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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, 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.