--- Log opened Sun Jul 17 00:00:59 2016 00:11 < CaptHindsight> kanzure: the dye stuff is to lend electrons to the photoprocesses 00:22 -!- ebowden_ [~ebowden@2001:8003:100e:c500:53e:a7e2:58b8:cd6f] has quit [Remote host closed the connection] 00:23 -!- ebowden_ [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has joined ##hplusroadmap 00:25 -!- Th3_Prince [~b3nszy@132.147.10.243] has quit [Remote host closed the connection] 00:31 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-eahkdezqbpeezcvl] has quit [Quit: Connection closed for inactivity] 00:56 -!- Burninate [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has joined ##hplusroadmap 00:57 -!- mabel [~mabel@unaffiliated/jacco] has joined ##hplusroadmap 00:58 -!- Burnin8 [~Burn@pool-108-31-204-167.washdc.fios.verizon.net] has quit [Ping timeout: 272 seconds] 01:00 -!- nildicit [~nildicit@unaffiliated/nildicit] has left ##hplusroadmap ["Leaving"] 01:03 -!- ebowden_ 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[~Gurkengla@dslb-178-005-223-183.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 252 seconds] 05:58 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 06:06 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ktpntvcegsjdbzfp] has joined ##hplusroadmap 06:09 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Remote host closed the connection] 06:09 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 07:31 < kanzure> from the department of "why did we bother looking into this, again?" http://voxeu.org/article/cheaper-flights-and-scientific-collaboration 07:39 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Remote host closed the connection] 07:56 < kanzure> "Microfluidic devices and methods for gene synthesis" https://patents.google.com/patent/US9216414B2/en?assignee=Gen9 (2009) 07:56 < kanzure> "Assembly of high fidelity polynucleotides" https://patents.google.com/patent/US9217144B2/en?assignee=Gen9 (2010) 08:00 < kanzure> "Mutant cas9 proteins" https://patents.google.com/patent/CA2930829A1/ 08:03 < kanzure> "Sequencing by structure assembly" https://patents.google.com/patent/CA2850509A1/ seems to be something about sequencing by hybridization or sequencing by ligase 08:03 < kanzure> mentions "Photocleavable biotin derivatives: a versatile approach for the isolation of biomolecules" 08:07 -!- Orpheon [~Orpheon@68.168.62.81.dynamic.wline.res.cust.swisscom.ch] has quit [Read error: Connection reset by peer] 08:08 < kanzure> "High-throughput single cell barcoding" https://patents.google.com/patent/CA2814049A1/ 08:13 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 08:14 < kanzure> "Barcoded protein array for multiplex single-molecule interaction profiling" https://patents.google.com/patent/WO2015148606A9/ 08:16 < kanzure> "Spatial sequencing of nucleic acids using DNA origami probes" https://patents.google.com/patent/US20150292007A1 08:18 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 240 seconds] 08:18 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 08:18 < kanzure> "Methods and compounds for chemical ligation" https://patents.google.com/patent/US8481258B2/ 08:43 -!- Orpheon [~Orpheon@68.168.62.81.dynamic.wline.res.cust.swisscom.ch] has joined ##hplusroadmap 08:49 < kanzure> "Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases" http://journal.frontiersin.org/article/10.3389/fgene.2014.00036/full 08:49 < kanzure> "The mechanism of nucleobase recognition by the class-II CCA-adding enzyme is distinct from that observed in the class-I CCA-adding enzyme (Figures 2D,E). The template for the CCA-addition by the class-II CCA-adding enzyme is composed of the protein itself, rather than the RNA–protein complex as in the class-I CCA-adding enzyme. The protein-template of the class-II CCA-adding enzymes was confirmed by the mutations of Asp and Arg in the ... 08:49 < kanzure> ... neck domain. The rational mutagenesis of the two key residues in the neck domain allowed the enzyme to add other nucleotides in vitro (Cho et al., 2007)." 08:50 < kanzure> "Cho et al., 2007" is "Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases" http://www.pnas.org/content/104/1/54.short 08:52 < kanzure> "... and we transformed the B. stearothermophilus CCA-adding enzyme into a poly(C,A) polymerase by mutations in helix J that appear, based on the apoenzyme structure, to sterically limit addition to CCA. We also transformed the B. stearothermophilus CCA-adding enzyme into a dCdCdA-adding enzyme by mutating an arginine that interacts with the incoming ribose 2′ hydroxyl. Most importantly, we found that mutations in helix J can affect ... 