So its just a transfer function or a lookup table for the calibrated device?
On Tue, Apr 24, 2012 at 12:58 PM, Simon Quellen Field
<sfield@scitoys.com> wrote:
> You are correct.
>
> Having an accurate thermometer in the lab is a good thing.
>
> But it does not need to be built into the incubator.
>
> It can be used for many different things, and it can be sterilized, and
> nicely
> portable, and easy to read, clean, and store. And it can be used to set the
> calibration point of the incubator for each run, giving you some confidence
> that nothing has gone out of calibration in the incubator between runs or
> during cleaning.
>
> -----
> Get a free science project every week! "http://scitoys.com/newsletter.html"
>
>
>
>
> On Tue, Apr 24, 2012 at 8:20 AM, Nathan McCorkle <nmz787@gmail.com> wrote:
>>
>> But if I need a reference, and I only have one incubator, I'll still need
>> to buy at least one good temp sensor. So I guess we should be talking about
>> two designs, a reference or golden standard, and "slave" devices which get
>> calibrated against that, as our lab needs grow
>>
>> On Apr 24, 2012 4:20 AM, "Cathal Garvey" <cathalgarvey@gmail.com> wrote:
>>>
>>> It's not the error in my own samples that matters, so much as the
>>> variance between incubators. Also, it's not about the cells' survival;
>>> it's about maintaining them at a known growth state.
>>>
>>> We grow mesophiles like E.coli at 37C because, for most of them, that's
>>> the ceiling for comfortable growth. Higher temperatures mean more
>>> reactions per second, meaning faster growth. However, any higher than
>>> this ceiling, and heat-shock starts to get induced. While the cells will
>>> survive, their gene expression profiles will change markedly.
>>>
>>> So, if you and I set our incubators to 37C, and mine hits 36.5 while
>>> yours hits 37.5, that could have a significant effect on our experiments
>>> with the same DNA constructs. If any protein folding effects are
>>> interrupted by heat-shock, you'll have reduced apparent expression. If
>>> we're using heat or chemically induced promoters, you'll seem to have
>>> higher expression at the same temperature.
>>>
>>> At the very least, you'll have faster growth than I will at the same
>>> apparent temperature, even controlling for all other factors.
>>>
>>> If this were unavoidable I wouldn't complain, but for the difference of
>>> €0.5, it's not worth skimping on accuracy. Science is about good
>>> experimental control and reproducible results. If our equipment has such
>>> significant error, you and I can't really compare or reproduce one
>>> anothers' work; that's bad science.
>>>
>>> On 24/04/12 00:23, Simon Quellen Field wrote:
>>> > This is an incubator, guys.
>>> > What organism do you know that maintains its temperature to 0.1C?
>>> > Why would you think that was important for anything you are going to
>>> > incubate?
>>> >
>>> > Let's suppose that you need to incubate something for 10 hours (600
>>> > minutes).
>>> > Suppose you set one incubator for 310 kelvin, and another for 310.1.
>>> > Thus one is to get 186,000 degree minutes, and the other gets 186,060
>>> > degree
>>> > minutes.
>>> >
>>> > You open them both, and immediately the air temperature changes by 11
>>> > degrees
>>> > to 26, the temperature of the Petri dishes full of agar.
>>> >
>>> > It takes both incubators 20 minutes to settle down to their set
>>> > temperature.
>>> > You have an average of 5 degrees below the set point during those 20
>>> > minutes.
>>> > That is 100 degree minutes off already, which is more than the 60
>>> > degree
>>> > minutes
>>> > by which the two incubators have been set.
>>> >
>>> > But more to the point, suppose we are incubating E. coli.
>>> > Let's look at some of the protocols in
>>> >
>>> > use<http://www.daff.gov.au/agriculture-food/food/regulation-safety/antimicrobial-resistance/antimicrobial_resistance_in_bacteria_of_animal_origin/appendix_2_bacterial_culturing_protocol_for_e._coli,_enteroccus_spp._and_cambylobacter_spp.>.
>>> > One says to incubate at 37 Celsius for
>>> > 18 to 24 hours. Another of
>>> > them<http://www.neb.com/nebecomm/products_intl/productC2988.asp>says
>>> > to expect a 2-fold loss
>>> > of transformation for
>>> > every 15 minutes that a 1 hour incubation at 37 Celsius. A
>>> >
>>> > third<http://openwetware.org/wiki/Maxiprep_of_plasmid_DNA_from_E.coli_protocol>calls
>>> > for incubating
>>> > at 37 Celsius for 30 minutes, then incubating 'at room temperature' for
>>> > 10
>>> > minutes.
>>> >
>>> > It does not look to me like anyone is calling for one tenth of a degree
>>> > of
>>> > accuracy in
>>> > temperature. But more to the point, given that how long the cultures
>>> > are
>>> > incubating
>>> > is so variable, being off by a couple degrees does not seem like it is
>>> > going to make
>>> > any difference.
>>> >
>>> > If it *does* make a difference, is temperature the right thing to be
>>> > measuring?
>>> > If the reason we incubate at 37 for an hour is to get a certain density
>>> > of
>>> > critters
>>> > per milliliter, why not incubate until the optical density is some
>>> > particular value?
>>> >
>>> > Maybe we shouldn't bother with electronics at all.
>>> > Run some hot water from the tap and adjust the temperature to 37.
>>> > Get a 5 gallon insulated beer cooler and fill it with water from that
>>> > tap.
>>> > Put your Petri dish in a zip-lock bag, set it in the water, and close
>>> > the
>>> > cooler lid.
>>> > Take it out an hour later. The water temp is still 37.
