Hello everyone, and welcome back for the final installment of the BioBoard blog! Today is the last day of the Great Global Hackerspace Challenge 2011, and thus our last chance to tell you about all the cool stuff we've been doing on this project over the last 6 weeks. In all fairness, those of you who've kept up with the blog already know most of this, but since this is our last post, please bear with us as we do a quick run-down of the project once again.

 

Our initial target with the BioBoard was to build a set of sensors that would allow us to monitor several different, biologically relevant parameters in luquid microbial cultures, such as bacterial or yeast fermentation. The parameters we settled on were temperature,  biomass / cell density, acidity (pH), and oxygen levels.

 

Temperature is the key parameter in this context, as almost all biological reactions and processes are strongly temperature-dependent, and in many cases almost linearly proportional to temperature, too, at least up to a certain point. Essentially, at low temperatures, the limiting factor in any reaction in a liquid medium is the rate of molecular movement; at high temperatures, the ceiling is usually set by the the denaturation (unfolding) of proteins, a process which rapidly causes the cessation of biological activity in any form. There are numerous exceptions, but none which are relevant in this context, nor in general for most DIY biologists. However, as well as explaining why refrigeration and / or heating works for preserving foodstuffs, temperature is also an important factor in pH and oxygen measurements. Both pH and oxygen sensors basically detect the concentration of chemical species in the medium - H+ for pH and O2 for oxygen - and the solubility of these varies with temperature, i.e. more oxygen can be dissolved in cold than in warm water. 

 

The idea of measuring biomass / cell density was obviously motivated by a strong desire to be able to visually convey this simple dependence on temperature. Furthermore, for many purposes, knowing which growth phase your culture is in can be crucial - a lot of conjecture in microbiology is based on the assumption of exponential growth, and mathematical models based on such assumptions are obviously only valid when the culture in question actually is in the exponential growth phase. Last, but not least, the rate of biological growth is what determines when your homebrew will be ready for harvest, and thus of prime importance to the much-famed kombucha fermentations that were the original inspiration for this entire mad scheme.

 

The kombucha was also our main reason for including pH, at least at first. Along with the aerobic yeast fermentation, the bacterial acidification process that takes place during kombucha production is what creates the distinctive, acidic flavour, and also what makes your kombucha turn into vinegar if you leave on the shelf for too long. In order to achieve consistent, reproducible results from our production, we first need to know how the acidification co-varies with temperature and biomass - not necessarily a linear relation! That way, we'll know which parameters to change in future set-ups to optimize our results.

 

Because yeast only make alcohol in the absence of oxygen, measuring dissolved oxygen is a lot more relevant in anaerobic fermentations, such as ethanol production. It's also often a limiting factor in aqautic environments, where (as Sean put it) oxygen levels basically determine whether you're going to get fish (need it!) or algae (don't need it) in your pond. Especially during the exponential growth phase of a bacterial or yeast culture, oxygen can very quickly become depleted, resulting in the formation of unwanted by-products, or even the eventual demise of your culture.

 

Monitored over time and displayed together, these parameters should give most students a basic understanding of the interdependence of several co-variable with a single independent key variable. However, over time we also hope to accumulate enough base-line data for mathematical modelling (and - perhaps someday - automation) of the biological processes we study. If you are interested in making your own BioBoard, and using the supporting software we've developed for it, you can use the documentation wikis and how-tos we've made for this project:

 

https://www.noisebridge.net/wiki/BioBoard - the initial project description and overview; also contains links to all the other pages

 

https://www.noisebridge.net/wiki/BioBoard/Documentation/Temperature - DTS and thermistor documentation and how-to

https://www.noisebridge.net/wiki/BioBoard/Documentation/pH - DIY pH electrode run-down

https://www.noisebridge.net/wiki/BioBoard/Documentation/Oxygen - how to build an optode

https://www.noisebridge.net/wiki/BioBoard/Documentation/Optical_loss - a home-built NIR sensor for <$10

https://www.noisebridge.net/wiki/BioBoard/Documentation/Arduino_protocol - microcontroller assembly and schematics

https://www.noisebridge.net/wiki/BioBoard/Documentation/PC_Software - documentation on the datalogging and visualization

 

Most of the pictures we've taken during the challenge can be found on Picasa: https://picasaweb.google.com/rikke.c.rasmussen/BioBoard20110412#

 

Last, but not least, we've finally managed to make a short video of the project which we've uploaded to YouTube. Here you go, hope you've all enjoyed this challenge as much as we have! This is Noisebridge and the BioBoard team signing off for now, and reminding you, as always, to be excellent to each other, dudes!

