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Page archived 3 May 2011 by [[User:Rikke|Rikke]]
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=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 wireless data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.
 
 
[[File:BioBoardOverview.png|200px|thumb|left|BioBoard overview]]
 
=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===
 
'''[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
* 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
* [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] - $19 from Omega
TC wire
* [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath] ~$1/foot, by the foot from McMaster Carr
* Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)
Amplifier
* [http://www.sparkfun.com/products/307 TC amplifier] - $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]
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'''
 
* 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 functional prototype digital thermometer which uses a DS18B20 DTS
 
[[File:One-wire_prototype.jpg|200px|thumb|left|One-wire prototype]]
 
 
'''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)
 
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'''
 
* [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] / [http://en.wikipedia.org/wiki/Absorbance Absorbance]'''
 
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
* Could be very hard to pack into a probe
 
 
'''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 [http://www.aber-instruments.co.uk/brewing/controlling-cell-culture-processes 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.]
 
'''Commercial resources'''
 
* [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]
** [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'''
 
* [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.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==
 
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) 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.
 
'''Resources'''
 
* Eric Allens has been kind enough to open source the [http://github.com/epall/templogger online templogger] he uses to [http://svallens.com/templogger/ live-monitor his house].
:He adds: ''"The installation is totally undocumented at this point, so I suggest using this as a guideline to build something new, as opposed to using it verbatim. I do recommend considering starting from scratch with [http://oss.oetiker.ch/rrdtool/ RRDtool]."''
* Labitat has a [http://space.labitat.dk/ live power usage graph] made with Comet
* [http://welserver.com/ Web Energy Logger]
 
=Other BioBoard pages=
 
For internal use mainly
 
*[[BioBoard/Equipment]]
*[[BioBoard/Time_line]]
*[[BioBoard/Documentation]]

Revision as of 16:41, 11 July 2014

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