| --- Log opened Thu Jul 11 00:00:22 2013 | ||
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Remote host closed the connection] | 00:03 | |
| -!- delinquentme [~asdfasdf@66.233.132.203] has joined ##hplusroadmap | 00:19 | |
| -!- delinquentme [~asdfasdf@66.233.132.203] has quit [Quit: Leaving] | 00:38 | |
| -!- 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 | 00:48 | |
| -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap | 00:51 | |
| -!- kmo is now known as kajetan | 00:51 | |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has joined ##hplusroadmap | 01:14 | |
| -!- klafka [~klafka@c-24-6-18-31.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] | 01:18 | |
| -!- chido [chidori@pasky.or.cz] has quit [Ping timeout: 240 seconds] | 02:11 | |
| -!- chido [chidori@pasky.or.cz] has joined ##hplusroadmap | 02:11 | |
| -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 02:26 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] | 02:28 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 02:59 | |
| -!- monkeynipples [monkeynipp@gateway/shell/xzibition.com/x-ajlxxhlqjhjzgswa] has quit [Ping timeout: 246 seconds] | 03:42 | |
| -!- monkeynipples [monkeynipp@gateway/shell/xzibition.com/x-isqvcjwfwiasbwmd] has joined ##hplusroadmap | 03:43 | |
| -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap | 03:50 | |
| -!- weles [~mariusz@71.234.3.169] has joined ##hplusroadmap | 04:15 | |
| -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has joined ##hplusroadmap | 04:20 | |
| -!- weles [~mariusz@71.234.3.169] has quit [Ping timeout: 240 seconds] | 05:01 | |
| -!- makoLime [~mako@103-9-42-133.flip.co.nz] has quit [Ping timeout: 248 seconds] | 05:18 | |
| -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap | 05:32 | |
| 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 | 05:56 |
| -!- 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 | 06:05 | |
| -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has joined ##hplusroadmap | 06:28 | |
| -!- mietek [mietek@bak.io] has left ##hplusroadmap [] | 06:43 | |
| -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap | 07:05 | |
| -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap | 07:22 | |
| -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 264 seconds] | 07:30 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 07:53 | |
| -!- 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 | 08:02 | |
| -!- hehelleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 248 seconds] | 08:12 | |
| -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap | 08:33 | |
| -!- ybit is now known as heath | 08:34 | |
| @kanzure | chris_99: that sounds like a lie ("first") | 08:36 |
| -!- HEx1 [~HEx@hexwab.plus.com] has quit [Ping timeout: 240 seconds] | 08:38 | |
| @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! | 08:39 |
| @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 | 08:42 |
| 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/ | 08:43 |
| heath | https://www.youtube.com/watch?feature=player_detailpage&v=HjR6hzAYygk#t=114s | 08:44 |
| 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..." | 08:45 |
| @kanzure | i met paul once. nice fellow. he also helped out on nanoengineer-1. | 08:46 |
| 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 | 08:47 |
| 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 | 08:48 |
| 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 | 08:49 |
| 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? | 08:50 |
| 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 | 08:51 |
| jonathan_ | " 29% reported they had snooped on someone else’s phone. Among those under 35, however, almost half – 47% – admitted snooping." | 08:56 |
| @kanzure | is it snooping if someone gives you their phone and lets you poke around? | 08:57 |
| jonathan_ | no | 08:57 |
| jonathan_ | it's snooping when a jealous girl sneaks over to your phone and goes thru it while you're in the bathroom. | 08:58 |
| * heath is looking for a project to work on.. | 09:00 | |
| * heath is considering making an open version of http://cando-dna-origami.org/ | 09:00 | |
| @kanzure | heath: how about fixing nanoengineer? https://github.com/kanzure/nanoengineer#readme | 09:02 |
| @kanzure | heath: or paperbot. :( | 09:02 |
| -!- 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 | 09:04 |
| 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 | 09:05 |