08:52 < kanzure> ... the specificity of the nucleotide binding site some 20 Å away, suggesting that the specificity of both class I and II enzymes may be dictated by an intricate network of hydrogen bonds involving the protein, incoming nucleotide, and 3′ end of the tRNA." 08:52 < kanzure> .wik polynucleotide adenylyltransferase 08:52 < yoleaux> "In enzymology, a polynucleotide adenylyltransferase (EC 2.7.7.19) is an enzyme that catalyzes the chemical reaction" — https://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase 08:53 < kanzure> ".. its two products are pyrophosphate and RNA with an extra adenosine nucleotide at its 3' end." 08:53 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 08:54 < kanzure> "The rate at which PAP adds adenine nucleotides is dependent on the presence of another regulatory protein, PABPII (poly-adenine binding protein II). The first few nucleotides added by PAP are added very slowly, but the short polyadenine tail is then bound by PABPII, which accelerates the rate of adenine addition by PAP. The final tail is about 200-250 adenine nucleotides long." 09:15 < kanzure> .wik GLD-2 09:15 < yoleaux> "GLD-2 (which stands for Germ Line Development 2) is a cytoplasmic poly(A) polymerase (cytoPAPs) which adds successive AMP monomers to the 3’ end of specific RNAs, forming a poly(A) tail, which is a process known as polyadenylation." — https://en.wikipedia.org/wiki/GLD-2 09:18 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Quit: Leaving] 09:21 < kanzure> "GLD2 poly(A) polymerase is required for long-term memory" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567210/ (2008) 09:24 < kanzure> er.. nevermind. seems obvious that translation would be required for that anyway. it would be more interesting if that was about storage of mRNAs. 09:28 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has joined ##hplusroadmap 09:48 -!- sandeepkr_ [~sandeep@111.235.64.4] has joined ##hplusroadmap 09:52 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Ping timeout: 240 seconds] 09:52 -!- juri_ [~juri@192.94.73.193] has joined ##hplusroadmap 10:07 -!- ArturSha1 [~ArturShai@37.218.162.107] has quit [Ping timeout: 276 seconds] 10:10 < CaptHindsight> besides http://www.the-odin.com/ who is making any DIY or open HARDWARE or PHYSICAL devices, biological components, tissues etc vs just software? 10:10 -!- sandeepkr__ [~sandeep@111.235.64.4] has joined ##hplusroadmap 10:11 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 10:12 < CaptHindsight> https://synbiota.com 10:14 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Ping timeout: 260 seconds] 10:15 < kanzure> there are many.. check the logs i guess. even as way back as openpcr, opentrons, schloendorn's company thing, p212121, simon's scikit stuff, .. 10:16 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 10:17 < kanzure> backyard brains.. 10:17 < kanzure> it's a really long list. i don't think that's a reasonable request. :P 10:18 < CaptHindsight> http://openpcr.org/ who does this with a straight face? 10:18 < kanzure> yeah i didn't say it's good 10:19 < CaptHindsight> did they do this mock some of the maker projects by using wood grain? 10:19 < kanzure> no they did it because they hate their primary audience 10:20 < kanzure> further evidence in favor of my assessment: they used adobe air 10:21 < chris_99> heh, apparently air isn't even supported on linux 10:21 < kanzure> right. like i said, they are a hateful group of people... 10:22 < CaptHindsight> ok, then how about a list of good projects :) 10:22 < CaptHindsight> looks like a really short list 10:23 < kanzure> hackteria does a lot of hardware projects 10:23 < kanzure> i really think it would be more efficient to read the logs than query me for the name of each and every hardware group out there 10:23 < kanzure> http://gnusha.org/logs/ 10:24 -!- augur [~augur@2602:304:cdac:e260:98b0:4555:519b:d116] has joined ##hplusroadmap 10:24 < CaptHindsight> so it looks like I really do have to do everything 10:24 < kanzure> biocurious does a bunch of hardware projects although i can't comment on quality 10:24 < kanzure> while you are busy doing everything, you should read all of the emails sent to https://groups.google.com/group/diybio 10:25 < kanzure> "pearl biotech" was the name of the openpcr crew 10:25 < CaptHindsight> thanks for the warning 10:25 < kanzure> :) 10:25 < CaptHindsight> I just expected more was already done 10:26 < kanzure> nmz787 was working on an open-source spectrophotometer setup, https://github.com/nmz787/open-spectrometer 10:28 < CaptHindsight> I figured maybe nmz787, fenn and chris_99 built some hardware 10:28 < chris_99> i'm attempting to work on a cheapo spectrometer next week, playing with the Pi camera, if that works i'll try a linear ccd 10:29 < CaptHindsight> http://www.openspectrometer.com/ domain for sale 10:29 < kanzure> probably a query like https://groups.google.com/forum/#!searchin/diybio/companies would work for your purposes 10:30 < CaptHindsight> I just assumed you might know since you want to build so many things 10:31 < kanzure> yeah but.. i mean.. it's not all loaded into working memory at the moment. 10:31 < CaptHindsight> but there's not much 10:31 < CaptHindsight> short list 10:32 < CaptHindsight> oh well 10:32 < kanzure> there's a bunch of different projects, they are just scattered in the channel logs 10:32 < kanzure> for example, there was an open-source optical microscopy setup 10:32 < kanzure> there was an open-source patch clamp device... that was pretty neat. but there's no way i'm going to spontaneously remember it's name. 10:32 < kanzure> POSAM counts, right? 10:33 < kanzure> *its 10:33 < CaptHindsight> I should look for someone to write a translator for the opentrons json files 10:34 < kanzure> what does it need to be translated into? 10:35 < CaptHindsight> so we can use it to generate proper G-code for use with Linuxcnc 10:35 < kanzure> can you give a link to the json file 10:35 < kanzure> this is pretty simple 10:36 < CaptHindsight> json to G-code 10:36 < kanzure> an example json file would be required to write a quick program to do this. it's only a 2d grid right? 