Curry Identification Project:
Similar idea to Food Phylogeny and Detecting GMOs - taking samples of
meat from various curry houses, and checking to see whether they're
actually the meat that they claim to be and whether they're
contaminated with any other species. I'm told (although have never
checked) that some years back, pork DNA was found in chicken breasts
sold in a UK supermarket (some pig product was used in the solution
that gets injected into cheap chicken breasts to bulk them up) which,
understandably, irked a load of religious people. So could be an
interesting one! Requirements are probably the same as those for
Detecting GMOs in foods.
Incubator:
We need a warm box (one or two cubic feet will be fine) with a shelf
inside, that we can keep at 37 degrees. Realistically, 35 degrees +/-
3 degrees should be OK. We discussed setting up a system relying on
peltier warmers/coolers with a fan to circulate the air. This would be
great, as we should have good control over temperature and be able to
set e.g. 16 hours at 37 degrees then stay around 4 degrees until
turned off, if we set up a bacterial culture overnight and no-one is
free to come in the next day.
That sounds very unscientific. Did you record the variety of cheese :-)
Unfortunately I couldn't make the meeting, it sounds like it was really interesting and that is a great list
of projects.
A few thoughts about equipment:
Although hacking our own PCR machine is a worthwile aim, buying a cheap one from ebay would
help kickstart things. Is this one suitable http://cgi.ebay.co.uk/270691363646 if it is then start a
pledge for it - I am up for �30, and may be able to collect it as well.
One thing that seems to be missing from the list is a power supply for electrophoresis. My limited
understanding of the subject suggests 100V or more is desirable, so the existing supplies in the space
probably aren't going to be very useful. What sort of voltage and current should we be looking for?
How many base pairs are we looking at running a gel for? A good while back I had a discussion
over a beer with a molecular biologist who enthused about the new FIGE (Field Inversion Gel
Electrophoresis) technique. He was working with upto 500,000 base pairs, probably rather more
than the current projects require but why limit our capabilities?
Things have probably moved on a lot since then, but the main requirement seemed to be a computer
controlled polarity switch, very expensive back then but high voltage FETs are fairly cheap now.
The switch timing was varied during the run, and I think the voltage was as well but not under
computer control. Building such a supply with built in switch should be fairly easy, so what
specification is required?
A final thought, would it be practical to modify a scanner to use UV leds as the illumination source
to get a dimensionally accurate high resolution scan of the finished gel?
Nigle
I someone on the Histonet group mention converting a flatbed scanner into a gel imager by replacing the light with a UV tube. This was done in a professional lab due to lack of funding for a commercial imager.
We are very close to having enough pledges to start bidding on this. Will you do the bidding on this or shall I?
Nigle
Great find Nigel!
I've added a pledge section to the biohacking page: http://wiki.hackspace.org.uk/wiki/Biohacking#Pledges
I can put Ł40 towards the thermal cycler.
Great find Nigel!
I've added a pledge section to the biohacking page: http://wiki.hackspace.org.uk/wiki/Biohacking#Pledges
I can put Ł40 towards the thermal cycler.
We are very close to having enough pledges to start bidding on this. Will you do the bidding on this or shall I?
Nigle
For the electrophoresis power supply:
120V DC is a sensible upper limit: you *can* go higher, but have to
start worrying about melting the gel. The speed at which a gel runs
scales linerarly (ish) with the voltage you put across it, so the
lower limit is defined by how patient you are. 20V will need to be
left overnight, 120V will take about 30-45min for the gel sizes that
we're interested in. I've never timed a gel running at 100V, but it's
probably OK.
Looks like we are sorted then, at least to begin with.
I like the idea of designing our own affordable supply in the longer term, but I need to finish several
existing projects before I start another one. Your higher voltage one may well be called upon!
Nigle
I have a friend who lives half the time in Kent - I'll ask him if he
can go and collect the machine for us. If that doesnt work out, does
anyone have a car we can use? Maybe the hackvan? I'll email the seller
and ask for their exact location.
On 16 Jan 2011, at 23:57, Nigel Worsley <nig...@googlemail.com> wrote:
>> Great find Nigel!
>> I've added a pledge section to the biohacking page: http://wiki.hackspace.org.uk/wiki/Biohacking#Pledges
>> I can put �40 towards the thermal cycler.
Or risk shipping it with parcel2go (cheap but only "96% success rate".)
m.
According to a website I found:
Weight: 57 lbs.
Measurements: 13 x 19 x 12
Not huge, but rather heavy!
Nigle
By my calculation it weighs 25.9kg. Plus packing.
