"M'Kenzie in the Kitchen - how to make a gel box"

[John Cumbers]

So a summary of the DIYBio home cooking show:

Proposed titles:   "M'Kenzie in the Kitchen - how to make a gel box"
Funders:
John C: $20
Jason M: $50
Biobarcamp: $100
Tito J: $50
Mac C: $100

So we're up to  $320 so far...

John






John Cumbers, Graduate Student
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.  
cell +1 (401) 523 8190, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA

On Thu, Oct 23, 2008 at 3:40 PM, Meredith L. Patterson <clon...@gmail.com> wrote:

FYI, TAP sells translucent amber-coloured acrylic, in 1/8" and 1/4" thicknesses.

http://www.tapplastics.com/shop/product.php?pid=341&

I like the blue LEDs idea too. I was just going to take an animator's
lightbox (a friend is getting rid of one) and replace the bulb with a
UV bulb, but LEDs are certainly cheaper.

--mlp

On Thu, Oct 23, 2008 at 3:34 PM, Tom Knight <t...@csail.mit.edu> wrote:
>
> If we're doing this, it would be good to do a version with a set of
> blue LEDs for under-gel illumination and an amber plastic cover for
> viewing the gel.  Both ethidium bromide and the sybr-safe and
> sybr-green gel bands would be very visible with this illumination.
> Done correctly, the illuminator and amber cover could be used to cut
> out bands as well, without the gel box being present.  We should
> experiment with LED and plexiglass color to determine which ones work.
> We might be able to arrange to use either the lab laser cutter or the
> water jet cutter to fabricate these in reasonable volumes.  Does anyone
> know the stability of the monel wire?  The pro boxes use platinum wire
> electrodes, which are essential indestructible, though a little pricey.
>
> On Oct 23, 2008, at 11:21 AM, Mackenzie Cowell wrote:
>
>> This thread is awesome :)  Let's build one like Meredith's and blog it
>> at DIYbio.org
>>
>> On Thu, Oct 23, 2008 at 12:27 AM, Peter Olson <pe...@peabo.com> wrote:
>>>
>>>  Source of monel wire:
>>>
>>> http://www.shopwiki.com/detail/
>>> d=20Lb_14%22_Monel_Wire_(30pc_per_tube)/jumpToFirst=t/
>>>
>>>  On Oct 22, 10:09 pm, "Meredith L. Patterson" <clonea...@gmail.com>
>>>  wrote:
>>> > I went to TAP Plastics in San Francisco and gave them the sizes
>>>  > specified in the PDF linked below. They cut the acrylic exactly to
>>>  > size (even the half-inch pegs), and the total came to just over
>>> $20.
>>>  > They will do mail-order. Putting the pieces together with acrylic
>>>  > cement took about an hour and a half. Do make sure to seal the
>>> seams
>>>  > on both sides -- the box needs to be watertight! The PDF shows a
>>>  > syringe with a curved plastic tip for the cement applicator. TAP
>>> has
>>>  > these, though I used a syringe with a blunt metal needle and that
>>>  > worked very well.
>>>  >
>>>  > If you spill some cement, just let it dry -- it will smear if you
>>> try
>>>  > to wipe it off.
>>>  >
>>>  > You could probably get away with just making the gel carrier from
>>>  > acrylic, and using a Tupperware and some terminal posts to seat the
>>>  > electrodes. If you go that route, you'll probably want to seal the
>>>  > holes for the electrode posts with hot glue or epoxy.
>>>  >
>>>  > They didn't have the Teflon, but it sounds like Mackenzie et al did
>>>  > pretty well with a used Charlie Card. You could also cut the comb
>>> from
>>>  > a Blockbuster Video card or any other smooth plastic wallet-sized
>>>  > card.
>>>  >
>>>  > Radio Shack's banana plugs aren't quite the right size, but I got
>>> it
>>>  > to fit together okay with a pair of stackable banana plugs and a
>>> pair
>>>  > of screw-in posts. I'll see if I can find my camera's battery and
>>> take
>>>  > a picture.
>>>  >
>>>  > Do use steel wire, as copper will stain the gel blue.
