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| nmz787 | https://hackaday.io/project/1620-the-human-connection-1st-impression | 00:33 |
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| FourFire | This looks potentially interesting for BCI | 05:53 |
| FourFire | but I'd be concerned about having a lot of LN² close to my head | 05:53 |
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| kanzure | not like i needed that body part anyway | 07:10 |
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| kanzure | beep bloop | 08:20 |
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| xtalmath | that magnet guy was ... | 08:56 |
| xtalmath | magneto? | 08:56 |
| kanzure | nah there are others playing around with finger magnets | 09:13 |
| kanzure | "LabCures (https://labcures.com) is trying a back-the-team rather than back-the-project approach to crowdfunding" ugh more crowdfunding | 09:14 |
| xtalmath | must be a pain in the ass to clean your finger after milling ferromagnetic materials... | 09:14 |
| kanzure | and lifepsan.io.... bleh. reason@fightaging.org really needs to reconsider his crowdfunding approach. | 09:14 |
| xtalmath | also MRI machine is no go zone for him if he has a serious accident, the doctors might not know about the magnet... | 09:16 |
| kanzure | can't they just leave his hand out of the machine | 09:17 |
| kanzure | anyway look up "grindhouse wetware" for more finger magnet stuff | 09:18 |
| xtalmath | thats gonna be a lot of fun, when it yanks his hand and arm until closest point, then rips the magnet out of his skin, and the magnet flies around the room until it hits the superconducting magnet housing, and shatters in all directions | 09:18 |
| kanzure | perhaps he has very long arms | 09:19 |
| xtalmath | MRIs and high tesla MS are places with lots of funny stories that people experience | 09:19 |
| xtalmath | at my university, somebody once brought a laptop in the room, but a little too close to the machine, and the magnet attracted the laptop to underneath the device | 09:20 |
| xtalmath | the person couldnt seperate the laptop on his own, one person had to lay under the magnet and grab the laptop with both arms, while the others pulled his legs to pull him from under the machine | 09:21 |
| xtalmath | longer arms just means longer period of acceleration before ripping out of his skin | 09:22 |
| kanzure | maybe 20 foot arms | 09:23 |
| xtalmath | his hand may collide with the machine before his arms are fully extended, ouch | 09:23 |
| xtalmath | might break a bone | 09:23 |
| xtalmath | so you wake up after coma from car accident, and they tell you "you had 2 accidents, but calm down" | 09:24 |
| xtalmath | "oh, you lost your partner too" | 09:24 |
| xtalmath | "but the good news is, life extension made you survive it, your 200yrs now btw" | 09:26 |
| kanzure | the life extension is because of the finger magnet? | 09:26 |
| xtalmath | no seperate development | 09:26 |
| kanzure | the partner death is because finger magnet? | 09:27 |
| xtalmath | no car acciden | 09:27 |
| kanzure | the car accident is because finger magnet? | 09:28 |
| xtalmath | yes | 09:28 |
| gradstudentbot | I hope they kick me out. | 09:28 |
| xtalmath | it pulled the keys out of the ignition | 09:28 |
| kanzure | keys are not a good idea anyway | 09:28 |
| xtalmath | which he normally got used to, but that time it was inconvenient | 09:28 |
| xtalmath | "good news is, we still have your car keys" "you can probably pick up the remains of your car, somewhere at lost and found, early 21st century section" | 09:29 |
| xtalmath | "oh, theres still the matter of your partner's family suing you for causing the accident" | 09:31 |
| kanzure | there's no way that the lawsuit wouldn't have been settled earlier | 09:32 |
| xtalmath | what about the right to a defense? | 09:32 |
| kanzure | huh? you can still have a defense. | 09:33 |
| xtalmath | so the lawsuit was not final | 09:33 |
| kanzure | almost all lawsuits aren't | 09:33 |
| xtalmath | indeed | 09:34 |
| xtalmath | "you still have the right to a defense, but formal verification tools have after heuristic search, found that there exists no defense" | 09:40 |
| kanzure | huh? no they just assign you a public defender or whatever, go ask the people stuck in comas how they deal with lawsuits | 09:44 |
| xtalmath | "also, your internationalized human rights gave you your daily proper share of average rent of all world resources, which amounts to millions now" | 09:44 |