10:36 < streety> I came across https://hackaday.io/project/4141-c12666ma-micro-spectrometer a little while ago. Doesn't go into the UV as would be needed but an interesting project and component 10:37 < chris_99> While LinuxCNC does seem cool, i'm confused by the advantage of using a PC over an MCU to control the axis, as doesn't LinuxCNC require a realtime kernel etc. 10:37 < kanzure> nothing wrong with a realtime kernel :) 10:37 < kanzure> throwing $3 linux boards into everything is not a big deal 10:37 < CaptHindsight> chris_99: how do you add more axis, cameras, lasers etc to a fing *dunio? 10:38 < chris_99> who said arduino 10:38 < kanzure> also if we're going to standardize around something, it seems like using a widely-supported operating system is a good idea 10:39 < kanzure> https://sites.google.com/site/neurorighter/ "NeuroRighter is an open-source system for multi-electrode closed-loop recording and stimulation" 10:40 < kanzure> CaptHindsight: https://upverter.com/hardware-startups/ 10:40 < CaptHindsight> kanzure: http://mix.bio/protocols/p10s 10:40 < CaptHindsight> they have a list of basic templates there 10:41 < kanzure> O_o they are pre-generated templates? wat 10:41 < CaptHindsight> you can mod them to your delight 10:43 < CaptHindsight> chris_99: IIRC they used a duino for the motion controller 10:43 < kanzure> "transfer": [{"from": {"container": "plate", "location": "A2", "touch-tip": false}, "to": {"container" : "plate", "location" : "A3", "tip-offset" : 0, "delay" : 0, "touch-tip" : false}, "volume": 10}] 10:43 < chris_99> CaptHindsight, i was thinking more of something like http://smoothieware.org/smoothieboard but yeah, cameras etc. are a good point 10:43 < CaptHindsight> oh sorry yeah they used a poopieboard 10:43 < CaptHindsight> idiots 10:44 < kanzure> you would want the pipette volume stuff to be controlled through gcode as well? 10:44 < CaptHindsight> everything 10:44 < CaptHindsight> well everything should be controllable 10:44 < CaptHindsight> not everything fits well into g-code 10:45 < kanzure> i bet maaku/transcriptic already has something that does this 10:45 < CaptHindsight> a frame buffer for an inkjet for instance 10:45 < kanzure> if they aren't using linuxcnc then i'm quitting life 10:45 < CaptHindsight> you can easily sync motion from gcode to trigger data to be read from a frame buffer 10:46 < CaptHindsight> but the image just doesn't fit into G-code 10:46 < chris_99> wouldn't you get higher precision if you used something other than a PC though, because of the CPU cache, context switching etc. though 10:46 < kanzure> are you using gcode for your inkjet frame buffers? 10:47 < CaptHindsight> chris_99: there's no issue with precision, the top manufacturers of CNC machines moved to x96 PC's 10-20 years ago 10:47 < CaptHindsight> x86 even :) 10:47 < kanzure> CaptHindsight: there's also a bunch of hardware stuff from marcin jakubowski's "open source ecology" crew... does any of that count? 10:47 < chris_99> ah interesting, i'm happy to be proven wrong, was just curious, the x86 chip drives the servos directly? 10:47 < kanzure> oh you wanted biotech-specific. nevermind. 10:47 < CaptHindsight> kanzure: gcode controls the inkjets motion 10:47 < kanzure> yes i know 10:48 < CaptHindsight> it can output a real time signal to the frame buffer 10:48 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 10:49 < CaptHindsight> it can also gate the encoder pulses to be a clock for the frame buffer that loads the printheads with data 10:50 < kanzure> you are doing that with gcode? 10:50 < CaptHindsight> chris_99: x86 + FPGA 10:51 < CaptHindsight> kanzure: all the g-code can do it setup an M code to output a real time signal that is triggered by some position of the machine... 10:51 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 10:52 < CaptHindsight> say when the machine reaches X 100, Y 100 it outputs a pulse 10:52 < kanzure> doing signal generation from gcode seems like a terrible horrible chore 10:52 < kanzure> yashgaroth: http://diyhpl.us/~bryan/papers2/polymerase/The%20evolution%20of%20DNA%20polymerases%20with%20novel%20activities.pdf.evolved-or-rationally-designed-polymerases.png 10:52 < chris_99> CaptHindsight, ah gotcha 10:53 < CaptHindsight> that pulse can be the gate for the clock that puts the fires the first drops out of the heads... 10:54 < CaptHindsight> then you gate the encoder pulses (lets say every 8 pulses the next row of drops should fire) to be the clock to fire drops out the printhead 10:55 < CaptHindsight> kanzure: the gcode doesn't do signal generation, it just triggers events in the vase of an inkjet or laser 10:55 < CaptHindsight> vase/case 10:57 < CaptHindsight> the opentrons team needs their 8020 catalog taken away from them 10:58 < CaptHindsight> they picked out some pretty flimsy extrusions 11:00 -!