Nigle
Nice to have, why do things by halves? :) :
20 to 200V
400mA (definitely with adjustable current limit, 80W at 200V)
programmable profile over time, including reverse
We would also need to pick a physical format and user interface
and a remote control interface.
Andrew
--
Andrew Cousins
A little inaccuracy sometimes saves tons of explanation.
-- H.H. Munro, "Saki"
On Saturday I also mentioned that for an incubator we could look
at what this guy uses for a DIY thermal chamber for electronics:
http://www.eevblog.com/2010/07/25/eevblog-101-hacking-your-own-peltier-lab-thermal-chamber/
It seems to be a 19 litre beer fridge / pie warmer, driven by a
peltier.
http://www.amazon.com/gp/product/B001F7H4RY?ie=UTF8&tag=ee04-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=B001F7H4RY
A search on Google UK for cooler and warmer turns up a 14 litre
food warmer/ cooler for �51 from Argos. I assume this is also
driven by a peltier, there are no specs on accuracy or how much
load it can handle:
http://www.argos.co.uk/static/Product/partNumber/9248832.htm?_$ja=tsid:11527|cc:|prd:9248832|cat:gifts+and+hobbies+%2F+mini+fridges+and+water+dispensers+%2F
It does say that it can only pull to 18 degrees below ambient,
which might not be enough.
To get a timed temperature profile we would have to hack it. If
we don't hack it for the timed profile we might as well get an
oven that can be set to 37C reasonably accurately (how often will
the space be warmer than that?).
If we use Adrian's proper environmental chamber then this is all
moot of course.
Andy
I was looking into doing an isolated 20-200V supply at 200mA, initially a dumb one and adding processor control
later.. It should be easy to increase to 400mA, but I suspect that will only be necessary for runnning multiple gels
and I prefer the flexibility of a pair of 200mA supplies independently controlled. The extra cost of doing it this way
should be less than �10.
> We would also need to pick a physical format and user interface
I was thinking og a graphic LCD, mainly because I already use them in a product. I have some small (2.4"?) TFT
displays that I haven't got around to using, over the top but it would look very nice, may use them instead.
> and a remote control interface.
USB is trivial, ethernet is a bit more work but would allow checking progress over the internet. Not at all sure about
allowing control over it though, could be dangerous.
Nigle
This one will cool by 27 degrees and heat up to 65 degrees (absolute I think, presumably the plastic won't cope with more)
http://cgi.ebay.co.uk/220725833946
I have already put a bid in on this as I can make use of it myself if the space doesn't want it.
> To get a timed temperature profile we would have to hack it.
That's what we do, isn't it?
How accurate does the temperature have to be? 1 degree is not too difficult but anything better will get expensive.
Nigle
This one will cool by 27 degrees and heat up to 65 degrees (absolute I think, presumably the plastic won't cope with more) http://cgi.ebay.co.uk/220725833946It does say that it can only pull to 18 degrees below ambient, which might not be enough.
I have already put a bid in on this as I can make use of it myself if the space doesn't want it.
I have a dual thermocouple digital thermometer. I can also borrow one of these from work:
http://www.picotech.com/thermocouple.html#buy It hasn't been used for years, nobody
would miss it for a while.
> The idea of putting a UV tube into a scanner is great. Are there any
> scanners in the space, or will we need to scrounge one?
One got junked a while back, I think it was because there were too many of them lying around.
> Are UV tubes expensive?
Depends on the wavelength. I was thinking of using LEDs, replace the RGB LEDs of the scanner with UV
ones and job done :-)
Maybe an interlock switch on the lid for safety.
> People who've pledged: as we've pledged quite a bit more than the cost
> of the thermal cycler, is it OK to redistribute the excess to other
> bits of essential kit for the DIYBio work?
Fine with me.
Nigle
Yes of course.
m.
Yes, please do.
Irwin
People who've pledged: as we've pledged quite a bit more than the cost
of the thermal cycler, is it OK to redistribute the excess to other
bits of essential kit for the DIYBio work?
Tom says he's happy to drive to Kent to pick the thing up, but is less
keen on driving through London. Do you think we'd be able to get it on
a train at Forest Hill and off again at Hoxton?
We will need a fairly beefy 12V power supply for it, is there a spare one in the space?
I should finally get the ethernet arduino board finished in the next few days, this would be
ideal for controlling it :-)
Nigle
James
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Somewhere between 5 and 10 amps at a rough guess. I have an 18 amp one I can loan
until we can sort out a flashy automated one.
Nigle
The cooler claims autoswitching between 12V and 24V, 2.5A may be enough. If not then it should be possible
to bodge a pair together. Are these proper supplies or something that the BBC kludged together?
Nigle