Re: [DIYbio] Microcontrollers

Well, the brachiopod project doesn't need a CO2 sensor, obviously. I mentioned it mainly to illustrate that there seems to be a wide variety of Arduino-compatible sensors out there, often with Arduino sample code. According to the datasheet, the Sandbox Electronics CO2 sensor (sold in a not-eBay fashion here: http://sandboxelectronics.com/store/index.php?main_page=product_info&cPath=66&products_id=197 ) uses 5.5V from the Arduino to condition the sensor signal, and requires a separate power supply for the sensor's heating circuit, so presumably that's how they get around the power issue.

Microcontrollers are not the big issue for a brachiopod project. The more I learn about the subject, the harder it looks. Even the first step, getting a laminar flow through a closed aquarium, is something that only became feasible relatively recently. I need a laminar flow system, a refrigeration system, and a moderately sophisticated filtration system, and you can get more complex from there (by using an algal turf scrubber, for example). One of the major problems we've encountered in keeping filter feeders is just knowing what they'll eat, and giving it to them-- you have to keep a culture of the plankton itself and introduce it to the tank without removing it via the filter. Progress on this problem has been made via the development of synthetic plankton substitutes(!!!), which I guess obviates the culture issue. Adding a microcontroller sensor system just makes the actual conditions in the tank more visible, and would hopefully make it less mysterious; eventually it would help maintain stable conditions.

All of this stands in stark contrast to the methods described in McCammon's paper, which sound pretty trivial by comparison. McCammon's methods might work! However, just GETTING brachiopods is not going to be easy. It's not going to be like buying a tiger shark or something, but we can't keep 'em, so if I go after this, someone has to get some. I'm not going to try McCammon's methods straight out when the creatures themselves are so hard to come by (commercially) and everything else I see says I'm in for a major challenge.

Evidently some of the progress in this area has been made by people who want to culture sponges to study their antibiotic properties?

This is a long-term project because I don't have the money to do it. It's not out of the question, I think-- I don't have to be the Monterey Bay Aquarium-- but it'd definitely require much more than I have.

I found a forum thread in which someone is attempting to use the Raspberry Pi and the Atlas Scientific sensors to make a tank monitor, so that's probably a thing you can do. (http://www.thereefuge.com.au/board/threads/raspberry-pi-tank-monitor-project.3475/ )

--T.

On Oct 1, 2012, at 2:11 PM, Cathal Garvey wrote:

> Small nitpick; gas sensors tend to draw a lot of power, and it's
> challenging to get even enough power to drive modest USB equipment from
> a RPi without a separate power hub. That's one nice feature of Arduino;
> a really wide input voltage band, and the potential to draw larger
> ampages straight from the voltage regulator than would otherwise be
> avaialble on the pins.
>
> Having said that, I'm not sure even the arduino can supply enough power
> for some of the more popular gas sensors like those used in alcohol
> breathalysers. It may or may not apply to your CO2 project.
>
> On 27/09/12 20:46, Tristan Eversole wrote:
>> The critical point, which I had not realized before Simon replied, is that my choice of microcontroller does not strongly constrain my choice of sensors. If it did, that would be a powerful argument in favor of the Arduino: I can type "arduino carbon dioxide sensor" into Google, and bang, there's one on eBay. (http://www.ebay.com/itm/MG811-MG-811-CO2-Carbon-Dioxide-Sensor-Module-for-Arduino-and-other-MCUs-/120804868793 ) However, if it's not that hard to connect the aforementioned carbon dioxide sensor (for example) to a Launchpad or a Raspberry Pi or a Propellor, then the choice of microcontroller is no longer any sort of huge limiting design decision-- particularly because the microcontroller is going to be quite cheap relative to the tank, the sensors, the refrigeration system, and the brachiopods themselves.
>>
>> So I really owe you guys for pointing this out.
>>
>> --T.
>>
>> On Sep 27, 2012, at 12:09 AM, Patrik D'haeseleer wrote:
>>
>>> On Wednesday, September 26, 2012 4:26:32 PM UTC-7, John Griessen wrote:
>>> Taking all you've said about your own experience level, this is sounding the most
>>> results-getting direction yet. Does the bioboard have cost levels you can fit to your want?
>>>
>>> Actually, the BioBoard *is* an Arduino platform. And it is far from a well-developed product - it's a couple of people at Noisebridge hacking some sensors. Really cool work though - they were building their own pH and DO probes.
>>>
>>> Given Tristan's lack of experience with Linux, OS's, programming, and electronics, I still think the fastest way to get him up and running would be Arduino. He'll have his hands plenty full setting up the aquarium, rigging the sensors, etc.
>>>
>>> I'd say get to the point where you can collect all the data you need on an SD card, and switch some relays on an Arduino. Pretty much everything you've learned up to that point will translate over directly if you do decide to move to a RasPi platform.
>>>
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>>
>
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