the diy equipment list?

[Jeswin]

Was there ever a list of DIY equipment that could be built?

Sure, we can all hobble together stuff but are there plans for more
kit style equipment like the OpenPCR or dremel-fuge? Should we work on
equipment that anyone can put together with only minimal knowledge of
theory outside biochemistry (EE, programming, etc)

[John Griessen]

On 10/10/2012 12:18 PM, Jeswin wrote:
> Should we work on
> equipment that anyone can put together with only minimal knowledge of
> theory outside biochemistry (EE, programming, etc)

Sure, I'm planning some, but no willing collaborators so far...
I suppose it will wait until I productize it. Not many seem to want to
design equip, but rather bio experiments, and they expect building blocks
to be ready. But the ones that are ready are fairly expensive.

If you mean, "Should we work on a list?", There's not much extant yet
of a cost reduced price. Most lab equip is low volume/high priced.

My first kit machines will be auto incubator, then
add fluid handling to get it to do auto-culturing of 100 ml.
The battery backed small refrigerator and small incubator mentioned awhile back is a good one too.
Small to mid sized flat boxed kit of parts to assemble a laminar flow bench.

All these need a good amount of time in more than design -- they need a lot of purchasing
effort and some capital to risk on batches of purchased parts and materials before sales
pay for them, because one at a time is not efficient. Some things are designed by trial and
error, like just how much fan is needed to push air through a HEPA filter? Probably the first fan
will be larger than is needed, cost more, use more power, and only the second or third batch will
get optimum sizing and still work well. Variable speed fans are best for a flow bench with a variable
opening made by the front window being up more or less... But who would want a flow bench with
a fixed front opening?, so that kind of complexity is a given. A flow bench needs a lighting system
that's good. It needs to be quiet and easy to clean, ( to sterile condition). Some built in UV
for sterilizing might be good, else offer a corded lamp to use for setting up and getting to sterility.
It needs to have real HEPA filter material, and real laminar flow -- those might not be perfect
the first time, and need some course correction. A kit will need instructions on assembling so it
is really air tight, and micron particle leak tight, so a good bit of writing will need to be done,
and offer some way to verify along with the kit.

Quick question: Is there any catch to having ports on the side walls for power cords, instrumentation
wires, drain tubes? I figure you can put a blanking plate on a port if not used, and caulk
it air tight around wires when used so no reducing positive pressure.

[Bryan Bishop]

On Wed, Oct 10, 2012 at 3:45 PM, John Griessen wrote:

If you mean, "Should we work on a list?", There's not much extant yet
of a cost reduced price.  Most lab equip is low volume/high priced.

Well, there's a bit of an equipment list:

http://diyhpl.us/wiki/diybio/faq/equipment/

(Formatting sucks. Editors-who-care wanted.)

And I mirror of the hardware repos here:

http://diyhpl.us/cgit

I think that's a fairly good start to a list.

- Bryan
http://heybryan.org/
1 512 203 0507

[Jeswin]

On Wed, Oct 10, 2012 at 4:45 PM, John Griessen <jo...@industromatic.com> wrote:

> get optimum sizing and still work well. Variable speed fans are best for a
> flow bench with a variable
> opening made by the front window being up more or less... But who would
> want a flow bench with
> a fixed front opening?, so that kind of complexity is a given. A flow bench

What do you mean by "fixed front opening"? I use an AirClean PCR
workstation with UV and HEPA filtered air-flow through the front. The
opening is hinged so you can have it half-open or fully open. Its good
for reducing cross-contamination.

> needs a lighting system
> that's good. It needs to be quiet and easy to clean, ( to sterile
> condition). Some built in UV
> for sterilizing might be good, else offer a corded lamp to use for setting
> up and getting to sterility.

I think having the consumer obtain a portable UV lamp would be a good
idea. Was it UV-B for sterilization? If you use UV, what material are
you using for the box? Must take safety precaution of accidental UV
exposure using UV-reflective (absorptive?) material and safety switch
that turns UV on only if box is closed.

