--- Log opened Mon Jul 02 00:00:56 2012
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06:21 <@kanzure> hi
06:38 < nsh> what's new?
06:40 <@kanzure> nsh: did you get arrested again
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06:47 < nsh> no, that was someone's idea of a joke
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06:51 < nsh> kanz, what are you working on currently?
06:52 <@kanzure> i'm working on waking up
06:56 < nsh> i've heard good things about caffeine
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08:44 <@kanzure> "Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense" http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000147
08:44 <@kanzure> "oop-mediated isothermal amplification (LAMP) of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions. In the present study, a LAMP test was designed from the serum resistance-associated (SRA) gene of Trypanosoma brucei rhodesiense, the cause of the acute form of African sleeping sickness, and used to detect parasite DNA from processed and heat-treated infected blood samples."
08:45 < nmz787> what makes the loop?
08:45 < nmz787> helicase or something?
08:53 <@kanzure> there should be a 'phd day' where scientists all upload their own papers
08:55 <@kanzure> hrmm i seem to be banned from the diybio-seattle mailing list
08:55 < nmz787> http://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification
08:55 < nmz787> whatt???
08:55 < nmz787> so lame
08:56 < nmz787> looks like people 'want' a diybio group in portland
09:01 <@kanzure> nmz787: this guy does too Emil Mcdowell <sir.galimore@gmail.com>
09:02 < nmz787> http://diybio.meetup.com/members/us/or/portland/
09:02 < nmz787> the "wanters"
09:28 <@kanzure> https://www.techdirt.com/articles/20120620/07513919403/how-extending-patent-protection-antibiotics-creates-perverse-incentives-to-render-them-useless.shtml
09:28 <@kanzure> also has comments. gah, i linked to techdirt? :(
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10:05 < nmz787> so NYC does not have what I am looking for
10:05 < nmz787> there is no science lounge
10:05 < nmz787> no gathering of minds that happens daily or ad hoc
10:05 <@kanzure> genspace?
10:05 <@kanzure> have you talked with them recently or are they still missing in action?
10:05 < nmz787> not really... emailed with ellen today, but they don't have AC and its hot as hell here
10:06 < nmz787> i on the other hand just got a window AC, so I'm not dying to get out of my apt now
10:06 <@kanzure> no AC?? they certainly charge enough on membership fees to afford it
10:06 < nmz787> i don't think the building is sealed at all for that to work
10:06 < nmz787> at least i dont think they have AC
10:07 < nmz787> you may be overestimating genspace membership, or underestimating NYC costs???
10:07 <@kanzure> probably both
10:07 <@kanzure> i think genspace was charging $300/class and $100/mo?
10:08 < nmz787> yea
10:08 <@kanzure> and i bet running an AC costs maybe $200-$300/mo for that large floor
10:08 < nmz787> i asked if they have ac
10:08 < nmz787> so if they dont have ac, thats a deal breaker for me hanging out there all day on the laptop
10:09 < nmz787> but otherwise seems like they don't really have 'open hours' or meet n greet times
10:09 < nmz787> where you can just go to be social
10:09 < nmz787> which might be because they only really have 1 room thats subdivided
10:10 < nmz787> so things could get bumped or stolen or contammed
10:10 <@kanzure> yeah, doing benchwork without AC is pretty dumb
10:17 < nmz787> well break out the faraday cage for cell phones
10:17 < nmz787> http://en.wikipedia.org/wiki/Power_analysis
10:18 < nmz787> or: "ther countermeasure strategies to reduce the effectiveness of DPA attacks involve hardware modifications: varying the chip internal clock frequency has been considered to desynchronize electric signals, which lead in return to algorithmic enhancements of traditional DPA."
10:18 < nmz787> so CPU freq selector should be goin nuts basically
10:23 < nmz787> genspace has a portable AC in the lab area... which they can turn on and I can sit near... lol
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10:40 < nmz787> WIKIPEDIA IS DOWN
10:41 < superkuh> Back up.
10:41 < nmz787> whew!
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11:04 < nmz787> why is there a term such as NGO??? by the explicit interpretation of the acronym, wouldn't walmart be an NGO???
11:07 < delinquentme> nmz787, probably used alot in government?
11:07 < delinquentme> i mean bc every part of gov is incestuous
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12:02 < nmz787> was first used by U.N.
12:03 < nmz787> basically walmart can have a mayor or something be a shareholder, all the way to a major politican playing a role
12:04 < nmz787> NGOs can be funded none, partially or fully by govt or its entities, but they cannot carry decision biasing
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13:15 <@kanzure> hi shin-to.
13:15 < shin-to> hi there
13:22 < shin-to> sorry not much input from me here yet…just stumbled upon this chan in the channel list and thought i'd lurk in, as I am quite curious in this (even if not that informed yet)
13:23 <@kanzure> okie dokie
13:40 < jmil> kanzure: RepRap video with 3D printed sugar for vascular tissue fabrication: http://www.youtube.com/watch?v=9VHFlwJQIkE
13:52 < ThomasEgi> jmil, bonus points for creating sweets^
13:52 < jmil> :D thanks ThomasEgi
13:55 < nmz787> nice vid!
13:56 < nmz787> so are you flowing endothelial cells in first to make a vascular system, then removing the remaining sugar and filling it in with myocytes or whatever organ you want?
13:57 < ThomasEgi> from what i heared they have no vascular system other than the holes
13:57 < ThomasEgi> so it would be the sugar frame. the actual cells.
13:57 < ThomasEgi> removing the sugar and pumping the liquid rigth through it
13:58 < ThomasEgi> could've misunderstood it tho.
