BioBoard

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=Abstract=
 
=Abstract=
  
"The BioBoard" is an Arduino-controlled sensor package that allowusers to monitor a range of physiochemical factors related to microbiological processes (e.g. algae growing, youghurt production, kombucha fermentation, sourdough culturing, etc.) in liquid media/cultures, with real-time wireless data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.  
+
"The BioBoard" is an Arduino-controlled sensor package that allow users to monitor a range of physiochemical factors related to microbiological processes (e.g. algae growing, youghurt production, kombucha fermentation, sourdough culturing, etc.) in liquid media/cultures, with real-time data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.
  
  
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==Sensors==  
 
==Sensors==  
  
Important considerations are affordability, accessibility and required precision.  
+
Important considerations are affordability, accessibility and required precision. Biologically relevant temperature range is approx. 0-100°C; accuracy should not be less than ±0.5°C at 25-35°C. pH range is (1-14), and required precision is approx. ±0.5, preferably better. dO probe should be able to measure % conc. with an accuracy of approx. ±2%, preferably better. Biomass probe will likely be measuring absorbance as a proxy for total biomass, and can be validated using classic spectrophotometer and CFU count.
  
 
===Thermometer===  
 
===Thermometer===  
 
'''[http://en.wikipedia.org/wiki/Thermocouple Thermocouples (TCs)]'''
 
 
Pros
 
* Very robust, good for nasty environments
 
* Wide temperature range (−200°C to +1350°C for type K)
 
* Relatively cheap (approx. $15 for a DIY model incl. amplifier)
 
Cons
 
* Voltage is very small so requires an amplifier with digital out (41 µV/°C for type K)
 
  
 
'''Digital Temperature Sensors (DTS)'''
 
'''Digital Temperature Sensors (DTS)'''
Line 32: Line 23:
 
* Good precision in biological range  
 
* Good precision in biological range  
 
** ±0.5°C accuracy from –10°C to +85°C for DS1820
 
** ±0.5°C accuracy from –10°C to +85°C for DS1820
** ±2°C for TC1047A at 25°C
 
 
* Very cheap ($0.75 to $3.95)
 
* Very cheap ($0.75 to $3.95)
 
Cons
 
Cons
Line 38: Line 28:
 
** –55°C to +125°C for DS1820
 
** –55°C to +125°C for DS1820
 
** -40°C to +125°C for TC1047A
 
** -40°C to +125°C for TC1047A
 +
* Accuracy only ±2°C for TC1047A at 25°C
 
* Sensitive to mechanical damage and liquid, so require protection/casing
 
* Sensitive to mechanical damage and liquid, so require protection/casing
  
Line 48: Line 39:
 
* Comparatively limited temperature range (-40°C to +125°C)
 
* Comparatively limited temperature range (-40°C to +125°C)
 
* Accuracy approx. ±1°C at 25°C
 
* Accuracy approx. ±1°C at 25°C
* Require casing
+
 
  
 
'''Commercial resources'''
 
'''Commercial resources'''
  
* TCs
+
DTS
** [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] $19
+
* [http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html DS18B20 digital temperature sensor] - $3.95 from Hacktronics
* TC wire
+
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-8&file=DSA-149089.pdf Datasheet for DS1820 1-wire DTS]
** McMaster Carr [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath for ~$1/foot, by the foot]
+
* [http://us.element-14.com/jsp/displayProduct.jsp?sku=89C8093&CMP=KNC-KEY-SKU-MIC&s_kwcid=TC|20219|tc1047avnbtr||S|b|6383206454 TC1047A microchip] - $0.60 from element14
** Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)
+
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-304&file=55284.pdf Datasheet for TC1047AVNBTR DTS microchip]
* Amplifier
+
Thermistor
** [http://www.sparkfun.com/products/307, $12 from Sparkfun]
+
* [http://www.hacktronics.com/Sensors/Thermistor-Temperature-Sensor/flypage.tpl.html Thermistor] - $1.75 from Hacktronics
* DTS
+
** [http://www.vishay.com/doc?29049 Datasheet for thermistor]
** [http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html DS18B20 digital temperature sensor] - $3.95 from Hacktronics
+
*** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-8&file=DSA-149089.pdf Datasheet for DS1820 1-wire DTS]
+
** [http://us.element-14.com/jsp/displayProduct.jsp?sku=89C8093&CMP=KNC-KEY-SKU-MIC&s_kwcid=TC|20219|tc1047avnbtr||S|b|6383206454 TC1047A microchip] - $0.60 from element14
+
*** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-304&file=55284.pdf Datasheet for TC1047AVNBTR DTS microchip]
+
  