> It needs to have real HEPA filter material, and real laminar flow -- those
> might not be perfect
> the first time, and need some course correction. A kit will need
> instructions on assembling so it
> is really air tight, and micron particle leak tight, so a good bit of
> writing will need to be done,
> and offer some way to verify along with the kit.

Why such air-tightness? What kind of experiments are you designing this for?

>
> Quick question: Is there any catch to having ports on the side walls for
> power cords, instrumentation
> wires, drain tubes? I figure you can put a blanking plate on a port if not
> used, and caulk
> it air tight around wires when used so no reducing positive pressure.

Well, if you want such an airtight box then that side vent is not
good. But it is very handy to run vacuum-manifold DNA purification
systems in the hood with the pump positioned outside. Also useful to
have the port if separate portable UV-lighting is used.

Final question: Are you modeling a commercial laminar flow hood and if
so, which one? I ask because I use the Airclean vertical laminar flow
hoods and they're not as air-tight as you want.

[John Griessen]

On 10/10/2012 04:06 PM, Jeswin wrote:
> On Wed, Oct 10, 2012 at 4:45 PM, John Griessen<jo...@industromatic.com> wrote:
>
>> get optimum sizing and still work well. Variable speed fans are best for a
>> flow bench with a variable
>> opening made by the front window being up more or less... But who would
>> want a flow bench with
>> a fixed front opening?, so that kind of complexity is a given. A flow bench
>
> What do you mean by "fixed front opening"? I use an AirClean PCR
> workstation with UV and HEPA filtered air-flow through the front. The
> opening is hinged so you can have it half-open or fully open. Its good
> for reducing cross-contamination.

Fixed as opposed to sliding up and down.

>
>> needs a lighting system
>> that's good. It needs to be quiet and easy to clean, ( to sterile
>> condition). Some built in UV
>> for sterilizing might be good, else offer a corded lamp to use for setting
>> up and getting to sterility.
>
> I think having the consumer obtain a portable UV lamp would be a good
> idea. Was it UV-B for sterilization? If you use UV, what material are
> you using for the box? Must take safety precaution of accidental UV
> exposure using UV-reflective (absorptive?) material and safety switch
> that turns UV on only if box is closed.
>
>> It needs to have real HEPA filter material, and real laminar flow -- those
>> might not be perfect
>> the first time, and need some course correction. A kit will need
>> instructions on assembling so it
>> is really air tight, and micron particle leak tight, so a good bit of
>> writing will need to be done,
>> and offer some way to verify along with the kit.
>
> Why such air-tightness? What kind of experiments are you designing this for?

The flow hood laminar flow is never perfect, and these are less perfect because of small size,
and people and things moving can make blasts of air,
so you want few leaks in a quality flow hood.
Not wanting to hold more than breeze pressure though.

>
>>
>> Quick question: Is there any catch to having ports on the side walls for
>> power cords, instrumentation
>> wires, drain tubes? I figure you can put a blanking plate on a port if not
>> used, and caulk
>> it air tight around wires when used so no reducing positive pressure.
>
> Well, if you want such an airtight box then that side vent is not
> good.

Not imagining a vent, but a port for a seldom moved wire or tube
to go through side wall, (and be caulked).

>
> Final question: Are you modeling a commercial laminar flow hood and if
> so, which one?

No particular one. All the ones I ever saw, which is not many, so asking questions.

[Nathan McCorkle]

positive pressure is fine for taking care of small leaks in a hood, as
long as you aren't aiming for a hood that also recycles the air near
the opening (to limit worker exposure to the stuff in the box, not
just keep the stuff in the box clean from outside)

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Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Cathal Garvey]

Rudiger (bcc'd) demo'd a DIY electrophoresis supply at the European
Bioethics meetup that was made by a friend of his. Sadly, his friend
didn't grok open source, and was wary of revealing his plans, despite
having no intention of actually making any use of them commercially
himself. It was just a weekend project for him, it seems..

--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey

[Jeswin]

Is it possible to develop methods and plans to repurpose other
equipment for DIYbio? For example, you can buy budget computer PSUs on
sale at $20-$30 from Corsair or Antec. Could someone write up a way to
*safely* use them in a bio-lab and improve their flaws, like ripple
and noise? I'm no EE so I'm just wondering.

