| --- Day changed Tue Aug 25 2009 | ||
| genehacker | is it that heat on the brain thing | 00:01 |
|---|---|---|
| genehacker | my airconditioning unit maintenance needs | 00:02 |
| genehacker | errr... this is bad | 00:08 |
| genehacker | I can see other people's file on the appserver | 00:08 |
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| kanzure | this looks like an interesting journal: "journal of reducing space mission cost" | 11:07 |
| 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" | 11:14 |
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| -!- Irssi: #hplusroadmap: Total of 30 nicks [0 ops, 0 halfops, 0 voices, 30 normal] | 11:26 | |
| ybit | http://c2.com/cybords/ | 11:38 |
| ybit | http://www.c2.com/cgi/wiki?ReciprocalityTheory | 11:38 |
| ybit | mostly cybords | 11:38 |
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| kanzure | xp_prg: can you please stop sending me two word emails? | 12:42 |
| xp_prg | ok, like what? | 12:49 |
| kanzure | like "Wow awesome!" | 12:52 |
| kanzure | don't send me that. | 12:52 |
| xp_prg | ok | 12:52 |
| xp_prg | I have an initial lesson plan for biopython from someone who teached it! | 12:53 |
| drazak_ | I know a little biopython | 12:54 |
| xp_prg | tell me how you use it and stuff | 12:54 |
| drazak_ | make primers | 12:55 |
| drazak_ | lulz | 12:55 |
| drazak_ | not that I ever got my script to work | 12:55 |
| drazak_ | but that's not because of biopython, it's because I don't know python | 12:56 |
| xp_prg | what is a primer? | 13:29 |
| 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 | 13:34 |
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| ybit | kanzure: did you ever write a script to extract the title of a pdf and rename the file? | 13:40 |
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| xp_prg | drazak_ is that right? | 14:00 |
| xp_prg | I was right! | 14:01 |
| drazak_ | no | 14:01 |
| drazak_ | it isn't right | 14:01 |
| 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 | 14:02 |
| 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? | 14:03 |
| 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? | 14:04 |
| drazak_ | I never said it was? | 14:05 |
| drazak_ | I was saying I used biopython to make primers | 14:06 |
| drazak_ | well, design primers | 14:06 |
| xp_prg | oh ok | 14:06 |
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| 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 | 14:08 |
| 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 | 14:09 |
| 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 | 14:10 |
| 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 | 14:11 |
| 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? | 14:12 |
| 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? | 14:13 |
| drazak_ | er | 14:15 |
| drazak_ | what's wrong mean? | 14:15 |
| drazak_ | what would cause it not to go into the gene? | 14:15 |
| drazak_ | also: depending on how you made the plasmid, it may not be a plasmid without the gene | 14:16 |
| xp_prg | well the cell membrane may not have the right receptor to allow the transcription factor in | 14:17 |
| 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? | 14:18 |
| 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 | 14:19 |
| 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 | 14:20 |
| 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 | 14:21 |
| 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 | 14:22 |
| 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 | 14:23 |
| xp_prg | but can't a protein enter a cell via endocytosis and bind to a promoter region of a gene? | 14:24 |
| parolang | /j #php | 14:25 |
| kanzure | ybit: look around for renamepdf.py | 14:28 |
| xp_prg | drazak_ ? | 14:32 |
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| novaxian | hello | 15:12 |
| -!- 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 :) | 15:13 |
| 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 | 15:14 |
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| novaxian | hello | 15:21 |
| novaxian | anyone here work with thermophilc bacteria? | 15:21 |
| 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 | 15:23 |
| kanzure | hello novaxian | 15:26 |
| drazak_ | novaxian: like the bacteria taq polymerase is from? | 15:27 |
| novaxian | drazak ill look into that | 15:29 |
| novaxian | afk | 15:29 |
| drazak_ | it's like thermophilus aquarius | 15:29 |
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| genehacker | did somebody say thermophilic bacteria? | 15:33 |
| parolang | <novaxian> anyone here work with thermophilc bacteria? | 15:33 |
| genehacker | yeah I know | 15:35 |
| genehacker | kanzure can heekscad make a curve through a given set of points | 15:36 |
| * 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? | 15:37 | |
| kanzure | you will get more if you send the hdd | 15:38 |
| kanzure | ybit: try searching for "rename pdf zotero py" | 15:38 |
| 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? | 15:39 |
| 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 | 15:40 |
| genehacker | you can adjust base radius | 15:41 |
| 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 | 15:42 |
| genehacker | but it makes pretty gear pictures for now | 15:43 |
| genehacker | how do Iadd a website to ubuntu's sudo repository thing? | 15:46 |
| kanzure | do you know what you want to add? | 15:47 |
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| 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? | 15:47 |
| 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 | 15:48 |
| kanzure | http://brlcad.org/~erik/glassbearing.png | 15:50 |
| genehacker | permission denied | 15:50 |
| kanzure | sudo it | 15:50 |
| kanzure | don't forget both >> | 15:50 |
| genehacker | not working | 15:51 |