'''Private resources'''
 
 
* Charlie has access to a good amount of Type K metal sheathed TC wire, plus assorted probes and a TC reader he can donate - as we go along our improving expertise will lead us to resources other people can use... like the relatively cheap McMaster Carr wire.
 
* We presently have a not-quite-functional prototype digital thermometer which uses a DS18B20 DTS; the sketch is compiling correctly, but there's de-bugging to be done (error msg reads: ''avrdude: stk500_getsync(): not in sync: resp=0x31'').
 
 
'''Other resources'''
 
 
* [http://www.instructables.com/id/Making-A-Thermocouple/ Instructable for how to build a thermocouple]. This soldering method will work with the Omega wire, and better junctions can be made with a welder or capacitive discharge.
 
* [http://www.chinwah-engineering.com/USBThermocoupleProject.html USB Thermocouple Project]
 
  
 
===pH-meter===  
 
===pH-meter===  
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'''Commercial resources'''
 
'''Commercial resources'''
  
* Probes
+
Probes
** [http://www.heavydutysupplies.com/servlet/the-15/Checker,-HI-98103,-HI98103/Detail HANNA Instruments HI 98103] $55
+
* [http://www.heavydutysupplies.com/servlet/the-15/Checker,-HI-98103,-HI98103/Detail HANNA Instruments HI 98103] $55
** [http://www.amazon.com/Milwaukee-pH600-Portable-pH-meter/dp/B004CZ8632 Milwaukee pH600] $20 - doesn't look like it needs specific buffers for calibration, but the accuracy is probably not great. Maybe it's enough, though.
+
* [http://www.amazon.com/Milwaukee-pH600-Portable-pH-meter/dp/B004CZ8632 Milwaukee pH600] $20 - doesn't look like it needs specific buffers for calibration, but the accuracy is probably not great. Maybe it's enough, though.
** [http://www.google.com/products/catalog?hl=en&q=ph+electrode&sqi=2&cid=15011737823946485839&os=sellers# Google shopping results] approx. $40 upwards  
+
* [http://www.google.com/products/catalog?hl=en&q=ph+electrode&sqi=2&cid=15011737823946485839&os=sellers# Google shopping results] approx. $40 upwards  
** [http://www.pulseinstruments.net/sotaphelectrode.aspx SOTA pH Electrode] $100 - expensive, but so so sweet: designed for continuous measurement, and comes with any kind of connector.
+
* [http://www.pulseinstruments.net/sotaphelectrode.aspx SOTA pH Electrode] $100 - expensive, but so so sweet: designed for continuous measurement, and comes with any kind of connector.
* pH tester units  
+
pH tester units  
** [http://www.jencostore.com/ph-meter/ph-testers.html?price=1%2C100 Jenco 610 pH tester] for $30 - perhaps it could be hacked?
+
* [http://www.jencostore.com/ph-meter/ph-testers.html?price=1%2C100 Jenco 610 pH tester] for $30 - perhaps it could be hacked?
  
'''Schematic'''
+
'''DIY resources'''
  
 +
* [http://phduino.blogspot.com/ pHduino] - Arduino-based pH-amplifier circuit for interfacing with a commercial pH probe.
 