| xtalmath | "in absence of your consciousness doctors decided it was in your best interest to spend it all on the best treatment during your stay here" | 09:44 |
| kanzure | are you just completely unaware of how the current system works, or are you just wasting my time for fun? | 09:45 |
| xtalmath | "we hope you enjoyed the holographic television you couldn't possibly perceive, well we enjoyed it" | 09:45 |
| xtalmath | not wasting your time, just fun | 09:45 |
| kanzure | it's a waste of my time to explain to you things that you might already know | 09:45 |
| kanzure | if you don't know how medical decisions and estate decisions are handled when someone is in a coma, that's one thing. knowing and still getting it wrong is another. | 09:45 |
| xtalmath | 150yrs passed in the hypothetical | 09:45 |
| kanzure | "oh noes stuff happens during 100s of years" so what? | 09:46 |
| gradstudentbot | The paper was rejected. | 09:47 |
| kanzure | on an only slightly related note, | 09:48 |
| kanzure | xtalmath: http://extropians.weidai.com/extropians.3Q97/4356.html | 09:48 |
| xtalmath | that text reminds me of ... | 09:50 |
| xtalmath | roko's basilisk | 09:50 |
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| kanzure | aww i missed the start of ludum dare 33 http://ludumdare.com/compo/ | 10:11 |
| kanzure | "guide an ambitious young fire hydrant to fulfill her dream of destroying the sun" http://ludumdare.com/compo/ludum-dare-32/?action=preview&uid=51259 | 10:19 |
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| jackybgood | paperbot doi:10.1038/nm.3820 | 13:05 |
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| jackybgood | paperbot: http://www.nature.com/nm/journal/v21/n4/full/nm.3820.html | 13:13 |
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| kanzure | hi rancyd | 13:37 |
| rancyd | hi kanzure | 13:37 |
| chris_99 | kanzure, did you know whether the nozzles on a printer are all individually addressable btw (i'm assuming they would be) | 13:38 |
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| kanzure | chris_99: yes | 14:27 |
| kanzure | we went over this with you yesterday | 14:28 |
| kanzure | or the day before. not sure. | 14:28 |
| chris_99 | nope, noone answered that | 14:28 |
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| kanzure | http://gnusha.org/logs/2015-08-21.log | 14:34 |
| kanzure | 15:39 < chris_99> is there a piezo per nozzle | 14:34 |
| kanzure | 15:39 < chris_99> or only per colour | 14:34 |
| kanzure | 15:40 < CaptHindsight> chris_99: with piezo yes, it's one piezo per nozzle | 14:34 |
| kanzure | 15:40 < kanzure> there is a piezo per nozzle | 14:34 |
| kanzure | 15:40 < kanzure> a better question would be "does the control circuitry allow individual piezo control" | 14:34 |
| chris_99 | yeah to which noone answered | 14:34 |
| kanzure | huh? | 14:40 |
| chris_99 | answered the question on whether they do allow individual piezo control | 14:42 |
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| CaptHindsight | yes, each piezo is individually controlled | 14:46 |
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| CaptHindsight | otherwise you'd just be firing (or not firing) all the nozzles at the same time | 14:47 |
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| CaptHindsight | chris_99: ^^ | 14:47 |
| chris_99 | gotcha, i had a look at an image of one of the bottom of the heads, it looked like each colour has a line of nozzles, so it's printing vertically over a fairly large surface at a time right? | 14:48 |
| CaptHindsight | it all depends on the printhead | 14:48 |
| CaptHindsight | some have only one fluid channel | 14:48 |
| CaptHindsight | some have multiple | 14:48 |
| gradstudentbot | May I ask what formula did you use? | 14:50 |
| chris_99 | i found you can get MEMS ultrasonic mics really cheap, so i'm gonna get one to see if you can pick up an interesting ultrasonic audio from the heads | 14:52 |
| CaptHindsight | so in the case of the Epson heads anywhere from 0-180 nozzles per channel can fire at a time... | 14:54 |
| CaptHindsight | and Epson has up to 8 channels per head (depending on model) | 14:55 |
| CaptHindsight | the piezo are also put into modes other than just firing ink, they are also used to churn up the ink | 14:55 |
| chris_99 | does 8channels mean 8 colours? | 14:56 |
| CaptHindsight | it can | 14:57 |
