| --- Log opened Sun Jul 17 00:00:59 2016 | ||
| CaptHindsight | kanzure: the dye stuff is to lend electrons to the photoprocesses | 00:11 |
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| kanzure | from the department of "why did we bother looking into this, again?" http://voxeu.org/article/cheaper-flights-and-scientific-collaboration | 07:31 |
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| 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) | 07:56 |
| kanzure | "Mutant cas9 proteins" https://patents.google.com/patent/CA2930829A1/ | 08:00 |
| 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" | 08:03 |
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| kanzure | "High-throughput single cell barcoding" https://patents.google.com/patent/CA2814049A1/ | 08:08 |
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| kanzure | "Barcoded protein array for multiplex single-molecule interaction profiling" https://patents.google.com/patent/WO2015148606A9/ | 08:14 |
| kanzure | "Spatial sequencing of nucleic acids using DNA origami probes" https://patents.google.com/patent/US20150292007A1 | 08:16 |
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| kanzure | "Methods and compounds for chemical ligation" https://patents.google.com/patent/US8481258B2/ | 08:18 |
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| 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)." | 08:49 |
| 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 | 08:50 |
| 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 | 08:52 |
| kanzure | ".. its two products are pyrophosphate and RNA with an extra adenosine nucleotide at its 3' end." | 08:53 |
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| 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." | 08:54 |
| 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 | 09:15 |
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| kanzure | "GLD2 poly(A) polymerase is required for long-term memory" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567210/ (2008) | 09:21 |
| 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. | 09:24 |
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| 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 |
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| CaptHindsight | https://synbiota.com | 10:12 |
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| 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, .. | 10:15 |
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| kanzure | backyard brains.. | 10:17 |
| kanzure | it's a really long list. i don't think that's a reasonable request. :P | 10:17 |
| CaptHindsight | http://openpcr.org/ who does this with a straight face? | 10:18 |
| kanzure | yeah i didn't say it's good | 10:18 |
| 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 | 10:19 |
| kanzure | further evidence in favor of my assessment: they used adobe air | 10:20 |
| 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... | 10:21 |
| CaptHindsight | ok, then how about a list of good projects :) | 10:22 |
| CaptHindsight | looks like a really short list | 10:22 |
| 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/ | 10:23 |
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| 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 | 10:24 |
| 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 | 10:25 |
| kanzure | nmz787 was working on an open-source spectrophotometer setup, https://github.com/nmz787/open-spectrometer | 10:26 |
| 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 | 10:28 |
| 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 | 10:29 |
| CaptHindsight | I just assumed you might know since you want to build so many things | 10:30 |
| 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 | 10:31 |
| 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? | 10:32 |
| kanzure | *its | 10:33 |
| CaptHindsight | I should look for someone to write a translator for the opentrons json files | 10:33 |
| kanzure | what does it need to be translated into? | 10:34 |
| 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 | 10:35 |
| 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 | 10:36 |
| 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? | 10:37 |
| 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 | 10:38 |
| kanzure | https://sites.google.com/site/neurorighter/ "NeuroRighter is an open-source system for multi-electrode closed-loop recording and stimulation" | 10:39 |
| 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 | 10:40 |
| kanzure | O_o they are pre-generated templates? wat | 10:41 |
| CaptHindsight | you can mod them to your delight | 10:41 |
| 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 | 10:43 |
| 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 | 10:44 |
| 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 | 10:45 |
| 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? | 10:46 |
| 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 | 10:47 |
| CaptHindsight | it can output a real time signal to the frame buffer | 10:48 |
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| CaptHindsight | it can also gate the encoder pulses to be a clock for the frame buffer that loads the printheads with data | 10:49 |