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14:35 < jmil> nmz7872 ThomasEgi there are a few methods we showed in this paper. we DID show that we can line all the vasculature with endothelial cells as they are in the human body. you can see a highlight of that image here: http://news.sciencemag.org/sciencenow/2012/07/a-sweet-way-to-grow-blood-vessel.html?ref=hp
14:35 < jmil> but strictly speaking you don't need the endothelial cells to keep the cells in the bulk gel alive
14:36 < ThomasEgi> in any case. the whole thing is pretty awesome
14:37 < nmz7872> gel?
14:37 < nmz7872> don't they start as suspension culture?
14:38 < yashgaroth> they'd just settle at the bottom then
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15:11 < nmz7872> yashgaroth: right, but suspension cultures can then form adhesion and form layers
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15:12 < yashgaroth> that seems like a lot more work than a gel though
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15:15 < nmz7872> how do you make a homogenous gel?
15:16 < nmz7872> ahh, ok i got it now
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15:27 < jmil> ThomasEgi: thanks!
15:27 < nmz7872> kanzure what was the CAD porting to python scheme you seemed tho think might work?
15:27 < nmz7872>  i think it had the word 'engine' in it
15:28 < jmil> the gels are viscous fluids and keep cells fairly neutrally buoyant during the first few minutes of crosslinking before the liquid gel hits its gel transition stage (where it becomes more solid than liquid). at that point, the cells are trapped.
15:29 < nmz7872> how quickly does the sugar harden? can you do really complex vasculature at this stage?
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15:29 <@kanzure> nmz7872: opencascade? brlcad? sorry, you need to describe it more
15:29 < nmz7872> i.e. does the sugar harden 1-3mm from the extruder head?
15:30 < nmz7872> it was a few days ago, you linked to some .py
15:30 < nmz7872> esolid
15:30 < nmz7872> that was it
15:30 <@kanzure> ah okay.. http://diyhpl.us/cgit/lolcad has esolid.py
15:31 <@kanzure> i don't recommend using esolid.py because it doesn't work and hasn't been tested
15:32 < nmz7872> do you think that's a real, viable route?
15:32 < nmz7872> (how do i change my name from nmz7872???)
15:32 <@kanzure> nmz7872: type /nick nmz787
15:32 < jmil> nmz7872: yes we freeze the sugar at room temperature shortly after extrusion
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15:33 < nmz787> do you think you could program it to do a supportless helix?
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15:33 <@kanzure> nmz787: who are you asking :)
15:33 <@kanzure> i think that question might work for either conversation happening here
15:34 < nmz787> jmil: re: supportless helix... slow enough extrusion and cold enough build stage?
15:34 < jmil> nmz787: yes the sugar formulation is very amenable to complex and curved fabrication strategies
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15:48 < ThomasEgi> http://www.natureasia.com/en/research/index/highlight/id/1890/
15:52 < nmz787> do we know scott janousek?
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16:11 <@kanzure> via avery/bosslab: "Some of you at the meeting saturday heard me talk about the bluegene project, basically we want to take a gene from one bacteria and transfer it to another bacteria.  This gene codes for an enzyme that breaks down indole, and turns it into indigo."
16:12 <@kanzure> "Right now, the team is Cat, Simon, and myself.If you want to join, please do so this week, by Friday.  The cost of the project is basically whatever we buy, divided between all the people in the project.  I estimate that if nothing goes wrong, cost will be under $200 per person."
16:12 <@kanzure> http://bosslab.org/BlueGene
16:12 <@kanzure> nmz787: nope i don't know him sorry
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21:57 < nmz7871> kanzure
21:57 -!- nmz7871 is now known as nmz787
21:58 <@kanzure> nmz787: hm?
21:58 < nmz787> can you reset my password on gnusha, i'm logged in via keys but i need to have pw for filezilla access
21:58 < nmz787> i tried passwd but i failed to remember :(
21:59 <@kanzure> uhhhhhh filezilla should be able to use your keys
21:59 <@kanzure> but sure.. let me pm you a new password
22:09 <@kanzure> nmz787: i sent you a new password in a pm
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22:13 < nmz787> how do i logon to this IRC?? [13:09] * Now talking in #Chemistry
22:13 < nmz787> [13:09] * chemistry.gravitywaves.com sets mode: +nt
22:15 <@kanzure> /join #Chemistry
22:15 < nmz787> its a private server though
22:15 < nmz787> chemistry.gravitywaves.com/logs/chatlog_11_11_08.log
22:15 < nmz787> will try to scrape for more logs
22:16 <@kanzure> oh do you mean how to connect
22:16 <@kanzure> /connect chemistry.gravitywaves.com
22:17 < fuztt> lol
22:17 < fuztt> My friends IRC does that
22:17 < fuztt> i doubt there is much interesting to find
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22:25 < jrayhawk> nmz787: filezilla can use pageant for authentication if you're using the sftp protocol
22:26 < jrayhawk> there's probably also a way to point it at your key, but that's more effort
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22:30 < ParahSailin> http://diggingintheclay.wordpress.com/2012/06/18/lead-them-not-into-temptation/
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22:37 < nsh> i think that dialogue misses the point somewhat
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22:38 < nsh> i don't recall anyone saying anthropogenic climate change will kill us all by negating the laws of thermodynamics
22:39 < nsh> it's more about having "local energy distribution" that's convenient for human/wider-ecological integrity
22:39 < nsh> *human survival
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22:47 < nmz787> http://gnusha.org/~nmz787/Hybrid%20error%20correction%20and%20de%20novo%20assembly%20of%20single-molecule%20sequencing%20reads.pdf
22:52 < nmz787> ParahSailin: good read
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23:51 < jrayhawk> "It has a few internal but steady state and minor energy sources." No, tidal friction and radioactivity are dynamic.
23:52 < jrayhawk> So's the sun, actually.
23:58  * nsh nods
--- Log closed Tue Jul 03 00:00:57 2012