| nmz787 | chris_99: I was just looking at this last night, uses MEMS mics and a MCU I might want to use (LPC4370) for an xray spectrometer https://hackaday.io/project/1620-the-human-connection-1st-impression | 14:57 |
| nmz787 | i can't tell how much code is here though, like if it is complete (seems not) https://github.com/ehughes/hc-1 | 14:58 |
| chris_99 | neat, i was looking at the knowles ones | 14:58 |
| chris_99 | let me check if that's the analog or digital one | 14:58 |
| nmz787 | I am guessing analog, because the person wanted to leverage the 80MSPS ADC | 14:59 |
| nmz787 | I thought | 14:59 |
| gradstudentbot | My experiment was working a second ago, but now it doesn't even work. | 14:59 |
| nmz787 | (maybe I was just assuming that?) | 14:59 |
| chris_99 | yeah thats analog | 14:59 |
| chris_99 | i'm looking at the digital PDM one | 15:00 |
| nmz787 | oh, I actually didn't pay much attention to the mic aspect | 15:00 |
| nmz787 | since I want to throw a photodiode in front with (probably a ton of) amplification | 15:00 |
| chris_99 | i wasnt sure whether to get an analog one or pdm one, as the analog one possibly has a slightly high freq. response | 15:01 |
| archels | nmz787: that's cool stuff, been waiting for something like that to come along | 15:01 |
| chris_99 | what are they using them for anyway, as it mentions x-rays? | 15:01 |
| nmz787 | what mentions xrays? | 15:02 |
| nmz787 | (I mentioned xrays here) | 15:02 |
| chris_99 | oh sorry, you did heh | 15:02 |
| nmz787 | yeah I just want really fast sampling so I can average to remove some noise | 15:03 |
| nmz787 | by oversampling | 15:03 |
| chris_99 | ahh | 15:03 |
| gradstudentbot | Yeah, I don't know. | 15:03 |
| nmz787 | since I want to get as much resolution as possible from the different xray photon energy levels | 15:03 |
| chris_99 | how are you detecting x-rays? | 15:04 |
| nmz787 | supposedly the PIN photodiodes commonly used for fiber optic communication in NIR can get something like 120eV of resolution in the xray area | 15:04 |
| chris_99 | yeah i've heard of people using PIN diodes for radiation, i think you can pick up gamma too with them? | 15:05 |
| nmz787 | which isn't as good as the single digit resolution that wavelength dispersion spectrometers can achieve, or the few 10s of eV that the SDD or SiLi detectors can get... but it seems pretty damn good | 15:05 |
| nmz787 | and PIN diodes are like $1 each | 15:05 |
| nmz787 | yeah | 15:05 |
| nmz787 | I actually probably don't need a spectrometer, but it would be a nice upgrade to the xray detector project I have in the works now with just a buzzer | 15:06 |
| nmz787 | and it is stressing so many areas of expertise... so it seems like a good goal to march toward. | 15:07 |
| chris_99 | i'd like a dental x-ray sensor, alas they're not exactly cheap | 15:07 |
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| nmz787 | http://arrc.ou.edu/~rockee/RIO/serialio-book.pdf | 15:42 |
| nmz787 | 'As one expert put it, “Radiated emission problems are really just signal integrity problems.”' | 15:42 |
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| nmz787 | "Before we think that gigabit serial I/O sounds too good to be true, let's look at the downsides. In our designs, we must first we must pay close attention to signal integrity issues. For example, one vendor reported a 90% failure rate on their first attempt with high-speed, multi-gigabit serial designs for a particular application. To improve the odds, we might need to perform analog simulations and use new, more complex bypassing schemes. ... | 15:43 |
| nmz787 | ... In fact, we may even need to simulate and model the bypassing scheme." | 15:43 |
| nmz787 | "We can also expect to pay more for impedance-controlled PC (printed circuit) boards, high-speed connectors, and cables. We will have to deal with complications and smaller time bases in digital simulations. And when taking advantage of a predefined protocol, we must plan time for integration and extra gates or Central Processing Unit (CPU) cycles for protocol overhead." | 15:43 |
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| nmz787 | """SERDES was initially used to talk box-to-box. But it exploded into the marketplace because of how nicely it handles chip-to-chip communication on the same circuit board. Chip-to-chip communication had previously been almost exclusively a parallel domain. The amount of logic needed to serialize and deserialize far outweighed any savings that come from pin count reduction.""" | 15:46 |