| kanzure | you are doing that with gcode? | 10:50 |
| CaptHindsight | chris_99: x86 + FPGA | 10:50 |
| 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 |
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| 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 | 10:52 |
| CaptHindsight | that pulse can be the gate for the clock that puts the fires the first drops out of the heads... | 10:53 |
| 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 | 10:54 |
| 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 | 10:55 |
| CaptHindsight | the opentrons team needs their 8020 catalog taken away from them | 10:57 |
| CaptHindsight | they picked out some pretty flimsy extrusions | 10:58 |
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| 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 | 11:01 |
| 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? | 11:03 |
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| 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) | 11:09 |
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| kanzure | cool a "compartmentalized ribosome display" technique | 11:10 |
| chris_99 | heh, what don't you like about the smoothieboard | 11:25 |
| chris_99 | do you use LinuxCNC with an FPGA? | 11:27 |
| 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." | 11:31 |
| 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 | 11:32 |
| CaptHindsight | a mistake kids often make | 11:33 |
| CaptHindsight | if I were designing a high volume dedicated Cartesian robot for an application I still would use a smoothie | 11:34 |
| CaptHindsight | sorry would not use a smoothie | 11:35 |
| chris_99 | so do you use an FPGA then? | 11:35 |
| 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? | 11:36 |
| 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 | 11:37 |
| chris_99 | yeah i can definitely see how with that config it'd be very customisable | 11:40 |
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| 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." | 11:47 |
| kanzure | we should stalk arizona's matt dunn | 11:52 |
| kanzure | and andrew hatch, who has done high-throughput microfluidics for polymerase evolution and other reasons | 11:53 |
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| 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 | 12:01 |
| CaptHindsight | chris_99: http://linuxcnc.org/docs/2.5/pdf/LinuxCNC_Developer_Manual.pdf page 4 for a block dia | 12:06 |
| chris_99 | ta | 12:07 |
| CaptHindsight | http://linuxcnc.org/docs/2.6/html/code/LinuxCNC-block-diagram-small.png | 12:08 |
| CaptHindsight | found just that page | 12:08 |
| chris_99 | so which bit would be the FPGA? | 12:11 |
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| 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." | 12:21 |
| 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 | 12:25 |
| CaptHindsight | chris_99: with the FPGA over ethernet the PC just needs a 1-4mS interval | 12:27 |
| 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") | 12:28 |
| chris_99 | nice CaptHindsight | 12:29 |
| CaptHindsight | chris_99: Linuxcnc has evolved around machine tools but it may be expanded to control robots, automation, interface to comedi | 12:30 |
| CaptHindsight | comedi.org is down :( | 12:31 |
| CaptHindsight | ^^ data acquisition | 12:31 |
| CaptHindsight | real time | 12:31 |
| chris_99 | ah cool | 12:33 |
| 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 | 12:37 |
| 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 | 12:38 |
| chris_99 | oh neat, i've played a teeny bit with opencv | 12:39 |
| CaptHindsight | chris_99: yes always have encoders | 12:39 |
| 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 | 12:42 |
| 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 ... | 12:43 |
| 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 | 12:44 |
| 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 | 12:47 |
| CaptHindsight | I build custom machines and robots | 12:48 |
| chris_99 | ahh nice | 12:48 |
| 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 | 12:49 |
| 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? | 12:51 |
| 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 | 12:52 |
| 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 | 12:53 |
| 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 | 12:54 |
| 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 | 12:55 |
| 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 | 12:56 |
| 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? | 12:57 |
| 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 | 12:58 |
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| 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 | 14:48 |
| nmz787 | or 'questionable' | 14:49 |
| kanzure | nmz787: phone for a few minutes? | 14:49 |
| nmz787 | sure, lemme go in the other room | 14:51 |
| nmz787 | ready | 14:52 |
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| 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 |
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| Jawmare | a lot of research scandal for biological chemistry stuff | 15:14 |
