| --- Log opened Thu Jul 02 00:00:58 2015 | ||
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| kanzure | justinzero: nope | 05:42 |
|---|---|---|
| kanzure | justinzero: whoops, not you, go away | 05:43 |
| kanzure | .tell justanotheruser there is not an hplusroadmap mailing list at the moment | 05:43 |
| yoleaux | kanzure: I'll pass your message to justanotheruser. | 05:43 |
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| FourFire | kanzure, is there another active channel besides IRC? | 05:56 |
| archels | 06:09 | |
| * archels runs | 06:09 | |
| chris_99 | heh | 06:15 |
| FourFire | archels, I was asking kanzure | 06:22 |
| kanzure | not really | 06:22 |
| kanzure | there's the diybio mailing list | 06:22 |
| kanzure | and there's the diyhpl.us wiki | 06:24 |
| FourFire | yeah I haven't made an account there yet | 06:26 |
| FourFire | don't feel like I have much to contribute yet, however I recall wanting to rewrite some of the front page stuff | 06:27 |
| kanzure | go for it | 06:27 |
| kanzure | the worst that can happen is only that an ai tortures you forever in an eternal simulated hell, which isn't that bad in the scheme of things | 06:28 |
| FourFire | Hmm it's rather slow to send the confirmation e-mail | 06:35 |
| kanzure | iirc you don't need to see the confirmation email | 06:36 |
| kanzure | jrayhawk: ping | 06:36 |
| FourFire | well I fail the login | 06:37 |
| kanzure | possibly something is broken | 06:37 |
| kanzure | your other option is to use git to edit the wiki | 06:38 |
| kanzure | .gc "kilometer-wide" | 06:43 |
| yoleaux | 109,000 (site), 11,700 (api) | 06:43 |
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| eleitl | We should have a subreddit for this channel. | 07:28 |
| eudoxia | i wouldn't be viscerally opposed to that | 07:33 |
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| kanzure | what have redditors ever done for me | 07:54 |
| kanzure | or this channel | 07:54 |
| kanzure | besides soil it | 07:54 |
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| kanzure | "personal dna sequencer" http://www.sigmaaldrich.com/life-science/genapsys.html | 09:04 |
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| nell | has anyone here installed caffe | 09:07 |
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| nell | nvm I got it :D | 09:23 |
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| kanzure | http://nbviewer.ipython.org/url/norvig.com/ipython/Gesture%20Typing.ipynb | 10:13 |
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| nmz787_i | "GENIUS Club members get: * One or more GENIUS Systems, including base-calling software and consumables for up to 10 runs, * Special GENIUS Club discount pricing on additional consumables for continued GENIUS System(s) use," ... | 10:34 |
| nmz787_i | 'Experience designing CMOS image sensors is a plus' | 10:39 |
| nmz787_i | from their job posting on analog engineers | 10:39 |
| nmz787_i | 'Practical knowledge in flow cell / chip fabrication is a plus. ' from their post for a bio-science researcher | 10:40 |
| nmz787_i | i'm guessing the analog guy will be able to pull 50-100% more salary | 10:41 |
| nmz787_i | "Applicants may apply for one or more GENIUS Systems. Each GENIUS System under the program, will arrive with base-calling software and consumables for up to 10 runs, for usage within 30 days of receipt." | 10:42 |
| nmz787_i | "Each GENIUS System received under the GENIUS Club program requires a deposit of $2,500 (US). Within the first 30 days after receipt, the deposit will be credited against the purchase of the GENIUS system(s) or the GENIUS system(s) may be returned for a full refund." | 10:42 |
| nmz787_i | "The device of any one of claims 1 to 38, comprising at least one sensor selected from a Fin FET, a nanoneedle, a nanobridge, an ISFET, a CHEMFET, a pH sensor, and a microcantilever." | 10:44 |
| nmz787_i | https://www.google.com/patents/WO2013082619A1 | 10:44 |
| nmz787_i | .title | 10:44 |
| yoleaux | Patent WO2013082619A1 - Systems and methods for high efficiency electronic sequencing and detection - Google Patents | 10:44 |
| kanzure | only 10 runs... | 10:48 |
| nmz787_i | "In the case of water hydrolysis near the positive electrode of a cell in the nanosensor array, 02 bubbles and H+ ions may be generated. In some embodiments, the bubble problem can be overcome by adding a chemical to the solution where the discharge potential of the chemical is less than that of water, and as a result no gas is generated. HQ has a hydrolysis voltage which is less than that of water (0.6V versus 1.2V, respectively) and thus a | 10:49 |