| nmz787 | """But with deep sub-micron geometry, an incredible amount of logic can be achieved in a very small amount of silicon. SERDES can be included on parts for a very low silicon cost. Add to that the everincreasing need for I/O bandwidth, and SERDES quickly becomes the logical choice for moving any significant amount of data chip-to-chip""" | 15:46 |
| nmz787 | .wik infiniband | 15:47 |
| yoleaux | "InfiniBand (abbreviated IB), a computer-networking communications standard used in high-performance computing, features very high throughput and very low latency. It is used for data interconnect both among and within computers." — https://en.wikipedia.org/wiki/Infiniband | 15:47 |
| chris_99 | 10Gbps infiniband cards are dirt cheap on fleabay | 15:49 |
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| nmz787 | """An unsettling aspect of the Gigabit SERDES is that they appear to be almost magical. They work with 3, 5, and even 10+ gigabits. How is that kind of speed possible? There are several techniques that provide this speed.""" | 15:50 |
| nmz787 | """One of the biggest advances in high-speed SERDES involves the PLLs used in clock and data recovery. A normal PLL requires a clock running at the data speed, but there are several techniques that can be used to avoid this requirement, including fractional rate phase detectors, multi-phase PLLs, parallel sampling, and over-sampling data recovery.""" | 15:52 |
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| nmz787 | """The 8b/10b encoding scheme was developed by IBM and has been widely adapted. It is the encoding scheme used in Infiniband, Gigabit Ethernet, FiberChannel, and the XAUI interface to 10 Gigabit Ethernet.""" | 15:54 |
| nmz787 | """first let’s examine how 8b/10b ensures a good DC balance""" | 15:54 |
| nmz787 | this is like RNA tiplets and amino acids or something... | 15:55 |
| nmz787 | triplets* | 15:55 |
| nmz787 | """8b/10b uses two different symbols assigned to each data value. In most cases, one of the symbols has six zeros and four ones, and the other has four zeros and six ones. The total number of ones and zeros is monitored and the next symbol is chosen based on what is needed to bring the DC balance back in line. The two symbols are normally referred to as + and - symbols.""" | 15:56 |
| nmz787 | """One additional benefit of the running disparity is that the receiver can monitor the running disparity and detect that an error has occurred in the incoming stream because the running disparity rules have been violated.""" | 15:57 |
| nmz787 | """Scrambling is a way of reordering or encoding the data so that it appears to be random, but it can still be unscrambled. We want randomizers that break up long runs of zeros and ones. Obviously, we want the descrambler to unscramble the bits without requiring any special alignment information. This characteristic is called a self-synchronizing code.""" | 15:58 |
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| nmz787 | wow | 15:58 |
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| xtalmath | chris_99: did the microphone move during the recording? | 15:59 |
| chris_99 | nope | 15:59 |
| xtalmath | is the recording taken straight from the video? | 16:00 |
| chris_99 | yup | 16:00 |
| chris_99 | its from a shotgun mic ontop of the camera | 16:00 |
| xtalmath | great | 16:01 |
| xtalmath | I'll tick your shoulders when I have something usefull | 16:02 |
| chris_99 | i'm planning on getting a MEMS mic to get up to 80kHz | 16:02 |
| chris_99 | or so | 16:02 |
| xtalmath | chris_99: I think piezo can easily get this? | 16:02 |
| xtalmath | just need fast enough ADC | 16:03 |
| chris_99 | the MEMS i'm looking at does PDM so i don't need an ADC | 16:03 |
| xtalmath | .wiki PDM | 16:03 |
| chris_99 | https://en.wikipedia.org/wiki/Pulse-density_modulation | 16:03 |
| chris_99 | i was also thinking of how to rip off the head from the printer, and have it print the same stuff without the mechanical belt noises etc | 16:05 |
| xtalmath | yes | 16:05 |
| xtalmath | at what frequency is the PDM? | 16:05 |
| gradstudentbot | That's definitely a Nature paper. | 16:05 |
| chris_99 | around 3MHz you clock the mic at | 16:05 |
| chris_99 | for ultrasound | 16:05 |
| xtalmath | well the belt noise should not be a problem as it will have a different spectrum | 16:06 |
| xtalmath | oh, I see what you mean | 16:07 |
| xtalmath | you might need the belt noise durations though | 16:07 |
| xtalmath | if the printer knows that for the rest of the line no ink will follow it can "newline" | 16:07 |
