28 Days later... The hardware layer was complete.

How does a bubble column bioreactor work?

We aren’t experts, but we can tell that a bubble column bioreactor needs mainly three things

• An illumination system
• A source of bubbles
• Algae for growing

The illumination system gives the radiant energy for the algae to grow, the bubbles carry oxygen, nitrogen and CO2 and all the remaining elements that compose the air, the algae also feeds on this. the ascending bubbles also generate water currents that inhibits the sedimentation of the algae and keeps a suspension of them. The culture is influenced by parameters as illumination, size of the bubble column, temperature, pH of the medium, CO2 dilute and many other that we don’t know, yet. Having the possibility of knowing those parameters and maybe controlling them was our main motivation for take hands on MARBLES project.

A bit of history

By Hardware, we mean a control unit that monitors all the sensors, and at the same time, controls all the peripherals that make the bioreactor work, (so the Algae keeps alive). We initially thought of using a ChipKit Uno32 as our control station, why?, well, the ChipKit Uno32 has Analog inputs, so we could connect our analog sensors “directly” to the device, and, using the digital outputs, we could control the state of on/off for the remaining electronic peripherals.  But we found that the included processor couldn’t handle well all the required tasks. Given that we also have a RaspberryPI (Rev B) as part of our “tools for success”, so we decided to explore all of our options.
So we decided to use the RaspberryPI for handling a web-based user interface, the data analysis and control the bubbling, the illumination system and the concentration measuring system. This last one is basically the Chipkit Uno32 connected on one side to a photodiode-resistor circuit and the other to the RasPI via USB for analog data transmission.

Control unit
The control unit contains the needed circuitry to manipulate the illumination intensity, the bubbling system and the laser through digital signals from the RasPI.
The circuit contains three optocoupler for protecting the RasPI and two transistors to increase the voltage on the laser and on the relay for them to function properly, the optocouplers ther operate as commutators when the GPIO (3.3V) HIGH signal arrives.
The sole optocoupler at the bottom operates in the same way but with the smal difference that the signal on the base is a PWM (Pulse-Width Modulation) which is not giving trustworthy results when the power of the illumination is measured. We must find another way around to control the intensity.

The circuit is every week mutating since we find other ways to get better results and more reliable signals, so it's still on a white and sad breadboard.

Black Metal Bioreactor

The system right now looks like this (kind of) but the user interface has changed a lot, next post will be about the software layer and the user interface.

Enter the Marbles

“-Your style is unorthodox.
-But effective.
-It is not the art but the combat you enjoy.
-The winning.
-We are all ready to win.
  Just as we are born knowing only life, it is defeat that you must learn to prepare for.
-I don’t waste my time with it. When it comes, I won’t even notice.
-Oh, how so?
-I’ll be too busy looking good”

Such a long time without bloggin’ anything related to our project. At least we have chosen a fancy name for it: MARBLES, which stands for Marvelous ADC and RaspberryPi Biorreactor’s Lightweight Electronic System

MARBLES is mainly composed of two components interacting with each other: A Software layer and a Hardware layer by means of both digital and analog signals.



The hardware layer is composed of an Arduino, a ChipKit or any ADC system that reads analog input and sends it via USB, and the software layer is a client-server web-based system that sends, receives, process and displays the information from the hardware layer.
Each of these layers will be explained in the next posts.

Episode I - A new hope: no more boring physicists

At the beginning: we were boring physicists

Hi Reader, this blog is meant to be the logbook of a science project.

A Physicist must have a lot of capabilities such as theoretical, experimental and computational; and sometimes this is forgotten (Even sometimes this is encouraged, by arguing that “you can only specialize on one thing”. F**k that s**t!). This time, two senior Physics students (at  University of Antioquia) engaged a research on a polemic field of application: Biological Sciences. You might ask, why polemic?, well, our institute has a long tradition on other fields of research such as quantum mechanics, optics and solid state physics, not related, not even a little, to Biology. That means that is pretty rare that some individuals follow a path different than the mentioned.

This time, we (Gerado and Me, Daniel) will make an experimental approach to the building of a Bioreactor system for the culture of microalgae. Our main goal is design a method to measure the microalgae concentration inside the bioreactor without opening it, which avoids the risk of contamine the microalgae culture. We detected this as an unsolved problem (at least locally) and that was highly motivating for us, so bad that we made a blog about it. We expect to make blog post and videos of our progress (but don’t expect hard details about it).

The interesting part is, that we will be using a Arduino Uno32 chipkit to automate stuff, (measurements basically) and a RaspberryPi to monitor and control all the processes, of course this involves circuit designing and building, also lots of programming, so we will be releasing code and maybe designs (licensed under GPL for hardware and GPL V3 for source code) in order to contribute to the community of free software and hardware.