SoylentNews is people
SoylentNews
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: 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.