| xtalmath | "carriage return" | 16:08 |
| xtalmath | chris_99: how do you record the PDM in the computer? you have a special soundcard/port for PDM? | 16:09 |
| chris_99 | i'll probably use an MCU devboard, that has usb on it | 16:10 |
| chris_99 | and it'll grab the PDM | 16:10 |
| chris_99 | decode to PCM | 16:10 |
| chris_99 | and shovel through USB | 16:10 |
| xtalmath | yeah | 16:10 |
| xtalmath | I was thinking in terms of what I have laying around, .. got an fpga with a 1 Msps adc | 16:11 |
| xtalmath | or was it 10 | 16:11 |
| xtalmath | but ... then you could connect a piezo to that :) well, your gear will probably give better result... | 16:11 |
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| xtalmath | so PDM seems basically the same as pulse width modulation? | 16:47 |
| xtalmath | ah no | 16:47 |
| xtalmath | its delta sigma modulation | 16:49 |
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| kanzure | http://www.sobify.com/the-lyubov-orlova-a-russian-cruise-ship-drifting-through-international-waters/ | 16:54 |
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| kanzure | "Meanwhile, the academic research industry is $1 trillion asset and runs on $2.5 billion/ week. Calico couldn't make it to Friday in that league. " | 17:00 |
| kanzure | not sure why someone would be comparing calico to the size of academia | 17:00 |
| kanzure | toxoplasma freezing http://www.protocol-online.org/biology-forums-2/posts/23756.html | 17:02 |
| kanzure | http://www.researchgate.net/post/how_can_i_isolate_and_culture_Toxoplasma_gondii_for_experimental_infection_in_details | 17:05 |
| kanzure | oh god i forgot how terrible biologists are at writing | 17:05 |
| delinquentme | anyone have suggestions for good reading on the evolutionary process by which novel insertions are bred out ... and ideally how to prevent that | 17:11 |
| delinquentme | OTHER than the JCVI play of simplifying the fuck out of the organism | 17:12 |
| delinquentme | also it gave me pause to think about if theres some way to robotically handle / sort / quantify cell excretion | 17:12 |
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| gradstudentbot | Holy crap, I need to add that to my slide collection. | 17:14 |
| yashgaroth | delinquentme: the normal way to prevent it is through constant antibiotic selection | 17:20 |
| yashgaroth | and to do your second question, sure put your stable cell line clone plates into a tecan that can do ELISA | 17:21 |
| yashgaroth | assuming this is related to you making a monoclonal in rpe1 cells | 17:21 |
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| nmz787 | "The ferrite bead has a low impedance at low frequencies and a very high impedance at high frequencies (Figure 4-12)." | 17:42 |
| xtalmath | yes | 17:44 |
| nmz787 | """As with any switching circuit, bypassing is critical. But, at these speeds, we cannot just insert few capacitors and say the bypassing is complete. That approach used to work a few years ago, so why not now? It still can work if we can find some ideal capacitors (no inductance or resistance) and get them on the board using ideal routes and vias (no inductance or resistance), and the package is ideal, and so on. As switching frequency and ... | 17:47 |
| nmz787 | ... current needs have increased, the ESR and ESL that at one time could be ignored now have to be considered.""" | 17:47 |
| nmz787 | """Another important aspect of bypassing is placement. As a general rule, the larger the cap value, the less critical the placement. The smallest values want to go as near a power and ground pin as possible. One way to do this that is often available when using MGTS inside FPGAs is to remove the trace and via of unused general IO to make room for the bypassing""" | 17:51 |
| nmz787 | (on the backside of the PCB, from the pin on the BGA or whatever) | 17:52 |
| nmz787 | """For best results, we should run differential pairs tightly coupled and closely matched. Trace length matching is essential. In FR-4, a 100-mil (1 tenth of an inch) difference in trace length results in approximately 18 picoseconds of difference between the positive and negative signal. This is also enough skew to start causing problems. And, while a tenth of an inch may sound like a lot if we just use normal trace routing from one BGA to ... | 17:54 |
| nmz787 | ... another, it is easy to end up with 300 - 400 mils of difference. If our PCB tool has an auto-trace matching, we need to use it. In general, we will want 50 mils or less difference in differential trace lengths.""" | 17:54 |
