon?
18:49 < xp_prg> I am not reusing plasmids, I am reusing bio brick parts which are genes
18:49 < xp_prg> I believe it is 3 bp
18:49 < xp_prg> could be a variable length
18:49 < xp_prg> depending on the gene
18:50 < xp_prg> yes I am fully aware of ampicillin and its use in wetware benchwork for killing those cells that do not get the new gene as part of a synthetic biology project
18:50 < xp_prg> primers for pcr are not necessary in synthetic biology
18:50 < xp_prg> *sigh* have you seen my diybio experiment video?
18:50 < xp_prg> we did all this
18:51 < xp_prg> drazak_ try again, I do know what I am talking about
18:52 < xp_prg> what is it again you think I don't know?
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18:53 < genehacker> well at least teach it with help from a biologist
18:54 < xp_prg> trying to do just that in here :>
18:55 < xp_prg> the diybio-sf group has passed igem meetings
18:56 < xp_prg> igem members I meant to say
18:56 < drazak_> xp_prg: so, codons are only the starts and stops of genese?
18:56 < drazak_> that must be a pretty fucking short gene
18:56 < drazak_> no amino acids if that's the case
18:57 < drazak_> and they aren't primers
18:59 < drazak_> don't worry, I'll wait while you wikipedia codons
19:00 < QuantumG> xp_prg: so does your group have access to a wet lab?
19:00 < xp_prg> yes!
19:00 < QuantumG> then you're one up on me.
19:00 < xp_prg> where are you located?
19:00 < QuantumG> australia :(
19:00 < drazak_> hm, I wonder if anyone is doing synbio at one of the other labs where I work
19:00 < xp_prg> fly out here, you can stay with me for a while till I get tired of you
19:01 < xp_prg> you can stay with me longer if you will teach me things in biology I don't know
19:02 < genehacker> quantumG are you a biologist?
19:03 < QuantumG> nah
19:03 < QuantumG> I did study molecular biology
19:03 < xp_prg> genehacker where are you located?
19:04 < genehacker> Conduct Satellite Hyperion currently stationed at L2
19:05 < drazak_> nobody's doing synbio at UB
19:05 < genehacker> aren't you located in San Franscisco xp_prg?
19:05 < xp_prg> you at university Berkely drazak_ ?
19:06 < xp_prg> no, I live by Stanford
19:07 < genehacker> visit venter's complex sometime for us xp_prg I think it's a bit south of that
19:07 < drazak_> xp_prg: university at buffalo
19:07 < xp_prg> wow cool, will they let me?
19:08 < xp_prg> guess what you guys can join us remotely cuz I am going to make these meetings virtual!
19:08 < xp_prg> I did that at the last meeting
19:08 < drazak_> venter lives in buffalo
19:08 < drazak_> :P
19:08 < genehacker> hehehe
19:08 < xp_prg> drazak_ can I get you to peer review my lesson plan and stuff?
19:08 < genehacker> but he's doing some stuff in california
19:08 < drazak_> xp_prg: uhm, maybe
19:09 < drazak_> xp_prg: you can send them to me if you want
19:09 < xp_prg> sweet thanks man
19:09 < xp_prg> happy to trade your help for like some biopython work you might need in the future
19:10 < drazak_> xp_prg: I get the impression that you don't know how to do what I want in biopython
19:13 < xp_prg> don't underestimate me, put me to the test!
19:13 < xp_prg> what do you need done?
19:13 < kanzure> xp_prg: why are you here
19:14 < xp_prg> cuz I love synthetic biology :)
19:14 < kanzure> that's the wrong answer
19:14 < drazak_> xp_prg: this is a channel for transhumanists
19:14 < drazak_> xp_prg: get off the grass kid
19:14 < xp_prg> heh, there is a transhumanist group at the Tech Shop
19:14 < xp_prg> I met with one of their leaders in my last meeting
19:14 < drazak_> uh huh
19:15 < xp_prg> he requested that I post an article to his magazine so don't front!!!!!!
19:15 < kanzure> oh please
19:15 < kanzure> it was probably james clement
19:15 < kanzure> and hplusmagazine sucks
19:15 < xp_prg> heh it was :>
19:16  * fenn watches television
19:16 < xp_prg> kanzure he mentioned you with great respect
19:16 < xp_prg> it is sad you can't at least reciprocate his good will
19:16 < kanzure> I've already talked with him about his magazine
19:16 < genehacker> xp_prg did you say you were at berkeley?
19:17 < xp_prg> nope by Stanford
19:17 < drazak_> xp_prg: ok, then do this with biopython, look up 20 genes from nucleotide, based on plaintext name and species, download the 20 genes, run the genes through primer3, returning 10 primers for each of the genes with a product length of 100-200nt, and check the primers for hairpins, and then return the acension number of the gene, the length of the product, the primers, and the name of the gene that the ascension number corresponds to
19:17 < genehacker> at stanford?