| 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>" | 15:52 |
| kanzure | since when is maradydd on lifeboat.com? | 15:54 |
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| kanzure | hey guido | 15:56 |
| 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 | 15:57 |
| 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? | 15:58 |
| 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 | 15:59 |
| 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 |
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| 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 | 16:00 |
| 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? | 16:01 |
| ybit | i corrected myself | 16:02 |
| ybit | ty novaxian | 16:02 |
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| ybit | should have been using emacs, poor fella | 16:02 |
| kanzure | well that can't be good | 16:02 |
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| 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 | 16:02 |
| 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? | 16:03 |
| kanzure | paper | 16:04 |
| ybit | if you have citations, i'm all eyes | 16:04 |
| 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 | 16:05 |
| 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 | 16:07 |
| OSGuido | so, | 16:11 |
| 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 | 16:12 |
| 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 | 16:15 |
| 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 | 16:16 |
| kanzure | lightbulbs generate heat | 16:17 |
| OSGuido | yes | 16:17 |
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| fenn | the goal is to raise and lower the temperature about 20 times | 16:17 |
| 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 | 16:18 |
| 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 | 16:19 |
| kanzure | ybit: these guys are thinking of spending $100k on us | 16:20 |
| kanzure | er, on Rob/Rik | 16:20 |
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| 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 :) | 16:20 |
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| kanzure | genehacker_: no. | 16:20 |
| kanzure | genehacker_: we can just use another design. | 16:21 |
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| 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 | 16:21 |
| * 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 | 16:22 |
| 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 | 16:23 |
| 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 | 16:24 |
| 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.. | 16:25 |
| 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 | 16:26 |
| 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 | 16:27 |
| 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 | 16:28 |
| 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 | 16:29 |
| fenn | how do you load samples into the lava amp tube? | 16:30 |
| OSGuido | that's a problem that we have to solve | 16:30 |
| 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? | 16:31 |
| 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 | 16:32 |
| 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 |
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| fenn | you will need a microcontroller to negotiate 500mA from the port | 16:34 |
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| * 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 | 16:34 |
| 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 | 16:35 |
| OSGuido | I was thinking (and, again, I am not an engineer, so please understand) | 16:36 |
| 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? | 16:37 |
| kanzure | no :( | 16:38 |
| OSGuido | temp 1= 95, temp 2= 65 temp 3= 72 | 16:38 |
| OSGuido | whatever | 16:38 |
| OSGuido | is this feasible? possible? could you do it with the Air Amp? | 16:39 |
| kanzure | fenn: thermodynamic analysis of manufacturing processes | 16:41 |
| 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? | 16:42 |
| 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 | 16:43 |
| OSGuido | OK | 16:44 |
| OSGuido | is there any major difference? | 16:44 |
| drazak_ | xp_prg: still want a biology lesson?> | 16:44 |
| 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? | 16:45 |
| 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* | 16:46 |
| 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: :( | 16:47 |
| 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 | 16:48 |
| 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 | 16:49 |
| 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 | 16:50 |
| 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 | 16:51 |
| 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 | 16:52 |
| 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 | 16:53 |
| 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 | 16:54 |
| 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 :( | 16:55 |
| 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? | 16:56 |
| 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 | 16:57 |
| 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 | 16:58 |
| 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 | 17:00 |
| 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? | 17:01 |
| 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 | 17:02 |
| OSGuido | I have no papers yet. My adviser is Concepción JL | 17:03 |
| OSGuido | Parasite ENzymology Lab. | 17:03 |
| 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 | 17:04 | |
| fenn | uh, so i guess that wasn't the paper i was thinking of | 17:05 |
| OSGuido | OK, these devices coupled to pumps, actually have an advantage | 17:07 |
| 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/ | 17:08 |
| 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 | 17:09 |
