--- Log opened Thu Apr 05 00:00:39 2018
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05:18 < JayDugger> https://patents.google.com/patent/US20180047462A1/en?oq=US20180047462A1
05:18 < JayDugger> "Encapsulating Magnetic Fields for Plasma Confinement"
05:18 < JayDugger> Lockheed Martin's fusion reactor patent
05:24 < JayDugger> "FIG. 2 illustrates an examples aircraft system 200 that utilizes one or more fusion reactors 110,..."
05:24 < JayDugger> "In some embodiments, hot coolant is a mixture of FLIBe (i.e., a mixture of lithium fluoride (LiF) and beryllium fluoride (BeF₂)) or LiPb."
06:04 < kanzure> schindler_: you're just going to have to hack the post install function yourself. run it in an interactive python interpreter until it works.
06:13 < kanzure> "Spatial organization of projection neurons in the mouse auditory cortex identified by in situ barcode sequencing" https://www.biorxiv.org/content/early/2018/04/03/294637 https://twitter.com/TonyZador/status/981693522276487174
06:16 < kanzure> "resolved neurons by combining the high throughput of DNA sequencing with the high spatial resolution of microscopy. We used BARseq to determine the projections of 1309 neurons in mouse auditory cortex to 11 targets. We observed 264 distinct projection patterns. ... By sequencing in situ, BARseq has the potential to bridge anatomical, transcriptomic, functional, and other approaches at single ...
06:16 < kanzure> ...neuron resolution with high throughput, and thereby offer unprecedented insight of the structure and function of a neural circuit."
06:17 < kanzure> "The development of loop-mediated isothermal amplification (LAMP) assays for the rapid authentication of five forbidden vegetables in strict vegetarian diets" https://www.nature.com/articles/srep44238 https://twitter.com/SynBio1/status/981506864692293632
06:18 < kanzure> uggghhh
06:18 < kanzure> .tw https://twitter.com/synbioSRI/status/981468670244409345
06:18 < yoleaux> EVENT- Join us 11 April @PantonArms for a talk with Todd Kuiken (@DrToddOliver @NCState) about ensuring safety within the rapidly expanding community of amateur biologists and the growing network of community labs. Co-organised w @CSERCambridge https://bit.ly/2pziz1D (@synbioSRI)
06:23 < kanzure> "AlterEgo: A personalized wearable silent speech interface" http://fluid.media.mit.edu/sites/default/files/p43-kapur.pdf
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07:23 < kanzure> "Highly efficient and versatile plasmid-based gene editing in primary T cells" http://www.jimmunol.org/content/200/7/2489
07:28 < kanzure> giulio prisco article on nectome https://motherboard.vice.com/en_us/article/43baam/uploading-the-mind-to-a-computer-cryonics
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08:08 < kanzure> various open-source software things for fgpa stuff http://www.fabienm.eu/flf/open-source-fpga-map/
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08:13 < kanzure> does addgene publish sequences? someone should scrape that.
08:13 < kanzure> http://www.addgene.org/popular-plasmids/
08:14 < kanzure> http://www.addgene.org/kits/zhang-tale-toolbox/
08:14 < kanzure> http://www.addgene.org/32185/
08:14 < kanzure> http://www.addgene.org/32185/sequences/
08:14 < kanzure> yeah ok we should scrape that
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08:22 < kanzure> https://www.addgene.org/crispr/
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09:40 < kanzure> https://www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676/
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13:24 < CaptHindsight> what's the lowest going price for custom oligos?
13:34 < kanzure> haha good luck finding that.. they don't advertise that well, because that would be a leak of confidential information.
13:34 < kanzure> try twist then try IDT, those are usually the best bets.
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15:06 < kanzure> http://www.nealelab.is/blog/2017/7/19/rapid-gwas-of-thousands-of-phenotypes-for-337000-samples-in-the-uk-biobank
15:06 < kanzure> https://hail.is/
15:12 < kanzure> a thing for generating papers from a pile of wrapped software experiments? https://github.com/systemslab/popper
15:30 < kanzure> "Cortical plasticity induced by inhibitory neuron transplantation" http://science.sciencemag.org/content/327/5969/1145 (2010)
15:42 < kanzure> https://bitcoinmagazine.com/articles/history-lightning-brainstorm-beta/
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16:50 < CaptHindsight> http://www.idtdna.com/pages/products/custom-dna-rna/dna-oligos/custom-dna-oligos
16:55 < CaptHindsight> http://www.operon.com/products/custom-oligos/custom-oligo-pricelist.aspx
16:56 < CaptHindsight> http://www.genelink.com/newsite/products/unmodoligosPRICELIST.asp
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16:57 < CaptHindsight> http://www.bionexus.net/product/Custom+Oligo%27s+by+email.html
16:57 < CaptHindsight> http://www.biosyn.com/dna-synthesis.aspx
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17:49 < CaptHindsight> http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30121-8
17:49 < CaptHindsight> Human Hippocampal Neurogenesis Persists throughout Aging
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18:10 < nmz787> schindler_: I get that error on ubuntu myself, because the python-BRLCAD script doesn't look at BRLCAD_PREFIX
18:11 < nmz787> schindler_: see my comments here http://gnusha.org/logs/2018-03-26.log
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18:12 < nmz787> schindler_: err, I guess I was talking about BRLCAD_PATH... but maybe that's also supposed to work?
