DIY Turbidostat
Jt
New to the DIYBio group.
I have created a turbidostat that I would like to share with the
community. In brief, it uses an Arduino to control a peristaltic pump
based on OD readings, includes temperature control as well as an
aquarium pump for aeration. Additionally, I have a version that
forgoes the pump and relies on air pressure and valves to move fluid
through the system. The system currently uses the Arduino Ethernet
Shield and HTML interface to control it, though an interface over
serial could be easily written for anyone who wants to go into the
code.
Besides the Arduino code, I have CAD drawings for the housings,
EAGLE .brd and .sch files for the additional "Turbidostat Shield" I
made that contains the electrical components, as well as the parts
list. I haven't created the How-To yet because I'm not sure where the
best place to publish the designs are and what the demand is from the
community. I read that there was an open source turbidostat project on
DIYbio, but cannot find its current progress.
In any case, the device is relatively cheap (especially depending on
what you have on hand and where you want to cut corners), and I think
it would be helpful the community.
Any direction would be greatly appreciated.
jt
Cathal Garvey
Very awesome! Would love to hear/see more on this! :)
Consider me very interested. I have a lot of potential uses for a
turbidostat, but that kind of equipment is out of my league for now. How
did you go about getting OD readings?
As for hosting the files, Thingiverse, Github and Brian Bishop's SKDB
are both good. The former is somewhat like an instructables with
inclusive source file hosting/rendering, the penultimate is, well,
Github, a source-hosting site, and the latter is (Brian, forgive my
crude interpretations if off the mark) intended to be a human/machine
readable source format/file system for building anything at all.
Of course, there's also Citizen Science Quarterly and DIYbio for writing
up a "How to" article if they're interested, and you can attach small
files to emails sent to this list, or host them online (you can use a
subdomain of my sites if you want free filehosting for a modest project,
I technically have unlimited bandwidth: indiebiotech.com or
cunningprojects.com)
Looking forward to hearing more,
Cathal
Jonathan Cline
> Besides the Arduino code, I have CAD drawings for the housings,
> EAGLE .brd and .sch files for the additional "Turbidostat Shield" I
> made that contains the electrical components, as well as the parts
> list. I haven't created the How-To yet because I'm not sure where the
> best place to publish the designs are and what the demand is from the
> community.
yourself a Notebook page using the template given. Document it
on the wiki. For the files, create a project on github and track the
files there, with references back to the openwetware.org pages.
Once the files are on github it is easy for others to browse,
download, or contribute back. Google Code might be an easier
interface, however it is still corporate owned and likely won't
last as long as github (i.e. measured in decades).
The benefit of tools can't usually be predicted. Unix, for example,
was created as a fun set of tools. Now it's the basis for all modern
smartphones and their apps. It's best to set your "child projects"
free and let them grow into surprising things.
The natural path for such a project might be manufacturing &
distribution through Sparkfun, once they see there is some volume
of interest in it.
Personally I would mate it to a UBW board.
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################
Cathal Garvey
if you make lasercuttable or printable enclosures and refine the design
into mostly sparkfun-derived electronics parts, you can define a whole
kit through the "Personal factory" that others can buy. Pretty awesome
idea IMHO.
John Griessen
> Besides the Arduino code, I have CAD drawings for the housings,
> EAGLE .brd and .sch files for the additional "Turbidostat Shield" I
> made that contains the electrical components, as well as the parts
> list. I haven't created the How-To yet because I'm not sure where the
> best place to publish the designs are and what the demand is from the
> community.
To have your own web site that you and others can update would be the best if you
are up for that level of effort. Otherwise I like Cathal's suggestion of
making a documentation directory structure full of files and publishing that on github.
I like Jonathan's favorite, openwetware.org wiki, also.
I have a latent project to learn enough django web framework coding to use
a content management system, (CMS), to allow community users to log in and add content,
while the style matches the rest of the site, and links and site wide features are
easy to use. I have plans in my head for turbidostat, chemostat, potentiostat
functions along with incubation and shaking. So, some day in 2012, I see
using some of your open design merged with my ideas, TAPR licensed and documented
in a community friendly CMS on my site. And I'll put it on the openwetware.org wiki,
with links to my site -- for the ones who just want to buy...rather than build.
John
Jt
openwetware and github seem like the right combination.
To give a full story, I work for Ginkgo BioWorks and have developed
this device for our own inhouse bug testing/polishing. Though the
current iteration is probably a little more sophisticated than a lot
of hobbyists would want to get into, there are pared down versions
which are totally within grasp. We don't have any intention of selling
the device so we want to open source it to kick start all the diy
bioers out there. So I don't know if I'll go through the lengths of
making it Sparkfun/Ponoko purchasable myself, but take Jonathan's
advice of setting it free. Also, a UBW is most definitely in the
works, which I am happy to share as well.