| 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 | 17:10 |
| xp_prg | what is the stuff that is used to plate petri dishes so the cells grow? | 17:14 |
| 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 | 17:15 |
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| xp_prg | write = wire | 17:16 |
| drazak_ | xp_prg: LB broth | 17:16 |
| xp_prg | I think it is powdered agar | 17:16 |
| 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 | 17:17 |
| genehacker | superkuh was here? | 17:18 |
| xp_prg | ok right we used plates | 17:18 |
| genehacker | pumps present a problem | 17:19 |
| genehacker | but only really if we need precise flow control | 17:19 |
| 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 | 17:20 |
| 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 | 17:21 |
| OSGuido | you could use it to identify bacteria, like you use differential media now | 17:22 |
| 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 | 17:23 |
| 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 | 17:24 |
| 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 | 17:25 |
| 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 | 17:26 |
| 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) | 17:27 |
| 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 | 17:28 |
| 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? | 17:29 |
| genehacker | yes | 17:30 |
| genehacker | xp_prg you can purchase microfluidic lego blocks | 17:30 |
| genehacker | as they are called | 17:30 |
| genehacker | I don't understand what you want to acomplish | 17:31 |
| xp_prg | synthetic biology on a microfluidic basis | 17:31 |
| 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 | 17:33 |
| 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 | 17:34 |
| 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 | 17:35 |
| OSGuido | genehacker: That's a potential use, but many others are possible, educational devices are possible | 17:36 |
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| genehacker | so do you want a device that does everything or one thing? | 17:36 |
| kanzure | hey embraceunity | 17:36 |
| embraceunity | yo | 17:36 |
| OSGuido | hey there! | 17:37 |
| 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? | 17:38 |
| 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? | 17:39 |
| OSGuido | something like that | 17:40 |
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| genehacker | hello superkuh | 17:40 |
| genehacker | microfluidics isn't very hackable | 17:40 |
| superkuh | Hello. | 17:40 |
| 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 | 17:41 |
| 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? | 17:42 |
| 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 | 17:43 |
| 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 | 17:44 |
| 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 | 17:45 |
| OSGuido | 1 PCR; 2 Amp. detection; 3 Moving the sample to different wells; 4 programmable | 17:46 |
| genehacker | what chemicals are needed needed? | 17:47 |
| drazak_ | OSGuido: so you want a qrt-pcr microfluidics machine | 17:47 |
| genehacker | the problem is that most microfluidic devices are one-shot deals | 17:48 |
| genehacker | its hard to clean microfluidics channels | 17:48 |
| 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 | 17:49 |
| 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 | 17:50 |
| genehacker | do any processes involve solvents? | 17:51 |
| OSGuido | just a simple loop around a heater with different temperatures | 17:51 |
| OSGuido | genehacker: I do not think so, but again, my idea is not very specific, I haven't thogut a lot about details | 17:52 |
| 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 | 17:53 |
| 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 | 17:54 |
| 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 | 17:55 |
| 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 | 17:56 |
| genehacker | but for now just need the max number at each step | 17:57 |
| 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 | 17:58 |
| 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 | 17:59 |
| genehacker | that presents a problem | 18:00 |
| genehacker | especially if we want something reusable | 18:00 |
| OSGuido | wait a second, please | 18:01 |
| 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 | 18:02 |
| 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 | 18:03 |
| OSGuido | does it makes any sense? | 18:04 |
| genehacker | yeah | 18:04 |
| OSGuido | good | 18:05 |
| OSGuido | but I think such a device is still far away | 18:05 |
| 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 | 18:06 |
| 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 | 18:07 |
| 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 | 18:08 |
| OSGuido | no turbulence | 18:09 |
| genehacker | yeah | 18:09 |
| genehacker | because fluid starts to behave like syrup on that scale | 18:09 |
| OSGuido | yes, | 18:09 |
| 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 | 18:10 |
| genehacker | I'd really like to see stuff like this take off | 18:11 |
| OSGuido | talk to you later | 18:11 |
| xp_prg | genehacker I am going to teach a class on synthetic biology, got any pointers on the content of such a class? | 18:14 |
| drazak_ | xp_prg: explain to me concisely what synthetic biology is | 18:15 |
| drazak_ | xp_prg: if you can't do that you can't teach synthetic biology | 18:16 |
| xp_prg | synthetic biology is the novel use of synthetic dna to solve problems via abstraction, reusability, formal methods, and synthetic design using cells | 18:17 |
| drazak_ | do you even know what the means? | 18:20 |
| xp_prg | drazak_ yes I do | 18:20 |
| drazak_ | then explain it | 18:20 |
| 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? | 18:23 |
| 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 | 18:25 |
