--- Log opened Thu Jul 11 00:00:22 2013 00:03 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Remote host closed the connection] 00:19 -!- delinquentme [~asdfasdf@66.233.132.203] has joined ##hplusroadmap 00:38 -!- delinquentme [~asdfasdf@66.233.132.203] has quit [Quit: Leaving] 00:48 -!- kmo [122@d30-138.icpnet.pl] has joined ##hplusroadmap 00:48 -!- kmo [122@d30-138.icpnet.pl] has quit [Changing host] 00:48 -!- kmo [122@unaffiliated/kmo] has joined ##hplusroadmap 00:51 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 00:51 -!- kmo is now known as kajetan 01:14 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap 01:18 -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] 02:11 -!- chido [chidori@pasky.or.cz] has quit [Ping timeout: 240 seconds] 02:11 -!- chido [chidori@pasky.or.cz] has joined ##hplusroadmap 02:26 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 02:28 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 02:59 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 03:42 -!- monkeynipples [monkeynipp@gateway/shell/xzibition.com/x-ajlxxhlqjhjzgswa] has quit [Ping timeout: 246 seconds] 03:43 -!- monkeynipples [monkeynipp@gateway/shell/xzibition.com/x-isqvcjwfwiasbwmd] has joined ##hplusroadmap 03:50 -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap 04:15 -!- weles [~mariusz@71.234.3.169] has joined ##hplusroadmap 04:20 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has joined ##hplusroadmap 05:01 -!- weles [~mariusz@71.234.3.169] has quit [Ping timeout: 240 seconds] 05:18 -!- makoLime [~mako@103-9-42-133.flip.co.nz] has quit [Ping timeout: 248 seconds] 05:32 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap 05:56 < chris_99> http://www.bbc.co.uk/news/science-environment-23244768 05:56 < chris_99> .title 05:56 < yoleaux> BBC News - Scientists building the world's first synthetic yeast 06:05 -!- biostudent_ [~chatzilla@46.208.19.205] has joined ##hplusroadmap 06:05 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 276 seconds] 06:05 -!- biostudent_ is now known as biostudent 06:28 -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has joined ##hplusroadmap 06:43 -!- mietek [mietek@bak.io] has left ##hplusroadmap [] 07:05 -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap 07:22 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap 07:30 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 264 seconds] 07:53 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 08:02 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] 08:02 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 08:12 -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 248 seconds] 08:33 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 08:34 -!- ybit is now known as heath 08:36 <@kanzure> chris_99: that sounds like a lie ("first") 08:38 -!- HEx1 [~HEx@hexwab.plus.com] has quit [Ping timeout: 240 seconds] 08:39 <@kanzure> "I am at SB6.0, and they just announced that in 2014 they will be inviting DIY teams to the IGEM competition" 08:39 <@kanzure> yawn.. 6-7 years too late. damn you, randy! 08:42 <@kanzure> http://what-if.xkcd.com/53/ "How quickly would the ocean's drain if a circular portal 10 meters in radius leading into space was created at the bottom of Challenger Deep, the deepest spot in the ocean? How would the Earth change as the water is being drained?" 08:42 <@kanzure> looks like they stole my idea for fixing the oil spill in the gulf of mexico 08:43 < heath> Rather, I am interested in how processes in biology and chemistry can actually act as computers and execute molecular algorithms. -- http://www.dna.caltech.edu/~pwkr/ 08:44 < heath> https://www.youtube.com/watch?feature=player_detailpage&v=HjR6hzAYygk#t=114s 08:45 < heath> .title 08:45 < yoleaux> 3d printing living things DNA by Cambrian Genomics - YouTube 08:45 < heath> "Proteins don't "execute". They fold and unfold. They bounce..." 08:46 <@kanzure> i met paul once. nice fellow. he also helped out on nanoengineer-1. 08:47 < heath> that last quote was from anselm 08:47 <@kanzure> yes, well, so was the one i told you to read yesterday, but i don't think you did 08:47 < heath> i read, that was from the thread 08:47 <@kanzure> ah okay. 08:47 <@kanzure> good 08:48 < heath> his coworker is equating dna to a computer code in that video 08:48 <@kanzure> yes, well, it's a very lucrative hype machine that the synthetic biology crowd has created 08:49 < heath> i don't think that he disagrees there's computation going on, he's just trying to state that it's not exactly like the digital computers we program today 08:49 <@kanzure> so in some cases i can see it's okay to say those things, like if you're raising venture capital 08:49 < gradstudentbot> Future work will focus on that. 08:49 <@kanzure> because in the context of billions of dollars of venture capital, sure, something interesting can be made to happen. like cheap dna synthesis. or genome synthesis. 08:49 < heath> paul is a collaborator for this project: http://www.cds.caltech.edu/~murray/wiki/index.php/Biomolecular_Breadboards_for_Prototyping_and_Debugging_Synthetic_Biocircuits 08:50 < heath> i was surprised to see his name on the list 08:50 <@kanzure> why would you be surprised to see rothemund anywhere? 08:50 <@kanzure> considering how much involvement he has in everything? 08:51 < heath> i've never seen his name associated with synbio 08:51 <@kanzure> he's cited very frequently 08:51 <@kanzure> he hangs out with lots of synthetic biology peeps 08:51 <@kanzure> ok whatever 08:56 < jonathan_> " 29% reported they had snooped on someone else’s phone. Among those under 35, however, almost half – 47% – admitted snooping." 08:57 <@kanzure> is it snooping if someone gives you their phone and lets you poke around? 08:57 < jonathan_> no 08:58 < jonathan_> it's snooping when a jealous girl sneaks over to your phone and goes thru it while you're in the bathroom. 09:00 * heath is looking for a project to work on.. 09:00 * heath is considering making an open version of http://cando-dna-origami.org/ 09:02 <@kanzure> heath: how about fixing nanoengineer? https://github.com/kanzure/nanoengineer#readme 09:02 <@kanzure> heath: or paperbot. :( 09:04 -!- cathalgarvey [~cathalgar@178.167.254.115.threembb.ie] has joined ##hplusroadmap 09:04 < cathalgarvey> paperbot: https://www.sciencedirect.com/science/article/pii/S0003269700950061?np=y 09:04 < cathalgarvey> Hi all! 09:04 < paperbot> http://libgen.org/scimag1/10.1006/abio.2000.5006.pdf 09:04 < cathalgarvey> Just going insane and need a ref, don't mind me.. 09:04 <@kanzure> cathalgarvey: hello 09:05 < cathalgarvey> Libgen.org now? Cool! 09:05 < gradstudentbot> Paper submitted. 09:05 < cathalgarvey> @kanzure You at synbio 6? 09:05 <@kanzure> nope. busy hacking. 09:05 <@kanzure> paperbot is now routing requests through the seedy underworld of russia 09:06 < cathalgarvey> Haha awesome 09:06 <@kanzure> cathalgarvey: have you met gradstudentbot? he's been working on a few papers. 09:06 < gradstudentbot> I coauthored a paper about that a few years ago. 09:06 < cathalgarvey> Actually, I tried sci-hub first, and it just kept forwarding me to scholar or pubmed 09:06 < cathalgarvey> Was v. disappointed, but I suspect it's something to do with my stringent anti-plugin/frames/cookies/popups browser.. 