* [http://www.ph-meter.info/pH-meter-construction pH meter construction] - this could perhaps be adapted to use an Arduino instead of a voltmeter - not necessarily cheaper than buying, although it’d certainly be both fun and informative.  
 
* [http://www.ph-meter.info/pH-meter-construction pH meter construction] - this could perhaps be adapted to use an Arduino instead of a voltmeter - not necessarily cheaper than buying, although it’d certainly be both fun and informative.  
* We could also build [http://xkcd.com/730/ this]
 
  
===Dissolved oxygen (DO) probes===
 
  
'''Membrane electrode''' (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)
 
  
* Pros
+
===Dissolved oxygen (DO) probes===
** New sensors for out of date cars are available on eBay for $10
+
** Contain required platinum, anodes, and teflon membrane
+
* Cons
+
** Sensors typically operate at ~300C
+
* Progress
+
** Ordered 3 $6-$10 probes on ebay to futz with
+
** Plan is to knock out the zirconium matrix and add a KCl electrolyte to see if we can get a reaction started at room temperature.
+
  
 
'''Optode''' (a.k.a. build an intensity- or time-based optode from scratch)
 
'''Optode''' (a.k.a. build an intensity- or time-based optode from scratch)
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Recently, people have been using a [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=85793|FLUKA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC ruthenium complex] as a visual (fluorescent) indicator of oxygen concentration. This complex is excited by a blue LED, then its transmission is measured by a filtered photoresistor (more details [http://www.env.gov.nl.ca/env/waterres/rti/rtwq/07_14.pdf here in pdf])
 
Recently, people have been using a [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=85793|FLUKA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC ruthenium complex] as a visual (fluorescent) indicator of oxygen concentration. This complex is excited by a blue LED, then its transmission is measured by a filtered photoresistor (more details [http://www.env.gov.nl.ca/env/waterres/rti/rtwq/07_14.pdf here in pdf])
  
* Pros
+
Pros
** All solid state (super low maintenance)  
+
* All solid state (super low maintenance)  
** No calibration needed  
+
* No calibration needed  
* Cons
+
Cons
** Could be some serious tecnical hurdles to overcome on this one
+
* Could be some serious tecnical hurdles to overcome on this one
** Ru molecule is expensive (~$70/mg)  
+
* Ru molecule is expensive (~$70/mg)
 +
 
 +
Film Contruction Ideas
 +
* Disperse catalyst in PVC powder, bake in oven on top of PET film under compression. May hit a rheology problem with the PET film. Melting point of PET is close to that of PVC.
 +
* Film coat: PVC dissolves in 2-butanone, whereas PET will not. Make a thin liquid layer, then allow to evaporate. PVC morphology may not provide necessary mechanical stiffness after this process.
  
 
'''Commercial resources'''
 
'''Commercial resources'''
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* [http://www.vernier.com/probes/do-bta.html DO-BTA Dissolved Oxygen Sensor] $209
 
* [http://www.vernier.com/probes/do-bta.html DO-BTA Dissolved Oxygen Sensor] $209
 
* [http://www.google.com/products/catalog?q=dissolved+oxygen+sensor&hl=en&safe=off&cid=1714170039035567861&os=sellers# Yellow Springs Dissolved Oxygen Meters] $80-104
 
* [http://www.google.com/products/catalog?q=dissolved+oxygen+sensor&hl=en&safe=off&cid=1714170039035567861&os=sellers# Yellow Springs Dissolved Oxygen Meters] $80-104
 
===Biomass===
 
  
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy]'''
+
'''Lab-Built Option'''
 +
* [http://www.cebtechservices.com/probe&sensorA.htm Diagram for the construction of a lead-silver galvanic probe]
 +
* [https://srac.tamu.edu/index.cfm/event/getFactSheet/whichfactsheet/167/ A discussion of the various types of dissolved oxygen probes from the Southern Regional Aquaculture Center. This article also contains a diagram of the typical polarographic sensor]
  
