Difference between revisions of "Open Source Bioreactor"

Latest revision as of 13:20, 6 December 2016

The Project

History

... Coming Soon ...

List of contributors

Project Coordinators

Dr. Luc Patiny, ISIC EPFL, Lausanne, CH: https://people.epfl.ch/148588
Pr. Julien Wist, DARMN Research Group, Univalle, Cali, CO: http://quimica.univalle.edu.co/index.php/profesores/julien-wist
Pr. Janeth Sanabria, GAOX Research Group, Univalle, Cali, CO: http://pisa.univalle.edu.co/investigacion/
Quentin Cabrol, MSc Micro and Nanosystems EPFL: https://ch.linkedin.com/in/quentincabrol

Current Collaborators, on Oct 2016

EPFL CODEV: http://cooperation.epfl.ch/
Clément Chenevas and Alice Leydier, Life Science Students EPFL, Sep to Dec 2017 : operation of Bioreactor v3 @ Univalle
Daniel Kostro and Michael Zasso, ISIC EPFL, Lausanne, CH : Bioreactor NodeJS GUI interface

Past Collaborators

Emilien Mingard	Eric Brunner	Marco Schukraft
David Lambalet	Samuel Benketaf	Raffael Tschui
Gabriel Laupré	Gael Grosch	Oliver Peric

Concept

This project is a collaboration between Univalle (Universidad Del Valle - Colombia) and EPFL (Polytechnical school of Lausanne - Switzerland). The goal was to build an Open Source Bioreactor that everyone could assemble and use, from their backyard to the universities around the world.

This Bioreactor can be used for many applications, such as growing bacterias in anaerobic conditions, with an automatised interface. The temperature, pH, weight, conductometry, feeding and flow of gas going in the reactor can be controlled. All the parameters are stored in a card for future use and can be changed or viewed remotely.

Once the Bioreactor is build, all you have to do is choose the conditions of your experiment (pH, temperature, time of sedimentation, flow of gas), and the Bioreactor will do the rest for you !

Central Unit

Requirements Specifications

BOM

...Coming Soon... List of required parts for BioV4.2 Assembly

Mechanical Design

The mechanical design of the parts for the current (11.2016) Bioreactor V4.2 revision is available on github at https://github.com/Bioreactor/Bioreactor_v4/tree/master/CAD/v4.2 .
Parts are to be cut out in plexiglass plates mainly, except fot the heating plate which is in Aluminum, the push button which is 3D printed and the recipient cut out in a polycarbonate cylinder.
A detailed Assembly manual is provided in pdf form at: https://github.com/Bioreactor/Bioreactor_v4/blob/master/Documentation/Plan%20de%20Montage.pdf .

Electrical Design

The Electrical design of the Bioreactor V4.3 Main Unit consists of 2 boards: the mainboard and an extension LCD board providing direct user interface. The hardware of the electronics is under MIT licence and freely accessible at: https://github.com/Bioreactor/Bioreactor_v4/tree/master/Eagle . Gerbers for each board are provided in zip format in each folder. The Gerbers files follow the seeedstudio design rules.

... Coming Soon == BOM in each board folder ...

Embedded Software

1. Arduino IDE isntallation of v1.0.5 2. unzip provided libraries 3. burn Leonardo bootloader (provide link for the JTAG surface connector) 4. flash the code dedicated to the board 5. brief explanation of USB interface with user 6. Idem for LCD interface

Remote Control & Visualizer

... Coming Soon ...

Dev of the remote control ws / NodeJS inteface available for now on https://github.com/qcabrol/NodeTest (no funcitonnal release yet). Information on the GUI platform that is used at http://www.cheminfo.org/

User Manual

This Bioreactor is based on the use of parameters that can either be read or changed. The parameters that can be read are the ph, temperature, weight, gas flow and conductometry. Depending on the needs of the experiment, the user can change the target pH and temperature of the solution, as well as the desired gas flow, the time of sedimentation and the level of emptying and filling of the Bioreactor.

Extension Modules

pH regulation and conductometry

The Bioreactor contains an optional pH board, that can be used with a standard gel probe containing reference electrode and a BNC/RCA (Cinch) 2-Wires output. You can choose to regulate or not the pH of your solution, by changing the pH state. In order to regulate the pH, the target pH should be set and solutions of acid and base should be prepared.

Another board can be added for the measure of the conductometry.

Dynamic gas Mix

The Anemometer board addresses the need to control the bioreactor atmosphere. It dispose of 4 flow measurement channels to dynamically analyze the input and output flows of gas in the reactor. It allows to obtain a desired mix out gas bottles with pure content (CH4, N2, CO2,...) and potentially to operate the system in anaerobic conditions by ensuring a constant overpressure. Though it, of course, requires a bit more of material both electronic and fluidic.