| delinquentme | yashgaroth, does science have an idea what is applying those pressures to breed out the novel modifications? | 17:56 |
| xtalmath | nmz787: what are you planning to use MGTS for? | 17:56 |
| delinquentme | also planar growth seems to make sense for antibody selection , idk about suspended growth ... unless of course im calculating out the expected cell yield along side the antibiotic load were placing in the reactor | 17:57 |
| delinquentme | which could be done | 17:57 |
| xtalmath | nmz787: sounds like you are reading some FPGA manual | 17:58 |
| nmz787 | oh someone pointed out that the LPC4370 has a 204MHz clock (with 3 cores) but even with that and maybe SIMD instructions, at 80 MSPS (12 bits per sample) you effectively only have 204/80 clocks (2.55... or 2 i guess) to get anything done with the data | 17:58 |
| nmz787 | so I'm thinking I'd have to pipe it over to an FPGA with some boxcar filtering and edge detection logic | 17:58 |
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| nmz787 | and then averaging the data within a certain pulse that was found... which would greatly reduce the data transmission afterwards | 17:59 |
| nmz787 | in fact at that point it would probably just be binning the values into a histogram | 17:59 |
| nmz787 | (this is for xray spectrometer idea) | 17:59 |
| yashgaroth | delinquentme the pressure is from natural selection, any cell that happens to methylate & repress the insert will be able to divide faster than the other cells, that + time = lower yields | 18:00 |
| xtalmath | what calculation do you need on the data? what is the register width on the core? | 18:00 |
| xtalmath | you have 3 cores, so depending on the task you can divide the workload by 3, and depending on SIMD instructions and register size you might get another 2-4 times speedup | 18:02 |
| nmz787 | basically its just taking the ADC values, which are oversampled... finding where a pulse starts and ends, then taking all the samples within the pulse and averaging them, then throwing them into a dictionary/map with the key being the average-value and the value being a counter that increments | 18:02 |
| nmz787 | then after some time, the dictionary keys and values would be flushed over USB or to an SD card or something | 18:03 |
| nmz787 | so you'd get a spectrum of photodiode readings over some amount of time | 18:03 |
| xtalmath | but yes FPGA sounds more reasonable, but with FPGA you could as well have used an ADC with parallel outputs, like a 120Mhz video ADC, so you get your samples at the rate of 120Mhz with 12bits in parallel in the FPGA | 18:03 |
| nmz787 | yeah but then I have to think about the PGA which I think comes built in to the LPC4370 | 18:04 |
| nmz787 | but yeah | 18:04 |
| nmz787 | I realized that | 18:04 |
| delinquentme | yashgaroth, is a continuous growth / selection bioreactor a thing? | 18:04 |
| delinquentme | like FACS + bioreactor | 18:05 |
| xtalmath | sounds like you want to identify isotopes? | 18:05 |
| nmz787 | someone in another room said the LDO on the LPC-Link-v2 adds noise to the ADC readings... but it would be awesome to be able to use that board as-is with a daughter card(s) for the ADC pre-amp and FPGA stuff | 18:05 |
| xtalmath | oh yeah, I forgot theres an FPGA in the FLP4370 | 18:06 |
| xtalmath | i should grab that devboard some day | 18:06 |
| yashgaroth | delinquentme, um most bioreactors are running continuous growth and selection, not sure how FACS fits into it, also you can't select with FACS for a secreted antibody unless you do some fancy multi-splicing expression where the cell produces both secreted and membrane-anchored antibody and you use the membrane-anchored as a proxy for secreted yield | 18:06 |
| nmz787 | xtalmath: with a SEM or FIB you can do elemental mapping... but in my case I want to support an application of thickness detection/monitoring as a FIB milling operation proceeds (as the depth of the hole increases, more xrays can be seen out the backside) | 18:06 |
| nmz787 | xtalmath: flp4370? | 18:07 |
| xtalmath | nmz, I see, so you are using the material's gamma ray stopping power to measure thickness while milling | 18:07 |
| xtalmath | LPC, typo | 18:07 |
| nmz787 | oh, no there's no FPGA there | 18:07 |
| nmz787 | hence the reading about high-speed links to other boards | 18:08 |