>>> >
>>> > But that takes all the fun out of building the device. So let's use the
>>> > device to
>>> > do *sous vide* cooking, or to incubate chicken eggs (which will hatch
>>> > in 21
>>> > days
>>> > even if you are off by 10 degrees). Your *sous vide* pork chop will
>>> > come
>>> > out great
>>> > even if you are off by 5 degrees.
>>> >
>>> > In other words, the temperature sensor in the microcontroller is
>>> > already
>>> > more
>>> > sensitive and accurate than you need.
>>> >
>>> > -----
>>> > Get a free science project every week!
>>> > "http://scitoys.com/newsletter.html"
>>> >
>>> >
>>> >
>>> >
>>> > On Mon, Apr 23, 2012 at 2:20 PM, John Griessen
>>> > <john@industromatic.com>wrote:
>>> >
>>> >> On 04/23/2012 03:28 PM, Cathal Garvey wrote:
>>> >>
>>> >>> Most other forms of temperature readout
>>> >>> that I've encountered are a bit batch-variable, and I wouldn't be
>>> >>> surprised if the same is true of something cool but hack-ey like your
>>> >>> onboard diode idea
>>> >>>
>>> >>
>>> >> It's the physics behind all the temp sensors, the differences are in
>>> >> the
>>> >> implementation details.
>>> >> Why would you pay more for a method or mechanism if you can't get any
>>> >> better results
>>> >> than with the low cost method? You don't just always pay more, you
>>> >> shop
>>> >> for a low accuracy need for low dollars
>>> >> and hi accuracy for hi dollars. Precision, or fine grained
>>> >> resolution, is
>>> >> inexpensive,
>>> >> and you can transfer the accuracy from another temp probe to your
>>> >> machine
>>> >> and get repeatable results
>>> >> without a temp standard built in.
>>> >>
>>> >> This particular MSP430, for example, MSP430G2230IDR, has a nicely
>>> >> engineered diode temp sensor
>>> >> inside, that can be switched in to one of its ADC channels to read the
>>> >> temperature of the chip.
>>> >> The diode will have a small batch to batch random variation, but will
>>> >> always repeat very closely
>>> >> as temperature differences happen. There is a temperature compensated
>>> >> volt reference for the
>>> >> ADC so volts measured are truly accurate. Temperature repeatability
>>> >> of
>>> >> .01 deg C is probably
>>> >> possible, although that's not accuracy, and would only agree that
>>> >> closely
>>> >> on long equilibration
>>> >> soak times after a temperature change.
>>> >>
>>> >> All you need is to put the chip in the stirred air you want to heat
>>> >> and
>>> >> you're accurate
>>> >> to a very reasonable precision, and you could get better accuracy by
>>> >> calibration.
>>> >> Repeatability and precision are easy to get with silicon
>>> >> microcontrollers.
>>> >> That one I mention costs $46/qty 100, or 46 cents each and has four
>>> >> channels of 10 bit analog converter.
>>> >>
>>> >> Is 0.1 degree C inherent reference standard accuracy necessary for
>>> >> incubation? No...
>>> >> repeatability is nice, an easy cal feature is nice... Your code can
>>> >> have
>>> >> a mode where
>>> >> when you press a calibrate button, it changes its look up tables to
>>> >> use
>>> >> what your external
>>> >> fancy temp sensor reference standard says. The code could take input
>>> >> as
>>> >> up/down buttons
>>> >> to adjust the temperature lookup table while controlling temp at 35
>>> >> deg C.
>>> >> You would put the tip
>>> >> of your hi res. platinum temp probe in the incubator for the
>>> >> calibration
>>> >> for a few minutes for each
>>> >> up/down command until stable at 35.0 deg C. Then it will repeat, and
>>> >> be a
>>> >> transfer standard
>>> >> for the cal thermometer for many months or years with as good accuracy
>>> >> and
>>> >> precision
>>> >> as the cal thermometer even though it does not have an internal temp
>>> >> standard that
>>> >> accurate. It does need a very stable, repeatable volt standard inside
>>> >> or
>>> >> on board, and
>>> >> to make no changes to the chips used to keep its cal.
>>> >>
>>> >> John
>>> >>
>>> >>
>>> >> --
>>> >> You received this message because you are subscribed to the Google
>>> >> Groups
>>> >> "DIYbio" group.
>>> >> To post to this group, send email to diybio@googlegroups.com.
>>> >> To unsubscribe from this group, send email to diybio+unsubscribe@**
>>> >> googlegroups.com <diybio%2Bunsubscribe@googlegroups.com>.
>>> >> For more options, visit this group at http://groups.google.com/**
>>> >> group/diybio?hl=en <http://groups.google.com/group/diybio?hl=en>.
>>> >>
>>> >>
>>> >
>>>
>>>
>>> --
>>> www.indiebiotech.com
>>> twitter.com/onetruecathal
>>> joindiaspora.com/u/cathalgarvey
>>> PGP Public Key: http://bit.ly/CathalGKey
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "DIYbio" group.
>>> To post to this group, send email to diybio@googlegroups.com.
>>> To unsubscribe from this group, send email to
>>> diybio+unsubscribe@googlegroups.com.
>>> For more options, visit this group at
>>> http://groups.google.com/group/diybio?hl=en.
>>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "DIYbio" group.
>> To post to this group, send email to diybio@googlegroups.com.
>> To unsubscribe from this group, send email to
>> diybio+unsubscribe@googlegroups.com.
>> For more options, visit this group at
>> http://groups.google.com/group/diybio?hl=en.
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "DIYbio" group.
> To post to this group, send email to diybio@googlegroups.com.
> To unsubscribe from this group, send email to
> diybio+unsubscribe@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/diybio?hl=en.
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/diybio?hl=en.
0 comments:
Post a Comment