- Aurelius_Work [~cpopell@static-108-28-104-83.washdc.fios.verizon.net] has quit [Ping timeout: 258 seconds] 11:01 < CaptHindsight> looking over their files again and I guess someone could spend a few days just using CAM in their head to rewrite the few files 11:03 < CaptHindsight> chris_99: is it something in the breakfast cereals during the 90's that causes people to think poopieboard or duino vs a PC and Linuxcnc when it comes to motion control? 11:05 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 11:09 < kanzure> "Taking fingerprints of DNA polymerases: multiplex enzyme profiling on DNA arrays" https://kops.uni-konstanz.de/bitstream/handle/123456789/9804/Kranaster_Angew_Chem_Int_Ed_2009.pdf?sequence=1&isAllowed=y (2009) 11:10 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 11:10 < kanzure> cool a "compartmentalized ribosome display" technique 11:25 < chris_99> heh, what don't you like about the smoothieboard 11:27 < chris_99> do you use LinuxCNC with an FPGA? 11:31 < kanzure> "Design and synthesis of digitally encoded polymers that can be decoded and erased" http://www.nature.com/ncomms/2015/150526/ncomms8237/full/ncomms8237.html 11:31 < kanzure> "Here we describe a non-natural information-containing macromolecule that can store and retrieve digital information. Monodisperse sequence-encoded poly(alkoxyamine amide)s were synthesized using an iterative strategy employing two chemoselective steps: the reaction of a primary amine with an acid anhydride and the radical coupling of a carbon-centred radical with a nitroxide. [...] Moreover, the formed sequences are easy to decode using ... 11:31 < kanzure> ... tandem mass spectrometry." 11:32 < chris_99> it's just driving servos directly with the PC and interface that confuses me, but i can understand doing that with an FPGA 11:32 < CaptHindsight> chris_99: it's missing lots of features and it's underpowered 11:32 < CaptHindsight> it's a shortsighted design 11:33 < CaptHindsight> a mistake kids often make 11:34 < CaptHindsight> if I were designing a high volume dedicated Cartesian robot for an application I still would use a smoothie 11:35 < CaptHindsight> sorry would not use a smoothie 11:35 < chris_99> so do you use an FPGA then? 11:36 < kanzure> "A General Approach to Sequence-Controlled Polymers Using Macrocyclic Ring Opening Metathesis Polymerization 11:36 < kanzure> " 11:36 < kanzure> their idea is to use a ring molecue structure, where the head and tail are bonded together i guess? 11:37 < CaptHindsight> chris_99: yes, usually, and especially with servos 11:37 < kanzure> i don't really see how they expect the two ends to be physically proximal.. 11:37 < chris_99> gotcha, cool 11:40 < chris_99> yeah i can definitely see how with that config it'd be very customisable 11:42 -!- Orpheon [~Orpheon@68.168.62.81.dynamic.wline.res.cust.swisscom.ch] has quit [Remote host closed the connection] 11:47 < kanzure> "Reverse transcription of threose nucleic acid by a naturally occurring DNA polymerase" http://onlinelibrary.wiley.com/doi/10.1002/cbic.201600338/abstract 11:47 < kanzure> "Geobacillus stearothermophilus (Bst) DNA polymerase I functions as an efficient and faithful threose nucleic acid (TNA)-dependent DNA polymerase. Bst DNA polymerase generates ~2-fold more cDNA with 3-fold fewer mutations than Superscript II (SSII), which was previously the best TNA reverse transcriptase. Notably, Bst also functions under standard magnesium-dependent conditions, while SSII requires manganese ions to relax the enzyme's ... 11:47 < kanzure> ... substrate specificity. We further demonstrate that Bst DNA polymerase can support the in vitro selection of TNA aptamers by evolving a TNA aptamer to human α-thrombin." 11:52 < kanzure> we should stalk arizona's matt dunn 11:53 < kanzure> and andrew hatch, who has done high-throughput microfluidics for polymerase evolution and other reasons 11:54 -!- Netsplit *.net <-> *.split quits: _hanhart, souljack, Aurelius_Home, poohbear, night, c0rw1n_, adamg 12:00 -!- Netsplit over, joins: c0rw1n_ 12:01 < chris_99> CaptHindsight, so with an FPGA+x86, is it essentially parsing the g-code with the x86, then say for an instruction like 'X-0.5 Y0.' passing it to the FPGA, to step to that position 12:06 < CaptHindsight> chris_99: http://linuxcnc.org/docs/2.5/pdf/LinuxCNC_Developer_Manual.pdf page 4 for a block dia 12:07 < chris_99> ta 12:08 < CaptHindsight> http://linuxcnc.org/docs/2.6/html/code/LinuxCNC-block-diagram-small.png 12:08 < CaptHindsight> found just that page 12:11 < chris_99> so which bit would be the FPGA? 12:13 -!- souljack [souljack@gateway/shell/xshellz/x-mydtqkezntxdjylm] has joined ##hplusroadmap 12:13 -!- poohbear [~poohbear@unaffiliated/tigger] has joined ##hplusroadmap 12:13 -!- night [~Adifex@unaffiliated/adifex] has joined ##hplusroadmap 12:14 -!- Aurelius_Home [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 12:14 -!- adamg [~akg@50.242.93.33] has joined ##hplusroadmap 12:15 -!