| 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.. | 09:06 |
| 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] | 09:07 | |
| 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: | 09:08 |
| cathalgarvey | PySplicer, which was such a mess to begin with that I basicaly rewrote it recently | 09:09 |
| 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 | 09:10 |
| 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. | 09:11 |
| 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. | 09:12 |
| @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 | 09:13 |
| 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 | :) | 09:14 |
| 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] | 09:15 | |
| heath | ParahSailin: me? | 09:16 |
| heath | ah, cathal | 09:16 |
| 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. | 09:18 |
| heath | i'm not sure | 09:19 |
| @kanzure | hey if you wanna be helpful can you go find the paper about cellular uptake of different dna origami shapes | 09:20 |
| heath | oooh, that sounds fun | 09:21 |
| heath | mirkin was talking about his SNAs yesterday and states his group had removed the sphere the nucleic acides were attached to | 09:22 |
| -!- 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? | 09:23 |
| heath | favorite quote of the day | 09:27 |
| heath | [11:14:03] <ParahSailin> just use genome compiler, i hear they've done all the heavy lifting on DNA programming languages | 09:27 |
| @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 ... | 09:31 |
| @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" | 09:32 |
| -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] | 09:38 | |
| jonathan_ | the defcon guys are mostly lame | 09:41 |
| 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. | 09:42 |
| jonathan_ | omg i can run a scanner and discover all the hidden ssid's around me! i'm so uber hax0r | 09:44 |
| 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 | 09:45 |
| 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 | 09:47 |
| @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? | 09:48 |
| jonathan_ | next step for diybio: double agents | 09:49 |
| jonathan_ | fake projects on kickstarter are not enough! | 09:49 |
| @kanzure | double agents? so the fbi will claim they are fbi, but really they are what? | 09:50 |
| jonathan_ | the diybio hax0rs will claim they are uber uber and really they are working for the nsa | 09:52 |
| jonathan_ | and also paid fbi informants | 09:53 |
| nmz787 | bring on the salary | 09:53 |
| jonathan_ | see? you're all sell outs | 09:53 |
| nmz787 | too many underground projects around, need unseen regulatory oversight | 09:54 |
| 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 | 09:55 |
| nmz787 | get em to start freezing themselves with a faulty process, to weed out the crowd | 09:56 |
| jonathan_ | then again, the fbi is not that clever, so... | 10:04 |
| 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 | 10:14 |
| -!- 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 | 10:24 | |
| nmz787 | so where is the SB6.0 torrent? | 10:36 |
| @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] | 10:47 | |
| -!- ParahSailin [~Rob@unaffiliated/parahsailin] has joined ##hplusroadmap | 10:49 | |
| 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 | 10:50 |
| @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/ | 10:51 |
| @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 | 10:52 |
| -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has left ##hplusroadmap ["Leaving"] | 11:02 | |
| -!- weles [~mariusz@wsip-70-183-164-169.ri.ri.cox.net] has joined ##hplusroadmap | 11:03 | |
| 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 | 11:17 |
| nmz787 | we're cool | 11:18 |
| nmz787 | wait | 11:18 |
| nmz787 | that isn't the right pdf | 11:18 |
| 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 | 11:19 |
| @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 | 11:20 |
| 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 | 11:21 |
| @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 | 11:22 |
| nmz787 | paperbot: http://link.springer.com/content/pdf/10.1007%2F978-3-642-02391-0.pdf | 11:23 |
| @kanzure | <xmp:CreatorTool>Arbortext Advanced Print Publisher 9.0.223/W Unicode</xmp:CreatorTool> | 11:23 |
| paperbot | http://libgen.org/scimag4/10.1007/978-3-642-02391-0.pdf | 11:23 |
| @kanzure | <pdf:Producer>Acrobat Distiller 8.1.0 (Windows)</pdf:Producer> | 11:23 |