* Pros
+
===Biomass===
** Currently lots of DIY spectroscopy projects under development
+
** Relatively easy build
+
** Can be made using a LED and an old cell phone [http://en.wikipedia.org/wiki/Charged_coupled_device CCD]
+
** Can be used for chemical analysis as well
+
** Verification of results with known absorbance values should be easy
+
* Cons
+
** Will likely need re-calibration for every use
+
  
'''[http://en.wikipedia.org/wiki/Absorbance Optical density/absorbance]'''
+
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy] / [http://en.wikipedia.org/wiki/Absorbance Absorbance]'''
  
* Pros
+
Pros
** Also a spectroscopy technique, so as above
+
* Currently lots of DIY spectroscopy projects under development
** Tried and tested method
+
* Relatively easy build, can be made using a LED and a photoresistor, phototransistor, an old cell phone [http://en.wikipedia.org/wiki/Charged_coupled_device CCD] or other simple photodetector
* Cons
+
* Validation of results with known absorbance values should be easy
** Re-calibration needed every time
+
Cons
 +
* Will likely need re-calibration for every use
 +
* Could be very hard to pack into a probe
  
'''Calibrated capacitance + conductivity sensor'''
+
'''Commercial resources'''
  
Industry has commercial probes available which measure living biomass; we think we may be able to retroengineer such a thing. With enough calibration, it might be possible to do this  by measuring capacitance alone.
+
* [http://www.optek.com/Product_Detail.asp?ProductID=12 ASD19-N Single Channel NIR Absorption Probe]
 
+
** [http://www.optek.com/Schematic_Single_Channel_NIR_LED_Probe.asp NIR probe schematic]
[The basic principle behind these probes is the different electrical properties of living and dead cells; both are conductive - being essential very long and folded chains of carbon molecules - but living cells also act as capacitors (batteries); active transport across the cell membrane of electrically charged ions/molecules establishes a negative potential/charge on the order of -70mV in resting mammalian neurons.]
+
** [http://www.optek.com/pdf/optek-ASD19-N_Data-Sheet_english.pdf ASD19-N datasheet]
 +
* [http://www.finesse.com/files/pdfs/app-tech-notes/TruCell.TN.AUvsOD.pdf TruCell] - NIR probe promotion PDF; basic intro to using spectrometry for biomass measurements, incl. calibration curves and equations 
  
 
'''Other resources'''
 
'''Other resources'''
  
* [finesse.com/files/pdfs/app-tech-notes/TruCell.TN.AUvsOD.pdf .pdf with technical notes about a commercial OD probe]
 
 
* [http://www.optek.com/Application_Note/Biotechnology/English/2/Fermentation_and_Cell_Growth_Monitoring.asp Industrial application of NIR spectroscopy] in fermentation and cell growth monitoring  
 
* [http://www.optek.com/Application_Note/Biotechnology/English/2/Fermentation_and_Cell_Growth_Monitoring.asp Industrial application of NIR spectroscopy] in fermentation and cell growth monitoring  
 
* [http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html Cell phone spectrophotometer]
 
* [http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html Cell phone spectrophotometer]
 
+
* [http://www.rsc.org/Education/EiC/issues/2007Sept/BuildYourOwnSpectrophotometer.asp Article] on how to build your own spectrophtometer
 +
* [http://topologicoceans.wordpress.com/2011/03/15/diy-spectro-ii/ DIY Spectrometer]
 +
** [http://topologicoceans.wordpress.com/2011/01/29/diy-spectro-faq/ DIY Spectrometer FAQ] - lots of useful links to other DIY spectro projects
  
 
==Microcontroller assembly==
 
==Microcontroller assembly==
  
Arduino is the microcontroller of choice; which board will depend on which assembly we choose.
+
A bare-bones Arduino set-up with USB connection to a dedicated lap-top initially; later - when we have more time for integration - an ethernet shield will be added to the assembly to give us wireless data transmission to the server.
 
