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umafuckitt writes:
Early microscopists and electrophysiologists were pathfinders who built their own hardware to perform their experiments. Today, whilst much cutting edge biology still requires the experimenter to develop new equipment, a huge amount of excellent work can be done with off-the-shelf hardware.
The problem, however, is that a lot of this equipment is over-priced for what it is and it's usually closed and so hard to hack. Thus, it may not be surprising that a home-brew hardware revolution is quietly taking place in biology. Rather than building novel equipment, a lot of today's scientists are coming up with much cheaper and more flexible solutions for existing commercial devices. Opensource hardware is a great way of stretching grant money, bringing science into schools, and allowing researchers in poorer countries to do more with their limited budgets. Central to most Opensource hardware projects are easy to use microcontroller packages, such as Arduino, Maple, and Teensy, allowing biologists with no engineering background to re-invent their closed, mass-produced, and expensive hardware. One reason this reinvention has been so effective is because a lot of the equipment still being sold today is based upon older designs that have not been updated in many years.
Here is a selection of some of what's out there now:
- OpenPCR is a $600 thermocycler used for amplifying DNA for detection and sequencing. OpenPCR is at least ten times cheaper than competing commercial alternatives.
- Open Ephys is a hardware/software platform for electrically recording neural activity from multiple electrode channels. Cost savings are huge.
- Pulse Pal is a arbitrary wavefrom generator, competing with far more expensive commercial alternatives such as the Master 8.
- OpenStage is a complete motor control system that provides sub-micron motions for microscope stages. A system can be assembled for about $1000, which is what what some commercial vendors are charging for just the joystick input to their controllers.
(Score: 3, Interesting) by Sir Garlon on Thursday March 27 2014, @01:22PM
Out of curiosity, what kind of biology work requires a waveform generator?
[Sir Garlon] is the marvellest knight that is now living, for he destroyeth many good knights, for he goeth invisible.
(Score: 5, Informative) by umafuckitt on Thursday March 27 2014, @01:36PM
Poster here. Since there is no original article, I'll be on hand to answer questions.
I can only speak from my own experience, but we use waveform generators for a bunch of tasks. Two common jobs that require very precise pulse trains are light activation (or deactivation) of neurons genetically engineered to express light-gated ion channels (optogenetics [openoptogenetics.org]). Similar waveforms are used to drive neurons directly using current injection from an electrode. This might be performed using extra-cellular electrodes or cell-attached electrodes [wikipedia.org].
There are other uses for precise pulse trains too (such as gating sensory stimuli to an animal), but the above uses are amongst the most time-critical I can think of.
(Score: 0) by Anonymous Coward on Thursday March 27 2014, @07:14PM
You're involved in research involving the genetic engineering of brain cells? Excellent - finally someone to ask this question that's been bothering me since I saw a TED talk on the subject a year or three ago:
What safeguards do you take to ensure that your engineering viruses don't escape into the wild? I understand that the original viruses are basically harmless, the sort of virus you'll likely never know has infected you. However you've altered them to make changes to some of the brain cells of their hosts - changes whose long-term consequences are completely unknown. After all even if there are no other side effects growing and maintaining the photo-receptors comes at a non-zero biological cost. Routinely allowing viruses to escape would seem lead to a large slice of the human population developing neural photoreceptors, probably many different kinds originating from many different experiments. Best-case scenario that renders them unsuitable as subjects for future research using this technique. Worst-case... well that would depend entirely on exactly what the probably subtle long-term effects are.
(Score: 2) by umafuckitt on Thursday March 27 2014, @08:32PM
I don't know what safeguards there are (I don't do the work) but there are a few things I can point out. Photoreceptors are the light-sensitive cells in your eye. These have nothing to do with optogenetics, which employs proteins derived from algae. As far as I know, most of the viruses used in these experiments are not infectious in the traditional sense. You inject them directly into the brain, they get taken up by neurons near the injection site, but they do not then infect other cells. They stay where they are. The only exception to this that I know of are viruses used for synaptic tracing: they enter a cell and then infect all cells connected to that cell. However, they stop at those neurons and do not infect further cells. So basically, the only way you'll get infected by one of these viruses is via needle stick. So really it's all very safe because the viruses are stripped of everything but what's needed to do the job.
(Score: 1) by Immerman on Thursday March 27 2014, @09:31PM
(Same AC, finally signed up)
Thank you, that is considerably less worrisome than I imagined.
Oh, and FYI while "photoreceptor" does refer to a specific class of cells when discussing biological vision systems, it is also a far more generic term spanning everything from the light-responsive proteins employed by such cells (or algae, etc), to silicon-based light detectors.
