BioBoard

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Ruslan Fedotenko {signs|indicators|indications|symptoms|signals|clues|warning signs|evidence|signs or symptoms|signs and symptoms|hints} {with|along with|together with|using|having|by using|utilizing|through|with the help of|by means of|by way of} {Philly|Philadelphia}  Thursday {July|This summer|Come july 1st|Come early july|September|August|June|May|Aug|February|Summer} #file_links<D>\keywords11.txt,1,S]  {5|Five|A few|Your five|5 various|Several|Some|6|7|4|10}, {2012|Next year} {3|Three|Several|Three or more|A few|3 or more|About three|4|Various|A variety of|Many}:{09|2009} {PM|Pm hours|Evening|Pm} {By|Through|Simply by|By simply|By means of|By way of|By just|As a result of|From|Just by|With} {Steve|David|Dorrie|Charlie|Bob|Ken|Gary|Sam|Ruben|Sara|Mark} Zipay  {Photo|Picture|Photograph|Image|Photography|Snapshot|Shot|Pic|Photographic|Graphic|Pics} {credit|credit score|credit rating|credit history|credit ratings|consumer credit|credit ranking|credit standing|consumer credit rating|credit scores|credit worthiness}: APThat's {the third|the 3rd|the next|another|your third|the last|the final|thirdly|the 3rd type of|finally|the middle} UFA {player|participant|person|gamer|gambler|battler|competitor|musician|professional|poker player|golfer} {in the|within the|inside the|inside|from the|while in the|during the|with the|on the|in your|through the} {Rangers|Ranger} bottom-six {who has|that has|who may have|who's|who's got|who have|having|who has got|with|posessing|which has} {fled|left}.{Of|Associated with|Regarding|Involving|Connected with|With|For|From|In|About|Involved with}  #file_links<D>\keywords15.txt,1,S] {the three|the 3|these|a few|several|a few of the|the|three of the|significant|important|useful}, ({John|Steve|David|Bob|Ruben|Sara|Mark|Kim|Tom|Diane|Jesse} Mitchell, {Colorado|Co|Denver colorado|Denver|Littleton|Denver co} {and|as well as|and also|along with|in addition to|plus|together with|and even|not to mention|and additionally|and then} Brandon Prust, Montreal) Feds, {at|from|with|in|on|during|for|within|located at|by|found at} {33|Thirty-three|Thirty three}, {is the|may be the|will be the|could be the|would be the|is definitely the|is a|stands out as the|certainly is the|is considered the|will be} {oldest|earliest|most ancient|most well-known|older|most seasoned|eldest|best|first born|first|son}, {and therefore the|and then the|and so the|therefore the|so the} {one|1|a single|one particular|just one|a person|an individual|a particular|you|a|single} {I|We|My partner and i|My spouse and i|I actually|I personally|I really|When i|I just|That i|Simply put i} belie {#|Number} #file_links<D>\keywords13.txt,1,S] file_links<D>\keywords12.txt,1,S] ved {most likely|probably|almost certainly|more than likely|possibly|most probably|in all probability|likely|in all likelihood|very likely|most certainly} {to depart|to go away|to go out of|end|to exit} {when|whenever|any time|while|as soon as|if|anytime|once|when ever|the moment|in the event that} {coach|trainer|mentor|instructor|private coach|guru|teacher|train|advisor|fitness instructor|tutor} {John|Steve|David|Bob|Ruben|Sara|Mark|Kim|Tom|Diane|Jesse} Tortorella {said|stated|mentioned|explained|claimed|reported|proclaimed|says|suggested|pointed out|talked about} {the team|they|the c's|the group} {would be|could be|will be|can be|could well be|is|might be|might possibly be|may be|is going to be|could possibly be} {getting|obtaining|acquiring|receiving|finding|having|becoming|gaining|possessing|buying|being} {younger|more youthful|youthful|young|newer|more radiant|the younger|much younger|smaller|10 years younger|ten years younger}.{Remember|Keep in mind|Bear in mind|Don't forget|Recall|Try to remember|Take into account|Consider|Do not forget|Just remember|Recollect}, {he|he or she|this individual|they|he / she|your dog|the guy|she or he|she|the person|this guy} {played in|took part in} {Philly|Philadelphia} #file_links<D>\keywords14.txt,1,S] {before|prior to|just before|ahead of|previous to|in advance of|well before|earlier than|previously|prior to when|right before}, {from|through|coming from|via|by|out of|with|as a result of|because of|right from|provided by} 1999-2002. {I like|I love|I prefer|I favor|I enjoy|I'm keen on|I really like|I appreciate|I want|I recommend|I'm keen} Feds, {who|that|which|whom|exactly who|who seem to|who actually|just who|what person|what individuals|who exactly} {didn't have|did not have|was lacking|was without|was missing} {the best|the very best|the most effective|the top|the most beneficial|the ideal|the perfect|one of the best|the right|the most suitable|the best quality} {season|period|time|time of year|year|year or so|couple of years|months|summer|time of the year|winter} (9-11-20),...
+
=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
 +
* [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]
 +
 
 +
 
 +
===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?
 +
 
 +
'''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.
 +
 
 +
 
 +
 
 +
===Dissolved oxygen (DO) probes===
 +
 
 +
'''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
 +
 
 +
'''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]
 +
 
 +
===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 a photoresistor, phototransistor, an old cell phone [http://en.wikipedia.org/wiki/Charged_coupled_device 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'''
 +
 
 +
* [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==
 +
 
 +
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=
 +
 
 +
*[[BioBoard/Documentation]]
 +
**[[BioBoard/Documentation/Temperature]]
 +
**[[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

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