| nmz787_i | lower discharge potential, as shown in FIG. 8, and this may allow for the application of lower voltages through the electrodes with a resulting signal that may be the same or increased as compared to solution without HQ. The HQ-Q redox reaction may address the bubble problem, but the redox reaction can generate H+ ions, thereby lowering the pH. In a further embodiment, this problem may be addressed by adding HQ to a sequencing and/or | 10:49 |
| nmz787_i | amplification buffer, in order to regulate the pH such that it may be closer to the desired pH, such as for example a pH level that is approximately 7." | 10:49 |
| nmz787_i | where HQ is hydroquinone | 10:49 |
| nmz787_i | "In some embodiments, Quinhydrone (QH), which is a complex of HQ and Q, may be added to the flow stream in the microfluidic nanoarray. By increasing the concentration of QH to increase the current, filming and deposition of QH on the electrodes can occur. The greater the increase in concentration of HQ, the more molecules may be available near the electrodes for a reduction oxidation (redox) reaction. If the concentration of HQ is low, then | 10:50 |
| nmz787_i | after a short period of time the area around the electrodes may become depleted of one product (for example, H2Q near anode and Q near cathode) and the reaction may stop at that point." | 10:50 |
| nmz787_i | they keep talking about being within the Debye length | 10:50 |
| nmz787_i | "In other embodiments, the charge or signal may be moved, in a manner similar to that of a CCD to a readout port. There may be one or more readout ports associated with each microfluidic device, said device containing a nanosensor array. In some embodiments, the circuitry at the readout ports may include one or more of an analog to digital converter, a row selector, a column selector, shift register, serial read out, multiplexer, etc." | 10:53 |
| nmz787_i | "Electrical nano-sensors can rely on label free detection of biochemical reactions that produce changes in charge and current. In one version of the sample embodiment, a NanoNeedle is used. The NanoNeedle is an ultra-sensitive, localized impedance biosensor that can allow the detection of changes in impedance via electrical current changes that occur following perturbation of the local solution resistance through, for example, proton release | 10:54 |
| nmz787_i | during the DNA incorporation reaction, protein binding, DNA hybridization, pH change, or other biochemical reactions." | 10:54 |
| nmz787_i | "In the sample embodiment, each of the sensors may be brought directly out to bondouts on the silicon sensor; each of these may be wire bonded to associated pads on a Chip Carrier PCB board, which may act as an intermediary to the signal processing board, wherein the current can be converted to a voltage by a transimpedance amplifier, and may subsequently be subjected to various linear transformations as needed for the sensor type, such as, for | 10:55 |
| nmz787_i | example, reference subtraction, multiplication to remove AC, filtration, etc. The processed analog signals can then sent to a DAC card, from whence they can be stored in a hard disk. " | 10:55 |
| nmz787_i | i'm gonna do all this, except not use a hard-disk... I think that's enough of an improvement to be considered a unique patent, right? | 10:56 |
| nmz787_i | "The characteristic time of the nucleotide incorporation signal and the number of sensors per array may dictate the data throughput requirements. Data acquisition of 20 independent channels at sampling rates of greater than 1 kHz is well within the capability of commercially available, data acquisition (DAQ) cards. Thus all 20 sensors can be monitored simultaneously, with individual trans-impedance amplifiers, multipliers, and filters as needed | 10:56 |
| nmz787_i | for the sensor type. Data can be acquired for every cycle from every sensor. Those sensors without a reaction may be used as references to remove any variation in buffer ion concentration, temperature influences on the system, or other systematic variables. All data can be acquired by a DAC card, which may then buffer the data to a hard disk on a computer prior to data analysis" | 10:56 |
| nmz787_i | "The NanoNeedle and NanoBridge sensors may be used to detect the incorporation of a nucleotide by DNA polymerase using a clonal DNA template. In an exemplary process, DNA templates were attached to magnetic beads, either via a streptavidin biotin linkage or directly conjugated, and hybridized to the sequencing primer. After pre-incubation of these beads with DNA polymerase, they were introduced into the sensor device followed by the delivery of | 10:57 |