09:07 < cathalgarvey> Love him, he fills so many social niches we struggle with right now 09:07 < cathalgarvey> :) 09:07 <@kanzure> ah, well, paperbot runs gecko, so it does that javascript/cookie/popup stuff for you 09:07 -!- nuba [~nuba@pauleira.com] has quit [Remote host closed the connection] 09:08 < cathalgarvey> Thank you, bot-friends and bot-maintainers 09:08 < cathalgarvey> May you stay out of prison for many years to come :) 09:08 <@kanzure> cathalgarvey: could you spend 2 minutes telling heath (in here) about your python/bioinformatics stuff? he is looking for a project to do. 09:08 < cathalgarvey> Hm! 09:08 < cathalgarvey> Two minutes, OK. That's my deadline anyway! 09:08 < heath> bring it 09:08 <@kanzure> i figured 09:08 < cathalgarvey> Hi Heath, I authored two sketchy and incomplete python synbio projects so far: 09:09 < cathalgarvey> PySplicer, which was such a mess to begin with that I basicaly rewrote it recently 09:10 < heath> "Fasta Compiler: a simple, extensible bash-style scripting language for synthetic biology." 09:10 < cathalgarvey> It performs codon optimisation using a weighted-random selection system ( you have to feed it codon frequency tables for your target species), while excluding specified DNA patterns and (most recently) trying to avoid secondary structures in the 5' portion of the RNA. 09:10 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has quit [Ping timeout: 276 seconds] 09:10 < cathalgarvey> And yes, Fasta Compiler, the other half of a not-yet-integrated cohesive compiler. I ultimately want PySplicer to be a part of FastaC, athough I also want to rewrite Fastac to be not-hideous 09:11 < cathalgarvey> FastaC is designed to be back-compatible with straight-Fasta, so you can use existing Fasta files as "libraries". I'm also planning to build a Genbank parser into the backend so you can treat bacterial genomes as namespaces in the compiler. 09:11 < cathalgarvey> Quite simply it allows you to treat multifasta files as namespaces of sequences, and perform some transforms and templating operations upon them. 09:12 < cathalgarvey> Which is 90% of what a "DNA programming language" according to our current level of mastery involves. 09:12 <@kanzure> cathalgarvey: i think something like that would be useful, but why does it have to be a new language? why not use an existing language like python, and then have a thing that loads a fasta file into an object, and then you can operate on that object using normal python conventions? 09:12 < cathalgarvey> @kanzure Partly because it was an exercise in building a (terrible) language of its own. 09:12 < cathalgarvey> And partly to keep the function separate from the implementation. 09:13 <@kanzure> do you know about parser generators and compiler grammars? 09:13 < cathalgarvey> Although since it ended up seeming very bash-script-ey, that's not much of a virtue really 09:13 < cathalgarvey> Ha, trying. Although every time I look into Parsers, everything I find is written assuming you already "get" everything. 09:13 <@kanzure> i think that's what the dragon book is for 09:13 < cathalgarvey> I'm thinking of ditching my effort at finding a nice python for-idiots parser and just writing a hideous regex-based parser.. 09:13 <@kanzure> http://www.amazon.com/Compilers-Principles-Techniques-Alfred-Aho/dp/0201100886 09:13 < cathalgarvey> Ah, cool 09:14 < cathalgarvey> will look into that 09:14 < ParahSailin> just use genome compiler, i hear they've done all the heavy lifting on DNA programming languages 09:14 < cathalgarvey> TY 09:14 <@kanzure> ParahSailin: how are you not banned yet 09:14 < ParahSailin> what does that even mean, dna programming language 09:14 < heath> i started working on a "compiler for genetic circuits" the other day, but then i was dissuaded 09:14 < cathalgarvey> Genome Compiler is closed source bullshit, no interest. At this point, I design most stuff by hand anyway, so I'm not missing out on any bizarre special sauce. 09:14 < cathalgarvey> Right, I'm off guys, sorry! 09:14 <@kanzure> seeya 09:14 < cathalgarvey> parenting calls 09:14 < cathalgarvey> :) 09:15 < ParahSailin> what is your bedrock abstraction going to be 09:15 -!- cathalgarvey [~cathalgar@178.167.254.115.threembb.ie] has left ##hplusroadmap ["With a vague gesture to the horizon"] 09:15 -!- kajetan [122@unaffiliated/kmo] has quit [Quit: Leaving] 09:16 < heath> ParahSailin: me? 09:16 < heath> ah, cathal 09:18 < heath> for me it was building off "amplifying genetic logic gates" by endy 09:18 <@kanzure> isn't that just a buzzwordy way of saying pcr. 09:19 < heath> i'm not sure 09:20 <@kanzure> hey if you wanna be helpful can you go find the paper about cellular uptake of different dna origami shapes 09:21 < heath> oooh, that sounds fun 09:22 < heath> mirkin was talking about his SNAs yesterday and states his group had removed the sphere the nucleic acides were attached to 09:23 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap 09:23 < heath> kanzure: http://dash.harvard.edu/handle/1/9556124?show=full 09:23 < heath> is that the one you're looking for? 09:27 < heath> favorite quote of the day 09:27 < heath> [11:14:03] just use genome compiler, i hear they've done all the heavy lifting on DNA programming languages 09:31 <@kanzure> "Feds, we need some time apart" https://groups.google.com/forum/#!topic/diybio/FPQeUtmTKDM 09:31 <@kanzure> https://www.defcon.org/#dc21fedbreak 09:31 <@kanzure> https://news.ycombinator.com/item?id=6024094 09:31 <@kanzure> "For over two decades DEF CON has been an open nexus of hacker culture, a place where seasoned pros, hackers, academics, and feds can meet, share ideas and party on neutral territory. Our community operates in the spirit of openness, verified trust, and mutual respect. When it comes to sharing and socializing with feds, recent revelations have made many in the community uncomfortable about this relationship. Therefore, I think it would be ... 09:32 <@kanzure> ... best for everyone involved if the feds call a "time-out" and not attend DEF CON this year. This will give everybody time to think about how we got here, and what comes next. - The Dark Tangent" 09:38 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] 09:41 < jonathan_> the defcon guys are mostly lame 09:42 < jonathan_> no better than diybio 09:42 < jonathan_> they build an LED cube and think it's the most amazing thing ever 09:42 < jonathan_> or write a perl cgi and think it's the most amazing thing ever 09:42 <@kanzure> hey man, fastcgi is rockin'.... ok maybe not. 09:44 < jonathan_> omg i can run a scanner and discover all the hidden ssid's around me! i'm so uber hax0r 09:45 < jonathan_> omg i can toggle an i/o line on the rasberry pi now i can control the world .. umm maybe not 09:45 < nmz787> while defcon is crying, feds be slacking with diybio meeting this year 09:47 < jonathan_> man freakin bernanke 09:47 < jonathan_> he's the uber hax0r 09:47 < nmz787> ben? 09:47 <@kanzure> the fbi drones are always slacking on organizing the diybio meeting 09:47 < jonathan_> he is crashing financial markets every da 09:48 <@kanzure> they usually end up a month or two behind schedule 09:48 <@kanzure> so i predict october or maybe september 09:48 < jonathan_> how much does the fbi pay for information? 