Can guidelines and re-purposing kits be developed for other equipment?

[John Griessen]

On 10/10/2012 06:30 PM, Nathan McCorkle wrote:
> as
> long as you aren't aiming for a hood that also recycles the air near
> the opening (to limit worker exposure to the stuff in the box

Just tackling a clean flow bench first rather than a safety cabinet.

[John Griessen]

On 10/11/2012 04:29 AM, Cathal Garvey wrote:
> Rudiger (bcc'd) demo'd a DIY electrophoresis supply at the European
> Bioethics meetup that was made by a friend of his. Sadly, his friend
> didn't grok open source, and was wary of revealing his plans, despite
> having no intention of actually making any use of them commercially
> himself. It was just a weekend project for him, it seems..

Many people have been indoctrinated such that they perceive product manufacturing
business as a fierce battle with the public at large and even their
customers, and see everything as a liability risk.

Of course, that also helps them rationalize why they have not done much...
besides stay safe from lawsuits.

Instead, I take the example of the publishing business, where information
has no liability. If you make few product claims in your selling literature,
demand that your customer does the final assembly, and provide
instructions on a site published to the world,
you defuse much liability. And you lower the market selling price a lot...
since most want to spend more for and "easy button" product.

[John Griessen]

On 10/11/2012 08:10 AM, Jeswin wrote:
> Could someone write up a way to
> *safely* use them in a bio-lab and improve their flaws, like ripple
> and noise?

Yes, that's possible, just clunky and my temperament doesn't like it.

Short story:

Take surplus PS unit. Identify desired output voltage and connectorize
that wire and the common wire. Add RC filtering and output connectors.
Repackage for safety in a larger clunkier box.

Short story 2:

Take surplus PS units modified with filtering. Stack as high as the output voltage
you want with the "in series" connector kit or according to the "in series" diagram.
Enjoy low volt electrophoresis with your giant stack of PS units.

Short story 3:
Order kit from John. Do final assembly of PCBs into custom molded enclosure.
Wire up with safety interlock connectors.
Enjoy FOSS programmable high or low volt or ramp soak controlled electrophoresis with your
small footprint device connected by USB or ethernet to a PC running Mac OS-X, linux, windows...

[Nathan McCorkle]

I would like to say, I think a power supply with a digitally controllable output would be fantastic at enabling lab automation. That way you could do things like pulsed field gel electrophoresis, or something as simple as watching the end of the gel for a band of DNA to trigger shutdown (so it doesn't run off the gel)

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[Nathan McCorkle]

To do PFGE the supply also need to be reversible.

[Rüdiger Trojok]

Hey,
here is Phillips contact if you'd like to have more info about
the gelelectrophoresis device. It was much more than a weekend project
(about 100 working hours).

Yestderday I successfully tested my DIY gene gun, which in the final version
was not much more than a pressure device for whip like this:
http://www.amazon.de/ISI001-Gourmet-Sahnespender-Edelstahl-geb%C3%BCrstet/dp
/B001U83TWW/ref=sr_1_2?s=kitchen&ie=UTF8&qid=1349997807&sr=1-2
It was even much simpler than expected. I tested it with Cyano fluorescent
protein
under a plant specific constitute promoter. the protein had a nuclea
localization sequence
and stained the nuclei of the onion phloem tissue I used.
I will soon upload evidence pictures of the experiment.
the gold particles were 10µm.
Best, Rüdiger


-----Ursprüngliche Nachricht-----
Von: Cathal Garvey [mailto:cathal...@gmail.com]
Gesendet: Donnerstag, 11. Oktober 2012 11:29
An: diy...@googlegroups.com
Betreff: Re: [DIYbio] the diy equipment list?

[John Griessen]

On 10/11/2012 01:44 PM, Nathan McCorkle wrote:
> To do PFGE the supply also need to be reversible.

For HV that's clunky in a way I can do. Big HV separated relays
that go clunk.

It would be an add-on module.

Maybe I should add an electrophoresis supply to my to do list...