- _hanhart [~hanhart@static.141.80.201.138.clients.your-server.de] has joined ##hplusroadmap 12:21 < kanzure> "Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces" http://www.nature.com/articles/srep12066 (2015) 12:21 < kanzure> "we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes." 12:25 < kanzure> "New oxidative labels for electrochemical detection of DNA" http://cccc.uochb.cas.cz/symposium_series/14/365/ 12:25 < CaptHindsight> chris_99: part of the PID and lower 12:27 < CaptHindsight> chris_99: with the FPGA over ethernet the PC just needs a 1-4mS interval 12:28 < chris_99> ah gotcha 12:28 < chris_99> i'm just looking at the mesa drivers 12:28 < CaptHindsight> chris_99: if you have faster IO that needs to interact with the trajectory planner then you can stick the FPGAin a PCIe slot 12:28 < kanzure> "Artificial genetic sets composed of size-expanded base pairs" http://onlinelibrary.wiley.com/doi/10.1002/anie.201305267/full (2013) (this seems to literally be "larger nucleotides") 12:29 < chris_99> nice CaptHindsight 12:30 < CaptHindsight> chris_99: Linuxcnc has evolved around machine tools but it may be expanded to control robots, automation, interface to comedi 12:31 < CaptHindsight> comedi.org is down :( 12:31 < CaptHindsight> ^^ data acquisition 12:31 < CaptHindsight> real time 12:33 < chris_99> ah cool 12:37 < chris_99> i'm sure i recall reading something about positioning robot arms being insanely hard for some reason 12:37 < CaptHindsight> look at all the axis 12:37 < CaptHindsight> and range of motion 12:38 < CaptHindsight> and there are multiple ways to be in the same position 12:38 < chris_99> ah, makes sense, do the arms tend to have any feedback information, so you know it's in the right place in the different axis 12:38 < CaptHindsight> chris_99: openCV also works with Linuxcnc 12:39 < chris_99> oh neat, i've played a teeny bit with opencv 12:39 < CaptHindsight> chris_99: yes always have encoders 12:42 < CaptHindsight> harmonic drives for joints 12:42 < chris_99> can the output from an encoder ever differ somewhat from the reality of its position, over time, so say i repeatedly tell it to move from X1,Y1,Z1 to X2,Y2,Z2 12:42 < chris_99> and back 12:42 < chris_99> continuously 12:43 < chris_99> will it drift 12:43 < CaptHindsight> it should not if operating properly 12:43 < chris_99> in accuracy 12:43 < chris_99> ah 12:43 < CaptHindsight> https://en.wikipedia.org/wiki/Harmonic_drive 12:43 < kanzure> "Temperature sensing using red fluorescent protein" http://link.springer.com/article/10.1007/s12257-014-0456-z 12:43 < kanzure> "Genetically encoded fluorescent proteins are extensively utilized for labeling and imaging proteins, organelles, cell tissues, and whole organisms. In this study, we explored the feasibility of mRFP1 and its variants for measuring intracellular temperature. A linear relationship was observed between the temperature and fluorescence intensity of mRFP1 and its variants. Temperature sensitivities of E. coli expressing mRFP1, mRFP-P63A and ... 12:44 < kanzure> ... mRFP-P63A[(4R)-FP] were −1.27%, −1.26% and −0.77%/°C, respectively. Finally, we demonstrated the potentiality of mRFP1 and its variants as an in vivo temperature sensor." 12:44 < CaptHindsight> https://en.wikipedia.org/wiki/Rotary_encoder#Absolute_and_incremental_encoders 12:44 < kanzure> "Engineering lead-sensing GFP through rational designing" http://pubs.rsc.org/is/content/articlelanding/2014/cc/c4cc07163h 12:44 < chris_99> CaptHindsight, thanks, never heard of that mechanism before 12:44 < CaptHindsight> chris_99: low to no lash 12:47 < CaptHindsight> chris_99: I have some with accuracy down to +- 0.002 deg 12:47 < chris_99> haha wow 12:47 < chris_99> what do you use them for 12:48 < CaptHindsight> I build custom machines and robots 12:48 < chris_99> ahh nice 12:49 < chris_99> what kind of encoder gives you that accuracy 12:49 < kanzure> "Directed evolution of DNA polymerases for next generation sequencing" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043640/ (2010) 12:49 < chris_99> along with the fancy mechanics of course 12:51 < CaptHindsight> chris_99: some are down to 32b per rev so 4 billion counts per turn 12:51 < chris_99> Wow, is that for a robot arm? 12:52 < CaptHindsight> installed +/- 1 arc second 12:52 < CaptHindsight> if you want 12:52 < CaptHindsight> the lobger the arm the lower the accuracy 12:52 < CaptHindsight> lobger/longer 12:52 < CaptHindsight> Staubli arms <1m in length have repeatability ~25um 12:53 < chris_99> why's the longer the arm the lower the accuracy, because it's hard to maintain the weight of a longer arm? 12:53 < CaptHindsight> yeah, flex 12:53 < chris_99> ah 12:54 < CaptHindsight> http://www.ebay.com/itm/STAUBLI-RX90-Robot-arm-with-CS7-RX90-controller-and-tech-/321410909135 12:54 < chris_99> i occasionally search for robot arms, but i imagine they're v. hard to get to work, without the controller 12:55 < CaptHindsight> we swap them and use Linuxcnc 12:55 < chris_99> oh neat, how hard is it to do that? like are the electronics of an arm fairly simple 12:55 < CaptHindsight> servo motor with encoder 12:56 < CaptHindsight> so you might have to swap the encoder if it has some proprietary format 12:56 < chris_99> do they not have their own weird controller before that 12:56 < CaptHindsight> you just yank it 12:56 < chris_99> which you'd bypass? 12:56 < chris_99> ah cool 12:57 < CaptHindsight> http://www.staubli.com/en/robotics/6-axis-scara-industrial-robot/low-payload-6-axis-scara-robot/6-axis-industrial-robot-tx2-40/ 12:57 < CaptHindsight> Repeatability ±0.02 mm ^^^ 12:57 < chris_99> oh also don't they use compressed air? 12:58 < CaptHindsight> some as a brake 12:58 < chris_99> ah, so the air isn't to actually alter the position? 