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18:19 < nmz787> schindler_: "sudo pip install -U brlcad"   seems to work for me (at least installation doesn't show obvious failure)... but when I run "sudo python setup.py install" from the github repo, it fails with your error message
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20:37 < juul> yashgaroth: yeah you're right about integration strategy. do you have experience with other methods of yeast chromosomal integration? and yes, respecting patents is a pain in the ass
20:37 < juul> the only good thing about patents is that they actually expire
20:38 < juul> and since a lot of the basics were discovered/invented more than 20 years ago it's mostly a matter of documenting this fact
20:38 < juul> of course due to the USPTO not having the resources to do decent prior arts searches you get patents on things that were invented years ago anyway
20:39 < juul> and if they sue you on what should be an invalid patent it's not like you're likely to have the money to fight
20:40 < juul> but there's a relatively new process where you can create a third-party pre-issuance submission
20:41 < juul> this allows anyone to look at the in-process patent application and submit relevant prior art for free
20:41 < juul> in a sense crowdsourcing the prior arts search
20:41 < juul> you can even set up search queries and the system will send you emails when a new hit appears
20:42 < juul> the unfortunate thing is that you can pay for and expedited process which can conclude in less than 18 months if you have all your ducks in a row (read: really good lawyers)
20:42 < juul> and patent applications do not become public until 18 months have passed
20:42 < juul> they used this trick for one of the core CRISPR patents
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22:13 < yashgaroth> juul: if you have antibiotic selection then random integration of plasmid should be enough for your purposes, but I haven't kept track of whether interesting stuff is/n't still patented
22:13 < juul> ok, well i can do the patent check if you know of any interesting methods
22:14 < juul> i would honestly prefer not to require use of zeocin
22:14 < kanzure> juul: let's scrape addgene.org
22:15 < kanzure> juul: do you know them? can we get a database dump?
22:15 < yashgaroth> maybe some of the transposases are out of patent, they've been around forever; that way you can maybe get duplication as it copies itself all over the genome
22:15 < juul> kanzure: yeah i know them. i've visited. but it would take a long long time to clear each plasmid of third party rights
22:16 < juul> what would you do with the database dump?
22:16 < juul> yashgaroth: thanks, i'll look into those :)
22:16 < kanzure> bury it in the ground for a rainy day
22:16 < juul> ah
22:17 < kanzure> these sequences are useful.
22:17 < juul> well our laywer is talking to them about integrating OpenMTA into their system so i'll ask
22:17 < yashgaroth> and yeah zeocin sucks, you pay out the nose for it
22:17 < kanzure> their amazon aws s3 bucket requires signatures for every file download so it's really annoying to scrape this stuff
22:17 < juul> ah
22:18 < kanzure> fucking scholars...
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22:18 < juul> they said they didn't have the IT resources to add an OpenMTA option for new submissions (i should think that would be a tiny tweak to a form somewhere) so i'm not hopeful
22:19 < kanzure> their thing is django
22:19 < kanzure> tell them that you'll add it yourself
22:19 < juul> i'd probably have to sign a bunch of NDAs. i don't like doing that
22:20 < kanzure> alright, sounds like it's time for a heist
22:21 < kanzure> http://www.addgene.org/browse/pi/3578/
22:21 < kanzure> Reverse for 'browse.pi' with arguments '(u'The_Genetically_Encoded_Neuronal_Indicator_and_Effector_Project_(GENIE)',)' not found. 1 pattern(s) tried: ["(?P<alias>[\\w\\s\\'\\.\\-]+_[\\w\\s\\'\\.\\-]+)/$"]
22:21 < juul> hah, they're moving headquarters so maybe intercepting their computers in transit. i'm thinking Italian Job style
22:31 < kanzure> they have physical computers wow
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23:08 < schindler_> nmz787, I'll try and fix the post install script like kanzure suggested. I'm still trying to figure out what paths work for it :P
23:09 < schindler_> nmz787: BRLCAD_PATH is supposed to point to what exactly? The build/bin folder or the trunk? I'm a little in the dark about this.
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--- Log closed Fri Apr 06 00:00:39 2018