| Jawmare | I wonder why | 15:14 |
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| fenn | spelled "writozyme" | 16:01 |
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| fenn | i thought it was more recent than 2010 though | 16:02 |
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| 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. | 17:31 |
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| delinquentme | Is there an IRC channel dedicated to MEMS / microfabrication ? | 18:58 |
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| nmz787 | #homecmos | 19:09 |
| 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 | 19:10 |
| kanzure | delinquentme: why do you ask | 19:13 |
| delinquentme | price to feature size | 19:16 |
| delinquentme | and costs for wafers per generation and feature size | 19:17 |
| delinquentme | fuck. blah. that senseless. | 19:17 |
| 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 | 19:18 |
| nmz787 | delinquentme: have you cold-called fab companies? | 19:21 |
| nmz787 | i.e. foundrycontact@intel.com | 19:22 |
| 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 | 19:24 |
| nmz787 | (well I got the email from that page) :) | 19:25 |
| delinquentme | nmz787: kanzure you guys know kent kemmish right? | 19:28 |
| delinquentme | hes looking for markets for mechanical nanopores | 19:28 |
| 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 | 19:30 |
| 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 | 19:39 |
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| 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? | 19:41 |
| 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? | 19:42 |
| delinquentme | nmz787: unsure how to answer whether its MEMS-ified | 19:44 |
| delinquentme | as in " are the lithographic masks already made ?" | 19:44 |
| 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 | 19:45 |
| yashgaroth | hmm? | 19:46 |
| kanzure | yashgaroth: up for a phone call? | 19:46 |
| yashgaroth | ya ok, you got my # right? | 19:46 |
| 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 | 19:47 |
| nmz787 | delinquentme: http://pdxscholar.library.pdx.edu/cgi/viewcontent.cgi?article=1114&context=phy_fac | 19:49 |
| nmz787 | "Field programmable gate array based reconfigurable scanning probe/optical microscope" | 19:50 |
| nmz787 | https://www.pdx.edu/nano-development-lab/tenom-tip-enhanced-near-field-optical-microscopy | 19:52 |
| 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 | 19:53 |
| delinquentme | " The instrument has the ability to image at room temperature and atmospheric pressure or under | 19:54 |
| delinquentme | liquid." | 19:54 |
| nmz787 | this also seems relevant http://biomed.tamu.edu/obsl/obsl/Documents/pdfs/Wang-SERSoptofluidic_labonachip.pdf | 19:55 |
| nmz787 | 'just add some gold dust to it' seems like magical leprechaun voodoo | 19:57 |
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| delinquentme | kanzure: waiting on that emailzu | 20:35 |
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| kanzure | huh? i had sent already. | 20:56 |
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| 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 | 21:45 |
| kanzure | i was looking at that earlier today (or yesterday) | 21:46 |
| 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 | 21:47 |
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| kanzure | at $0.01/genome you could synthesize 100 million unique mutant protein sequences (say ~3.5kbp) for $1 | 22:34 |
| kanzure | although you probably wouldn't need to make 100 million mistakes before getting the protein right | 22:36 |
| kanzure | it's not enough bp to iterate through all amino acid space but you shouldn't be doing that anyway. | 22:38 |
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| 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 ) | 23:10 |
| kanzure | "Recent progress in atomistic simulation of electrical current DNA sequencing" http://arxiv.org/pdf/1411.3437 | 23:11 |
| kanzure | that polymerase electrical conductance paper is pretty cool. you could probably monitor for incorporation events. | 23:18 |
| 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. | 23:19 |
| 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 | 23:38 |
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| kanzure | citing yourself is pretty common | 23:39 |
| kanzure | "citing yourself is pretty common" - me | 23:40 |
| chris_99 | heh | 23:43 |
| nmz787 | yeah it is just very vague | 23:45 |
| kanzure | maybe it's in a patent :\ | 23:45 |
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| 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) | 23:50 |
| kanzure | "Reading Single DNA with DNA Polymerase Followed by Atomic Force Microscopy" http://pubs.acs.org/doi/abs/10.1021/ja5063983 | 23:52 |
| 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 | 23:53 |
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| nmz787 | this is a pretty fun game http://www.zachtronics.com/tis-100/ | 23:58 |
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| --- Log closed Mon Jul 18 00:00:00 2016 | ||
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