(Score: 2) by umafuckitt on Thursday March 27 2014, @10:00PM
I guess the usage of the term is field-specific. The usage I'm familiar with sees "photoreceptor" referring to a cell type, such as retinal rods and cones, and "photopigment [wikipedia.org]" referring to the light-sensitive proteins within them. This is a useful disambiguation for neuroscience. I imagine people who study algae might well refer to chanelrhodopsin as a "photoreceptor." That's certainly what the Wikipedia page seems to imply [wikipedia.org].
(Score: -1, Troll) by Anonymous Coward on Thursday March 27 2014, @01:49PM
i wonder what it smells like
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(Score: 2, Interesting) by sbgen on Thursday March 27 2014, @03:30PM
Thanks for the links. I would like to checkout the OpenPCR. Do you know how efficient &/ accurate its ramping is? The latest PCR machines are pretty useful for very fast PCRs with their extreme ramping abilities. While we are here, do you know of any opensource alternative to the sonicators? They are not only expensive but also sadly unreliable. I would also love to find some reporter vectors that one can synthesize quickly and cheaply. The market price currently is quite unrealistic.
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 3, Informative) by Anonymous Coward on Thursday March 27 2014, @03:50PM
It's worth noting that PCR was a patent protected process until 2006. Those of us who bought systems before then had to pay a premium for licensing, and since everyone got used to paying thousands of dollars for a microprocessor controlled Peltier, that became (and has largely stayed) the market price.
Some of the taq enzymes are still patent protected. "Real time" PCR is still patent protected. If you're really thinking about rolling your own system, you may have a maze of intellectual property rights to sort out before you can publish. If you're primarily education, then having a group build and calibrate their own PCR system would be a great way to teach them and to provide a tool for future class-generations.
Speed is going to depend on how many peltiers and how much current you can drive. Accuracy is going to depend on how much effort you're willing to put into calibration. That is: you can't put thermal sensors in the wells during an actual run, so you need some relationship between the actual well temperature and the sensors you do have. Make a few "fake" runs using tubes filled with water and thermistors, and you should be able to calibrate at least as well as the commercial devices.
(Score: 3, Informative) by umafuckitt on Thursday March 27 2014, @04:13PM
Yes, exactly. It would help if the OpenPCR guys published the ramp curves on their site. That would help potential users decide if the product would be suitable for their needs (might be worth e-mailing them to ask). I've heard that someone in our institute is using an OpenPCR box with success, but I don't know more than that.
(Score: 2, Interesting) by sbgen on Thursday March 27 2014, @07:12PM
I went to their site and no they do not have ramp curves for their instrument. Besides it is limited to 16 tubes and that necessarily excludes it from most research labs, a minimum of 96-wells is a must. However, it is a very good platform for education, especially for high-schools. Interestingly, I saw that they are developing a qPCR (realtime, quantitative PCR) machine which will be sold through "Chai Biotechnologies" (there is a link on OpenPCR site somewhere). This is the company that is also selling their OpenPCR kit at the moment.
The AC replying to my post makes some good points in terms of the patents on PCR process coming in the way of research. Unfortunately I have no modpoints to make that post more visible, some body please mod that post.
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 4, Interesting) by nukkel on Thursday March 27 2014, @04:56PM
I'm not familiar with the field, but I think it is a good thing to reduce the income these established equipment companies get out of their old cash cows. It will hopefully motivate them to divert more resources to R&D and come up with new, interesting equipment (and after N years, the cycle can repeat).
(Score: 1) by sbgen on Thursday March 27 2014, @07:15PM
I completely agree. You might want to read the post by AC (replying to my post above) to get some idea why things are so expensive in the above field.
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 3, Informative) by umafuckitt on Thursday March 27 2014, @07:39PM
Some things are patented, yes, but that's likely not the general reason why stuff is so expensive. For example, take the link to the joystick in the original post. Nothing is patented there, but the thing still costs a grand. So why is some stuff absurdly expensive?
One reason is time savings. You're a stressed academic and you need data. You know you can buy widget X to solve your problem and it'll be here this week. If you design it yourself it will take longer; maybe much longer. This initial time investment will go down as more opensource hardware is released and researchers can begin modifying existing designs rather than building from scratch. Leveraging what's available in the hobby electronics movement has really helped in this regard.
The second reason these companies can charge absurd money is that a lot of researchers, particularly in the "soft" sciences, can't program and have few technical skills. They'll pay whatever is asked of them because they have no choice and consider all this stuff to be magic. I'll give you an example. Someone I know works on human gait and purchased a 3-D tracking system that records human locomotion and converts it into some useful stats they need. They were excited recently because the company has just produced a new version of the software which allows the data to exported as .csv or .xls and so they can get stuff into Excel directly. Prior to this they were printing out the data and typing it in manually into Excel. I don't know what format the software used to produce, but clearly there must have been some way to automate the export process before (even if it required programming knowledge to read proprietary binary files). For a lot of people, however, if their software can't do X then they assume X isn't possible. A second great example was a guy I know who bought a $10k system to track animal position over time. The system arrived and it was just a crappy $100 frame made out of parts from McMaster Carr, a CCD camera, and a PC with some simple software to read out the animal's position. Most people in my lab could have made such a system in an afternoon with a web cam.