>>>  >
>>>  > --mlp
>>>  >
>>> > On Wed, Oct 22, 2008 at 6:08 PM, Jason Kelly
>>> <ja...@ginkgobioworks.com> wrote:
>>>  >
>>>  > > that's neat.  gel boxes are a complete rip off.
>>>  >
>>>  > > Meredith, which plastic supplier did you use - and can you post
>>> the
>>>  > > specifications you sent them?
>>>  >
>>>  > > thanks,
>>>  > > jason
>>>  >
>>>  > > p.s. apologies for the several emails to follow in a row --
>>>  > > apparently, i wasnt properly registered for the list so was just
>>>  > > sending mail into the ether for last week or two.
>>>  >
>>>  > > On Tue, Oct 21, 2008 at 3:28 PM, Meredith L. Patterson
>>> > > <clonea...@gmail.com> wrote:
>>>  >
>>>  > >> The University of Utah's gel box is quite easy to build (well,
>>> to be
>>>  > >> fair, I did get the plastic supplier to cut the pieces for me)
>>> and
>>>  > >> cost about $30 in parts all told.
>>>  >
>>>  > >>http://learn.genetics.utah.edu/content/labs/gel/gelchamber/
>>>  >
>>>  > >> --mlp
>>>  >
>>> > >> On Tue, Oct 21, 2008 at 12:22 PM, Mackenzie Cowell
>>> <macow...@gmail.com> wrote:
>>>  > >>> Great link, Jason.
>>>  >
>>>  > >>> I did a quick search for proposals that included the word
>>> "DNA".  The
>>>  > >>> average donation requested was something like $400.  This
>>> usually was for a
>>>  > >>> thermocycler and and some kind of PCR reagents or DNA
>>> extraction kit.
>>>  >
>>>  > >>> I agree wholeheartedly that we could do way better than $400.
>>>  >
>>>  > >>> Additionally, many of the teachers cited the physical,
>>> hands-on experience
>>>  > >>> that hardware provides as the main reason for wanting it for
>>> their class.
>>>  > >>> But think about how cool it would be for kids to be *building*
>>> their own
>>>  > >>> tools and then using them to do PCR.  Man, I for one felt like
>>> I got a
>>>  > >>> better understanding of gel electrophoresis when we tried to
>>> do it for $20
>>>  > >>> with tupperware and agar-agar.
>>>  >
>>>  > >>> So I think there is a huge potential for us to develop a
>>> robust, diy biotech
>>>  > >>> lesson plans for high school biology classes.
>>>  >
>>>  > >>> We could start with the gel electrophoresis protocol.
>>>  >
>>>  > >>> Mac
>>>  >
>>> > >>> On Mon, Oct 20, 2008 at 3:08 PM, Jason Morrison
>>> <jason.p.morri...@gmail.com>
>>> > >>> wrote:
>>>  >
>>>  > >>>> The following might be interesting for learning what kinds of
>>>  > >>>> supplies/labs/equipment should be cheaper to help promote
>>> biology research
>>>  > >>>> in schools, and I think high schools' budgets are interesting
>>> to consider,
>>>  > >>>> when we are considering DIY budgetary constraints.
>>>  >
>>> >
>>> >>>>http://www.donorschoose.org/donors/search.html?
>>> sourceid=qs&keywords=b...
>>> >
>>>  > >>>> "DonorsChoose.org is a simple way to provide students in need
>>> with
>>>  > >>>> resources that our public schools often lack. At this
>>> not-for-profit web
>>>  > >>>> site, teachers submit project proposals for materials or
>>> experiences their
>>>  > >>>> students need to learn. These ideas become classroom reality
>>> when concerned
>>>  > >>>> individuals, whom we call Citizen Philanthropists, choose
>>> projects to fund."
>>>  >
>>>  > >>>> Example:
>>>  >
>>> >>>>http://www.donorschoose.org/donors/proposal.html?id=195775&zone=0
>>>  > >>>> $284 for 4 DNA extraction kits?  Not sure what's included,
>>> perhaps
>>> >
>>> >>>>www.carolina.com/text/teacherresources/instructions/biotech/
>>> dna_neckl...
>>> > >>>> ?
>>>  >
>>>  > >>>> I think we can do better!
>>>  >
>>>  > >>>> -Jason
>>>  >
>>>  > >>>> --
>>>  > >>>> Jason Morrison
>>> > >>>> jason.p.morri...@gmail.com
>>> > >>>>http://jayunit.net
>>>  > >>>> (585) 216-5657
>>>
>>
>>
>>  >
>
>
> >
>

[Norman Wang]

I'll put in $40.