| @kanzure | <xmpMM:DocumentID>uuid:0d239f6c-0a54-4aca-94d3-00b018e3db1a</xmpMM:DocumentID> | 11:23 |
| nmz787 | huh, so my ezproxy can get the whole book, but libgen cant | 11:23 |
| @kanzure | <x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Adobe XMP Core 4.2.1-c043 52.372728, 2009/01/18-15:08:04 "> | 11:23 |
| @kanzure | <?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"? | 11:24 |
| nmz787 | wait so why is that paper on diyhplus? | 11:29 |
| nmz787 | pdx doesnt have access to it | 11:29 |
| 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 | 11:30 |
| nmz787 | so are pdfs on libgen assumed to be stable or not? | 11:31 |
| 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 | 11:32 |
| 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? | 11:33 |
| nmz787 | yes | 11:34 |
| nmz787 | well | 11:34 |
| 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 | 11:35 |
| 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 | 11:37 |
| gradstudentbot | Who's in charge of the master mix? | 11:38 |
| 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 | 11:46 |
| @kanzure | they might have saved them on livestream.com already. or they might be the type that will upload them in 4 months. | 11:47 |
| 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 | 11:49 |
| nmz787 | didnt work | 11:50 |
| nmz787 | .wa 0.5mL 10mM datp to grams | 11:57 |
| 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 | 11:58 |
| 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 | 11:59 |
| nmz787 | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/2443811 | 12:09 |
| 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 | 12:12 |
| 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 | 12:13 |
| 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 | 12:14 |
| -!- marciogm [~textual@177.106.57.86] has quit [Quit: Textual IRC Client: www.textualapp.com] | 12:16 | |
| -!- randalla1ordon is now known as randallagordon | 12:18 | |
| -!- 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) :) | 12:21 |
| 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? | 12:23 |
| nmz787 | accented magician | 12:24 |
| -!- oblique [~oblique@87-143-95.netrun.cytanet.com.cy] has quit [Read error: Connection reset by peer] | 12:24 | |
| nmz787 | how have your projects been coming along cathalgarvey | 12:25 |
| -!- kmo [~kmo@unaffiliated/kmo] has quit [Remote host closed the connection] | 12:25 | |
| 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 | 12:26 |
| 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. | 12:27 |
| 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 | 12:28 |
| nmz787 | ala kazam, wtGFP just got mutated into betterGFP | 12:29 |
| 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 | 12:30 |
| 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. | 12:31 |
| 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. | 12:32 |
| 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.. | 12:33 |
| cathalgarvey | ..sequence? | 12:34 |
| cathalgarvey | I said Free/Libre, I'm not gonna be keeping the source secret ffs | 12:34 |
| nmz787 | he's saying if you stomp other patents | 12:35 |
| 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 | :) | 12:36 |
| 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? | 12:37 |
| gradstudentbot | Have you read this paper? | 12:38 |
| 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 | 12:39 |
| nmz787 | an engineer that's good with poetry! | 12:40 |
| 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. | 12:41 |
| @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. | 12:42 |
| 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 | 12:43 |
| 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 | 12:44 |
| 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] | 12:45 | |
| 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 | 12:46 |
| 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 | 12:47 |
| ParahSailin | i bet you dont jaywalk either | 12:48 |
| nmz787 | i was born in the city that invented jaywalking | 12:50 |
| nmz787 | but that's a bit less penalized and certainly less financially risky | 12:51 |
| @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] | 12:52 | |
| 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 | 12:53 |
| 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 | 12:54 |
| @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 | 12:55 |