[Phil]

On Wednesday, 10 October 2012 16:45:59 UTC-4, John Griessen wrote:

>My first kit machines will be auto incubator, then
>add fluid handling to get it to do auto-culturing of 100 ml.
>The battery backed small refrigerator and small incubator mentioned awhile back is a good one too.
>Small to mid sized flat boxed kit of parts to assemble a laminar flow bench.

That is exactly what should be done first, except the small incubator is not essential as you can get them on ebay.
Compact incubators include the Lab-Line 100 and the GCA Precision Model 2 Gravity Convection Incubator.
Beware smaller "incubators" that are uninsulated and are really warming ovens.
I don't know if using used incubators provides contamination problems (they often have rust spots), or problems with uneven temperature in small incubators.

Next up: Small -80 freezer; a 3-day backup power supply for that freezer, a small -20 freezer (probably an off-the-shelf dorm freezer), and an incubator.

[shamrock]

To keep cells you can use a cooler filled with dry ice. I've found that a standard cooler filled with dry ice keeps about 5 -6 days and if you beefed up the insulation and had better seals it might keep longer. I've been keeping some cells that way for the past 3 months and haven't noticed any decrease in viability. 

Fetching the dry ice is a pain and because of that I'm in the market for a used -80 freezer. The going rate for a used -80 is about equal to a years worth of dry ice. Still the dry ice/cooler combo is a decent temporary alternative. 

Off the shelf chest or upright freezers work fine. If your going to store enzymes make sure it is not a frost-free freezer or keep the enzymes in a cooler block. 

[John Griessen]

On 10/16/2012 02:55 PM, Phil wrote:
>
> Next up: Small -80 freezer;

I studied this some a while back and it's not easy at all to get that cold.
Too much technical hurdle for me -- needs a refrigerator ME expert
and even then hard to make it inexpensive.

Unless you're talking a TE cooler for a 2 ml thimble full of volume only.

200 ml of volume is 100X as much as a thimble full and still not
what one thinks of as an ice box.

[Phil]

On Wednesday, 17 October 2012 08:57:25 UTC-4, John Griessen wrote:

On 10/16/2012 02:55 PM, Phil wrote:
>
> Next up: Small -80 freezer;

I studied this some a while back and it's not easy at all to get that cold.
Too much technical hurdle for me -- needs a refrigerator ME expert
and even then hard to make it inexpensive.

I'm thinking of taking a conventional -20F freezer, and putting in a 30L liquid nitrogen dewar with a thermometer and a valve that releases more NO2 when the temperature goes over -80F.  You need to vent the nitrogen from the dewar and from the freezer.  This would be cheap, and it might stay cold even if the power goes out for a few days.

[Sebastian S. Cocioba]

Dry ice and ethanol can cool to -70. Its used in table top freeze dryers. Just throwing that out there.

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

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[John Griessen]

On 10/17/2012 01:21 PM, Phil wrote:
> thinking of taking a conventional -20F freezer, and putting in a 30L liquid nitrogen dewar with a thermometer and a valve that

> releases more lN2 when the temperature goes over -80F. You need to vent the nitrogen from the dewar and from the freezer. This

> would be cheap, and it might stay cold even if the power goes out for a few days.

Sounds reasonable, maybe even workable with dry ice at -79 deg C (-109 deg F) too? Could be regulated by
a slight turning of a stirring fan, the whole -80F part jacketed by a -20F piston compressor freezer.

On 10/17/2012 01:37 PM, Sebastian S. Cocioba wrote:
> Dry ice and ethanol can cool to -70.

Are you talking -70 deg C? Which is the minimalist desirable temp? -80F or -80C?

[Nathan McCorkle]

Scientific standards are metric, and -70 to -80 is a common range for deep veto freeze

[Patrik D'haeseleer]

Is there some biological reason for -80 specifically? Or is it simply the colder the better, and -80 is what a certain refrigeration technology can easily achieve?

A -60 or -50C freezer may be orders of magnitude easier to achieve using DIY methods, and still be biologically acceptable. Let's not be fixated on -80 if we don't need to...