 

Hey folks! Just a quick peep from yours truly here to give y'all a quick insight into the hectic last-minute tinkering of the BioBoard team. We're now 2 days, 23 hours and 38 minutes from the GGHC 2011 dead-line - that'll be Tuesday 3rd May at 00:00 hours - and officially in crunch mode. The project has shaped up really nicely in the last week - the two thermal sensors are finished, have been successfully wired up to Arduino boards, as has the NIR probe, and we've had live data transmission and graphing from the home-built digital thermometer. Rolf has also succeeded in bulding a pH amplifier circuit that let's us use a regular aquarium pH probe with our Arduino board. Otute unfortunately couldn't make the last meeting, so we've yet to see whether his home-built electrodes will work with the amp circuit. As for the dissolved oxygen sensor, we've come up pretty square against the same consistent problem every time, namely getting the dissolved ruthenium ion to form an even film across the mylar sheet. Surface tension keeps pulling all the solvent to the edges of the little glue enclosures (see the picture below), and Sean has been forced to go out of town on work, so it looks like we're going to have to accept that we won't make this happen before the dead-line. We're close enough to be fairly pleased with the collective effort nonetheless - I've taken a look at our original goals as stated in our project overview wiki:

 

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.

 

A quick comparison to current status: we are able to monitor temperature, pH and biomass by proxy. We've built two thermometers and a near-infrared (NIR) probe ourselves, and built a circuit for interfacing a commercial pH probe. We've not managed to build the dissolved oxygen sensor, but strongly anticipate to do so before Maker Faire. We've got standardised data protocols, supporting microcontroller software, a running database server and real-time data visualization. Pretty much what we set out to do. On top of that, it's been a great experience, everyone's made new friends in the process, we have a cool new device for our DIY bio projects, and a new global network of hackerspaces that weren't talking much before. All in all a straight win, no matter who takes the final prize home!

 

We're meeting again both Sunday and Monday, and will focus on getting all probes wired up to the same Arduino board and the data displaying on a single graph, making some cool video footage of the final build and getting our documentation squared away - the temperature and NIR probe wikis are coming along very nicely, but there's still lots of work to be done. We'll make sure to post everything in the final project blog post on Tuesday, but until then, here are some quick pictures from Wednesday's meeting:

 

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The NIR probe wired up to a BoArduino

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The NIR probe calibration setup - the glass beaker on the left contains green tea kombucha, while the cups contain a dilution series of Hibiscus extract.

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Data from the NIR probe - the difference in optical loss between the kombucha and the darkest Hibiscus tea is 56% - pretty neat!

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The oxygen probe, painted black inside to minimize internal reflection of the flourescing ruthenium complex - the uneven distribution of the film is clearly visible.

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Real-time graph of data from our home-built digital thermometer!

 

That's all for now - we'll be back soon with the final installment of our BioBoard blog. Until then: be excellent to each other, dudes!

As promised, here's the second half of the BioBoard GGHC 2011 project:

 

At yesterday's meeting, our two chemists really got their act together to show off some truly awesome skills - Sean's long-awaited ruthenium catalyst for the dissolved oxygen sensor had finally arrived, and Otute brought in what initially appeared to be some rather odd Christmas decorations, but turned out to be one of the coolest hacks I've ever seen: home-made pH sensors from glass baubles! It turns out that the glass in those things is thin enough to be permeable to hydrogen ions (H+), which is what we want to measure when we're talking pH, so all you have to do is strip off the metal coating, remove the little hanger, and you have the makings of a rather large, but perfectly functional glass pH electrode. Take a look at this:

 

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Isn't that just the coolest thing ever?! Only one problem - they're huge (approx. 2 inch diameter), and in order to work, they need to be filled with potassium chloride (KCl), and attached to a reference electrode in a separate, also KCl-filled chamber, so any pH probe built using these is going to be seriously bulky. Obviously, Otute had already figured that one out, so he's gone ahead and built a second variety based on the paper we referenced in last week's update - this one made from disposable pipettes using a PVC matrix membrane instead of permeable glass. We managed to at least get a response when we measured them with a voltmeter (although it's rather far off the mark), so with a little more research on the current flow between the electrodes, and a little more tinkering with the pH amplifier circuit that Rolf is trying to create using the pHduino as a model, we might actually end up with a real pH probe. I managed to get a quick shot of Otute himself holding up one of the pipette prototypes filled with KCl and silver wire in place:

 