09:49 < jonathan_> next step for diybio: double agents 09:49 < jonathan_> fake projects on kickstarter are not enough! 09:50 <@kanzure> double agents? so the fbi will claim they are fbi, but really they are what? 09:52 < jonathan_> the diybio hax0rs will claim they are uber uber and really they are working for the nsa 09:53 < jonathan_> and also paid fbi informants 09:53 < nmz787> bring on the salary 09:53 < jonathan_> see? you're all sell outs 09:54 < nmz787> too many underground projects around, need unseen regulatory oversight 09:55 < jonathan_> or, fake projects which raise visibility 09:55 < jonathan_> "the secret cryogenics project that really works" then wait for diybio kiddies to join in 09:55 < nmz787> lol 09:56 < nmz787> get em to start freezing themselves with a faulty process, to weed out the crowd 10:04 < jonathan_> then again, the fbi is not that clever, so... 10:14 < nmz787> paperbot: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=995823&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F97%2F21489%2F00995823 10:14 < paperbot> http://libgen.org/scimag/get.php?doi=10.1109%2F97.995823 10:24 -!- kmo [~kmo@apn-5-60-167-144.dynamic.gprs.plus.pl] has joined ##hplusroadmap 10:24 -!- kmo [~kmo@apn-5-60-167-144.dynamic.gprs.plus.pl] has quit [Changing host] 10:24 -!- kmo [~kmo@unaffiliated/kmo] has joined ##hplusroadmap 10:36 < nmz787> so where is the SB6.0 torrent? 10:47 <@kanzure> nobody torrents it because they are all lame 10:47 <@kanzure> wrong subculture 10:47 -!- ParahSailin [~Rob@50-194-178-148-static.hfc.comcastbusiness.net] has quit [Remote host closed the connection] 10:49 -!- ParahSailin [~Rob@unaffiliated/parahsailin] has joined ##hplusroadmap 10:50 < ParahSailin> lol sci-hub pdfcache does not require proxy 10:50 < ParahSailin> i guess this should not surprise me 10:50 < ParahSailin> not sure why that didnt occur to me earlier 10:51 <@kanzure> well it's not that useful though 10:51 <@kanzure> there's only ~100 files stored there at a time 10:51 < jonathan_> pdfcache? 10:51 < ParahSailin> still, simplifies the code 10:51 < ParahSailin> dont need to pass that cookie when getting those 10:51 <@kanzure> jonathan_: http://sci-hub.org/pdfcache/ 10:52 <@kanzure> oh this is much more than ~100 10:52 <@kanzure> there seems to be about 15 files from 2013-03-01 and then the rest are from 2013-07-11 11:02 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has left ##hplusroadmap ["Leaving"] 11:03 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap 11:17 < nmz787> paperbot: http://link.springer.com/chapter/10.1007/978-3-642-02391-0_26 11:17 < paperbot> http://libgen.org/scimag4/10.1007/978-3-642-02391-0.pdf 11:18 < nmz787> we're cool 11:18 < nmz787> wait 11:18 < nmz787> that isn't the right pdf 11:19 < nmz787> that's just the TOC 11:19 < nmz787> of the book that i asked for a chapter of 11:19 < nmz787> huh 11:19 < nmz787> so there are two pdf links on the signed-in journal page 11:20 <@kanzure> you hsould use the exact link to the chapter 11:20 < nmz787> 'Download Book (5,551 KB) Download Chapter (275 KB)' 11:20 <@kanzure> *should 11:20 < nmz787> unsigned-in it didn't show me 11:20 < nmz787> and the link i pasted is to the whole chapter 11:21 < nmz787> 'As a courtesy to our readers, the eBook is provided DRM-free. However, please not that an invisible watermark has been included to safeguard the author's interests' 11:21 <@kanzure> they are lying, it's just metadata 11:21 < nmz787> paperbot: link.springer.com/content/pdf/10.1007%2F978-3-642-02391-0_26.pdf 11:22 <@kanzure> paperbot: link.springer.com/content/pdf/10.1007%2F978-3-642-02391-0_26.pdf 11:22 <@kanzure> erm 11:22 <@kanzure> paperbot: http://link.springer.com/content/pdf/10.1007%2F978-3-642-02391-0_26.pdf 11:22 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/5555ba56a955075b676993cf3ce11a15.pdf 11:22 < nmz787> so it got it that time 11:23 < nmz787> paperbot: http://link.springer.com/content/pdf/10.1007%2F978-3-642-02391-0.pdf 11:23 <@kanzure> Arbortext Advanced Print Publisher 9.0.223/W Unicode 11:23 < paperbot> http://libgen.org/scimag4/10.1007/978-3-642-02391-0.pdf 11:23 <@kanzure> Acrobat Distiller 8.1.0 (Windows) 11:23 <@kanzure> uuid:0d239f6c-0a54-4aca-94d3-00b018e3db1a 11:23 < nmz787> huh, so my ezproxy can get the whole book, but libgen cant 11:23 <@kanzure> 11:24 <@kanzure> wait so why is that paper on diyhplus? 11:29 < nmz787> pdx doesnt have access to it 11:30 < ParahSailin> invisible watermark is isomorphic to metadata 11:30 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S0956713509000759 11:30 < paperbot> http://libgen.org/scimag4/10.1016/j.foodcont.2009.03.002.pdf 11:31 < nmz787> so are pdfs on libgen assumed to be stable or not? 11:32 < nmz787> wtf is this e=reader http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2218926/ 11:32 < nmz787> it sucks 11:32 < nmz787> and i can't figure out how to change it 11:32 < nmz787> paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2218926/ 11:32 < ParahSailin> libgen pdfs are stable 11:32 < paperbot> http://libgen.org/scimag/get.php?doi=10.1155%2F2007%2F82612 11:33 < ParahSailin> thats functionality is broken though, sorry 11:33 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S0963996912005443 11:33 < ParahSailin> libgen html is quite irregular, so detecting whether a pdf is on there or not is not straightforward 11:33 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Producing%20more%20with%20less%3A%20Strategies%20and%20novel%20technologies%20for%20plant-based%20food%20biofortification.txt 11:33 < nmz787> :( 11:33 < ParahSailin> is http://sci-hub.org/pdfcache/f7f94bc6454fc29132ce230638244d8f.pdf it? 11:34 < nmz787> yes 11:34 < nmz787> well 11:35 < nmz787> yes 11:35 < nmz787> so the last paper, paperbot should have local access to 11:35 < nmz787> paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271165&_user=1694017&_pii=S0963996912005443&_check=y&_origin=article&_zone=toolbar&_coverDate=28-Dec-2012&view=c&originContentFamily=serial&wchp=dGLbVlV-zSkzV&md5=b395b9d413092d45e17ba46272fae58e&pid=1-s2.0-S0963996912005443-main.pdf 11:35 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/6caca47e4bd220d5e36c036f15ac5556.pdf 11:37 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S0278691512007533 11:37 < paperbot> http://libgen.org/scimag4/10.1016/j.fct.2012.10.016.pdf 11:37 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S0278691508003797 11:37 < paperbot> http://libgen.org/scimag4/10.1016/j.fct.2008.06.092.pdf 11:38 < gradstudentbot> Who's in charge of the master mix? 11:46 < nmz787> well seems like sb6.0 must be over now 11:46 < nmz787> '1) Access videos of the plenary sessions live online, while the conference is taking place for free.' 11:46 < nmz787> and i guess that means i can't see the free videos 11:47 <@kanzure> they might have saved them on livestream.com already. or they might be the type that will upload them in 4 months. 11:49 < nmz787> seems unlikely "2) Within 24 hours of each session, professionally edited videos of all the presentations made in the main auditorium from all three days of the conference will be available online for viewing in a stable, encoded, compressed format for reliable, smooth playback at your convenience. You must register for this portion of the SB6.0 Digital Conference. The fee is $199." 