| delinquentme | yashgaroth, yeah thats what I was thinking but could be complex. closely co-located antibody + GFP ... could possibly allow GFP to act as proxy for antibody secretion | 18:08 |
| nmz787 | also I work on board design automation at work, so I've been thinking of what it would take to integrate signal-integrity simulations/modelling into my software | 18:08 |
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| gradstudentbot | My code works. I have no idea why... | 18:09 |
| yashgaroth | delinquentme, depends on the cell line, oftentimes they're limited by their secretory procesing pathway, but usually we use the antibiotic resistance protein as a proxy instead of like gfp | 18:09 |
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| xtalmath | ah no its not stopping power, its Beer Lambert law | 18:11 |
| yashgaroth | you will be hard pressed to find a method that is both reliable, and doesn't require months of tissue culture work of expanding single cells, endless ELISAs and pipetting media and oh god I'm getting flashbacks | 18:11 |
| delinquentme | yashgaroth, Yessss. Ok so this is why it would be a good idea to start w highly secreting cell line instead of just saying " all cells have capacity to secrete" | 18:11 |
| delinquentme | ( which is what my gut feeling said , but I had nothing to back it up w ) | 18:11 |
| nmz787 | xtalmath: umm, I think its just some bandgap thing | 18:11 |
| delinquentme | yashgaroth, you're saying that antibiotic selection is just a really simple well-known path | 18:11 |
| gradstudentbot | Have you read this paper? | 18:12 |
| xtalmath | nmz787: electric apparently can do some signal integrity calculations, uses FastHenry etc if self-inductance | 18:12 |
| yashgaroth | delinquentme, uhh what am I backing you up on specifically; also antibiotic selection or some other very similar principle is used 99% of the time for this | 18:12 |
| nmz787 | the photons warp the electron field in the thickness of the PIN silicon and convert all their energy before they make it to the end | 18:12 |
| nmz787 | yashgaroth: i feel like there could be a self-selection system setup though | 18:12 |
| xtalmath | nmz787: no I meant what you use it for, during milling | 18:13 |
| nmz787 | oh, to detect when you milling to a specified thickness, so you can change to a smaller milling diameter | 18:13 |
| xtalmath | "but in my case I want to support an application of thickness detection/monitoring as a FIB milling operation proceeds (as the depth of the hole increases, more xrays can be seen out the backside)" | 18:13 |
| nmz787 | which would otherwise not be effective to mill through so much thickness without getting redeposition | 18:14 |
| yashgaroth | sure there's ways you don't need traditional selection, like with the bicistronic antibody where you have beads with the target on them, run cells over it and pull off the high binders, or use a fluorescent target and do FACS I guess | 18:14 |
| xtalmath | so you are measuring the transmission signal strength of xrays | 18:14 |
| nmz787 | .wik bremstralung radiation | 18:14 |
| yoleaux | nmz787: Sorry, that command (.wik) crashed. | 18:14 |
| nmz787 | .gc bremstralung radiation | 18:14 |
| yoleaux | nmz787: Sorry, that command (.gc) crashed. | 18:14 |
| nmz787 | .g bremstralung radiation | 18:14 |
| yoleaux | https://en.wikipedia.org/wiki/Bremsstrahlung | 18:14 |
| xtalmath | yes bremstralung | 18:14 |
| nmz787 | yeah | 18:14 |
| nmz787 | .wik Bremsstrahlung | 18:14 |
| yoleaux | "Bremsstrahlung (German pronunciation: [ˈbʁɛmsˌʃtʁaːlʊŋ] ( listen), from bremsen "to brake" and Strahlung "radiation", i.e. "braking radiation" or "deceleration radiation") is electromagnetic radiation produced by the deceleration of a charged particle when deflected by another charged particle, typically an electron by an atomic nucleus." — https://en.wikipedia.org/wiki/Bremsstrahlung | 18:14 |
| nmz787 | so as you mill, that happens... and at some thickness, the material you're milling stops being able to absorb all the radiation, and it leaks out | 18:15 |
| nmz787 | so when you detect a leak, you know you're at some thickness | 18:15 |
| yashgaroth | the problem is no one uses non-traditional methods for cell line production since the normal ones work fine, assuming you have a few months to do the endless plating; sure you could try a new method but the development will take even longer to test out, for probably negligible gain | 18:15 |