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Meanwhile, Sean has been waiting for three weeks for the elusive ruthenium complex catalyst for his dO sensor to arrive - and at long last, it has! So he was very excited last night, and understandably so - finally, we got to test whether the basic theory actually held. The idea is that the ruthenium complex is excited by blue light (approx. 470nm), and glows a bright orange in the presence of oxygen, the concentration of which can then be extrapolated from either the  intensity or the lifetime of the flourenscence. In order to do this with any accuracy, we need to be able to correct for background light, so the ruthenium complex is layered between mylar (oxygen permeable) and vinyl (impermeable) and irradiated two different LEDs, one blue and one red, and the flourenscence is then meaured with a broad-spectrum photoresistor. It sounds complicated - and it is - but not quite as bad as one might fear...no lab required, so you can do this on your kitchen counter, as long as you clean it thoroughly afterwards. None of the ingredients are toxic, but your food might taste funny. Anyhow, we managed to capture some shots of Sean playing around with the chemicals, and a beatiful shot of the Ru glowing brightly orange under blue light:

 

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That's all for this time, folks. Hope you'll stay tunes as we forge ahead on this last mad rush to get all the sensors built, tested, wired up, talking to the Arduino and transmitting all their lovely lovely data to our database. Whether or not you do, just don't forget: Be excellent to each other, dudes!

Howdy, and welcome to another installation of the BioBoard project! While the guys wind down tonight's meeting in the background, I've gone straight to the box to tell you all about our latest progress, because I am really, really excited about this! Although yesterday was originally meant to be our final deadline for the sensor build, we've decided to extend that by another 10 days (until April 27th), leaving ourselves only a single week to make sure that all components communicate and do what they're supposed to. That might seem a little rash - and admittedly, we'll probably be feeling the pressure at the end - but after having seen a home-built pH probe made from Christmas baubles, a ruthenium catalyst glowing beautifully bright orange under pure blue light, and an near-infrared probe for less than $15, we all agreed that there was no way we could stop building now. Hopefully this means that by the end of the challenge, we'll be able to provide designs and tutorials for DIY temperature, NIR, pH and dissolved oxygen sensors, as well as schematics and Ardunio sketches for two different microcontroller set-ups, with and without wi-fi shield, respectively.

 

Last week, I showed you pictures of the circuitry and read-out from the digital thermo sensor, which has been encased in acrylic tube and hot glue (probably not food safe, so don't try this at home just yet), wired up, and is now a fully functional, perfectly waterproof digital thermometer. This is a really important accomplishment for os, as temperature is a key parameter in most of the microbial processes we expect to be monitoring. Additonally, both pH and oxygen concentation are temperature dependent, so to celebrate our first real victory, here's a shot of the finished thing, and the Boarduino it's running off:

 

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Last week's edition also included a picture of Rolf's initial NIR circuit mock-up incl. an obviously lit infrared LED, and a rather rough hand-drawn sketch of my probe design. One of the interesting challenges of this project is the fact that we intend to measure in liquids, so all our probes have to be 100% watertight, as they need to be able to stand being fully submerged for weeks at a time. This, I assure you, is a non-trivial task. First of all, welding acrylic with acetone is not as easy as it sounds when your personal pet chemist says piece of cake. Not nearly. In fact, to weld acrylic using acetone (or other water thin solvent or glue), both surfaces have to be perfectly planed, and perfectly smooth, which is in practice impossible to achieve with a hacksaw, a file and sandpaper. A Dreml and finer file works better, but acrylic cement of the syrupy variety is really what you need for this sort of rough-job. Hot glue also works fairly well, and in the end, a combination of the two turned out to be our best bet against the wet.

 

So, having solved that problem, we wired the IR LED and phototransistors (nowly safely encased in acrylic and hot glue - not a worry in this case, since it's enclosed in food safe acrylic) up to a voltmeter, and started measuring the output from the phototransistor and started testing it under different conditions. We got nice, steady readings of about 3.8V (almost theoretical max.) in open air and 3.7V in tap water - much encouraged by the fact that the readings seemed much less sensitive to distance, angle and background light than we had feared - and then dumped the probe in a cup of kombucha - only to see the strangest thing: starting at around 1.5V, the readings kept drifting steadily (and quite rapidly) to as high as 2.8V! We talked it over, brought in  the oscilloscope, mused at the possibility of microbial locomotion as a cause of the phenomenon, light absorbance vs. light scattering, all without coming to any useful conclusion - until it suddenly occured to one of us to actually look at the thing. So we moved kombucha and probe to a clear glass, let it sit for a while, and sure enough: tiny bubbles of CO2 were forming all over glass, probe, and - hence our troubles - LED and phototransistor. A problem we'll only have in carbonated liquids, but since we're fairly fond of both beer and kombucha around here, that's bad enough, and something that would have to be fixed. It turned out to be a relatively simple hack: since shaking the sensor dislodges the bubbles, we merely attached an old cell-phone motor (safely encased) to the assembly with rubber bands. Next step will be to make a daylight shade and outer case for the whole thing from a piece of 1-inch opaque PVC tube. Thankfully, we've still got time to improve upon the design, and will be sure to keep you posted. We'll also be making a thorough How-To wiki for all parts of this project on the Noisebridge website, but for now, pictures will speak more than...well, several hundred words, at least:

 

 

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Tomorrow, I'll tell you all about what the crazy chemists have been up to - stay tuned for part 2, and don't forget: be excellent to each other, dudes!