(Score: 1) by sbgen on Thursday March 27 2014, @08:22PM
That is interesting - you are making me curious. If I may ask, what is the software your buddy bought to track animals? And which animal/s can it track? Our lab could probably find it useful. I agree with your assessment about time constraint and unfamiliarity with coding contributing to the expense of the instruments and fleecing thereof. Hopefully this will change with time as you suggest. However, patents do hinder research and particularly applied side of it.
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 2) by umafuckitt on Thursday March 27 2014, @08:40PM
Ha, ha... The guy in question was a work dodger (now fired) and never used the system (or did any experiments at all, for that matter). I have no idea what the system is (it has no labels on it). He bought it to track fly larvae. It was a particularly dumb thing for him to do, given that we already had two different pieces of in-house software to track adult flies. There's also this [sourceforge.net]. So it's really an easy problem for 2-D. There are published 3-D solutions too.
(Score: 1) by sbgen on Thursday March 27 2014, @08:53PM
Thanks, ctrax is a good software, I had forgotten about it. We have software from CleverSys to track rodents.
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 2) by nukkel on Friday March 28 2014, @07:01AM
Very good points.
(Score: 2, Interesting) by gumby on Thursday March 27 2014, @07:40PM
really hit home. Experiments are so expensive and we get used to buying expensive sterile bottles of PBS from Fisher that we forget we don't need to waste money with Fisher for prosaic stuff.
For example a single steel secondary containment vessel is $160 from Fisher. Or you can get a dozen rectangular deep dish (1.5 inch deep) pizza pans from restaurant supply for $120. That 254 nm UV light? Shockingly it's the same wavelength as an EPROM eraser, though you pay 10X the price for the privilege.
For stuff that will be submitted for regulatory purposes I might pay the extra Danegeld [wikipedia.org]. But for regular old R&D, a lot of lab supply is expensive. Save that money for reagents and pipetter tips.
(Score: 2, Interesting) by moondrake on Thursday March 27 2014, @09:24PM
Even although there is no news article I like this post. I am a biologist as well and for the past few weeks have been creating up some new experimental setups. To read data from thermocouples, balances and various other sensors we use various dataloggers [campbellsci.com], but they are quite expensive. In addition, though (especially the older models) are well documented, they come with crappy windows software that usually fails to do what I want, so I write my own stuff and then interface it with the wonderful kst [kde.org] to have instant and beautiful graphing abilities.
I have been asking myself why I should not buy and Arduino or similar to do the same things, I just worry a bit about the reliability and accuracy. I usually do not need the fancy satellite uplinks of our current equipment, but I do need to be able to read out a thermocouple accurately and reliably. I am just not sure of this with a consumer product, but perhaps someone can chime in on that.
In my experience, it gets worse with more complex analyzers. Anything over $50,000 seems to come with its own embedded windows version (well, linux if you are lucky), but completely closed source and with a horrible interface. I asked several times to various companies to provide me the source and there are very few who comply (blahblah quality control blah blah). This pisses me off if the software does not output raw data and I want to know exactly how it is treated before I use the numbers. It is sometimes even necessary to make changes as I use the machine in a non-standard way where its assumptions do not hold.
So I spend weeks applying my (quite bad) coding skills on reimplementing 90% of the provided software based on RS232 output just to change a single parameter. Madness!
(Score: 2) by umafuckitt on Thursday March 27 2014, @10:21PM
I've had zero problems with Arduino reliability. If you design your circuits correctly, things really ought to be problem free. The accuracy may be an issue, but it depends what you want. Most Arduinos have 10 bit ADCs so if your inputs are badly scaled this certainly won't be enough. Even if they're well scaled, it could be too low. The Teensy 3.1 [pjrc.com] has 13 bits of usable resolution and the Arduino Due has 12 bits, so those are better. The cost of entry (both time and money) is so low, that you might as well buy a starter kit and have a play.
At about $150 NI do some small USB units: USB-6000 [ni.com] and USB-6008 [ni.com]. Those are also 12 bit. Then you move on to NI's PCI and PCIe cards, which have higher sampling rates and ADC resolutions. I use those to drive a scanning microscope. You can get quite reasonable 16 bit units for about a grand. Breakout box is extra. They can be controlled with MATLAB or NI's own software. The drivers are free to download and you can use the dlls to write code in the software of your choice.
All the above hardware will work. The trick is to define exactly what you want to measure: accuracy and sampling rate. Then buy a device which will be adequate for the job and has no frills. An Arduino Uno might be perfectly OK. Alternatively, you might indeed need the speed and resolution of a $1.5k board.