Re: [DIYbio] Microcontrollers

On Sep 25, 2012, at 3:42 PM, Simon Quellen Field wrote:

> Because the Pi is basically a laptop computer without the screen and keyboard,
> what you know about the computers you use for home, school, and work will
> apply to it. The Arduino is nothing like what you are used to, and will take
> longer to learn, even though it is very simple.

> The advantage of a multitasking web connected controller is that you can monitor
> it from anywhere on your phone or laptop, and it can send you alerts if something
> goes wrong with pumps, temperature, power failure (use a UPS for your router),
> oxygen, pH, or anything you'd like to monitor.
>
> It can keep a record of all the sensors on the hard drive, so when you kill your
> first batch, you can find out what went wrong and fix it before trying again.
>
> You can watch graphs of all the things you are measuring, and adjust things in
> response over the web, without having to be home watching it all the time.

You make a compelling argument for the Raspberry Pi. I hadn't spent much time looking at the Pi before, but it's clearly warranted now.

Nonetheless, I think you really hit the main issue on the head in that first paragraph above. The Pi is basically a laptop computer without the screen and keyboard, but that doesn't help me much:

1) I have no familiarity with Linux, Python, PHP, Apache, bash, etc. I currently have no idea how to set up THIS computer as a web server, or have it display continuously-monitored data as a graph. (Can I use R?) Maybe this is much, much easier than I think it is, or maybe I can get someone to help me, but I wouldn't count on it. I'm hardly averse to learning this stuff, either, but I have a very hard time not exploding into twenty different topics as it is, and I need to watch that.

2) I also have no idea how to connect this computer to a bunch of sensors designed to monitor environmental parameters. The Phidgets are easy, I think, but too expensive. In my particular case, the legacy of my long-standing and wholly unsuccessful attempts to get into robotics is a slightly greater familiarity with things like H-bridges than with things like sorting algorithms or data structures, so the low-level nature of the Arduino isn't as big a barrier to me as you might expect, although it's still substantial.


1) is unquestionably very nice. In the case of brachiopods (and possibly marine filter feeders in general), nobody actually knows what the relevant boundaries on these parameters are, so easy viewing of them would have serious value; I might have an easier time figuring out what kills brachiopods. But 2) is essential. The entire project is dead in the water (har) unless I can do 2).

The advantage of the Arduino, on this score, is that I know that I can actually go out and buy sensors for water flow, temperature, pH (https://www.sparkfun.com/products/10972 or http://atlas-scientific.com/product_pages/sensors/ph-sensor.html), dissolved oxygen (http://atlas-scientific.com/product_pages/sensors/do-sensor.html ), and oxidation-redox potential (http://atlas-scientific.com/product_pages/sensors/do-sensor.html ). Like, right now. If I want to go in the direction of a digester, a fermentation tank, a hydroponic system, an aeroponic system, or a terrarium, I can sense methane, carbon monoxide, alcohol, hydrogen (all at https://www.sparkfun.com/categories/146 ), humidity (http://www.seeedstudio.com/depot/grove-temperaturehumidity-sensor-pro-p-838.html ), and light. Sensing salinity is a problem, but at least I can find attempts at Arduino-compatible salinity sensors.

Similarly, I know that a bunch of people have tried to do these things before; the most recent find was the BioBoard project at Noisebridge (https://www.noisebridge.net/wiki/BioBoard ). It's clearly possible to make the Arduino do some data logging and PID control, as well, so I know I can continue beyond the sensing step using an Arduino.

Here, the sheer *seniority* of the Arduino is a substantial advantage-- unless it's trivial to connect all these things to the Raspberry Pi, in which case, hey, awesome. As this is a long term project, I could just sit around and wait for the Pi to "catch up", in terms of the availability or compatibility of sensors; how long do you think that would take?

Now, I obviously haven't looked into these issues in any remotely comprehensive way. It seems as if there's a significant overlap between many of these different environmental control problems, so it may be possible to design a board or something with general utility, one that could be used in everything from reef tanks to chemostats. (I guess this is the goal of the BioBoard project, really. Maybe I should talk to them, because they're roughly in the area and all.) DIYBio people: Would it be useful to you for me to go down this road? Do lots of you think you might need an environmental monitoring/control system? I'll probably do it anyway, because I'm pretty serious about the brachiopods, but I'd love to know.

--T.

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