| ParahSailin | nmz787: but his customers are just gonna be kids playing with toys | 12:56 |
| ParahSailin | any grownup customer making a business out of it would presumably be competent enough to know how to navigate IP law | 12:57 |
| @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 | 12:58 | |
| 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" | 12:59 |
| 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. | 13:00 |
| 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 | 13:01 |
| 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 | 13:02 |
| 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 | 13:03 |
| 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 | 13:04 |
| 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 | 13:05 |
| 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 | 13:06 |
| gradstudentbot | Who got mustard on my cell culture? | 13:07 |
| ParahSailin | so it sounds like customers using his stuff would be taking legal risks in using it anyway | 13:08 |
| 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) | 13:09 |
| @fenn | how about doing it the hard way, send your customer a jellyfish and a truckload of restriction enzymes | 13:10 |
| 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 | 13:11 |
| nmz787 | i think you can buy domenstically bred jellyfish | 13:12 |
| 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 | 13:13 |
| -!- 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 | 13:14 |
| 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? | 13:15 |
| @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 | 13:16 |
| 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? | 13:17 |
| 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 | 13:18 |
| 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 | 13:19 |
| 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" | 13:20 |
| cathalgarvey | I ordered this prior to DNA 2.0 releasing three fluorophores under the BPL (FML) | 13:21 |
| -!- 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. | 13:22 |
| @fenn | by resolution do you mean signal to noise ratio? | 13:23 |
| cathalgarvey | Yea | 13:23 |
| 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 | 13:24 |
| 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 | 13:25 |
| 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 | 13:26 |
| 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.. | 13:27 |
| 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 | 13:28 |
| 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. | 13:29 |
| ParahSailin | it says they're all unpatented | 13:30 |
| ParahSailin | https://www.dna20.com/wp-content/uploads/2013/04/Intellectual_Property_Statement.pdf | 13:30 |
| cathalgarvey | But, the BPL protects against *all future* assertions of IP, too | 13:34 |
| -!- 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 | 13:35 |
| 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 | 13:36 |
| 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 | 13:37 |
| @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? | 13:38 |
| @fenn | https://biobricks.org/bpa/faq/ | 13:39 |
| @kanzure | oh that's bpa not bpl | 13:39 |
| @kanzure | hmm | 13:39 |
| @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 | 13:40 |
| @fenn | i wonder why they don't retroactively apply the BPA to earlier biobricks | 13:41 |
| @kanzure | because they don't have the licensing figured out laready | 13:42 |
| @kanzure | *already | 13:42 |
| @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 | 13:43 |
| ParahSailin | they only distribute to academic institutions | 13:45 |
| @kanzure | it's not as free as they claim it, yo | 13:45 |
| ParahSailin | i remember talking to cathal 3 years ago, offering him biobricks | 13:46 |
| ParahSailin | dont think hes accomplished anything in the meantime | 13:46 |
| @kanzure | he's written some software | 13:47 |
| ParahSailin | wet, i mean | 13:47 |
| @kanzure | i think he just described some of his progress above | 13:48 |
| 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 | 13:49 |
| @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 | 13:50 |
| ParahSailin | protein purification columns? we have division of labor so that you dont have to make sundry commodities for yourself | 13:52 |
| @kanzure | but i can if i so choose to | 14:01 |
| ParahSailin | amish is not the future of humanity | 14:04 |
| 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 | 14:05 |
