BioBoard

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#REDIRECT [[BioBoard/Equipment]]
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=Abstract=
 +
 
 +
 
 +
 
 +
=Goals / Features=
 +
 
 +
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===
 +
 
 +
'''[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)'''
 +
 
 +
* 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
 +
*** ±2°C for TC1047A at 25°C
 +
** 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
 +
** Sensitive to mechanical damage and liquid, so require protection/casing
 +
 
 +
'''Commercial resources'''
 +
 
 +
* TCs
 +
** [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] $19
 +
* TC wire
 +
** McMaster Carr [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath for ~$1/foot, by the foot]
 +
** Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)
 +
* Amplifier
 +
** [http://www.sparkfun.com/products/307, $12 from Sparkfun]
 +
* DTS
 +
** [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===
 +
 
 +
'''Commercial resources'''
 +
 
 +
* Probes
 +
** [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.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.
 +
* 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?
 +
 
 +
'''Schematic'''
 +
 
 +
* [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
 +
** 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 [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
 +
** 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'''
 +
 
 +
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=85793|FLUKA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC ruthenium complex]
 +
* [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
 +
 +
===Biomass===
 +
 
 +
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy 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 [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]'''
 +
 
 +
* 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'''
 +
 
 +
* [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.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html Cell phone spectrophotometer]
 +
 
 +
==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
 +
** 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=
 +
 
 +
==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'''
 +
 
 +
* Eric Allens has promised to open source his [http://svallens.com/templogger/ online templogger]
 +
* Labitat has a [http://space.labitat.dk/ live power usage graph] made with Comet
 +
* [http://welserver.com/ Web Energy Logger]

Revision as of 17:09, 25 March 2011

Contents

Abstract

Goals / Features

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
      • ±2°C for TC1047A at 25°C
    • 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
    • Sensitive to mechanical damage and liquid, so require protection/casing

Commercial resources

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

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