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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: 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].