On Oct 24, 6:40 am, "John Cumbers" <johncumb...@gmail.com> wrote:
> So a summary of the DIYBio home cooking show:
>
> Proposed titles:   "M'Kenzie in the Kitchen - how to make a gel box"
> Funders:
> John C: $20
> Jason M: $50
> Biobarcamp: $100
> Tito J: $50
> Mac C: $100
>
> So we're up to  $320 so far...
>
> John
>
> John Cumbers, Graduate Student
> NASA Ames Research Center
> Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
> cell +1 (401) 523 8190, fax +1 (650) 604-1088
>
> Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
> Brown University, Box G-W Providence, RI, 02912, USA
>
> On Thu, Oct 23, 2008 at 3:40 PM, Meredith L. Patterson

> <clonea...@gmail.com>wrote:

[Jim H]

I can't help imagining....

Mac in an apron, thick framed black glasses, 4 day beard growth,
spatula in hand....

Priceless

[Jason Kelly]

im in for 25 bucks, but it's contingent on mac wearing an apron.

jason

[Jason Morrison]

Hah Jason that $25 should go straight to a diybio-logo'd apron ;)

--
http://jayunit.net
(585) 216-5657
(Sent from my mobile)

On Oct 24, 2008, at 10:56 PM, "Jason Kelly" <ja...@ginkgobioworks.com>
wrote:

>

[Josh Perfetto]

Would be happy to chip in $50 - that NanoDrop video was great :)

-Josh

[Alec Nielsen]

I'd love to see this too. Count me in for $40.

 

Alec

[JonathanCline]

I would also appreciate seeing such a video series
- though I wanted to throw one idea out there.

It should be possible to get industry itself to host
& present both the content and the materials for a
biotech-how-to show. A healthy 1/3 of industry
respondents to industry survey have indicated they
would act as guest speaker to a class, AND host
worksite visits, AND donate equipment for
educational purposes, AND help develop
career-preparatory programs for biotech technicians.

Industry, in general, usually enjoys small donations
to dedicated groups in niche markets which
ultimately grow the markets and thus make industry
more money. It's a symbiotic relationship.

So if industry were to present the class, then you
video it yourselves, and I don't see that there is
any real cash involved (only time to attend the
class, and time to do video production -- which
amounts to half a dozen hours).


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

On Oct 25, 12:40 am, "John Cumbers" <johncumb...@gmail.com> wrote:
> So a summary of the DIYBio home cooking show:
>
> Proposed titles:   "M'Kenzie in the Kitchen - how to make a gel box"
> Funders:
> John C: $20
> Jason M: $50
> Biobarcamp: $100
> Tito J: $50
> Mac C: $100
>
> So we're up to  $320 so far...
>
> John
>
> John Cumbers, Graduate Student
> NASA Ames Research Center
> Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
> cell +1 (401) 523 8190, fax +1 (650) 604-1088
>
> Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
> Brown University, Box G-W Providence, RI, 02912, USA
>
> On Thu, Oct 23, 2008 at 3:40 PM, Meredith L. Patterson

> <clonea...@gmail.com>wrote:

[Jim H]

At Life Technologies (and ironically it appears that Invitrogen+ABI
merger is going to be re-renamed back to Life Technologies), I used to
go out to local high schools and talk about careers in biotech and we
had a whole training center for our customers. Pretty sure IVGN got
rid of that concept, or at least moved it to Carlsbad. The problem is
that a lot of Industrial activity is monitored by the lawyers, who get
freaked out by liability issues.

That said, NCI-Frederick has a program for local HS students to work
in the labs and most local colleges have internship programs to work
at local industry. The big guys (like IVGN, MedImmune and Lonza in my
hometown), shy away from this becasue of the liability issues, but we
have 2 interns now and I am think ing about taking on another in the
winter.

The other hook with having industry involved is that this kind of
activity is automatically handed off to the Marketing guys. If you
have never worked in industry, it'll be hard to understand how
"threatened" the marketing guys get when you actually let someone in
the lab have face to face contact with a customer.

OK, I'll get off my rant. Stupid people...

[Mackenzie Cowell]

Jon,

Could you point us towards the results of the survey you mentioned?  Or was it more of a "raise your hand if..." type of thing that you informally conducted?

thanks,
Mac

[Jim H]

Mac,

I spoke with a company that can cut the plastic for DIY gel boxes.
The same ones who made the old BRL gel apparatus. He recommended
making the parts with interlocking, "tongue & groove" where they'll be
glued to make it easier. Apparently, this is not as easy as it sounds
to glue two pieces of acrylic plastic together and make a liquid tight
seal.

He said it would be less than $1.00 per piece, assuming some volume of
about 100-200 pieces per order.


Would you like me to keep going on this?