It's been quite a while since our last blog update - I shamefully admit to have neglected my duties as project correspondent somewhat this last week. Everyone (else) has day jobs, which means that most of us are working in our separate dens most of the time, and only really come together once a week, so I haven't been keeping up to date with the rest of the team quite as much as I should have. What's worse, though, is having brought my vidcam to the second meeting in a row, only to get so wrapped up the discussions and following work that I entirely forgot to do the Noisebridge tour and team intro I was planning. I'll remedy in part tomorrow and take you all on a quick tour of my favourite (and admittedly, only) hackerspace. Right now, though, I want to introduce you to our two new team members, Rolf and Otute, tell you how we're coming along with the project, and show you some pictures of what the team's been up to.

 

Otute is also a chemistry-dude-by-day, and has taken on the non-trivial task of building a DIY pH probe. A pH sensor is composed of two electrodes, a measuring electrode, which are normally encased in a special type of glass that is permeable to hydrogen (H+) ions. Both electrodes are made of silver chloride AgCl and bathed in a potassium chloride solution. The measuring electrode builds up potential directly related to the concentation of H+, but the reference electrode is in a separate chamber, and thus not in electrical contact with the solution being measured, so it provides a baseline measurement for calibration. The selectively permeable glass is expensive and difficult to come by, though, so instead Otute is going to try to make a selectively permeable membrane by dissolving polyvinylchloride (PVC, a plastic) in tetrahydroflouride (THF, a solvent) and mixing it with tribenzylamine to form a matrix. Still waiting for reagents, though, so it'll be a little while yet before we see the results of his efforts. The recipe is taken from a recipe in M.J. Goldcamp et al. (2010) "Inexpensive and Disposable pH Electrodes". Journal of Chemical Education, Vol. 87, no. 11, pp. 1262-64, and the major challenge here is presumably going to be getting the membrane solution to set right in the tube.

 

Meanwhile, Rolf's been hacking away at an amplifier circuit for the pH sensor based on the pHduino project - I've no idea what Rolf does by day, but by night, he's obviously busy solving any and all issues with regards to circuitry and electronics components on this project. There will be much refining of the whole package after the challenge, but we're going with the viable functionality model for now, so unfortunately Rolf will not be getting his much-desired custom-made PCBs just yet - we're going with strip boards for now - although I highly doubt I'll be able to stop him from designing them. As a small compensation, he's been mandated by the group to get a regular pH probe to play with while he fine-tunes the amp circuit.

 

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The strip board Sean and Rolf are building their circuits on

 

As I believe I've already mentioned, Rolf has also taken over the sensor part of the NIR probe from me (much to my relief), which is modeled on a commercial Optek probe and composed of a near-infrared LED emitting at 850nm and a phototransistor with equivalent reception. Both look exactly like regular LEDs to the untrained eye (i.e. mine), and will eventually be silicone-mounted in a pair of acrylic discs fused onto the end of a pair of acrylic tubes. The major challenge with this set-up is going to be firmly mounting these directly opposed to each other across an open gap, while water-proofing the leads + wires coming off both. All other components will be on the board end for now, so it'll be wires only, but the fact that the leads are at 180° could make it tricky nonetheless. I'll be buying/sourcing acrylic tubes of appropriate diameter and a tube of aquarium silicone (we're assuming it's food as well as fish-safe) tomorrow, so pictures of this soon to come.

 

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The basic NIR sensor circuit

 

 

 

 

 

 

A rough sketch of the NIR probe design

 

Otute and Sean are still waiting for chemicals/reagents...will possibly be using low-porosity filter (PVC matrix THF tetrahydroflouride solvent) instead of membrane - pH sensor consists of two probes, KCl and AgCl
no time to make own pcbs, so we're using strip boards
Sean missing catalyst, but circuitry is done (will be soldered tonight)

 

On the oxygen front, Sean is still missing the catalyst for his dissolved oxygen sensor, but the circuitry is (almost) done - he was still waving a smoking soldering iron like mad hacker when I left Noisebridge at close to midnight, so I feel pretty sure we'll be hearing more from him soon. At this stage, the whole thing seems to be coming along pretty much according to plan - except for the darned catalyst - so we're not expecting any major difficulties. There's always the potential outcome that we fail miserably and it doesn't work at all, but Sean's a pretty sound dude, and I'm confident that he's got this sussed out.