11:49 < nmz787> http://sb6.biobricks.org/digital-conference/ 11:49 < nmz787> they want some kind of access code 11:49 < nmz787> i tried the sample they have there 11:50 < nmz787> didnt work 11:57 < nmz787> .wa 0.5mL 10mM datp to grams 11:58 < yoleaux> convert 0.500 mL of 10 mM 2'-deoxyadenosine 5'-triphosphate to grams: 0.00246 grams; Unit conversions: 2.46 mg (milligrams); 2.46×10⁻⁶ kg (kilograms); Comparisons as mass: ~(0.03 ~1/37) × typical large sand grain mass (~9×10⁻⁵ kg); ~0.8 × mass of a typical snowflake (~3×10⁻⁶ kg); ~mass of a typical mosquito (~1×10⁻⁶ kg); Interpretation: mass 11:58 < nmz787> bitchin 11:59 < gradstudentbot> I had to remind my professor who I was today. 11:59 < nmz787> huh, so phosphoramidite nucleotides are cheaper than triphosphate nucleotides 11:59 < nmz787> phosphoramidite is $50/g those are $8500 12:09 < nmz787> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/2443811 12:12 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/0076687987520110 12:12 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/%5B8%5D%20Electrophoresis%20in%20agarose%20and%20acrylamide%20gels.txt 12:12 < nmz787> paperbot: http://www.sciencedirect.com.proxy.lib.pdx.edu/science?_ob=MiamiImageURL&_cid=273025&_user=1694017&_pii=0076687987520110&_check=y&_origin=article&_zone=toolbar&_coverDate=31-Dec-1987&view=c&originContentFamily=serial&wchp=dGLbVlB-zSkzS&md5=a8f3aa5bf83e0521703afe7c28184b35&pid=1-s2.0-0076687987520110-main.pdf 12:12 < paperbot> http://libgen.org/scimag3/10.1016/0076-6879%252887%252952011-0.pdf 12:13 < nmz787> Not Found 12:13 < nmz787> 'The requested URL /scimag3/10.1016/0076-6879%2887%2952011-0.pdf was not found on this server.' 12:13 < nmz787> paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=273025&_user=1694017&_pii=0076687987520110&_check=y&_origin=article&_zone=toolbar&_coverDate=31-Dec-1987&view=c&originContentFamily=serial&wchp=dGLbVlB-zSkzS&md5=a8f3aa5bf83e0521703afe7c28184b35&pid=1-s2.0-0076687987520110-main.pdf 12:14 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/a7a9a12e7fe167c34cf561065802cf77.txt 12:14 < nmz787> well this one's for the world: http://diyhpl.us/~nmz787/pdf/Electrophoresis_in_Agarose_and_Acrylamide_Gels.pdf 12:16 -!- marciogm [~textual@177.106.57.86] has quit [Quit: Textual IRC Client: www.textualapp.com] 12:18 -!- randalla1ordon is now known as randallagordon 12:21 -!- cathalgarvey [~cathalgar@79.97.71.97] has joined ##hplusroadmap 12:21 <@kanzure> welcome back 12:21 < cathalgarvey> Hey all, decided to come back and lurk now that Clara's asleep (or pretending to be) :) 12:23 < nmz787> you're like Harry Potter's Irish counterpart 12:23 < nmz787> except more real 12:23 <@kanzure> the star of a billion dollar franchise? 12:24 < nmz787> accented magician 12:24 -!- oblique [~oblique@87-143-95.netrun.cytanet.com.cy] has quit [Read error: Connection reset by peer] 12:25 < nmz787> how have your projects been coming along cathalgarvey 12:25 -!- kmo [~kmo@unaffiliated/kmo] has quit [Remote host closed the connection] 12:26 < cathalgarvey> Confused, but it's not the first time I've been compared to harry potter.. mostly by mild resemblance to the protagonist (and this weird scar on my forehead..) 12:26 < cathalgarvey> My projects are going indeterminably 12:27 < cathalgarvey> Because I've discovered what any oldtimer coulda told me about wild type GFP 12:27 < cathalgarvey> it sucks 12:27 < cathalgarvey> and E.coli itself is autofluorescent in roughly the same bands as wtGFP 12:27 < nmz787> huh 12:27 < cathalgarvey> as is most media containing yeast extract 12:27 < gradstudentbot> I'm so doing industry. 12:28 < gradstudentbot> I haven't written the abstract. 12:28 -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap 12:28 < nmz787> as far as the harry potter comment, you're close to england which i think is where he was from, and biotech is way cooler than whatever cool magic he was portrayed with 12:29 < nmz787> ala kazam, wtGFP just got mutated into betterGFP 12:30 < nmz787> cathalgarvey: so are mutated species allowed over there? 12:30 < cathalgarvey> Yea he was Londonese :) 12:30 < cathalgarvey> Mutants are OK, but artificial mutants are a gray area 12:30 < ParahSailin> you could only get wt gfp? 12:30 < nmz787> cathalgarvey: i was reading about all these mutant foods on the market over here, and there is almost no food safety testing been done or required 12:31 < cathalgarvey> Nope, I was hoping that if it worked well in testing then I could sail straight to release, but anything better than GFP is patented, AFAIK 12:31 < cathalgarvey> So I said "stick with wtGFP, it doesn't have to be that bright" 12:31 < nmz787> found a paper saying transcriptional changed are all over the place compared to GMO 12:31 < cathalgarvey> and how wrong I was 12:31 < cathalgarvey> @nmz787 Yea, I had a plant science prof who used to pump mutation breeding as the way forward because it was less regulated or blanket scaremonger-bombed than GMO. 12:32 < ParahSailin> you dont have to obey patents 12:32 < cathalgarvey> Had some funny stories about running a plantation in..Lebanon? :) 12:32 < cathalgarvey> @ParahSailin that's cute, but actually I do, because I'm hoping to run a business out of this and refuse to implement defensive patenting. 12:32 < cathalgarvey> And I'm in Europe, where we (for once) actually have a worse patent situation biotech-wise than the US, now. 12:33 < ParahSailin> business out of what? 12:33 < cathalgarvey> although even in US, eGFP et al are still explicitly patentable. 12:33 < cathalgarvey> Business out of Free/Libre DNA tools for cheap, easy molecular biology. 12:33 < cathalgarvey> Sadly much of that involves soul-destroying patent evasion 12:33 < ParahSailin> and someone's gonna sequence your constructs to check if you're infringing on anything? 12:33 < cathalgarvey> You'd be surprised how many seemingly silly, desperate things have been patented.. 12:34 < cathalgarvey> ..sequence? 12:34 < cathalgarvey> I said Free/Libre, I'm not gonna be keeping the source secret ffs 12:35 < nmz787> he's saying if you stomp other patents 12:36 < ParahSailin> it sounds like you're tilting at windmills here 12:36 < nmz787> what's that mean? 12:36 < nmz787> bringing your head close to a choper? 12:36 < nmz787> chopper 12:36 < nmz787> chopping device 12:36 < cathalgarvey> :) 12:37 < ParahSailin> before he became a character in a fighting game, the mexican known as cervantes wrote a book 12:37 < nmz787> don quixote 12:37 < cathalgarvey> Speaking of Free/Libre, @kanzure: You gave out once that I used the AGPL, without saying what exactly was wrong with it.. got a link or ref to arguments against? 12:37 < cathalgarvey> Besides virality, which is the selling point AFAIC. 12:37 < nmz787> you're saying the megacorps are just windmills, and cathalgarvey thinks they're attackers? 12:38 < gradstudentbot> Have you read this paper? 12:39 < ParahSailin> tilting at windmills is a poetic way of saying doing impractical things for idealistic reasons 12:39 <@kanzure> cathalgarvey: no, i don't have a good link to explain why i don't like AGPL 12:40 < nmz787> an engineer that's good with poetry! 