| xp_prg | formal methods: like biomodels.net, sbml, a formal way of describing reactions, chemical signaling networks | 18:26 |
| xp_prg | synthetic design: cell designer, modeling and simulation before raw experimentation | 18:27 |
| xp_prg | what is it you think I don't know? | 18:28 |
| 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 | 18:30 |
| 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? | 18:31 |
| drazak_ | because people make shit up | 18:32 |
| 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 | 18:33 |
| genehacker | learned that from the guy who heads up zyvex | 18:34 |
| 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 | 18:38 |
| 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 | 18:39 |
| xp_prg | drazak_ ? | 18:40 |
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| 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 | 18:45 |
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| 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? | 18:48 |
| 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 | 18:49 |
| 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 | 18:50 |
| xp_prg | drazak_ try again, I do know what I am talking about | 18:51 |
| xp_prg | what is it again you think I don't know? | 18:52 |
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| genehacker | well at least teach it with help from a biologist | 18:53 |
| xp_prg | trying to do just that in here :> | 18:54 |
| xp_prg | the diybio-sf group has passed igem meetings | 18:55 |
| 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 | 18:56 |
| drazak_ | and they aren't primers | 18:57 |
| drazak_ | don't worry, I'll wait while you wikipedia codons | 18:59 |
| 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 | 19:00 |
| xp_prg | you can stay with me longer if you will teach me things in biology I don't know | 19:01 |
| genehacker | quantumG are you a biologist? | 19:02 |
| QuantumG | nah | 19:03 |
| QuantumG | I did study molecular biology | 19:03 |
| xp_prg | genehacker where are you located? | 19:03 |
| genehacker | Conduct Satellite Hyperion currently stationed at L2 | 19:04 |
| 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_ ? | 19:05 |
| xp_prg | no, I live by Stanford | 19:06 |
| 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? | 19:07 |
| 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 | 19:08 |
| 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 | 19:09 |
| drazak_ | xp_prg: I get the impression that you don't know how to do what I want in biopython | 19:10 |
| 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 | 19:13 |
| 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 | 19:14 |
| 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 :> | 19:15 |
| * 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? | 19:16 |
| 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 :> | 19:17 |
| 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 | 19:18 |
| xp_prg | drazak_ I will make the solution opensource | 19:19 |
| drazak_ | xp_prg: just do it | 19:20 |
| QuantumG | parolang: xchat does | 19:21 |
| parolang | QuantumG: I stand corrected. | 19:21 |
| QuantumG | it can be annoying if you accidentally paste something large | 19:22 |
| parolang | QuantumG: Then the client should prompt you with a "are you sure?" if the post is greater than n characters. | 19:23 |
| xp_prg | I am just curious do you like biopython or bioperl more? | 19:24 |
| xp_prg | I hear mostly of bioperl | 19:24 |
| 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? | 19:30 |
| 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 | 19:31 |
| kanzure | I wish someone at my uni knew what R was. | 19:32 |
| drazak_ | I often chat him up about computers and shit | 19:32 |
| xp_prg | what is R? | 19:34 |
| drazak_ | it's like C but with statistics shit | 19:34 |
| kanzure | http://r-project.org/ | 19:34 |
| xp_prg | kanzure that is not a valid url | 19:36 |
| kanzure | http://www.r-project.org/ | 19:36 |
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| xp_prg | hmm... that is not a high speed biology library | 19:41 |
| 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 | 19:44 |
| 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 | 19:45 |
| 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 | 19:46 |
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| kanzure | Sounds like you have a virus. | 19:46 |
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| drazak_ | I run linux | 19:47 |
| drazak_ | it just says... here look | 19:49 |
| drazak_ | http://heybryan.org/books/Biology/Biology%20-%20Protocols%20-%20Current%20Protocols%20in%20Molecular%20Biology.pdf | 19:50 |
| kanzure | what about it? | 19:50 |
| 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? | 19:54 |
| 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 | 19:55 |
| 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 | 19:56 |
| kanzure | ok confirmed | 19:58 |
| kanzure | that's just the way the scraper worked | 19:58 |
| 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 | 20:00 |
| drazak_ | I might have someone print it and put it in a few giant binders for me | 20:02 |
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| drazak_ | anyone in here know about vpns? | 20:52 |
| 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_ ? | 21:11 |
| drazak_ | this is a ciscovpn | 21:14 |
| xp_prg | hmm... | 21:21 |
| xp_prg | well I know the theory, I can try to help you | 21:22 |
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| genehacker | superkuh didn't you try to make tamiflu? | 21:48 |
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| genehacker_ | http://nextbigfuture.com/ | 23:23 |
| genehacker_ | Jurassic Park for reals | 23:23 |
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