19:17 < xp_prg> no I live by Stanford
19:17 < fenn> drazak_: you keep getting cut off by your irc client
19:17 < drazak_> fenn: I keep typing really long lines
19:17 < xp_prg> drazak_ ok :>
19:18 < drazak_> fenn: it's actually a standard message length at the server that the client respects
19:18 < xp_prg> drazak_ thanks for giving me an opportunity to show you what I can do
19:18 < genehacker> drazak just curious what do hairpins do?
19:18  * parolang wonders why it seems that no IRC client is smart enough to cut up a long post into multiple posts.
19:18 < drazak_> genehacker: they make it harder to denature the primers
19:18 < genehacker> ok
19:19 < xp_prg> drazak_ I will make the solution opensource
19:20 < drazak_> xp_prg: just do it
19:21 < QuantumG> parolang: xchat does
19:21 < parolang> QuantumG: I stand corrected.
19:22 < QuantumG> it can be annoying if you accidentally paste something large
19:23 < parolang> QuantumG: Then the client should prompt you with a "are you sure?" if the post is greater than n characters.
19:24 < xp_prg> I am just curious do you like biopython or bioperl more?
19:24 < xp_prg> I hear mostly of bioperl
19:30 < QuantumG> I find it incredibly sickening that large scale biology projects are being done with either.
19:30 < QuantumG> they go on about their super computers and how many petabytes of data they are processing and it all sounds impressive
19:30 < genehacker> but the content is what matters correct?
19:31 < QuantumG> then they casually mention they are using python and it's like "that's why you need a super computer"
19:31 < drazak_> QuantumG: the bioinformatics guy on our floor uses R
19:32 < kanzure> I wish someone at my uni knew what R was.
19:32 < drazak_> I often chat him up about computers and shit
19:34 < xp_prg> what is R?
19:34 < drazak_> it's like C but with statistics shit
19:34 < kanzure> http://r-project.org/
19:36 < xp_prg> kanzure that is not a valid url
19:36 < kanzure> http://www.r-project.org/
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19:41 < xp_prg> hmm... that is not a high speed biology library
19:44 < drazak_> kanzure: do all of pages in http://heybryan.org/books/Biology/Biology%20-%20Protocols%20-%20Current%20Protocols%20in%20Molecular%20Biology.pdf work for you?
19:44 < kanzure> do they render?
19:44 < drazak_> kanzure: most of them render but some of the sections say 404 not found
19:45 < drazak_> kanzure: or rather, access denied
19:45 < drazak_> kanzure: I'm asking if they work for you because if they do I'll go through the vpn for where I work
19:45 < kanzure> yes they render for me
19:46 < drazak_> all of them, if you look down the table of contents?
19:46 < kanzure> I just page-downed through the whole book
19:46 < kanzure> what else do you want me to do?
19:46 < drazak_> nah, that sounds good
19:46 < drazak_> thanks
19:46 < drazak_> I wonder if there's a way to save it so it doesn't ahve to go out to the internet when it loads
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19:46 < kanzure> Sounds like you have a virus.
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19:47 < drazak_> I run linux
19:49 < drazak_> it just says... here look
19:50 < drazak_> http://heybryan.org/books/Biology/Biology%20-%20Protocols%20-%20Current%20Protocols%20in%20Molecular%20Biology.pdf
19:50 < kanzure> what about it?
19:54 < drazak_> well I can't get the pages that that refers to
19:54 < kanzure> just type in the page numbers
19:54 < drazak_> into where?
19:55 < kanzure> your pdf reader
19:55 < drazak_> into what box?
19:55 < drazak_> for the username?
19:55 < kanzure> how do you view pdfs?
19:55 < kanzure> ghostview, kpdf, xpdf, ?
19:55 < drazak_> gnome document reader
19:55 < drazak_> I could use xpdf
19:56 < kanzure> there should be a way to tell it which page number you want to look at
19:56 < drazak_> I actually prefer xpdf, but this is what started by default
19:56 < drazak_> well yeah, but there's no table of contents, and there are sections of pages missing
19:56 < kanzure> can you give me a page number to look at?
19:56 < drazak_> I don't know what page I want to look at, and I'm fairly sure the pages for electrophoretic mobility shift assay are missing
19:56 < drazak_> 212
19:58 < kanzure> ok confirmed
19:58 < kanzure> that's just the way the scraper worked
20:00 < drazak_> is there a way to get those pages, or to delete the ones out of there?
20:00 < kanzure> you can delete them with imagemagick if you want
20:02 < drazak_> I might have someone print it and put it in a few giant binders for me
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20:52 < drazak_> anyone in here know about vpns?
21:11 < xp_prg> I do
21:11 < xp_prg> I just setup a vpn with openvpn
21:11 < xp_prg> how can I help you drazak_ ?
21:14 < drazak_> this is a ciscovpn
21:21 < xp_prg> hmm...
21:22 < xp_prg> well I know the theory, I can try to help you
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21:48 < genehacker> superkuh didn't you try to make tamiflu?
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23:23 < genehacker_> http://nextbigfuture.com/
23:23 < genehacker_> Jurassic Park for reals
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