Open and Modular Photobioreactor for Quantiative and Theoretical Biology

• Code repository for a modular photobioreactor, based on arduino and raspberry pi controlled sensor and control devices.
• Initiated at the 1st QTB PBR Hack`a'thing, March 2-4 2016, at the Quantitative and Theoretical Biology Group of the Heinrich-Heine University Düsseldorf. See QTB wiki page.
• Inspired by prior work from Dougie B. Murray and Rob Lehmann, fuelled by the DIY spirit.

SET-UP ARDUINO & LIBRARIES

Installing Arduino IDE

1. E.g., on Fedora: sudo dfl install arduino or on Ubuntu/Debian: sudo apt-get install arduino arduino-core
2. Running arduino requires permissions to communicate with the USB port; this will either be managed by the software arduino, which will prompt you for a root password to add you to dialout and tty groups, or you can do it manually (on commmand-line) with sudo usermod -a -G tty yourUserName; sudo usermod -a -G dialout yourUserName. To take effect you'll need to logout and login again.
3. To access this ocde (PBR/code) from the arduino IDE easily, you can simply add a symbolic link to arduino's sketchbook directory, e.g. by ln -s ~/programs/PBR/code ~/sketchbook

Installing Required Libraries

There are two+ ways to install additional libraries for Arduino. Either download a .zip file of the library and import them via the arduino IDE (Import Library > Add Library and select the .zip file), or unpack (or e.g. git clone) them into your local arduino library path (e.g., ~/sketchbook/libraries). The latter requires closing and re-opening the arduino IDE.

• Touch screen: Our common module control is via the Arduino Mega 2560 board with Sainsmart's touch screen (SSD1289). These work with Rinky-Dink's libraries. Download UTFT.zip, UTFT_Buttons.zip and UTouch.zip and install them via the arduino IDE's .zip file import.
• Time library
• HX711 library for the scale module (liqometer)

Using Emacs for Arduino Code

i. Download emacs mode (arduino-mode.el), e.g., to ~/.emacs.d/lisp ii. Add the following code to your ~/.emacs file:

;; adding local .el files
(add-to-list 'load-path "~/.emacs.d/lisp")
(progn (cd "~/.emacs.d/lisp")
       (normal-top-level-add-subdirs-to-load-path))
;; auto-recognize arduino files via file-ending:
(setq auto-mode-alist (cons '("\\.\\(pde\\|ino\\)$" . arduino-mode) auto-mode-alist))
(autoload 'arduino-mode "arduino-mode" "Major mode for editing Arduino." t)

iii. In the arduino IDE activate "Use External Editor" in File > Preferences