12:41 < cathalgarvey> @kanzure Fair 'nuff! So it's not something special to the AGPL, similar reasons to why one might like GPL, then? 12:41 <@kanzure> ParahSailin: i thought it was 'chasing windmills' not 'tilting windmills' 12:41 < ParahSailin> simple solution if you actually think someone would take legal action against you, just declare bankruptcy with the shell corporation that is liable and you can keep all the salary you paid yourself 12:41 < ParahSailin> kanzure: among illiterate people yes 12:41 <@kanzure> cathalgarvey: AGPL has some specific problems of the same style that CC-NC has. i just don't remember the details. 12:42 <@kanzure> ParahSailin: i have never claimed literacy. in fact, i'm not even reading your messages. i'm making them up as i go. :) 12:42 < ParahSailin> tilt is an archaic verb for what the cataphracts do in a jousting match 12:42 < cathalgarvey> @ParahSailin That saves you, but the product you released is still not legal for others to build upon without risk of patent assault. 12:43 < cathalgarvey> @ParahSailin That's why FLOSS software avoids patents instead of going bullheaded and shell-company'd: it achieves nothing ultimately because the software remains patented. 12:43 < ParahSailin> thats safely not your problem 12:43 <@kanzure> floss software does not avoid patents always 12:43 < cathalgarvey> It is if my mission is FLOS Bio and not just a salary. 12:43 <@kanzure> in fact, that's why you agree to CLAs and copyright assignment agreements 12:43 < ParahSailin> thought you said you wanted to make a living out of it 12:43 <@kanzure> and i imagine there would even be patent agreements for downstream contributions 12:44 < cathalgarvey> @ParahSailin a living is required to continue hacking and making the end-goal happen. 12:44 < ParahSailin> your customers can either do the same thing or be non-profit 12:44 < ParahSailin> whats the problem 12:44 <@kanzure> non-profit status does not make you immune to patent litigation 12:45 < cathalgarvey> And in US, private individuals are not allowed break patents, either 12:45 < ParahSailin> you can cross that bridge when you come to it 12:45 < ParahSailin> http://en.wikipedia.org/wiki/Research_exemption 12:45 < cathalgarvey> If you think you can develop better/faster by just ignoring patents and crossing the mass-litigation bridge as it arises, be my guest. Not my cup of tea. 12:45 <@kanzure> that's research-only, like in an institution 12:45 -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap 12:45 <@kanzure> non-institutional research is unprotected 12:45 -!- marciogm [~textual@177.106.57.86] has quit [Client Quit] 12:46 < nmz787> ParahSailin: i thought duke law school did a good dissection and found there legally is no exemption 12:46 < cathalgarvey> Or even justifiably research-oriented amateur activity. Courts aren't stupid in that particular regard, they can tell a bullshitter 12:46 -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap 12:46 < ParahSailin> and university of california is gonna go after every kid on the diybio list you sold egfp to? 12:46 < cathalgarvey> Off for dinner, AFK 12:47 < ParahSailin> i seriously doubt that 12:47 -!- zubaz_ [~hexane@24.229.127.72] has joined ##hplusroadmap 12:47 -!- marciogm [~textual@177.106.57.86] has quit [Client Quit] 12:47 < ParahSailin> as i said, this is all tilting at windmills 12:48 < ParahSailin> i bet you dont jaywalk either 12:50 < nmz787> i was born in the city that invented jaywalking 12:51 < nmz787> but that's a bit less penalized and certainly less financially risky 12:52 <@kanzure> well, it just means you have to sell it anonymously and in bitcoins 12:52 <@kanzure> and then dont care about patent litigation 12:52 -!- upgrayeddd [uid2969@gateway/web/irccloud.com/x-zgykrscmvaumwbes] has quit [Ping timeout: 246 seconds] 12:52 -!- zubaz [~hexane@unaffiliated/zubaz] has quit [Ping timeout: 246 seconds] 12:52 -!- gradstudentbot [~gradstude@131.252.130.248] has quit [Ping timeout: 246 seconds] 12:53 < nmz787> i guess that duke thing is a bit old 12:53 -!- gradstudentbot [~gradstude@131.252.130.248] has joined ##hplusroadmap 12:53 < ParahSailin> my solution of declaring bankruptcy in the infinitely improbable event that someone actually trolls your for money would work 12:53 < nmz787> there has been newer precedent 12:53 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 240 seconds] 12:53 < nmz787> seems like he's right about other people not wanting to build on shaky ground 12:54 < ParahSailin> hes not trying to sell counterfeit avastin here 12:54 < ParahSailin> come to think of it, pirate avastin seems quite appropiate 12:54 < nmz787> yes 12:55 <@kanzure> ParahSailin: gimme a small writeup and how much cash you want, it will be received by a black suitcase on the 18th 12:55 < nmz787> i'm working with some folks on a shikimate project 12:55 < ParahSailin> yar, avastin matey 12:56 < ParahSailin> nmz787: but his customers are just gonna be kids playing with toys 12:57 < ParahSailin> any grownup customer making a business out of it would presumably be competent enough to know how to navigate IP law 12:58 <@kanzure> grownupbot 12:58 < ParahSailin> you're gonna be 20-30 years behind if you obey every law and bootstrap absolutely everything 12:58 <@kanzure> bootstrapping doesn't take 20 years 12:58 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 12:59 < ParahSailin> developing your own, unencumbered egfp might only take 1 year 12:59 < ParahSailin> developing your own, unencumbered YYY might only take another year 12:59 < ParahSailin> by the time you have enough components for your kit, thats about 20 years of work 12:59 -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has joined ##hplusroadmap 12:59 <@kanzure> it's not like you're constantly working on egfp 12:59 <@kanzure> most of the time i find that projects are 'set and forget, until the timer fucking beeps" 13:00 < ParahSailin> not to mention all the cost of reagents you're pouring into this quixotic black hole 13:00 < gradstudentbot> The real reason I wanted to join this lab was because I love to clean glassware. 13:01 < nmz787> i think there's merit and value in what cathalgarvey desires 13:01 -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has quit [Ping timeout: 240 seconds] 13:01 < nmz787> if it was done right, grownups would use the stuff too 13:01 < ParahSailin> yes there's merit and value, but value < cost 13:02 < nmz787> doing it right is complex here though, since it's both legal doing right, and molbio doing right 13:02 <@kanzure> of avoiding all things ever specified by patents? yeah, if you were going to do that, you might as well get venture capital to pay for that, because those are the only people that would care. 13:02 < nmz787> wtGFP isn't as useful/'right' as eGFP 13:03 < ParahSailin> im ignorant of exactly what he intends to do here 13:03 < nmz787> he basically already told you 13:03 < nmz787> FLOSbio 13:03 < ParahSailin> thats what 13:04 < nmz787> Free Libre Open Source bio 13:04 < nmz787> what parts he'll focus on i dunno 13:04 < ParahSailin> yes im familiar with the acronym 13:04 < nmz787> or systems 13:04 < nmz787> or subsystem 13:04 < nmz787> ss 13:04 < nmz787> he was working on some easier transformation process 13:05 < nmz787> and was trying to fit some GFP vector into the EU law stuff 13:05 < nmz787> so people could legally buy a transformation kit with all the parts, even if when they shoved DNA into the vector it would be crossing-the-legal-line 13:05 < nmz787> the sale and transfer of the base requirements wouldn't be encumbered 13:06 < nmz787> something about mutating a natural e.coli/bacillus plasmid 13:06 < nmz787> since EU doesn't care if it's cisgenic 13:06 < ParahSailin> i thought possiblity of customers breaking any laws was a dealbreaker 13:06 < nmz787> or something 13:06 < nmz787> not buying into anything that's encumbered by IP is more like it, I think 13:07 < gradstudentbot> Who got mustard on my cell culture? 