+
'''Ethernet shield set-up'''
+
* Pros
+
** Cheap and simple
+
* Cons
+
** Perhaps not enough power + pins for sensors
+
 
+
'''Sensor shield + biffer board set-up'''
+
 
+
* Pros
+
** More power + pins for sensors
+
** [http://bifferos.bizhat.com/ The biffer board] is excellent and tiny (1W)
+
* Cons
+
** No experience with use of the sensor shield
+
** More parts = more $
+
** More parts also = more work + more potential complications
+
 
+
  
 
=Software=
 
=Software=
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'''Data transmission'''
 
'''Data transmission'''
  
* Data should be timestamped, categorized (pH, temperature, etc)  
+
Data should be timestamped, categorized (pH, temperature, etc) and transmitted in real-time
 
* JSON data serialization format
 
* JSON data serialization format
 
* HTTP for transmission to server
 
* HTTP for transmission to server
Line 190: Line 143:
 
'''Web server'''  
 
'''Web server'''  
  
* Custom Rails app  
+
Custom Rails app  
** Receives data
+
* Receives data
** Logs to database  
+
* Logs to database  
** Generates graphs on demand
+
* Generates graphs on demand
*** Add Comet server for live-updated graphs   
+
** Add Comet server for live-updated graphs   
 
* Include 'export to CSV' function to allow users to extract data for analysis with tool(s)  
 
* Include 'export to CSV' function to allow users to extract data for analysis with tool(s)  
 
* All code on github so others can fork and add features
 
* All code on github so others can fork and add features
Line 200: Line 153:
 
* We could add features that lets new users sign up and get a unique key which they use when transmitting their own data to the JSON web service on our server. The server then uses the key to associate the data with the user, and the user can look at their graphs and share them with others.  
 
* We could add features that lets new users sign up and get a unique key which they use when transmitting their own data to the JSON web service on our server. The server then uses the key to associate the data with the user, and the user can look at their graphs and share them with others.  
  
'''Resources'''
+
=BioBoard documentation=
  
* Eric Allens has promised to open source his [http://svallens.com/templogger/ online templogger]
+
*[[BioBoard/Documentation]]
* Labitat has a [http://space.labitat.dk/ live power usage graph] made with Comet
+
**[[BioBoard/Documentation/Temperature]]
* [http://welserver.com/ Web Energy Logger]
+
**[[BioBoard/Documentation/pH]]
 +
**[[BioBoard/Documentation/Oxygen]]
 +
**[[BioBoard/Documentation/Optical loss]]
 +
**[[BioBoard/Documentation/Arduino protocol]]
 +
**[[BioBoard/Documentation/PC Software]]
 +
*[[BioBoard/Time_line]]
 +
*[[BioBoard/Equipment]]
 +
*[[BioBoard/Archive]]

Revision as of 11:36, 3 May 2013

Contents

Abstract

"The BioBoard" is an Arduino-controlled sensor package that allow users to monitor a range of physiochemical factors related to microbiological processes (e.g. algae growing, youghurt production, kombucha fermentation, sourdough culturing, etc.) in liquid media/cultures, with real-time data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.


Goals / Features

As a minimum, we want to be able to monitor temperature, pH and dissolved oxygen. We'd also like to be able to measure biomass, either directly or by proxy. The current plan is to build a thermometer, a dissolved oxygen sensor and a biomass probe ourselves, and supplementing with a commercial pH meter. Failing that, we'll buy a thermometer and an oxygen probe as well and attempt to hack them instead, and concentrate on standardising data protocols, building the supporting controller hardware and making the graphics look pretty.