| xtalmath | nmz787: with milling to thickness, you mean thickness of the target along the direction of the ion beam? | 18:15 |
| xtalmath | nmz787: this was experimentally observed I assume | 18:16 |
| nmz787 | yashgaroth: well i'm pretty sure those systems must already exist as well | 18:17 |
| nmz787 | umm, like if you want to make a really small hole, you will waste time if you set the machine to a tiny beam diameter... because milling will take so long | 18:17 |
| nmz787 | also, you get redeposition at some point | 18:18 |
| nmz787 | so you need to widen your hole before continuing downwards | 18:18 |
| yashgaroth | nmz787 I'm sure someone is running a startup based on one of those systems, and/or published a few papers, but for manufacturing biosimilars no one is really bothering | 18:18 |
| nmz787 | so normally you use a big diameter which is higher power to start, then later switch to a finer diameter | 18:18 |
| xtalmath | nmz787: the bremstralung can be seen as a source of xrays, and the remaining material as an absorber, so you expect intensity on the back I = I_0 * exp(-x*mu) | 18:18 |
| xtalmath | where mu is a material constant | 18:19 |
| nmz787 | so you want to know when you're deep enough to switch over | 18:19 |
| xtalmath | I see | 18:19 |
| nmz787 | umm, idk if that would be the equation... but yes metal absorbs xrays | 18:19 |
| xtalmath | yeah, I had to do this calculation like for 3 or so different experiments at university | 18:20 |
| nmz787 | so for a metal piece, or silicon, etc... you will need to calibrate for given beam power/diameter and signal detected | 18:20 |
| nmz787 | but you can just turn the working piece and take an image, and use geometry to calculate the depth you're at, etc | 18:20 |
| xtalmath | yes, I_0 will depend on milling settings | 18:20 |
| nmz787 | i was looking at this, $89, but am not sure if I could mate it with the LPC4370 (easily) http://www.element14.com/community/docs/DOC-69210/l/fpga-development-board-for-the-raspberry-pi | 18:21 |
| xtalmath | but if you have a seperate xray source, then I_0 will be constant | 18:21 |
| nmz787 | it has some diff-pairs routed to a decent connector | 18:21 |
| nmz787 | nah no separate source, from PIXE only | 18:22 |
| nmz787 | .wik PIXE | 18:22 |
| yoleaux | "Particle-induced X-ray emission or proton-induced X-ray emission (PIXE) is a technique used in the determining of the elemental make-up of a material or sample. When a material is exposed to an ion beam, atomic interactions occur that give off EM radiation of wavelengths in the x-ray part of the electromagnetic spectrum specific to an element." — https://en.wikipedia.org/wiki/PIXE | 18:22 |
| xtalmath | nmz787: heh I have a Spartan 6 LX9 dev board, but not that one | 18:22 |
| nmz787 | I wish there was someone around here that wanted to be an electronics apprentice or something... someone I could get to do a lot of the non-research aspect of this design process | 18:23 |
| xtalmath | I am not familiar enough with LPC4370, so even if I advised you, you should take my word with a grain of salt | 18:23 |
| nmz787 | heh | 18:23 |
| nmz787 | nah even another ADC would be OK | 18:24 |
| nmz787 | especially if I already need an FPGA | 18:24 |
| nmz787 | I've done one other slower ADC design before for a CCD... but I never really tested that for signal integrity or anything | 18:24 |
| nmz787 | and I wasn't oversampling | 18:24 |
| xtalmath | nmz787: I think it will be simpler to start with an ADC with parallel outputs, but not sure how suitable video ADC's are, as they may or may not assume/need a specific timing reference in the input signal | 18:25 |
| xtalmath | is it possible to output the 12 bits on 12 pins with the LPC? | 18:26 |
| xtalmath | if so its straightforward to connect fpga | 18:26 |
| xtalmath | OTOH, if the LPC has SerDes, the spartan can interface with lots of signalling standards | 18:27 |
| xtalmath | oh crap, have to wake up in 4 hours, and visit my sister, help a little with their house rebuilding | 18:28 |
| xtalmath | talk to you later! | 18:28 |
| xtalmath | I will think about the apprenticeship | 18:28 |
| xtalmath | XD | 18:29 |
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| rancyd | is the mailinglist still going? i recieve a 404 when visiting https://groups.google.com/diybio | 21:23 |
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| kanzure | you want https://groups.google.com/group/diybio | 21:25 |
| rancyd | kanzure: thank you | 21:28 |
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