13:08 < ParahSailin> so it sounds like customers using his stuff would be taking legal risks in using it anyway 13:09 < nmz787> i think so, if they're adding exogenous noncisgenic DNA 13:09 < nmz787> for a transformation helloworld no laws would be broken 13:09 -!- HEx [~HEx@hexwab.plus.com] has joined ##hplusroadmap 13:09 < nmz787> (i believe) 13:10 <@fenn> how about doing it the hard way, send your customer a jellyfish and a truckload of restriction enzymes 13:11 < ParahSailin> nah, that jellyfish might have been illegally harvested 13:11 < ParahSailin> sell them a boat instead 13:11 < ParahSailin> and those restriction enzymes are encumbered too 13:11 <@fenn> no way, all that stuff was done in the 70's 13:11 < ParahSailin> those were all enhanced 13:12 < nmz787> i think you can buy domenstically bred jellyfish 13:13 < nmz787> it's a recent thing on kickstarter 13:13 < ParahSailin> that raises issues of animal cruelty 13:13 < nmz787> some dude selling the whole tank and feeder 13:13 < nmz787> aren't they invertebrates? 13:13 < ParahSailin> yeah but they have neurons 13:13 < nmz787> but the original wt parents were illegally caught and held captive in most cases i blieve 13:14 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 13:14 < nmz787> so law only dictaces the children are legal to sell 13:14 <@fenn> it's illegal to catch jellyfish? 13:14 < ParahSailin> possibly, consult a lawyer 13:14 < nmz787> i think it's the captivity thing that's an issue 13:14 < nmz787> or breeding them 13:14 < nmz787> or something 13:14 <@fenn> i thinnk you're going to have a hard time doing anything if you assume everything is illegal 13:14 < nmz787> breeding a wild one is illegal maybe 13:15 < nmz787> everything is illegal 13:15 <@fenn> then kill yourself 13:15 <@fenn> fuck 13:15 <@kanzure> btw selling jellyfish is actually somewhat profitable right now 13:15 <@kanzure> because nobody has any 13:15 < nmz787> what's the best gauge needle to interact with a SureSeal vial? 13:16 <@kanzure> i think it's breeding them that is currently the issue 13:16 <@kanzure> not captivity 13:16 < cathalgarvey> Man, you guys are still talking about me 13:16 < cathalgarvey> I'm touched 13:16 < cathalgarvey> Also, you're all off the mark 13:16 < nmz787> you don't show up enough, we've a queue 13:17 < cathalgarvey> GFP is a red herring here. I'd like to sell something, so I'm using unencumbered fluorophores, but the fluorescence is incidental, just a nice way to test the real thing 13:17 < cathalgarvey> The project is a patent-free, cheap, easy protein purification (by affinity) system 13:17 < cathalgarvey> Existing systems are either patented, meaning startups implementing with them are liable for patent assault, expensive, or just plain terrible 13:17 < ParahSailin> so you're not even going to be selling the fluorophores? 13:18 < cathalgarvey> I have a potential system that's workable, cheap, and the resin is available cheaply anywhere. 13:18 < cathalgarvey> No, I'd happily sell it as a "hello world" if it works, too. But it's basically an experimental platform on which to design other products 13:19 < cathalgarvey> And, being fluorescent, it'd make a great positive control for use with those other products, too 13:19 < cathalgarvey> but as I've never had cause to UV illuminate E.coli cultures on TB prior to this, I had underestimated just how fluorescent normal cells are :x 13:20 < cathalgarvey> and the literature on wtGFP prior to eGFP didn't make a big point of how bad resolution was with wtGFP. 13:20 < cathalgarvey> Because, I guess, they didn't expect better at the time.. 13:20 < cathalgarvey> So I'm in this position which, it turns out in retrospect, was considered normal "at the time", where "my cells are fluorescent green but then all E.coli are" 13:21 < cathalgarvey> I ordered this prior to DNA 2.0 releasing three fluorophores under the BPL (FML) 13:22 -!- nuba [~nuba@pauleira.com] has joined ##hplusroadmap 13:22 < cathalgarvey> So I'm sorely tempted to ditch the effort of working with wtGFP, confirming with DNA2.0 that they are pretty certain their fluorophores are otherwise unencumbered, and using those BPL-licensed ones instead. The yellow one has a nice exitation/emission gap and yellow is very different from the E.coli autofluorescent green. 13:23 <@fenn> by resolution do you mean signal to noise ratio? 13:23 < cathalgarvey> Yea 13:24 < cathalgarvey> E.coli and anything containing yeast extract are both fluorescent under blue/UV, emitting green 13:24 < cathalgarvey> and wtGFP is 20 times weaker than eGFP even when it's working well, but it's so fragile to high temperatures, overexpression, redox etc, that it's hard to know for sure it's even expressing well 13:25 < cathalgarvey> I'm in the uncomfortable position of having no negative controls, too 13:25 < cathalgarvey> which is kind of pissing me off, too. 13:25 < ParahSailin> huh https://www.dna20.com/products/protein-paintbox#3 13:25 < ParahSailin> anyone have these yet? 13:25 < cathalgarvey> My DH10B got corrupted and I'm finding it bizarrely hard to find a vendor.. 13:25 < cathalgarvey> Those are the ones I meant: three of them are BPL licensed now 13:25 < cathalgarvey> I added them to the fastac libs folder 13:26 < ParahSailin> theyre all ip-free it says 13:26 < cathalgarvey> DNA 2.0 have a bad history of not really understanding what IP-free means 13:26 < cathalgarvey> so take them at their word only when they've signed a license saying so: as they did for 3, but not all, of their fluorphores. Are there only three in that kit? (looks) 13:26 <@fenn> how about a different (non-fluorescent) protein indicator such as lactase and X-GAL 13:27 < cathalgarvey> https://gitorious.org/fastac/fastac/blobs/master/libs/FluorescentProteins.fasta 13:27 <@kanzure> DNA2.0 has other weird history- like at fbi-diybio-2012 they said something about selling to non-institutional individuals, but then in their talks about dna filtering, they said the opposite. 13:27 < cathalgarvey> @fenn I could, yes. I just assumed, naively, that wtGFP wasn't that bad. 13:27 < cathalgarvey> lol, DNA filtering 13:27 < cathalgarvey> enzymatic synthesis for the win 13:27 < cathalgarvey> someday.. 13:28 < ParahSailin> i dont see where it says the licenses 13:28 < cathalgarvey> (I wonder what programming language Gitorious thinks my FASTA files are.. Odd syntax highlighting) 13:28 < gradstudentbot> I am kind of curious what he has a Ph.D. in, I can't really find this anywhere, it could be underwater basket weaving for all I know. 13:28 < cathalgarvey> The link to the BPL license is in the comments in the repo link I posted 13:28 < cathalgarvey> Right 13:28 < cathalgarvey> It's been fun folks 13:29 < cathalgarvey> but my laptop is about to become a glorified DVD player for a while 13:29 < cathalgarvey> so gotta logoff 13:29 < gradstudentbot> I think I'll be done in 4 years. 