Hardware

Sensors

Important considerations are affordability, accessibility and required precision. Biologically relevant temperature range is approx. 0-100°C; accuracy should not be less than ±0.5°C at 25-35°C. pH range is (1-14), and required precision is approx. ±0.5, preferably better. dO probe should be able to measure % conc. with an accuracy of approx. ±2%, preferably better. Biomass probe will likely be measuring absorbance as a proxy for total biomass, and can be validated using classic spectrophotometer and CFU count.

Thermometer

Digital Temperature Sensors (DTS)

Pros

  • Avaliable as one-wire devices, use single digital pin
  • Require no amplification or moderation to connect to Arduino
  • Good precision in biological range
    • ±0.5°C accuracy from –10°C to +85°C for DS1820
  • Very cheap ($0.75 to $3.95)

Cons

  • Comparatively limited temperature range
    • –55°C to +125°C for DS1820
    • -40°C to +125°C for TC1047A
  • Accuracy only ±2°C for TC1047A at 25°C
  • Sensitive to mechanical damage and liquid, so require protection/casing

Thermistors

Pros

  • Single analog pin use
  • Very cheap ($1.75 from Hacktronics)

Cons

  • Comparatively limited temperature range (-40°C to +125°C)
  • Accuracy approx. ±1°C at 25°C


Commercial resources

DTS

Thermistor


pH-meter

Commercial resources

Probes

pH tester units

DIY resources

  • pHduino - Arduino-based pH-amplifier circuit for interfacing with a commercial pH probe.
  • pH meter construction - this could perhaps be adapted to use an Arduino instead of a voltmeter - not necessarily cheaper than buying, although it’d certainly be both fun and informative.


Dissolved oxygen (DO) probes

Optode (a.k.a. build an intensity- or time-based optode from scratch)

Recently, people have been using a ruthenium complex as a visual (fluorescent) indicator of oxygen concentration. This complex is excited by a blue LED, then its transmission is measured by a filtered photoresistor (more details here in pdf)

Pros

  • All solid state (super low maintenance)
  • No calibration needed

Cons

  • Could be some serious tecnical hurdles to overcome on this one
  • Ru molecule is expensive (~$70/mg)

Film Contruction Ideas

  • Disperse catalyst in PVC powder, bake in oven on top of PET film under compression. May hit a rheology problem with the PET film. Melting point of PET is close to that of PVC.
  • Film coat: PVC dissolves in 2-butanone, whereas PET will not. Make a thin liquid layer, then allow to evaporate. PVC morphology may not provide necessary mechanical stiffness after this process.

Commercial resources

Lab-Built Option

Biomass

NIR spectroscopy / Absorbance

Pros

  • Currently lots of DIY spectroscopy projects under development
  • Relatively easy build, can be made using a LED and a photoresistor, phototransistor, an old cell phone CCD or other simple photodetector
  • Validation of results with known absorbance values should be easy

Cons

  • Will likely need re-calibration for every use
  • Could be very hard to pack into a probe

Commercial resources

Other resources

Microcontroller assembly

A bare-bones Arduino set-up with USB connection to a dedicated lap-top initially; later - when we have more time for integration - an ethernet shield will be added to the assembly to give us wireless data transmission to the server.

Software

Data logging and visualization

Data transmission

Data should be timestamped, categorized (pH, temperature, etc) and transmitted in real-time

  • JSON data serialization format
  • HTTP for transmission to server
    • Include "export to CSV" function with option for data set selection - should allow people to use a variety of programming languages and data analysis tools without a lot of work on their part or ours

Web server

Custom Rails app

  • Receives data
  • Logs to database
  • Generates graphs on demand
    • Add Comet server for live-updated graphs
  • Include 'export to CSV' function to allow users to extract data for analysis with tool(s)
  • All code on github so others can fork and add features
  • We could add features that lets new users sign up and get a unique key which they use when transmitting their own data to the JSON web service on our server. The server then uses the key to associate the data with the user, and the user can look at their graphs and share them with others.

BioBoard documentation

Personal tools