12:58 < CaptHindsight> bbl 12:58 < chris_99> toodles 12:58 < CaptHindsight> pneumatic robot would not be that accurate 13:26 -!- sandeepkr_ [~sandeep@111.235.64.4] has joined ##hplusroadmap 13:30 -!- sandeepkr__ [~sandeep@111.235.64.4] has quit [Ping timeout: 244 seconds] 13:37 -!- AmbulatoryC0rtex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 13:40 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Ping timeout: 260 seconds] 13:40 -!- sandeepkr__ [~sandeep@111.235.64.4] has joined ##hplusroadmap 13:43 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Ping timeout: 252 seconds] 13:57 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 14:04 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 14:06 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 14:06 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 14:08 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 252 seconds] 14:10 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 14:13 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 14:48 < nmz787> http://www.todayonline.com/singapore/spore-researchers-papers-retracted-ntu-professor-fired-over-falsified-data 14:48 < kanzure> i seem to be missing a chunk of data 14:48 < kanzure> i am pretty sure we have discussed a "writeozyme" before 14:48 < kanzure> but it's not showing up in the logs? 14:48 < nmz787> we should start a blacklist of bad scientists 14:49 < nmz787> or 'questionable' 14:49 < kanzure> nmz787: phone for a few minutes? 14:51 < nmz787> sure, lemme go in the other room 14:52 < nmz787> ready 14:58 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 240 seconds] 15:00 -!- ebowden_ [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has joined ##hplusroadmap 15:01 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 15:05 -!- ebowden_ [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has quit [Ping timeout: 260 seconds] 15:09 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 15:10 < kanzure> hmm i sent an email in 2008 saying i knew how to make polymerase pause. but i didn't write down the method? wat? 15:10 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 240 seconds] 15:14 < Jawmare> a lot of research scandal for biological chemistry stuff 15:14 < Jawmare> I wonder why 15:21 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Ping timeout: 244 seconds] 15:22 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 264 seconds] 15:25 -!- Dumuzi [Dumuzi@gateway/shell/panicbnc/x-fhiexdzhlpqdugse] has quit [Ping timeout: 258 seconds] 15:32 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 15:35 -!- GeneralK47 [~urchin@89.17.3.60] has joined ##hplusroadmap 15:35 -!- nildicit [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 15:57 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 240 seconds] 16:01 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 16:01 < fenn> spelled "writozyme" 16:01 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 16:02 < fenn> i thought it was more recent than 2010 though 16:06 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 16:30 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 16:43 -!- GeneralK47 [~urchin@89.17.3.60] has quit [Quit: Leaving] 16:55 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 17:00 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 17:17 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 17:31 < kanzure> template-independent DNA polymerase http://diyhpl.us/~bryan/papers2/polymerase/Genetic%20information%20'created'%20by%20archaebacterial%20DNA%20polymerase%20-%201997.pdf 17:31 < kanzure> nmz787: ^ 17:31 < kanzure> (not TdT) 17:31 < kanzure> fenn: apparently it was emailed to the original hplusroadmap mailing list. ancient history. 17:49 -!- augur [~augur@2602:304:cdac:e260:98b0:4555:519b:d116] has quit [Remote host closed the connection] 17:56 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has joined ##hplusroadmap 18:00 -!- ebowden_ [~ebowden@2001:8003:100e:c500:a541:dba1:12a4:b193] has quit [Ping timeout: 260 seconds] 18:26 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 252 seconds] 18:41 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has joined ##hplusroadmap 18:43 -!- delinquentme [ad0b667c@gateway/web/cgi-irc/kiwiirc.com/ip.173.11.102.124] has joined ##hplusroadmap 18:46 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 18:58 < delinquentme> Is there an IRC channel dedicated to MEMS / microfabrication ? 19:01 -!- ebowden_ [~ebowden@101.180.249.107] has joined ##hplusroadmap 19:09 < nmz787> #homecmos 19:10 < nmz787> it is relatively quiet, but there are ppl you just need to idle 19:10 < nmz787> or maybe they have logs 19:10 < nmz787> if they do just ask and mention you'll check the logs 19:13 < kanzure> delinquentme: why do you ask 19:16 < delinquentme> price to feature size 19:17 < delinquentme> and costs for wafers per generation and feature size 19:17 < delinquentme> fuck. blah. that senseless. 19:18 < delinquentme> I want to make grids of given sizes and determine whats the best way to get the largest wafer of these per minimum feature size corresponding to generation of machine 19:21 < nmz787> delinquentme: have you cold-called fab companies? 