13:29 < cathalgarvey> All the best! 13:29 < cathalgarvey> @gradstudentbot You won't, nobody is 13:29 < gradstudentbot> I think the centrifuge is broken. 13:30 < ParahSailin> it says they're all unpatented 13:30 < ParahSailin> https://www.dna20.com/wp-content/uploads/2013/04/Intellectual_Property_Statement.pdf 13:34 < cathalgarvey> But, the BPL protects against *all future* assertions of IP, too 13:35 -!- makoLime [~mako@103-9-42-133.flip.co.nz] has joined ##hplusroadmap 13:35 < cathalgarvey> until they BPL license or their window for patenting expires, they're not truly "IP free" 13:35 < cathalgarvey> Anyways, gotta go! 13:35 < cathalgarvey> Best, all 13:35 -!- cathalgarvey [~cathalgar@79.97.71.97] has left ##hplusroadmap ["Leaving"] 13:35 < nmz787> i am dang 13:35 < ParahSailin> sanctimonious wanker 13:35 < nmz787> dang 13:35 < nmz787> i wanted to ask him something 13:36 < nmz787> I don't even know wha tBPL is, Bit Pulse Logic??? 13:36 < nmz787> (i know it's not that) 13:36 < ParahSailin> who gives a fuck 13:36 <@kanzure> it's probably the biobrick public license or sometihng 13:36 <@kanzure> *something 13:37 < ParahSailin> public domain is just fine 13:37 <@bkero> is biobrick CC-approved? 13:37 < ParahSailin> i think stallman is probably more pragmatic than that kid 13:38 <@kanzure> BPL is some marketing stunt by the biobricks foundation, but sadly there's only 2 biobricks licensed under that license 13:38 <@kanzure> i guess this fluorophore is a possible addition ? 13:38 <@kanzure> so maybe 5 now? 13:39 <@fenn> https://biobricks.org/bpa/faq/ 13:39 <@kanzure> oh that's bpa not bpl 13:39 <@kanzure> hmm 13:40 <@fenn> BPA's are bad mmkay 13:40 <@kanzure> the plastic junk? 13:40 <@fenn> it's evil industrial chemicals, i know that because it's not natural 13:41 <@fenn> i wonder why they don't retroactively apply the BPA to earlier biobricks 13:42 <@kanzure> because they don't have the licensing figured out laready 13:42 <@kanzure> *already 13:43 <@kanzure> probably the individual schools would assert ownership 13:43 <@fenn> that seems to go against the whole point of having a library of free-to-use parts 13:45 < ParahSailin> they only distribute to academic institutions 13:45 <@kanzure> it's not as free as they claim it, yo 13:46 < ParahSailin> i remember talking to cathal 3 years ago, offering him biobricks 13:46 < ParahSailin> dont think hes accomplished anything in the meantime 13:47 <@kanzure> he's written some software 13:47 < ParahSailin> wet, i mean 13:48 <@kanzure> i think he just described some of his progress above 13:49 < ParahSailin> spend years dicking around then realize that wtgfp is crap and should have just disregarded law? 13:49 < nmz787> no that was just the last year i think 13:50 <@kanzure> huh? it's okay to have to replace a small part of your project. 13:50 <@kanzure> "oh my god something doesn't work, let's stop everything" 13:50 <@kanzure> 1) delete the computer 2) throw out your reagents 3) .. 13:50 <@kanzure> s/delete/wipe 13:52 < ParahSailin> protein purification columns? we have division of labor so that you dont have to make sundry commodities for yourself 14:01 <@kanzure> but i can if i so choose to 14:04 < ParahSailin> amish is not the future of humanity 14:05 < delinquentme> nmz787, do you remember the chemistry paper about 3 months back which was 3d printing crucibles for chemistry? 14:05 <@kanzure> it's not amish 14:05 <@kanzure> just because amish choose to do something that might seem similar doesn't mean it's amish 14:06 <@kanzure> "OH MY GOD THE AMISH USE IPHONES AND SMARTPHONES, THEREFORE WE SHOULDN'T EITHER" 14:06 <@kanzure> also electricity 14:06 <@kanzure> fuck off 14:07 < gradstudentbot> Nobody has tried this before. 14:09 < nmz787> ParahSailin: i just watched a BBC documentary on amish ppl last night 14:10 < nmz787> ParahSailin: they were doing damn well 14:10 < nmz787> delinquentme: yes, it wasn't that amazing 14:10 < delinquentme> nmz787, sure but how can I locate it ? Is "crucuble" the right term? 14:12 < ParahSailin> the amish are pretty rich, i know 14:13 < ParahSailin> i just dont think there's anything particularly virtuous or productive about making your life more difficult 14:15 < nmz787> they mentioned Jesus a lot 14:16 < nmz787> delinquentme: http://www.rsc.org/chemistryworld/2012/08/3d-printed-miniaturised-fluidic-devices 14:17 < delinquentme> nmz787, tyvms! 14:17 -!- Juul [~Juul@208.87.217.74] has joined ##hplusroadmap 14:17 < delinquentme> nmz787, this paper?! 14:20 < nmz787> http://www.nature.com/news/homegrown-labware-made-with-3d-printer-1.10453 14:20 < nmz787> http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.1313.html 14:20 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnchem.1313 14:20 < nmz787> http://www.youtube.com/watch?v=NCfpxA1q4uk 14:53 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 256 seconds] 14:54 <@fenn> jeez $200 just to watch recorded conference talks? what's the world coming to 14:56 -!- oblique [~oblique@unaffiliated/oblique] has joined ##hplusroadmap 14:56 < nmz787> yeah i'm in no position to splurge on that 14:57 < nmz787> i hoped someone who did had posted their code 14:57 <@fenn> .title 14:57 < yoleaux> Chemical Reactors Made By 3-D Printing - YouTube 14:57 < nmz787> i'm sure we could manage a logged-in vimeo scraper 14:57 <@fenn> youtube-dl works on vimeo too 14:58 <@fenn> or do you mean for sb6.0 videos? 14:58 < nmz787> yeah 14:58 < nmz787> the latter 15:01 <@fenn> btw pretty sure most amish use smartphones these days 15:03 <@fenn> at work at least 15:04 -!- upgrayeddd [uid2969@gateway/web/irccloud.com/x-yycmulcjvmupyqsi] has joined ##hplusroadmap 15:11 -!- Ummon [~chatzilla@nmd.sbx05699.placeca.wayport.net] has joined ##hplusroadmap 15:21 <@kanzure> ParahSailin: it's not about making your life more difficult, it's about making reagents more cheaply by owning your own infrastructure. it's about making other downstream things possible that aren't otherwise available if you have to pay $40 million per genome you synthesize. 15:28 -!- HEx [~HEx@hexwab.plus.com] has quit [Read error: Connection reset by peer] 15:43 -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has quit [Remote host closed the connection] 16:20 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 16:22 -!- pan4x [panax@131.247.116.193] has quit [] 16:33 < heath> [15:07:19] Who got mustard on my cell culture? 16:33 < gradstudentbot> Dude, you contaminated my experiment. 16:33 < heath> [15:10:34] how about doing it the hard way, send your customer a jellyfish and a truckload of restriction enzymes 16:44 < ParaSa1lin> its smart to weigh cost and benefits 16:45 < ParaSa1lin> multiply the probability of being liable for 40 million by 40 million, and subtract by the cost of avoiding that risk 16:45 < ParaSa1lin> if its positive, dont do it 16:46 <@fenn> i guess it would be an integral of the probability of being liable for any given amount, summed from negative infinity to positive infinity 16:48 <@fenn> how do you do integrals of functions with uncertainties? 