| nmz787_i | dNTP solution to initiate polymerization. The signals from multiple and single base incorporation were recorded. Sensor optimization involves factors such as total current (I), delta current (ΔΙ), ΔΙ/Ι, S/N, short and long term stability and response time. The rate limiting step for signal generation was the reagent delivery through the channel rather than the polymerization reaction (averaging 20ms). The signal strength may be dependent on t | 10:57 |
| nmz787_i | number of DNA templates as well as polymerase, nucleotide and salt concentration.For proof of concept studies, both sensor type chips were fabricated with an array of functional sensing units (20 to 100 for initial design and 2 million or more in the next step) in a microfluidic channel, for example a PDMS based one. With respect to the chips without integrated magnets within the sensor array, removable magnets underneath the sensor chip were | 10:57 |
| nmz787_i | used to capture beads that flowed into the channel. Sequencing was performed using beads preloaded with a single DNA template, primer, and Klenow (exo-) DNA polymerase followed by injection of dNTPs. Other types of DNA polymerase such as BST, Sequanase, Phi29, T4, etc. can be used." | 10:57 |
| nmz787_i | http://genapsys.com/about-us/management-team/hesaam-esfandyarpour/ | 11:00 |
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| nmz787_i | .wik sal 10^-6 | 11:10 |
| yoleaux | "Sterility assurance level (SAL) is the probability of a single unit being non-sterile after it has been subjected to sterilization." — https://en.wikipedia.org/wiki/Sterility_assurance_level | 11:10 |
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| kanzure | so their method is just "point many sensors at magnetic beads with streptavidin-connected dna/polymerase complexes" | 11:15 |
| nmz787_i | it seems more like micro/nano well, flow in dNTPs, watch for molecular evolution via nano-sensors (i.e. a change in current, impedance), correlate sensor reading with dNTP ju | 11:23 |
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| nmz787_i | just flowed in | 11:23 |
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| nmz787_i | and it seems the magnet part is only to enable movement/positioning of the bead in the channel | 11:26 |
| nmz787_i | channel/well | 11:26 |
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| nmz787_i | jrayhawk: that 4k monitor seems like it was a pretty good deal. so far i'm happy with it, and there were no issues other than the cables were loose in the box and I initially was worried they may have scratched the screen or damage it. | 11:42 |
| nmz787_i | these deals on computers these days are pretty tempting for a techie like me... but I really don't need another chromebook, and I'm not sure if parent-types would like using one either | 11:43 |
| nmz787_i | http://slickdeals.net/f/7950037-acer-11-6-chromebook-laptop-cb3-111-c8ub-manufacturer-refurbished-110-free-shipping-ebay-daily-deal | 11:43 |
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| archels | .title http://motherboard.vice.com/read/exotic-nanomaterials-claimed-their-first-major-workplace-injury | 12:11 |
| yoleaux | Exotic Nanomaterials Claimed Their First Major Workplace Injury | Motherboard | 12:11 |
| archels | isn't this a non-issue? When you're dealing with something even potentially hazardous, just do it in a fume hood | 12:12 |
| archels | (and upgrade your filters) | 12:12 |
| genehacker | seems like a lot of scaremongering | 12:21 |
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| archels | snoonet/#futurology is just a bot announcing reddit posts and nothing else | 13:13 |
| archels | I think there should definitely not be a subreddit for ##hplusroadmap | 13:14 |
| kanzure | :-) | 13:17 |
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| kanzure | also the mailing list back in 2007 didn't really work out either | 13:19 |
| kanzure | but that's partly my fault | 13:19 |
| catern | doesn't somewhere here archive all their browsing history | 13:22 |
| catern | and also have a blogpost about how they do it | 13:22 |
| kanzure | i archive most of my browsing history but i don't have a blogpost about it | 13:23 |
| catern | well how do you do it? | 13:24 |
| kanzure | nsh uses onetab, i use bookmarks, there are extensions i think | 13:24 |
| kanzure | ideal way is squidproxy to record all inbound http traffic | 13:25 |
| kanzure | on a related note, i was thinking at some point of using my phone to display a vertical list of open tabs from my laptop, but i didn't go through with this because i would feel bad about not being able to quickly type-to-search through the list | 13:28 |