19:22 < nmz787> i.e. foundrycontact@intel.com 19:24 < nmz787> http://www.intel.com/content/www/us/en/foundry/overview.html 19:24 < nmz787> huh, there is a lot more info on there I didn't know was public 19:24 < delinquentme> nmz787: have i told you you're my fav person ever for having htose emaulz 19:25 < nmz787> (well I got the email from that page) :) 19:28 < delinquentme> nmz787: kanzure you guys know kent kemmish right? 19:28 < delinquentme> hes looking for markets for mechanical nanopores 19:30 < kanzure> yes 19:30 < kanzure> well... we run into him. i have at least. 19:30 < kanzure> it's hard to not run into people when you're as large as neptune 19:39 < nmz787> delinquentme: if you were provided the raman spectroscope/microscope setup... could you build the scanning system out of a 32kHz RTC crystal for this: https://en.wikipedia.org/wiki/Tip-enhanced_Raman_spectroscopy 19:41 -!- delinquentme [ad0b667c@gateway/web/cgi-irc/kiwiirc.com/ip.173.11.102.124] has quit [Quit: http://www.kiwiirc.com/ - A hand crafted IRC client] 19:41 -!- delinquentme [ad0b667c@gateway/web/cgi-irc/kiwiirc.com/ip.173.11.102.124] has joined ##hplusroadmap 19:41 < nmz787> delinquentme: is the idea already MEMS-ified? last I knew, it was two huge macro plates with super-fine positioning control on them... I mean, is the cubic space requirement in the 100nm x 100nm x 100nm size range? 19:42 < nmz787> or is this part of your challenge? 19:42 < nmz787> finding someone that needs the devices, and also a company to help MEMS-ify it? 19:44 < delinquentme> nmz787: unsure how to answer whether its MEMS-ified 19:44 < delinquentme> as in " are the lithographic masks already made ?" 19:45 < delinquentme> no. but we know were' after grids of holes in an insulating material 19:45 < nmz787> no, as in, could you black-box the device into a given volume that someone would incorporate further into a nano/micro machine? 19:45 < kanzure> yashgaroth: hey where are you 19:45 < delinquentme> yeah thats possible 19:46 < yashgaroth> hmm? 19:46 < kanzure> yashgaroth: up for a phone call? 19:46 < yashgaroth> ya ok, you got my # right? 19:47 < delinquentme> I was actually just looking into chromatography as some resins have a upper limit on the pressures they're capable of handling ... whereas what hes working on... would be able to handle much higher pressures as its doesnt operate on a porous / crushable resin 19:47 < kanzure> seered into my heart 19:49 < nmz787> delinquentme: http://pdxscholar.library.pdx.edu/cgi/viewcontent.cgi?article=1114&context=phy_fac 19:50 < nmz787> "Field programmable gate array based reconfigurable scanning probe/optical microscope" 19:52 < nmz787> https://www.pdx.edu/nano-development-lab/tenom-tip-enhanced-near-field-optical-microscopy 19:53 < nmz787> so the scanning probe microscope is basically just some gold tip scanned above the sample 19:53 < delinquentme> fuckkkk 19:53 < delinquentme> thats a cool piece of equipment 19:54 < delinquentme> " The instrument has the ability to image at room temperature and atmospheric pressure or under 19:54 < delinquentme> liquid." 19:55 < nmz787> this also seems relevant http://biomed.tamu.edu/obsl/obsl/Documents/pdfs/Wang-SERSoptofluidic_labonachip.pdf 19:57 < nmz787> 'just add some gold dust to it' seems like magical leprechaun voodoo 20:09 -!- ebowden_ [~ebowden@101.180.249.107] has quit [Remote host closed the connection] 20:10 -!- ebowden_ [~ebowden@2001:8003:100e:c500:817d:2034:73eb:c66] has joined ##hplusroadmap 20:11 -!- justanot1eruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 20:11 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 20:12 -!- justanot1eruser is now known as justanotheruser 20:30 -!- ebowden_ [~ebowden@2001:8003:100e:c500:817d:2034:73eb:c66] has quit [Remote host closed the connection] 20:30 -!- ebowden_ [~ebowden@2001:8003:100e:c500:817d:2034:73eb:c66] has joined ##hplusroadmap 20:35 < delinquentme> kanzure: waiting on that emailzu 20:37 -!- delinquentme [ad0b667c@gateway/web/cgi-irc/kiwiirc.com/ip.173.11.102.124] has quit [Quit: http://www.kiwiirc.com/ - A hand crafted IRC client] 20:44 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-vmljbnehirggzula] has joined ##hplusroadmap 20:55 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 272 seconds] 20:56 < kanzure> huh? i had sent already. 21:03 -!- Filosofem [~Jawmare@unaffiliated/jawmare] has joined ##hplusroadmap 21:06 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has quit [Ping timeout: 240 seconds] 21:24 -!- AmbulatoryC0rtex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Read error: Connection reset by peer] 21:28 -!- ArturSha1 [~ArturShai@37.218.162.107] has joined ##hplusroadmap 21:45 < nmz787> kanzure: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502528/ 21:45 < nmz787> .title 21:45 < yoleaux> Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces 21:46 < kanzure> i was looking at that earlier today (or yesterday) 21:47 < nmz787> http://www.google.je/patents/WO2007039305A1?cl=en 21:47 < nmz787> .title 21:47 < yoleaux> Patent WO2007039305A1 - Pleckstrin-based fusion protein and method for monitoring of enzyme ... - Google Patents 21:50 -!- augur [~augur@2602:304:cdac:e260:95f8:628b:53e6:bb26] has joined ##hplusroadmap 21:55 -!