BioBoard

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'''[http://en.wikipedia.org/wiki/Thermocouple Thermocouples (TCs)]'''
 
'''[http://en.wikipedia.org/wiki/Thermocouple Thermocouples (TCs)]'''
  
Pros
+
* Pros
* Very robust, good for nasty environments  
+
** Very robust, good for nasty environments  
* Wide temperature range (−200°C to +1350°C for type K)
+
** Wide temperature range (−200°C to +1350°C for type K)
* Relatively cheap (approx. $15 for a DIY model incl. amplifier)
+
** Relatively cheap (approx. $15 for a DIY model incl. amplifier)
Cons
+
* Cons
* Voltage is very small so requires an amplifier with digital out (41 µV/°C for type K)
+
** 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)'''
  
Pros
+
* Pros
* Avaliable as one-wire devices, use single digital pin  
+
** Avaliable as one-wire devices, use single digital pin  
* Require no amplification or moderation to connect to Arduino
+
** Require no amplification or moderation to connect to Arduino
* 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
+
** Comparatively limited temperature range
* Comparatively limited temperature range
+
*** –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
  
 
'''Thermistors'''
 
'''Thermistors'''
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* 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
+
TCs
** [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] $19  
+
* [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] $19  
* TC wire
+
TC wire
** McMaster Carr [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath for ~$1/foot, by the foot]  
+
* McMaster Carr [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath for ~$1/foot, by the foot]  
** Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)
+
* 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 ($)
* Amplifier  
+
Amplifier  
** [http://www.sparkfun.com/products/307, $12 from Sparkfun]
+
* [http://www.sparkfun.com/products/307, $12 from Sparkfun]
* DTS
+
DTS
** [http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html DS18B20 digital temperature sensor] - $3.95 from Hacktronics
+
* [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://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://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]
+
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-304&file=55284.pdf Datasheet for TC1047AVNBTR DTS microchip]
 +
Thermistor
 +
* [http://www.hacktronics.com/Sensors/Thermistor-Temperature-Sensor/flypage.tpl.html Thermistor] - $1.75 from Hacktronics
 +
** [http://www.vishay.com/doc?29049 Datasheet for thermistor]
  
 
'''Private resources'''
 
'''Private resources'''
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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'''
 
'''Schematic'''
Line 96: Line 99:
 
'''Membrane electrode''' (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)
 
'''Membrane electrode''' (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)
  
* Pros
+
Pros
** New sensors for out of date cars are available on eBay for $10
+
* New sensors for out of date cars are available on eBay for $10
** Contain required platinum, anodes, and teflon membrane  
+
* Contain required platinum, anodes, and teflon membrane  
* Cons
+
Cons
** Sensors typically operate at ~300C
+
* Sensors typically operate at ~300C
* Progress  
+
Progress  
** Ordered 3 $6-$10 probes on ebay to futz with
+
* 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.
+
* 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)
Line 109: Line 112:
 
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)  
  
 
'''Commercial resources'''
 
'''Commercial resources'''
Line 126: Line 129:
 
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy]'''
 
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy]'''
  
* Pros
+
Pros
** Currently lots of DIY spectroscopy projects under development
+
* Currently lots of DIY spectroscopy projects under development
** Relatively easy build
+
* 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 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
** Can be used for chemical analysis as well
+
* Verification of results with known absorbance values should be easy  
** Verification of results with known absorbance values should be easy  
+
Cons
* Cons
+
* Will likely need re-calibration for every use
** Will likely need re-calibration for every use
+
  
 
'''[http://en.wikipedia.org/wiki/Absorbance Optical density/absorbance]'''
 
'''[http://en.wikipedia.org/wiki/Absorbance Optical density/absorbance]'''
  
* Pros
+
Pros
** Also a spectroscopy technique, so as above
+
* Also a spectroscopy technique, so as above
** Tried and tested method
+
* Tried and tested method
* Cons
+
Cons
** Re-calibration needed every time
+
* Re-calibration needed every time
  
 
'''Calibrated capacitance + conductivity sensor'''
 
'''Calibrated capacitance + conductivity sensor'''
Line 161: Line 163:
  
 
'''Ethernet shield set-up'''
 
'''Ethernet shield set-up'''
* Pros
+
 
** Cheap and simple  
+
Pros
* Cons
+
* Cheap and simple  
** Perhaps not enough power + pins for sensors  
+
Cons
 +
* Perhaps not enough power + pins for sensors  
  
 
'''Sensor shield + biffer board set-up'''
 
'''Sensor shield + biffer board set-up'''
  
* Pros
+
Pros
** More power + pins for sensors
+
* More power + pins for sensors
** [http://bifferos.bizhat.com/ The biffer board] is excellent and tiny (1W)
+
* [http://bifferos.bizhat.com/ The biffer board] is excellent and tiny (1W)
* Cons
+
Cons
** No experience with use of the sensor shield
+
* No experience with use of the sensor shield
** More parts = more $
+
* More parts = more $
** More parts also = more work + more potential complications
+
* More parts also = more work + more potential complications
  
  
Line 184: Line 187:
  
 
* Data should be timestamped, categorized (pH, temperature, etc)  
 
* Data should be timestamped, categorized (pH, temperature, etc)  
* JSON data serialization format
+
** JSON data serialization format
* HTTP for transmission to server
+
** 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  
+
*** 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'''  
 
'''Web server'''  

Revision as of 18:02, 25 March 2011

Contents

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.


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.

Thermometer

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)

  • 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

TCs

TC wire

Amplifier

DTS

Thermistor

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

pH-meter

Commercial resources

Probes

pH tester units

Schematic

  • 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 this

Dissolved oxygen (DO) probes

Membrane electrode (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)

Pros

  • 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)

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)

Commercial resources

Biomass

NIR spectroscopy

Pros

  • Currently lots of DIY spectroscopy projects under development
  • Relatively easy build, can be made using a LED and an old cell phone 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

Optical density/absorbance

Pros

  • Also a spectroscopy technique, so as above
  • Tried and tested method

Cons

  • Re-calibration needed every time

Calibrated capacitance + conductivity sensor

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.

[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.]

Other resources


Microcontroller assembly

Arduino is the microcontroller of choice; which board will depend on which assembly we choose.

Ethernet shield set-up

Pros

  • Cheap and simple

Cons

  • Perhaps not enough power + pins for sensors

Sensor shield + biffer board set-up

Pros

Cons

  • No experience with use of the sensor shield
  • More parts = more $
  • More parts also = more work + more potential complications


Software

Data logging and visualization

Data transmission

  • Data should be timestamped, categorized (pH, temperature, etc)
    • 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.

Resources

Personal tools