| superkuh | I just save session files (since they have per-tab history) | 13:30 |
| jrayhawk | kanzure: the web frontend requires a confirmation email, ssh doesn't | 13:38 |
| jrayhawk | though i guess it's possible one of us enabled pushes on git | 13:39 |
| jrayhawk | i will go poke at that web thing | 13:39 |
| kanzure | perhaps email stuff broke | 13:40 |
| kanzure | also it strikes me as weird how low activity that wiki is | 13:40 |
| jrayhawk | oh my god recaptcha has gotten uninterpretable | 13:41 |
| jrayhawk | fucking AI ruining our lives already | 13:41 |
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| jrayhawk | hmm. i guess recaptcha's noscript iframe is just completely goddamned broken | 13:49 |
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| FourFire | lol @ sponsored by lobsters | 13:59 |
| archels | jrayhawk: yeah I've been getting that too | 14:00 |
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| jrayhawk | FourFire: Can you try http://diyhpl.us/piny-commands/newuser/ again? | 14:21 |
| jrayhawk | I have made some corrections and added better logging and alerts for future problems. | 14:22 |
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| nmz787_i | .title https://www.youtube.com/watch?v=bB5iWzsztdc | 14:41 |
| yoleaux | Intentionally Shattering Wafers | Inside the Fab | Intel - YouTube | 14:41 |
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| FourFire | jrayhawk, sure | 14:43 |
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| chris_99 | nmz787_i, got your microscope out of storage? | 14:46 |
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| kanzure | http://www.wired.co.uk/magazine/archive/2015/07/features/airware-drones/viewall | 14:57 |
| nmz787_i | chris_99: nah, it's still over there... but it's at the FIB lab anyway, so it's in good company | 15:01 |
| chris_99 | aha | 15:04 |
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| jrayhawk | well, that's at least further along the mail routing chain than before | 15:11 |
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| jrayhawk | did you get it? | 15:13 |
| kanzure | hmph nonresponsive users hmph | 15:16 |
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| FFFFFFFF | FFFFFF! | 15:18 |
| FFFFFFFF | I get a nearly blank page upon using the e-mailed link | 15:18 |
| FFFFFFFF | "Missing captcha parameters" | 15:18 |
| FFFFFFFF | I hope I will be able to activate my account tomorrow | 15:19 |
| FFFFFFFF | I must sleep now | 15:19 |
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| jrayhawk | huh, that shouldn't even be checking for captcha parameters | 15:19 |
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| jrayhawk | apparently i was very dumb when writing this interface | 15:23 |
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| jrayhawk | Okay, I just repeated that GET request and it created the account. | 15:29 |
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| knobuddy | gene hack-man | 15:43 |
| knobuddy | played lex luthor | 15:43 |
| knobuddy | who cloned superman | 15:43 |
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| kanzure | fenn: would you be interested in picking mike darwin's brain for a whole week or two? with audio recording equipment. | 16:25 |
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| delinquentme | kanzure, existing open source projects for directed evolution ? | 16:52 |
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| kanzure | not aware of any | 16:54 |
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| kanzure | https://www.youtube.com/watch?v=ZeZL2R9jDJM | 17:51 |
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| kanzure | hmm i want software-generated screams of the dead | 20:04 |
| kanzure | "tenderized cow corpse" | 20:04 |
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| nmz787_ | .tell knobuddy I think this is the closest thing to that far-side comic that I guess (and hope) is a joke http://www.theallium.com/policy/taylor-swift-announces-she-will-no-longer-review-for-nature/ | 20:40 |
| yoleaux | nmz787_: I'll pass your message to knobuddy. | 20:40 |
| nmz787_ | is that a site similar to the onion? | 20:40 |
| nmz787_ | .wik allium | 20:40 |
| yoleaux | "The onion genus Allium comprises monocotyledonous flowering plants and includes the onion, garlic, chives, scallion, shallot, and the leek as well as hundreds of wild species." — https://en.wikipedia.org/wiki/Allium | 20:40 |
| nmz787_ | http://phys.org/news/2015-07-soundproofing-quantum-physics.html | 20:45 |
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| --- Log closed Fri Jul 03 00:00:59 2015 | ||
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