- augur [~augur@2602:304:cdac:e260:95f8:628b:53e6:bb26] has quit [Ping timeout: 250 seconds] 22:11 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 244 seconds] 22:13 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has quit [Remote host closed the connection] 22:32 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ktpntvcegsjdbzfp] has quit [Quit: Connection closed for inactivity] 22:34 < kanzure> at $0.01/genome you could synthesize 100 million unique mutant protein sequences (say ~3.5kbp) for $1 22:36 < kanzure> although you probably wouldn't need to make 100 million mistakes before getting the protein right 22:38 < kanzure> it's not enough bp to iterate through all amino acid space but you shouldn't be doing that anyway. 22:52 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 22:52 -!- augur [~augur@2602:304:cdac:e260:44f6:295a:746e:a7c8] has joined ##hplusroadmap 23:10 < kanzure> "DNA sequencing using electrical conductance measurements of a DNA polymerase" http://www.nature.com/nnano/journal/v8/n6/abs/nnano.2013.71.html 23:10 < kanzure> "Here, we show that single DNA molecules can be sequenced by monitoring the electrical conductance of a phi29 DNA polymerase as it incorporates unlabelled nucleotides into a template strand of DNA. The conductance of the polymerase is measured by attaching it to a protein transistor that consists of an antibody molecule (immunoglobulin G) bound to two gold nanoparticles, which are in turn connected to source and drain electrodes. The ... 23:10 < kanzure> ... electrical conductance of the DNA polymerase exhibits well-separated plateaux that are ~3 pA in height. Each plateau corresponds to an individual base and is formed at a rate of ~22 nucleotides per second. Additional spikes appear on top of the plateaux and can be used to discriminate between the four different nucleotides. We also show that the sequencing platform works with a variety of DNA polymerases and can sequence difficult ... 23:10 < kanzure> ... templates such as homopolymers." 23:10 < kanzure> ( https://ir.nctu.edu.tw/bitstream/11536/22351/1/000319979400018.pdf ) 23:11 < kanzure> "Recent progress in atomistic simulation of electrical current DNA sequencing" http://arxiv.org/pdf/1411.3437 23:18 < kanzure> that polymerase electrical conductance paper is pretty cool. you could probably monitor for incorporation events. 23:19 < kanzure> and then if you get the wrong incorporation, maybe you can trigger some sort of reversal error correction mechanism to fix the previous mistake. not sure. 23:38 < nmz787> kanzure: that "DNA sequencing using electrical conductance measurements of a DNA polymerase" I feel like had non-reproducible methods section 23:38 < kanzure> hrm 23:38 < nmz787> like the paper they quoted for the transistor attachment method was their own publication 23:39 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 23:39 < kanzure> citing yourself is pretty common 23:40 < kanzure> "citing yourself is pretty common" - me 23:43 < chris_99> heh 23:45 < nmz787> yeah it is just very vague 23:45 < kanzure> maybe it's in a patent :\ 23:49 -!- drewbot [~cinch@ec2-54-162-141-64.compute-1.amazonaws.com] has quit [Remote host closed the connection] 23:50 -!- drewbot [~cinch@ec2-174-129-100-67.compute-1.amazonaws.com] has joined ##hplusroadmap 23:50 < kanzure> "Editorial note: significant concerns have been raised about the validity of the data reported in this work. After an internal inquiry, we contacted the authors’ institution, the National Chiao Tung University, and asked them to launch a formal investigation into the matter. This investigation is now underway." 23:50 < kanzure> well..... there you go. 23:50 < nmz787> we need a better molecular viewer than what pdb gives us... this may already exist... I want to say something like, delete all atoms that aren't DNA and that are not touching the DNA within 2 or 3 amino acids from the DNA (in a polymerase PDB file) 23:52 < kanzure> "Reading Single DNA with DNA Polymerase Followed by Atomic Force Microscopy" http://pubs.acs.org/doi/abs/10.1021/ja5063983 23:53 < kanzure> "In our approach, four surface-conjugated nucleotides were examined sequentially with a DNA polymerase-immobilized AFM tip. By observing the specific rupture events upon examination of a matching nucleotide, we could determine the template base bound in the polymerase’s active site. The subsequent incorporation of the complementary base in solution enabled the next base to be read. Additionally, we observed that the DNA polymerase ... 23:53 < kanzure> ... could incorporate the surface-conjugated dGTP when the applied force was controlled by employing the force-clamp mode." 23:53 < nmz787> I think that paper may have been auto-generated by our dreams and some AI bot 23:53 * nmz787 AI bots read logs, generate fake papers to keep DIYers busy chasing their tails 23:53 < kanzure> yeah maybe it's a really advanced spearphishing campaign targeted specifically to members of this irc channel 23:53 < nmz787> :D 23:56 -!- adamg [~akg@50.242.93.33] has quit [Ping timeout: 276 seconds] 23:58 < nmz787> this is a pretty fun game http://www.zachtronics.com/tis-100/ 23:58 -!- ebowden_ [~ebowden@2001:8003:100e:c500:817d:2034:73eb:c66] has quit [Remote host closed the connection] --- Log closed Mon Jul 18 00:00:00 2016