 

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Sean's dO probe circuitry

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The schematics for the dO sensor circuit

 

Last you heard from us was an update from Charlie, who's been working on testing several different thermal sensor designs. His latest iteration of the thermistor (I believe this is a 10kΩ model?) has produced beautifully linear results within the desired range (15-40°C) and an estimated resolution of about 0.1°C, with an as-of-yet unknown absolute accuracy, likely within the ±0.2-0.5°C range. This is really encouraging (and frankly better than I had dared hope for), and since water-proofing thermistor leads + wires is really simple (don't worry, we'll make sure to show you how), we don't foresee much of a challenge with this part of the project - and that's critical, as temperature is a key parameter both in the biological processes we're hoping to measure, as well as in pH and dO calculations. Rolf also got the DTS (digital thermal sensor) to work, so we'll have two different thermometers at once - also useful, as time response may vary, and could potentially be important, at least in the dO measurements.

 

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The Dallas 1-Wire DTS (black semi-circle in the lower left-hand corner of the board) and the Arduino read-out

 

On the software end, Marc now has both the Arduino + ethernet shield assembly successfully transmitting data to a Rails server, which type- and timestamps all data values, logs them to a database, and plots them on a basic graph. The next feature add-ins are going to be a Comet server which will give us real-time graphics, a pared-down version of the Arduino (pure board, no shield, just a USB cable to any old box), and a de-centralized version of the data logging app so we don't have to host a server for this project indefintely, but can instead enable people to do it themselves. We're all pretty excited about this end of the project, as the data visualization really is very central to the educational perspective. Seeing is believing!

 

Alright, folks, that's all for now - stay tuned for the hectic rush to get all the sensors finished before next week's meeting, and don't forget: be excellent to each other, dudes!

Ho All!  I'm Charlie and I imagine that I am a materials scientist - designing and manufacturing such things as rare earth magnets and medical devices.  My task is to address some of the temperature measurement aspects of the BioBoard - we want something that is inexpensive, robust, sensitive enough for bio-systems in the appropriate range of interest (say -20 C to 150 C), and reasonably accurate.  We considered a bunch of different choices - thermocouples (TC), resistance temperature devices (RTD), digital temperature sensors (DTS), and thermistors being some of them.  My training says "Go with the thermocouple, it is well known, extremely robust, has a wide temperature range, etc.", but we got some reality checks once we started looking into them - while they indeed work over a very wide temperature range, it is much bigger than we need for biological systems.  And what good is it if there is the additional cost of an amplifier circuit ($12 here http://www.sparkfun.com/products/307) to boost the millivolt signal, and also TCs are just a bit hard to find and/or make - great for professionals, but not students.  We have been unable to initially choose between a DTS (like here http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html for $4) and a thermistor (available from all kinds of places that deal in electronics components - Digikey, Newark, etc. for less than $1) so we are testing both!  Rolf is managing the DTS efforts and I have the thermistor work on my plate.  They come in all shapes and sizes, but unfortunately they are no longer as easily available in retail stores as they used to be - everything is mostly on the web - so I had to initially take what I could get locally, a big clunky sensor (a centimeter in diameter!) rated at 100 ohms at room temperature.

 

Besides the size, which will be determined by your application but small is usually preferred, the two features you will be looking for will be that room temperature resistance value (anywhere from 1 ohm to 1 mega-ohm) and whether the resistance increases with temperature (positive temperature coefficient, PTC) or decreases with temperature (negative temperature coefficient, NTC); as always, Wikipedia is a good first resource for finding out about such things (http://en.wikipedia.org/wiki/Thermistor).  In any case, we'll be using the analog inputs to the Arduino boards, so we mainly need to determine what simple circuit we can use to measure the electrical resistance of our thermistor as the temperature is changing in our bio-system.  We'll do it with a voltage divider, and it really is no different than using the Arduino to monitor a photoresistor or a potentiometer - here is my first simple circuit:

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I've borrowed Rikke's Diecimila (just one of the Arduino models that we are exploring for our sensing platform) and while I was buying that 100 ohm thermistor I picked up a resistor with the same value to use in my voltage divider (big ones are no more expensive than small ones, so I bought the largest one they had) - that is the thermistor up at the top of the image.  We're using a 5 VDC excitation and I had it up and running in a matter of minutes, just using the AnalogReadSerial sketch that is widely used as an example tutorial when beginning with the Arduino.  I tested that everything was working OK by first dunking the sensor in ice water and then dropping it into boiling water - we'll talk later about calibrating, but this just told me all was fine.  I am just using the serial monitor to view the streaming data (logging at 1 Hz for now - plenty fast enough for most bio-systems, and certainly faster than this high thermal mass version of a thermistor warrants) and next need to drill into the details of the Steinhart-Hart equation to convert the analog input to the board (in volts) to an accurate temperature.  And I am waiting for my improved sensors - 10 kilo-ohms at room temperature with a very tiny sensor volume - to appear in the mail.  Stay tuned and next time we'll talk about selecting the right thermistor for your application, mathematically fitting the resistance vs. temperature curve, distinguishing between precision and accuracy and resolution, etc.

Hi kids -


Sean here. I'm the dude trying to make a dissolved O2 (DO) sensor from scratch! You may be asking yourself why you care about dissolved oxygen in the first place...the short version is that dissolved oxygen is an important factor to know when determining if a biologic system will live or die. Only a tiny bit of oxygen, and you wind up in a system that you readily see in ponds: most organisms survive based on photosynthesis alone (like algae). A lot of oxygen? You get a system like the ocean, dominated by giant killer fishies and more advanced animals. In fermentation of beer, you need to suppress the amount of oxygen your yeast sees, or else it will make carbon dioxide only, not tasty tasty ethanol. To this hacker...dissolved oxygen is a really interesting parameter.

 

So, why don't people monitor this all the time? Dissolved oxygen probes are *expensive*. They typically involve platinum catalysts and silver systems (details available here: http://en.wikipedia.org/wiki/Clark_electrode). This, combined with low demand, put commercial DO probes near $200 at a bare minimum...and that doesn't even include a meter to read the signal! If that price could get slashed by an order of magnitude, I have no doubt that all sorts of interesting correlations could be derived by hackers. Is this even possible?

 

Enter the optode. Instead of using a typical electrode system where oxygen concentration is related to a voltage or current from a chemical reaction, otpodes work by relating oxygen concentration to fluroescence of a fancy pants material (in this case, its a crazy Ruthenium based complex). The main advantage to using an optode is that it removes the need to build a sensitive analog circuit to amplify a tiny current. Also, it reduces the number of expensive materials needed from 2 to one. Handy! The hardest part in building this sensor is trying to determine a way to expose the system to the catalyst without degrading the catalyst or exposing the system to a ruthenium ion (this could allow some unexpeted zany reactions to occur).

 

I'm a chemistry dude by day, so I had some ideas in the back of my head to solve these problems. Rather than using the bare catalyst, I thought of encapsulating the catalyst inside a set of cheap, clear, food approved polymers that were also oxygen permeable. Mylar is oxygen permeable and food approved, so it seemed to make an ideal outer layer. Cost? $0.85/foot...yes! The downer with mylar is that it doesn't fuse to itself very easily. However, vinyl fuses to other polymers really really well and is also optically clear, and $1.25/yard...double yes!

 

Before blowing any expensive catalyst, I decided to demo the fusing process using the polymers and a solvent that the Ru complex would be dissolved in. Great successes were had! Here's the lowdown:

 

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Here's a drop of acetone (available at any home improvement store) on top of a ~2"x2" square of mylar. A similar sized piece of vinyl was cut and placed on top. This spreads out the acetone in a beautiful, thin layer (if you've ever put a cover slip on top of a microscope slide, you know exactly what I'm talking about). Next, this assembly was sandwiched between 2 aluminum plates, and heated with a heat gun:

 

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After doing this for about 5 minutes (aluminum plates should be too hot to touch), the assembly was removed from the vice. Don't have some aluminum plates and/or a vice? Unfortunately, you'll need to borrow one for this step. The results below show what happens if you don't happen to use a compression based technique:

 

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Far left: No compression at all. Mylar shrinks and buckles a bunch from the applied heat. Middle: one aluminum plate on top...so minimal pressure. Most of the severe bubbles are gone, but you can still see a lot of bubbles that didn't get their way out of the film layer. Far right: beautiful bilayer that is essentially bubble free, and awaiting some catalyst sandwiching!

 

 

So, in short, good news everybody! Looks like the film creation for this sensor will work out well...now to build the sensing array and do all the math...more on that next post!