External Resources

Media

Cali Summer Internships 2014: http://univalle.epfl.ch/page-111363.html
Collaboration EPFL - Univalle, CODEV: http://univalle.epfl.ch/
Presentation ALAM 2014: https://goo.gl/mMvKWo
ALAM 2014 Cartagena de las Indias: http://alam2014.acmicro.org/
Bioreactor Isobar : https://www.youtube.com/watch?v=AM8Rpxd9WJg
Bioreactor V3.0 2014 : https://www.youtube.com/watch?v=9sCRF4vdtTM
Presentation CODEV 2016: https://goo.gl/ixcJ2y

For Developers

Github Bioreactor V3 (soon to be abandoned): https://github.com/Bioreactor/Bioreactor_v3
Github Bioreactor V4 (in development 30.11.2016): https://github.com/Bioreactor/Bioreactor_v4
Extensive Developer Manual (in development 30.11.2016): https://goo.gl/il9WWs

@@ Line 4: / Line 4: @@
 ===History===
-http://univalle.epfl.ch/
+... Coming Soon ...
 ===List of contributors===
@@ Line 10: / Line 10: @@
 ''' Project Coordinators'''
-Pr. Luc Patiny, ISIC EPFL-UNIL, Lausanne, CH <br>
+Dr. Luc Patiny, ISIC EPFL, Lausanne, CH: https://people.epfl.ch/148588 <br>
-Pr. Julien Wist, DARMN Research Group, Univalle, Cali, CO <br>
+Pr. Julien Wist, DARMN Research Group, Univalle, Cali, CO: http://quimica.univalle.edu.co/index.php/profesores/julien-wist <br>
-Pr. Janeth Sanabria, GAOX Research Group, Univalle, Cali, CO <br>
+Pr. Janeth Sanabria, GAOX Research Group, Univalle, Cali, CO: http://pisa.univalle.edu.co/investigacion/ <br>
-Quentin Cabrol, MSc Micro and Nanosystems EPFL <br>
+Quentin Cabrol, MSc Micro and Nanosystems EPFL: https://ch.linkedin.com/in/quentincabrol <br>
 '''Current Collaborators, on Oct 2016'''
-Clément Chenevas, Life Science Student EPFL : operation of Bioreactor v3 @ Univalle <br>
+EPFL CODEV: http://cooperation.epfl.ch/ <br>
-Alice Leydier, Life Science Student EPFL : operation of Bioreactor v3 @ Univalle <br>
+Clément Chenevas and Alice Leydier, Life Science Students EPFL, Sep to Dec 2017 : operation of Bioreactor v3 @ Univalle <br>
-Daniel Kostro, ISIC EPFL-UNIL, Lausanne, CH
+Daniel Kostro and Michael Zasso, ISIC EPFL, Lausanne, CH : Bioreactor NodeJS GUI interface
-Michael Zasso, ISIC EPFL-UNIL, Lausanne, CH
 '''Past Collaborators'''
-Emilien Mingard <br>
-Eric
-Marco Schukraft <br>
-(1 more ?)
-David Lambalet <br>
-Samuel Benketaf <br>
-Raffael Tschui
-Gabriel Laupré
-Gael Grosch
-Oliver Peric
+{| class="wikitable"
-Add project contacts here with roles in the project.
+|-
+| Emilien Mingard
+| Eric Brunner
+| Marco Schukraft
+|-
+| David Lambalet
+| Samuel Benketaf
+| Raffael Tschui
+|-
+| Gabriel Laupré
+| Gael Grosch
+| Oliver Peric
+|}
 == Concept ==
@@ Line 48: / Line 49: @@
 === Requirements Specifications ===
+=== BOM ===
+...Coming Soon... List of required parts for BioV4.2 Assembly
 === Mechanical Design ===
+The mechanical design of the parts for the current (11.2016) Bioreactor V4.2 revision is available on github at https://github.com/Bioreactor/Bioreactor_v4/tree/master/CAD/v4.2 . <br>
+Parts are to be cut out in plexiglass plates mainly, except fot the heating plate which is in Aluminum, the push button which is 3D printed and the recipient cut out in a polycarbonate cylinder. <br>
+A detailed Assembly manual is provided in pdf form at: https://github.com/Bioreactor/Bioreactor_v4/blob/master/Documentation/Plan%20de%20Montage.pdf .
 === Electrical Design ===
+The Electrical design of the Bioreactor V4.3 Main Unit consists of 2 boards: the mainboard and an extension LCD board providing direct user interface. The hardware of the electronics is under MIT licence and freely accessible at: https://github.com/Bioreactor/Bioreactor_v4/tree/master/Eagle . Gerbers for each board are provided in zip format in each folder. The Gerbers files follow the seeedstudio design rules.
+... Coming Soon == BOM in each board folder ...
 === Embedded Software ===
+. Arduino IDE isntallation of v1.0.5
+. unzip provided libraries
+. burn Leonardo bootloader (provide link for the JTAG surface connector)
+. flash the code dedicated to the board
+. brief explanation of USB interface with user
+. Idem for LCD interface
 === Remote Control & Visualizer ===
+... Coming Soon ...
+Dev of the remote control ws / NodeJS inteface available for now on https://github.com/qcabrol/NodeTest (no funcitonnal release yet).
+Information on the GUI platform that is used at http://www.cheminfo.org/
 === User Manual ===
 This Bioreactor is based on the use of parameters that can either be read or changed. The parameters that can be read are the ph, temperature, weight, gas flow and conductometry. Depending on the needs of the experiment, the user can change the target pH and temperature of the solution, as well as the desired gas flow, the time of sedimentation and the level of emptying and filling of the Bioreactor.
-=== Bill of Materials ===
 == Extension Modules ==
@@ Line 84: / Line 107: @@
 Bioreactor Isobar : https://www.youtube.com/watch?v=AM8Rpxd9WJg <br>
 Bioreactor V3.0 2014 : https://www.youtube.com/watch?v=9sCRF4vdtTM <br>
-Presentation CODEV 2015: https://goo.gl/ixcJ2y
+Presentation CODEV 2016: https://goo.gl/ixcJ2y
 === For Developers ===