| @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 | 14:06 |
| gradstudentbot | Nobody has tried this before. | 14:07 |
| nmz787 | ParahSailin: i just watched a BBC documentary on amish ppl last night | 14:09 |
| 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? | 14:10 |
| ParahSailin | the amish are pretty rich, i know | 14:12 |
| ParahSailin | i just dont think there's anything particularly virtuous or productive about making your life more difficult | 14:13 |
| nmz787 | they mentioned Jesus a lot | 14:15 |
| nmz787 | delinquentme: http://www.rsc.org/chemistryworld/2012/08/3d-printed-miniaturised-fluidic-devices | 14:16 |
| delinquentme | nmz787, tyvms! | 14:17 |
| -!- Juul [~Juul@208.87.217.74] has joined ##hplusroadmap | 14:17 | |
| delinquentme | nmz787, this paper?! | 14:17 |
| 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 | 14:20 |
| -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 256 seconds] | 14:53 | |
| @fenn | jeez $200 just to watch recorded conference talks? what's the world coming to | 14:54 |
| -!- oblique [~oblique@unaffiliated/oblique] has joined ##hplusroadmap | 14:56 | |
| nmz787 | yeah i'm in no position to splurge on that | 14:56 |
| 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 | 14:57 |
| @fenn | or do you mean for sb6.0 videos? | 14:58 |
| nmz787 | yeah | 14:58 |
| nmz787 | the latter | 14:58 |
| @fenn | btw pretty sure most amish use smartphones these days | 15:01 |
| @fenn | at work at least | 15:03 |
| -!- upgrayeddd [uid2969@gateway/web/irccloud.com/x-yycmulcjvmupyqsi] has joined ##hplusroadmap | 15:04 | |
| -!- Ummon [~chatzilla@nmd.sbx05699.placeca.wayport.net] has joined ##hplusroadmap | 15:11 | |
| @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. | 15:21 |
| -!- HEx [~HEx@hexwab.plus.com] has quit [Read error: Connection reset by peer] | 15:28 | |
| -!- EnLilaSko [EnLilaSko@unaffiliated/enlilasko] has quit [Remote host closed the connection] | 15:43 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] | 16:20 | |
| -!- pan4x [panax@131.247.116.193] has quit [] | 16:22 | |
| heath | [15:07:19] <gradstudentbot> Who got mustard on my cell culture? | 16:33 |
| gradstudentbot | Dude, you contaminated my experiment. | 16:33 |
| heath | [15:10:34] <fenn> how about doing it the hard way, send your customer a jellyfish and a truckload of restriction enzymes | 16:33 |
| ParaSa1lin | its smart to weigh cost and benefits | 16:44 |
| 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 | 16:45 |
| @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 | 16:46 |
| @fenn | how do you do integrals of functions with uncertainties? | 16:48 |
| gradstudentbot | The gel is streaking. | 16:49 |
| * brownies pokes gradstudentbot | 17:02 | |
| gradstudentbot | Yeah, but his project was so easy. | 17:02 |
| -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] | 17:12 | |
| -!- Ummon [~chatzilla@nmd.sbx05699.placeca.wayport.net] has quit [Ping timeout: 240 seconds] | 17:14 | |
| -!- yorick [~yorick@oftn/member/yorick] has quit [Remote host closed the connection] | 17:34 | |
| -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Quit: the neuronal action potential is an electrical manipulation of reversible abrupt phase changes in the lipid bilayer] | 17:37 | |
| -!- teleko [~teleko@pool-96-235-9-40.pitbpa.east.verizon.net] has joined ##hplusroadmap | 17:58 | |
| ParaSa1lin | fenn, bayes theorem | 18:08 |
| -!- 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 | 18:10 | |
| -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has joined ##hplusroadmap | 18:11 | |
| -!- 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 | 18:12 | |
| -!- ParahSailin_ [~ropoctl@unaffiliated/parahsailin] has joined ##hplusroadmap | 18:15 | |
| -!- 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 | 18:17 | |
| -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has quit [Ping timeout: 240 seconds] | 18:20 | |
| -!- biostudent_ [~chatzilla@46.208.19.205] has joined ##hplusroadmap | 18:31 | |
| -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] | 18:33 | |
| -!- biostudent_ is now known as biostudent | 18:33 | |
| -!- Juul [~Juul@208.87.217.74] has quit [Ping timeout: 248 seconds] | 18:37 | |
| -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has quit [Read error: Connection reset by peer] | 18:40 | |
| -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has joined ##hplusroadmap | 18:41 | |