We are now one week into the Great Global Hackerspace Challenge, and the activity level on mailing lists, Google groups and blogs really spells out that everyone is gearing up for what will undoubtedly be a truly epic competition! So far, the communication between the hackerspaces has been pretty massive, and I'm starting to get my hopes up that - as well as all the inherent benefits of 30+ groups of talented, creative, determined people working on 30+ projects that will enhance education world-wide - this challenge could also be a major contribution to a much tighter global network of hackerspaces.

 

On a somewhat smaller and more immediate scale, though, it's time for a summary of the first week of work on the BioBoard project at Noisebridge. So far, we've introduced the crew, built a wiki, laid out a fairly detailed project plan, delegated main tasks, set major dead-lines, tested (so far unsuccessfully) our first prototype sensor build, held our first meeting and posted (almost) 3 updates to this blog. Which, when you put it like that, seems not too shabby at all for a bunch of geeks, freaks, and mad scientists.

 

So, in the very sketchiest of outlines, our plan is this: to build a thermometer, a dissolved oxygen sensor and a NIR spectrophotometer ourselves within 3 weeks, and supplementing with a commercial pH meter. Failing that, we'll buy a thermometer and an oxygen probe as well and spend the last 2 weeks attempting to hack them instead, concentrating on standardising data protocols, building the supporting controller hardware and making the graphics look pretty. There's a somewhat more detailed time line here if you want to know more about who will be doing what when.

 

In other news, your truly heaved a great sigh of relief earlier this evening, when Charlie and Rolf (whom I will introduce if he turns out to be a recurring member of the cast) took over the DS18B20 digital temperature sensor prototype project - Charlie took home the set-up I posted pictures of on Friday, while Rolf got the spare chip I had. After much agitation and bugging of friends, I'd finally managed to get the sketch to compile correctly and upload it succesfully to the Arduino board, only to receive absolutely zero signal in return. Somewhat dismayed, I figured I had probably fried the chip when encasing it in heat glue, so I wired up the other chip, triple-checking my circuit before I plugged it in, only to get the same result: nothing. Not exactly an impressive feat, considering that the 1-wire devices must be about the simplest thing in the world to work with, at least as home electronics go. -1.

 

Fortunately, we not all as hopeless as this shamed geek; Sean has already made quite a bit of progress on the dissolved oxygen sensor (dO) or optode, which is basically a solid state probe that uses a ruthenium complex as a visual (fluorescent) indicator of oxygen concentration. He has promised pictures and progress reports documenting his trials, so those should be coming up shortly. Stay tuned to this blog for more exciting updates on his exploits into the world of modern-day alchemy, and don't forget: Be excellent to each other, dudes!

 

 


As some of you readers may already know, Noisebridge (a hackerspace in San Francisco - http://www.noisebridge.net) is a big place, big enough that we initially had two different projects entered in the Great Global Hackerspace Challenge 2011, but as of today, we're down to just one. I just received an email from the mastermind behind the other project to the effect that they've chosen to withdraw from the challenge - no reason given, but I'm guessing that the problem is finding enough people to take on the responsibility of making it happen. Sad...I really wanted to see a electromagnetoscope in real life.

 

On a somewhat brighter note, we've got a new addition to the team: Bill, who may or may not have read the same book on project management that Mike derives his wisdom from, but he's certainly been helpful in prodding me to get some structure established. He's also made this neat little diagram of the project:

 

BioBoardSchematic.png

 

We haven't settled on the exact details of the set-up yet, but at least this gives you an idea of what we're working towards.

 

Speaking of work: all the other hackerspaces are having project start-up meetings and I'm jealous! Sean's been in Canada on business since Monday morning (talk about rotten timing!), which means we haven't been able to get the whole group all together at once, yet, and I'm really impatient to start building stuff! Despite my frustration, however, I must admit that all the mailing back and forth has been very useful for developing a solid project plan, as well as providing lots of written documentation of the initial development phase.  We've been busting behinds all week to get the project plan laid out, figuring out what needs to be done by whom, when, where, using what, how and why. I won't bore you with all the details, but as a result, we now have a lovely new wiki ( https://www.noisebridge.net/wiki/BioBoard) you can take a look at if you'd like to know more about our plans.

 

Apart from being busy talking and mailing with the rest of the team, your truly has also been doing a little bit of meddling with a 1-wire digital thermometer set-up. Unfortunately, in spite of all the geek lingo, programming is very far from being my main strength, so I'm stuck with an error message I don't understand (avrdude: stk500_getsync(): not in sync: resp=0x31), and not enough basic knowledge to identify the problem, let alone ask the right questions to find a solution. In the hope that someone out there might have a better idea of what I'm doing than I do (trust me, that's highly likely), I've thrown in some pictures of my set-up a little further down. Meanwhile, I'm doing my best to lay hands on an ethernet shield before Monday, hoping we'll be able to use this to build a simple prototype of the BioBoard so Marc can start working on the software. Our first proper meeting is Monday night, and I can't wait to get the whole group together and start making this thing real!