16:49 < gradstudentbot> The gel is streaking. 17:02 * brownies pokes gradstudentbot 17:02 < gradstudentbot> Yeah, but his project was so easy. 17:12 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 17:14 -!- Ummon [~chatzilla@nmd.sbx05699.placeca.wayport.net] has quit [Ping timeout: 240 seconds] 17:34 -!- yorick [~yorick@oftn/member/yorick] has quit [Remote host closed the connection] 17:37 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Quit: the neuronal action potential is an electrical manipulation of reversible abrupt phase changes in the lipid bilayer] 17:58 -!- teleko [~teleko@pool-96-235-9-40.pitbpa.east.verizon.net] has joined ##hplusroadmap 18:08 < ParaSa1lin> fenn, bayes theorem 18:10 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 256 seconds] 18:10 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 18:11 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has joined ##hplusroadmap 18:12 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has joined ##hplusroadmap 18:12 -!- weles [~mariusz@c-71-234-3-169.hsd1.ct.comcast.net] has joined ##hplusroadmap 18:15 -!- ParahSailin_ [~ropoctl@unaffiliated/parahsailin] has joined ##hplusroadmap 18:17 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has quit [Quit: ChatZilla 0.9.90 [SeaMonkey 2.19/20130630011339]] 18:17 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has joined ##hplusroadmap 18:20 -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has quit [Ping timeout: 240 seconds] 18:31 -!- biostudent_ [~chatzilla@46.208.19.205] has joined ##hplusroadmap 18:33 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] 18:33 -!- biostudent_ is now known as biostudent 18:37 -!- Juul [~Juul@208.87.217.74] has quit [Ping timeout: 248 seconds] 18:40 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has quit [Read error: Connection reset by peer] 18:41 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has joined ##hplusroadmap 18:42 -!- underscor [~quassel@192.210.211.75] has joined ##hplusroadmap 18:42 -!- underscor is now known as Guest28997 18:43 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] 18:44 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] 18:46 -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 18:50 -!- Juul [~Juul@208.87.217.74] has joined ##hplusroadmap 18:54 -!- ParahSailin_ [~ropoctl@unaffiliated/parahsailin] has quit [Quit: ParahSailin_] 19:00 -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap 19:03 -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has quit [Ping timeout: 245 seconds] 19:05 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] 19:15 -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has joined ##hplusroadmap 19:17 <@kanzure> bayes bayes bayes 19:17 <@kanzure> stupid gotomeeting why do i even bother 19:24 -!- Juul [~Juul@208.87.217.74] has quit [Ping timeout: 245 seconds] 19:29 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 19:29 -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap 19:37 -!- weles [~mariusz@c-71-234-3-169.hsd1.ct.comcast.net] has quit [Ping timeout: 264 seconds] 19:53 -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has joined ##hplusroadmap 20:04 < heath> benchling launched at sb6.0 20:04 < heath> Benchling just launched at the SB6.0 conference here in London. You're welcome to come check it out at https://benchling.com/signup, with invite code "SB60" 20:04 < heath> We literally just got the last build out the door, so we haven't had much time outside of fixing bugs and server crashes, but rest assured we'll contribute some of our more interesting modules back to the community, as well as pushing some biopython patches upstream. 20:15 < ParaSa1lin> hm i had some patches for biopython 20:16 < heath> ParaSa1lin: what happened to them? 20:16 < ParaSa1lin> forgot what they were though 20:17 <@kanzure> heath: meh, yet another product announcement for something nobody wants 20:17 < ParaSa1lin> oh, yeah i use some c extensions with it 20:17 <@kanzure> biopython changes would be nice, but whatever 20:17 <@kanzure> n 17 20:17 <@kanzure> jdfladjfka 20:17 < ParaSa1lin> but actually all i did was paste the same source into cython and build 20:17 < ParaSa1lin> 20x speedup 20:18 < gradstudentbot> Yeah, I read the paper, I just don't remember the details. 20:18 * brownies pokes gradstudentbot 20:18 < gradstudentbot> Yeah, it should take me about 2 days. 20:25 < heath> gradstudentbot: faster! 20:25 < gradstudentbot> I lost my pipette. 20:26 < heath> gradstudentbot: no excuses 20:26 < gradstudentbot> It's not really significant, but there's definitely a trend. 20:27 < heath> i'm impressed with the bot's past two responses 20:31 < mensch> gradstudentbot: melatonin 20:31 < gradstudentbot> Should this be on ice? 20:31 * kanzure pokes gradstudentbot 20:31 < gradstudentbot> I can't help it, I just like science so much. 20:32 < heath> [11:20:20] hey if you wanna be helpful can you go find the paper about cellular uptake of different dna origami shapes 20:32 < heath> kanzure: did you find that 20:32 <@kanzure> no, you did 20:32 < heath> great 20:32 <@kanzure> you even linked me to it 20:33 < heath> wasn't sure that's the one you wanted 20:37 -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap 20:44 < heath> http://www.kickstarter.com/projects/formlabs/form-1-an-affordable-professional-3d-printer 20:44 < heath> .title http://www.xconomy.com/boston/2013/06/24/formlabs-3d-systems-in-settlement-talks-over-3d-printing-patent/ 20:44 < yoleaux> Formlabs, 3D Systems in Settlement Talks over 3D Printing Patent | Xconomy 20:47 -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has quit [Ping timeout: 240 seconds] 20:52 <@kanzure> isn't that old stuff by now 20:55 -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap 21:26 -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has quit [Quit: Leaving] 21:47 < heath> paperbot: http://onlinelibrary.wiley.com/doi/10.1002/yea.1412/abstract 21:47 < paperbot> http://libgen.org/scimag1/10.1002/yea.1412.pdf 21:50 < heath> paperbot: http://www.annualreviews.org/doi/abs/10.1146/annurev-bioeng-070909-105238?journalCode=bioeng 21:51 < paperbot> http://libgen.org/scimag/get.php?doi=10.1146%2Fannurev-bioeng-070909-105238 21:53 -!- delinquentme [~asdfasdf@66.233.132.203] has joined ##hplusroadmap 21:57 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 22:17 -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has quit [Quit: Lost terminal] 22:18 -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has quit [Ping timeout: 245 seconds] 22:26 < ParaSa1lin> (http://libgen.org/scimag1/10.1002/yea.1412.pdf 22:27 < delinquentme> you know what I like BOUT my projects 22:27 < delinquentme> they're benign 22:33 -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] 23:01 -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has quit [Ping timeout: 246 seconds] 23:04 -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap 23:18 -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap 23:37 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] 23:44 -!- marciogm [~textual@177.106.57.86] has quit [Quit: Computer has gone to sleep.] 23:57 -!- kmo [122@unaffiliated/kmo] has joined ##hplusroadmap --- Log closed Fri Jul 12 00:00:23 2013