Look forward to the openwetware How-To and please continue posting any
suggestions you have!
jt
Also to respond to your question Cathal: a IR LED and photodiode pair
work perfectly well to measure OD and can be more accurate than a lot
of common laboratory cuvette readers, especially if you can get the
optics down (super cheap too).
Cathal Garvey
Ginkgo like DIYbio. The feeling is mutual! :)
Looking forward to hearing more. Already planning to make an IR-OD
measurement thing in the meantime, OD measurements would be very handy
for catching B.subtilis at the right stage for competence; a problem
I've grappled with in the past. You've made my day, I always figured
debugging a DIY diode rig wasn't worth the effort.
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John Griessen
> Though the
> current iteration is probably a little more sophisticated than a lot
> of hobbyists would want to get into, there are pared down versions
> which are totally within grasp.
Thanks for the offer to free publish.
I was researching the state of the art of various "stats" and came across
a nice concept from 1991, (patent expired) that could help do some culture growth-stat
functions.
==========
The permittistat: a novel type of turbidostat
http://mic.sgmjournals.org/content/137/4/735.full.pdf
==========
"Baker’s yeast was grown in a novel type of turbidostat in which the steady-state biomass level was controlled not by
the optical turbidity but by the dielectric permittivity of the suspension at appropriate radio frequencies. Dry
weight, fresh weight, the optical density at 600 nm, percentage viability (from methylene blue staining), bud count
and ethanol concentration were measured off-line and the cell size distribution was recorded using flow cytometry.
Any changes in the physiological properties of the yeast had a negligible effect on the ratio between the permittivity
set (and measured) and the steady-state dry weight, fresh weight or optical density of the cultures. The permittistat
was found to provide an extremely convenient means for carrying out turbidostatic culture."
==========
The method they talk of is using an oscillating voltage to measure the permittivity of the space
between electrodes as frequency is varied. They used a four-terminal dielectric spectrometer designed for the
registration of microbial biomass, a BugmeterTM, produced by Aber
Instruments, Aberystwyth, UK. We all know how easy it is to control volt signals
with an Arduino or similar now, so this kind of "stat" could get around any fouling up of
OD detector windows by growing bugs with low costs and fairly low complexity of control code and
instrumentation gear. The frequencies used in the above paper were 400 kHz and 9.5 MHz, which
are easy for some inexpensive chips to output.
Besides keeping a batch at a constant mass density of bugs in water/nutrient mix, when you sweep
the frequency along you can tell other subtle qualities of the mix. Search on "dielectric spectroscopy".
John
Mac Cowell
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Nathan McCorkle
So would you PWM a line at 400khz? How do you watch the effect?
Sent from my mobile Android device, please excuse any typographical errors.
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John Griessen
> So would you PWM a line at 400khz?
How do you watch the effect?
The dielectric spectrometer instrument they used is not defined much in the article.
From what I've read so far, it is just a capacitance meter -- i.e. the capacitance doesn't
change much with parameters like volts applied, so permittivity is == pico Farads x a scale factor.
The live stuff in the zone between four gold plated pins (for a four terminal Kelvin measurement of some sort)
varies conduction a lot as you change frequency. the difference in capacitance measured at 400kHz and 9.5MHz
is what they found was a fairly linear indicator of density by weight when assayed by dessicating and weighing.
So, the meter pF reading at 9.5MHz - meter pF reading at 400kHz is a delta. As the delta changes you
feed that back to a control loop and keep it close to constant, (the "stat" part of the the machine).
To measure capacitance you would use PWM square waves, but sine waves that a are pretty pure.
Pure sine waves because that is what has historically been used observing cells different conductivity
due to AC e-fields. cell wall behavior enters into it.
JG
Mackenzie Cowell
jt
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Alex Hoekstra
Have you constructed a How-To yet? I'd love to see what all's gone
into it.
Johann SynBio
thanks to JT first for his amazing project and sharing it as well as the content around it. Just to compelete this thread here a few links of more turbidostat and chemostat systems that were built by the Dunham and the Klavin lab:
DIY Turbidostat Array:
https://depts.washington.edu/soslab/turbidostat/pmwiki/pmwiki.php
DIY Chemostat Array:
http://dunham.gs.washington.edu/DunhamLabMinistats.pdf
I find these projects really inspiring especially as considering this patent solves the problems of biofilms/ dilution resistant strains! https://www.google.de/patents/WO2003004656A9?dq=mutzel&ei=im-mVI2uK4e-PK6OgMgO&cl=en
So by using two culture vessels and transfering the culture from one to the other vessel and cleaning out the one that is not in use - you can actually grow ou bugs for unlimited generations. So basically you can adapt bugs to grow on any waste media by just waiting until they are adapted (talking it easy).
I am currently planning to built a low cost model of the Evolinator and optionally combing it with another vessel. We will see :). However, I intend to culture anaerob archeae that grow really slow (doubling time 4h) so I will start with the normal Evolvinator set up under a DIY anaerobic chamber. Does anybody has experience with anaerobes? Are they suitable for such an automated culturing endeavor?