 

Stay tuned to this blog for more updates on the BioBoard - and don't forget: Be excellent to each other, dudes!

 

 

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The entire set-up: my Samsung N140 netbook (Odin), an old Arduino Diecemila and a Dallas 1-wire DS1820 digital thermometer, encased in hot glue and a piece of straw. 2 x 10K Ohm resistors (in parallel = 5K Ohm) and a braid of old single-core ethernet cable wires make up the bit-and-bobs.   

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The wiring: Orange is signal (digital pin no. 3), Blue is 5V and White is GND; the resistors are parallel-wired between digital pin no. 3 and 5V.

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The digital thermometer: the naked Dallas 1-Wire DS1820 chip, and the hot-glue-and-plastic-straw encased prototype (probably not food safe, so don't try this at home just yet, kids.)

Howdy, one n' all, and welcome to Noisebridge, a hackerspace in the Mission district of San Francisco, CA, and home of the Biobridge group (represented in this context by yours truly), one of the teams competing in the Great Global Hackerspace Challenge (GGHC). I'll introduce both myself and the rest of the team a little further down, but first a little bit about Noisebridge itself.

 

Noisebridge is my favourite place in the whole world for a gazillion reasons, but first and foremost among them is this: that the entire place - several hundred more-or-less regular users sharing 5000 sq ft. of workspace, toys, kitchen, dark room, wood shop, etc. - rests and runs on a quote from a 1989 pseudo-sci-fi B-movie poster (and of Keanu Reeves, of all people!): "Be excellent to each other, dudes!" [Bill & Ted's Excellent Adventure]

 

It seems somewhat hard to believe at first that such a  basic sentiment, such a simple statement, can really replace all the rules and regulations we're used to imposing on each other to keep our monkey minds in check, but it is none the less exactly what makes Noisebridge special - that the lack of imposed structure forces each and every one of us to regulate our own behaviour, communicate (and often compromise) with others, relate to all issues on an open case-by-case basis, and generally just be overall excellent to one another.

 

I sometimes hear that Noisebridge is not for everyone - to this, I say: that's a matter of choice. Everyone is free to choose to live by self-imposed codes of conduct rather than externally enforced rules. It's just...challenging...at times. It requires willpower and determination to strive for excellence in all things, but it is excatly that willpower and determination, that conscious choice to be excellent to ourselves and each other, which makes the community around Noisebridge such a singularly awesome group of people. And since such is the good fortune of yours truly that I count myself among them, without further ado I will now introduce myself and the fantastic team I'm working with:

 

We are part of Biobridge, a new group at Noisebridge dedicated to furthering DIY, open-source, practical (micro)biology. Our first project is the BioBoard, the above-mentioned GGHC entry (read the original project proposal and follow our progress under 'Projects'), an Arduino-controlled sensor package that allows users to monitor a range of physio-chemical parameters related to microbial processes, with wireless data transmission and supporting data visualization. The core project team consists of: Marc, a Danish software engineer working in synthetic biology with an inspiring dedication to futhering open source synthetic biotechnology and enabling citizen science - he's also a decent electronics hobbyist, our main technical capacity, and (being the only computer geek on the team) is primarily in charge of software development; Sean, an organic chemist currently leasing his soul to the pharmaceutical industry is awesomely enthusiastic about all things hackable, including vodka, cake and laboratory scales - he's also mean with a soldering iron, and will be in charge of building a probe to measure dissolved oxygen in liquid medium; Charlie, engineer,  home-brewer, handy man and all-round DIY old-timer, who is going to be leading our efforts to build the best possible DIY thermal sensor (several avenues of research will be pursued); Mike, man of many contacts, source of all things big, small, odd, pink and minimally draggable, who has read the book on project management and promised to share the wisdom therein - his eye for detail is unique, and apart from being in charge of sourcing, he'll also be keeping close watch that nothing is dropped during the inevitably hectic build process; and myself, Rikke, a  (coincidentally also Danish) DIY fanatic, mad biologist and cyberpunk futurist, currently doing my level best to coordinate the efforts of this group, document our progress as we go and hopefully even entertain you, dear reader, in the process. I'll also be attempting to develop a DIY biomass probe with my good friend and personal electronics guru, Dzl, as advisor - don't miss it, it's going to be...(guess).......(oh, go on, guess)..........(yay, you guessed it!)...EXCELLENT!

 

Stay tuned for next blog post, and don't forget: Be excellent to each other, dudes!