[Cathal Garvey]

I imagine answering that question would require some background reading
on ice crystal formation. The main reason to go lower than 20 is that
lower temperatures favour less destructive crystal structures, so
there's probably a pretty clear threshold you want to dip under to
protect cells.

Of course, there are some hacks to work around the ice issue; I've
successfully kept a few stocks in a -20C freezer as a film of
glycerol-rich cell suspension coated on the outside of very tiny beads.
The combination of the curved surface (discourages long crystals
forming) and glycerol (discourages ice to begin with) seems to be a nice
combination, and subculturing is as simple as tipping out a few beads
and rolling across agar, or tipping into broth.

Mind you, those stocks haven't broken out successfully last time I tried
a few days ago, so there's still an "expiry" on cells in -20, it seems.

[Marc Dusseiller]

hoi zäme,

as with many biological protocolls, i think the -80° has purely practical and historical resons. if you get some protocoll working, biology stayle, dont change it anymore.....

-80° is the sublimation temperatur of CO2, this is how they used to freeze their samples and cultures before the development of refrigerators for such low temeratures.

and so for doing DIY bio, always look how people used to do this stuff looooooong ago. cos 100 years ago most of science was DIY anyway, and soon will be again  :-)

best,

marc

[Brian Degger]

Great insight Marc. Now if only I lived next to a dry ice factory :)
Brian

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[Cathal Garvey]

You *are* a dry ice factory, it just comes off the production line a
little hot! :)

On 19/10/12 09:15, Brian Degger wrote:
> Great insight Marc. Now if only I lived next to a dry ice factory :)
> Brian
>
> On Friday, October 19, 2012, Marc Dusseiller <dus...@gmail.com> wrote:

>> hoi z�me,

[John Griessen]

On 10/19/2012 02:29 AM, Marc Dusseiller wrote:
> -80° is the sublimation temperatur of CO2, this is how they used to freeze their samples and cultures before the development of
> refrigerators for such low temeratures.

Ah ha! So maybe there is some use in a dry ice metering system surrounded by a -20 deg C freezer
that's ordinary. Another thing that lets a cold spot last is not opening the door, so maybe a robot handler
through a tiny door would be a good add on nowadays.

[Dakota]

http://www.ebay.com/sch/i.html?_trksid=p2050601.m570.l1313&_nkw=eppendorf+5415C&_sacat=0&_from=R40

I just got some Eppendorf 5415C centrifuges for really cheap.  $75 and $100 respectively.  They hit 15-16k max, though 13k is what most mobio protocols call for I think.   I had to wait a few days to find the right deal, but it was worth it.  Most are $200+ and some are in pretty shoddy condition, so be patient and diligent and you'll find a good deal on a nice looking machine.  Especially check out the ones with "Make an Offer" as a lot of times people want to move stock and will take a good deal.

You can get 5415's for $100 or less, but I'm 99% sure they do NOT come with a rotor cover, so they are loud.  The 5415C's do come with rotor covers, and are much more quiet, but use turn knobs like a cooking timer for the spin time.  The 5415D's are the digital ones and are really nice, but I havn't seen one sell for below $500, and they are usually $700-$1000

I wish I had purchased this for $125

http://www.ebay.com/itm/150948524512?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649

Lab resellers in my area just jack up the price so high, though I have found one decent looking place I still need to scope out.

Other than that, Ebay has re-affirmed the notion in my head that it really does have everything you need.  I've noticed Incubators and heat baths / water baths can be gotten for a pretty decent price on ebay.  Micro-pipettes are still kind of expensive for the nice ones, but I havn't put in the time to hunt for good deals.   

-50 or lower freezer would be nice, but I imagine shipping on that might be massive, plus I think they need a special dedicated 220V line?  I could be mistaken though.

Stir / hot plates + vortexers are also pretty cheap, $50 or less sometimes.

So in conclusion - EBAY!