Cheers and thanks for feedback
Johann
Nathan Brown
We have almost finished building the Evolvinator according to JT Saul's design. We're currently optimizing light levels from white LEDs to suit growth of photosynthetic bacteria. We also opted to use a stirring system to agitate the culture rather than a bubbling system, but we may return to a bubbling system as we try to parallelize the design. A friend of mine is working on implementing the control instructions in Python for a Pi or Beaglebone (Python is friendlier to biologists like me!). We think that we will be able to transfer JT Saul's PCB design to a Pi using a Pi-to-Arduino adapter shield, so that we don't have to rebuild the PCB.
Nice to see a fresh post on this thread!
John Griessen
> A friend of mine is working on implementing the control instructions in Python for a Pi or Beaglebone (Python is friendlier to
> biologists like me!). We think that we will be able to transfer JT Saul's PCB design to a Pi using a Pi-to-Arduino adapter shield
and it has plenty of python for measuring and sequencing things that change at audio speeds or slower.
Cathal Garvey
just plug Raspberry Pi's spiritual successor*, "Black Swift":
https://www.kickstarter.com/projects/1133560316/black-swift-tiny-wireless-computer
..unlike the Pi, it's fully open source, around SD-card sized, and has
onboard wifi. Plus, one microUSB-host for a peripheral (or hub?), power
line-in through microUSB, and runs OpenWRT: the "standard" in embedded
linux for home projects for years prior to Raspbian.
It's also cheap, beautiful, and has charismatic russian designers. :)
*dearly needed now that they're going Windows-by-default and still never
released bootloader blob source code: RIP Raspberry Pi idealism
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Apply for the Summer programme in Ireland:
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Nathan Brown
John Griessen
> ..unlike the Pi, it's fully open source, around SD-card sized, and has onboard wifi. Plus, one microUSB-host for a peripheral (or
> hub?)
desktop data, and firewalling. I'll have to back that at the 3 modules level.
They've cost reduced this so it's an easy decision to build in as is for low volume projects -- and then they
are available for customized production runs too.
The only little glitch is they do not say they have FCC certification done yet, and how long it will take.
I'm glad kickstarter changed rules to allow multiple quantities of deliverables. For a while you
had to choose to either deliver a five pack or a one pack and not both...
" If it comes wifi-ready, then I'm sold! I'm a bit of a russophile, too!"
At 120 mA typical power consumption it is a little more than the micropython board,
but then it's linux + openwrt which is allowing a huge range of code to run easily
without having to fiddle with C language on underpowered microcontrollers,
so the only thing micropython has on it is lower cost bill of materials.
I see micropython as being good for very cost reduced machines that are going to be used
in automation systems as a group to do a task. Each component needs to be inexpensive
almost to the point of throw away. Those kinds of systems will use Bluetooth Low Energy
to communicate with a gateway black swift and from there go on a LAN, not
the internet... A BLE add on daughter-card might be the first thing I do with one of my three black swifts.
John Sauls
On Saturday, January 31, 2015 at 5:00:43 PM UTC-8, Johann SynBio wrote:
Markos
Very interesting project.
I just made my registration to the forum:
https://groups.google.com/group/mixture-controlled-turbidostat
But I'm curious to understand in more detail the system for measuring turbidity.
What was the source and detector used for turbidity measurements. And what is the electronic circuit to the turbidity readings?
I'm thinking about doing something similar for a respirometer project that I have worked: http://www.c2o.pro.br/en/automation/x73.html
Congratulations for the amazing work.
Markos
On 31-01-2015 22:16, Johann SynBio wrote:
Hi jt,
thanks again for sharing your amazing project and also linking to the other turbidostats and chemostat systems from the dunham and kalvin lab. You mentioned in your Evolvinator that for anaerobic samples one could just flush the system with an anoxic gas. I don't think this will work especially working with oxygen atolerant anaerobes. I was thinking about building your system under a diy anaerobic chamber (there are lot of diy projects for those out).
Do you have any idea, papers, literature that could help me in cultivating Archeae in turbidostat system (does it make sense with an doubling time of 4h) ? Also for your problem with the formation of biofilms : there has been a patent out to solve that. They seem to use a combination of two culture vessels - changing vessels frequently to kill of biofilm producers and dilution resistant strains. Since you used yout system at Ginko Bioworks you can not really use it for commercial interest as it is patented but mabe there is a clever design around.
I think a DIY turbidostat - especially one that enables growing bugs for thousands of generation - would be powerful in changing substrate affinities and cleaning up waste streams.
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Nathan Brown
http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6860873
They weren't able to measure impedance at a frequency above 100kHz. I've written the first author on the paper to find out what the barriers to measuring at frequencies greater than 100kHz are.
Avery louie
If you want to know more about measuring dielectric properties, read up on the Si70XX series of humidity sensors or on capacitive touch sensing. You could probably do something decent in the permittistat area with a decent capacitive touch IC.
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