| -!- underscor [~quassel@192.210.211.75] has joined ##hplusroadmap | 18:42 | |
| -!- underscor is now known as Guest28997 | 18:42 | |
| -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] | 18:43 | |
| -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 240 seconds] | 18:44 | |
| -!- helleshin [~talinck@69-61-156-24.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap | 18:46 | |
| -!- Juul [~Juul@208.87.217.74] has joined ##hplusroadmap | 18:50 | |
| -!- ParahSailin_ [~ropoctl@unaffiliated/parahsailin] has quit [Quit: ParahSailin_] | 18:54 | |
| -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap | 19:00 | |
| -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has quit [Ping timeout: 245 seconds] | 19:03 | |
| -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] | 19:05 | |
| -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has joined ##hplusroadmap | 19:15 | |
| @kanzure | bayes bayes bayes | 19:17 |
| @kanzure | stupid gotomeeting why do i even bother | 19:17 |
| -!- Juul [~Juul@208.87.217.74] has quit [Ping timeout: 245 seconds] | 19:24 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 19:29 | |
| -!- biostudent [~chatzilla@46.208.19.205] has joined ##hplusroadmap | 19:29 | |
| -!- weles [~mariusz@c-71-234-3-169.hsd1.ct.comcast.net] has quit [Ping timeout: 264 seconds] | 19:37 | |
| -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has joined ##hplusroadmap | 19:53 | |
| 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. | 20:04 |
| ParaSa1lin | hm i had some patches for biopython | 20:15 |
| heath | ParaSa1lin: what happened to them? | 20:16 |
| ParaSa1lin | forgot what they were though | 20:16 |
| @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 | 20:17 |
| 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. | 20:18 |
| heath | gradstudentbot: faster! | 20:25 |
| gradstudentbot | I lost my pipette. | 20:25 |
| heath | gradstudentbot: no excuses | 20:26 |
| gradstudentbot | It's not really significant, but there's definitely a trend. | 20:26 |
| heath | i'm impressed with the bot's past two responses | 20:27 |
| 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. | 20:31 |
| heath | [11:20:20] <kanzure> 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 | 20:32 |
| heath | wasn't sure that's the one you wanted | 20:33 |
| -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap | 20:37 | |
| 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 | 20:44 |
| -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has quit [Ping timeout: 240 seconds] | 20:47 | |
| @kanzure | isn't that old stuff by now | 20:52 |
| -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap | 20:55 | |
| -!- delinquentme [~asdfasdf@192-195-81-250.PUBLIC.monkeybrains.net] has quit [Quit: Leaving] | 21:26 | |
| heath | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/yea.1412/abstract | 21:47 |
| paperbot | http://libgen.org/scimag1/10.1002/yea.1412.pdf | 21:47 |
| heath | paperbot: http://www.annualreviews.org/doi/abs/10.1146/annurev-bioeng-070909-105238?journalCode=bioeng | 21:50 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1146%2Fannurev-bioeng-070909-105238 | 21:51 |
| -!- delinquentme [~asdfasdf@66.233.132.203] has joined ##hplusroadmap | 21:53 | |
| -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap | 21:57 | |
| -!- mensch [~mensch@c-50-157-136-178.hsd1.ma.comcast.net] has quit [Quit: Lost terminal] | 22:17 | |
| -!- ianmathwiz7 [~chatzilla@ip65-46-170-6.z170-46-65.customer.algx.net] has quit [Ping timeout: 245 seconds] | 22:18 | |
| ParaSa1lin | (http://libgen.org/scimag1/10.1002/yea.1412.pdf | 22:26 |
| delinquentme | you know what I like BOUT my projects | 22:27 |
| delinquentme | they're benign | 22:27 |
| -!- biostudent [~chatzilla@46.208.19.205] has quit [Ping timeout: 245 seconds] | 22:33 | |
| -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has quit [Ping timeout: 246 seconds] | 23:01 | |
| -!- Juul [~Juul@50-0-83-158.dsl.static.sonic.net] has joined ##hplusroadmap | 23:04 | |
| -!- marciogm [~textual@177.106.57.86] has joined ##hplusroadmap | 23:18 | |
| -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] | 23:37 | |
| -!- marciogm [~textual@177.106.57.86] has quit [Quit: Computer has gone to sleep.] | 23:44 | |
| -!- kmo [122@unaffiliated/kmo] has joined ##hplusroadmap | 23:57 | |
| --- Log closed Fri Jul 12 00:00:23 2013 | ||
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!