[Derek]

You really don't need a -80 (or -50 even) for most things. I was keeping my strains in liquid nitrogen for the first while and it was cool to have around, but a prof at school told me he kept his E. coli strains in a -20 for all 7 years of his grad school and didn't have any problems. I've got strains that are 4 years old now from my -20 regular chest freezer and are still fine (no defrost cycle, of course.) The only thing I haven't been able to reliably do in the -20 is keep competent cells very good for more than a couple days. I usually just make them as I need them now with the PEG/DMSO protocol unless I need particularly high competency for something.

--Derek

On Monday, 3 December 2012 19:30:35 UTC-8, Nick F wrote:

-50 or lower freezer would be nice, but I imagine shipping on that might be massive, plus I think they need a special dedicated 220V line?  I could be mistaken though.

this can be achieved by replacing the gas with r22 or 134a, I'm having a friend (and expert) researching if a normal freezer can use this with som small mods like better insulation and stuff 

and i really digg your centrifuge part, that is almost cheaper than diy solution ^^ definitely gonna look into this when i get to that point in lab setup

[Josh Perfetto]

I've had much the same experience and while used to want a -80 I recently passed up a cheap one as I didn't want the energy expenditure and -20 was working for everything. However I now find myself needing to make a library so need cells of high transformation efficiency and all the commercial cells I find say they require -80. So questions:

1. Anyone have experience storing high competency commercial cells at -20?

2. What does the minimal liquid nitrogen environment look like? I suppose I need a dewar, how long will the liquid nitrogen last? Any tips on what to get?

-Josh

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[Derek]

I've stored university-lab made CCMB80 competent cells in a -20, I can dig back for my lab notebook if you want more accurate numbers, but as I recall on pUC19 they were high 10^6 range initially and degraded to high 10^3 or low 10^4 within a week in the -20.

LN2 minimal setup for me was a 15L transport dewar and an 80L storage dewar, I think I paid about $100 for the transport dewar and $250 for the storage dewar. It was costing me about $80 a month to keep it full, though. I think it was about $4 a litre for the LN2.

--Derek

[Chris Templeman]

as far a an incubator this summer we were incubating some microbial fuel cells in a broken fridge (provides good insulation, not plugged in obviously) and just a small incandescent light bulb.  We didn't even control the bulb state....just by trial found the right wattage of bulb at steady state that provided the right temp.

On Monday, December 3, 2012 5:08:13 PM UTC-5, Nick F wrote:

Sorry for reviving an old thread (and hello to you all, first post here)

During the next 6-8 months I'll be setting up a small home laboratory and it will all be done
at a low budget, which means that alot of the inventory will be home made.
first things of the plan is:

-50 freezer (will try to get as close to -70 as possible, but talking to an expert it requires the use of ammonium, not happy about that plus it's pricy)
-highspeed centrifuge
-autoclave
-incubator (will try and look into adding CO_2 control)

Suggestions?

So when making these things I'll provide my stepthrough for others to look at or perhabs follow if sufficient

[John Griessen]

On 12/04/2012 02:33 AM, Josh Perfetto wrote:
>how long will the liquid nitrogen last?

Longer inside the -20 freezer. Might make it too cold though.
Would too cold be a problem?

What about frozen CO2? Any cell users data at the temp dry ice
sublimates (−78.5 °C)?

[Eugen Leitl]

On Tue, Dec 04, 2012 at 09:24:00AM -0600, John Griessen wrote:
> On 12/04/2012 02:33 AM, Josh Perfetto wrote:
>> how long will the liquid nitrogen last?
>
> Longer inside the -20 freezer.

I doubt it would make a large difference, but if
anyone has the time to do the experiment, I would
be interested in the results.

Do not used a locked door on the fridge, but one which will
vent by popping the lid.

> Might make it too cold though.

No, because a dewar is rather good at what it does.

> Would too cold be a problem?
>
> What about frozen CO2? Any cell users data at the temp dry ice

> sublimates (-78.5 �C)?

You would have to store the dry ice in an insulated
box (e.g. styrofoam) to prevent air circulation.
There will be pressure buildup, so it's more suitable
for chest-type freezers which will close by gravity.

Do not stick your head inside your freezer with dry
ice in it, and inhale.

This goes doubly for liquid nitrogen -- you will pass
out suddenly, and fall in, and suffocate.