On Nov 6, 3:24 pm, "Mackenzie Cowell" <m...@diybio.org> wrote:
> Jon,
>
> Could you point us towards the results of the survey you mentioned?  Or was
> it more of a "raise your hand if..." type of thing that you informally
> conducted?
>
> thanks,
> Mac
>

[JonathanCline]

On Nov 7, 4:24 am, "Mackenzie Cowell" <m...@diybio.org> wrote:
> Jon,
>
> Could you point us towards the results of the survey you mentioned?  Or was
> it more of a "raise your hand if..." type of thing that you informally
> conducted?
>
> thanks,
> Mac

The results are based on a "funded industry survey" not "raise your
hand if..." -- so there's some basis to the idea..

I've seen a few similar pubs, however this one has a good breakdown,
it is from last year. Most of the white papers I've seen are designed
for spurring funding (public or private) or academic interest so the
results may be on the optimistic side, and any survey has some bias.
Anyway here's the relevant quote:

Biotechnology/Bioscience Training & Workforce Needs Assessment
© Ventura County Workforce Investment Board,
Central Coast Biotechnology Center,
Moorpark College & Ventura College
2007
http://www.ccbcweb.net/pdf/Biotech_Final_Report_2007.pdf

EXECUTIVE SUMMARY

BIOTECHNOLOGY/BIOSCIENCE TRAINING & WORKFORCE NEEDS ASSESSMENT


The Ventura County Workforce Investment Board, The Central Coast
Biotechnology Center, Moorpark College and
Ventura College contracted with The Resource Group–a Southern
California-based market research firm–to assist with
conducting an assessment of biotechnology and bioscience firms in San
Luis Obispo County, Santa Barbara County,
Ventura County and portions of both Kern and Los Angeles Counties.
The 2006 Biotechnology/Bioscience Training and
Workforce Needs Assessment project brought together these key
providers to assess the needs of companies to ensure
local training and workforce development programs continue to be
relevant to the workplace and to the changing
requirements of businesses in the biotechnology and bioscience
industries.

A total of 33 biotechnology/bioscience businesses participated in the
survey project by returning a completed survey.
Responding companies provided a detailed look at their business, the
characteristics of their workforce, the specific skills
and training needed by current and future employees, preferred
training delivery methods and their interest in career
preparation activities. Following is a presentation of the key trends
and issues expressed by these responding companies.


[[ excerpts: ]]
50% of surveyed area employers indicate there are industry-specific
skills needed by their current workforce
Top skills needed by current employees: engineering, equipment
calibration, field biology,
phlebotomy

73% of responding organizations employ 25 or fewer employees
65% of responding employers indicate individuals do not need more
than AA/AS degree for entry-level
production jobs
63% of businesses indicate some interest in low-cost, effective
training for staff
63% of responding organizations currently offer training programs to
staff
71% of those that offer training programs to staff have in-house
training resources
42% of responding firms prefer training at a college or other
district training sites
58% of those interested in training at a college or other district
site prefer such training on weekday evenings
33% would be interested in on-site training
69% interested in on-site training prefer weekdays during the day
78% of businesses responding to the survey indicate there are
specific skills and abilities they would like to see
in a pool of applicants for their industry
Top skills needed for future employees: computer, basic skills,
chemistry, engineering, lab skills
33% of responding organizations indicated an interest in serving as a
guest speaker to a class or offering course
instruction
24% of firms have an interest in hosting worksite visits for
students
18% each would be willing to donate equipment and materials, offer
worksite internships or provide entry-level
jobs for screened program graduates


......

So 1/3 are open to visiting as a guest speaker, 1/4 are open to
hosting students onsite, 1/5 are open to donating equipment &
materials for worksite internships (translation: "if it helps me hire
someone highly qualified next year, then I'll donate a couple bucks
now.").

But we already knew that, right? Researchers work in bio because they
enjoy bio and are willing to talk to others who enjoy bio (usually).
Otherwise they'd be working in mortgage lending for bigger bonuses
(well maybe not anymore, lol).

I agree with Jim H too, approach it the right way, otherwise might get
bogged down / shot down in executive committee. Go grassroots, thru
the backdoor, ask a researcher on the inside to lend an "informal
talk" (aka: "hey, you wanna come tell us / teach us about this cool
technology?") rather than the mkting side for "an official sponsorship
& training for a diy foundation". If going to the mkting side, then
approaching it as a "web 2.0 sales positioning using viral marketing
for your company" might sell the idea, depends on the company though.