Hive13 Research Labs - Biology Division
3 views
Skip to first unread message
XiO2
Oct 26, 2009, 8:54:30 PM10/26/09
to The Cincinnati Hackerspace Project
Please see the email correspondence I had with a certain Tito
Jankowski, founder of Pearl Biotech at the bottom of this message for
more information. Sorry this is so jumbled, I'm still working out my
plan. Feel free to add to this
------------------------------------------------------------------------------------------------
For the future Hive13 Research Labs - Biology Division:
Open Source Gel Electrophoresis Kit
Assembled: $200
UnAssembled: $125 (Of course I'll be getting this one)
http://www.pearlbiotech.com/
This, among other things like a good microscope with nice camera
functionality for use with a PC, a PCR Thermal Cycler (this can be
built), and more equipment that can surely be built DIY style
(Biohacking is the proper term I suppose).
My first set of goals was to splice GFP (Glowing Fluorescent Protein)
with some form of vegetation, making it naturally fluoresce. This can
be useful for detecting the activation or status of various genes, and
also the presence of any number of chemicals (please forgive my
nonstandard vernacular, I'm still picking up the lingo).
This equipment will be useful for any of the algae experiments I know
people have expressed interest in. The photo-bio-reactor being one of
them. Perhaps we could increase lipid production or alter the type of
lipid it produces, or even what it produces altogether. Perhaps
altering basic bacterial structures as well, I know ecoli has been
sequenced heavily, having only around 5000 base pairs. A lot of this
stuff has been done in garages for years, and I know there is a lot of
info out there now. I'm reading and listening to basic biology
lectures to get up to snuff on everything before I/we invest any
funding.
Let me know if anyone is interested, and forward this on to anyone in
the group who might have any interest in possibly going in on any
equipment or parts for eventual DIY equipment. I'll be creating a more
detailed wiki page with some of my suggested goals.
Some Links:
http://diybio.org/ - DIYbio is an organization dedicated to making
biology an accessible pursuit for citizen scientists, amateur
biologists, and DIY biological engineers who value openness and
safety.
http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/ - DIYbio at
Noisebridge hackerspace in San Fransisco
EMAIL CORRESPONDENCE
------------------------------------------------------------------------------------------------------------------
Hey Justin,
Great to hear from you, I'm happy to see that hackerspaces are
springing up all across the world!
A Pearl Gel box kit that puts your soldering iron and some silicone
glue to work is $125, and the assembled box is $199 - Paypal link. The
gluing and soldering steps are fun and teach the user about how a gel
box works, and will take a new builder about 2 hours to finish.
Let me know what other questions you have!
Tito
Founder, Pearl Biotech
On Mon, Oct 26, 2009 at 10:51 AM, Justin Sovine <xi...@hive13.org>
wrote:
>
> To whom it may concern,
>
> We here at the cincinnati hackerspace Hive13 (hive13.org / wiki.hive13.org), are setting up a basic biology lab and have been interested in the possibility of building a gel electrophoresis system, among other things. When I stumbled upon your site I was immediately enthused. Is there a price drop for the unassembled kit, as opposed to the normally assembled version?
>
> Also, are there any other sites promoting open source biohacking that you could recommend as we are definitely interested in being a part of a larger open source DIY community.
>
> Thank you for your time!
>
> Justin (XiO2)
> Hive13 Labs
> Alternate Energies / Biology
----------------------------------------------------------------------------------------------------------------------
Jankowski, founder of Pearl Biotech at the bottom of this message for
more information. Sorry this is so jumbled, I'm still working out my
plan. Feel free to add to this
------------------------------------------------------------------------------------------------
For the future Hive13 Research Labs - Biology Division:
Open Source Gel Electrophoresis Kit
Assembled: $200
UnAssembled: $125 (Of course I'll be getting this one)
http://www.pearlbiotech.com/
This, among other things like a good microscope with nice camera
functionality for use with a PC, a PCR Thermal Cycler (this can be
built), and more equipment that can surely be built DIY style
(Biohacking is the proper term I suppose).
My first set of goals was to splice GFP (Glowing Fluorescent Protein)
with some form of vegetation, making it naturally fluoresce. This can
be useful for detecting the activation or status of various genes, and
also the presence of any number of chemicals (please forgive my
nonstandard vernacular, I'm still picking up the lingo).
This equipment will be useful for any of the algae experiments I know
people have expressed interest in. The photo-bio-reactor being one of
them. Perhaps we could increase lipid production or alter the type of
lipid it produces, or even what it produces altogether. Perhaps
altering basic bacterial structures as well, I know ecoli has been
sequenced heavily, having only around 5000 base pairs. A lot of this
stuff has been done in garages for years, and I know there is a lot of
info out there now. I'm reading and listening to basic biology
lectures to get up to snuff on everything before I/we invest any
funding.
Let me know if anyone is interested, and forward this on to anyone in
the group who might have any interest in possibly going in on any
equipment or parts for eventual DIY equipment. I'll be creating a more
detailed wiki page with some of my suggested goals.
Some Links:
http://diybio.org/ - DIYbio is an organization dedicated to making
biology an accessible pursuit for citizen scientists, amateur
biologists, and DIY biological engineers who value openness and
safety.
http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/ - DIYbio at
Noisebridge hackerspace in San Fransisco
EMAIL CORRESPONDENCE
------------------------------------------------------------------------------------------------------------------
Hey Justin,
Great to hear from you, I'm happy to see that hackerspaces are
springing up all across the world!
A Pearl Gel box kit that puts your soldering iron and some silicone
glue to work is $125, and the assembled box is $199 - Paypal link. The
gluing and soldering steps are fun and teach the user about how a gel
box works, and will take a new builder about 2 hours to finish.
Let me know what other questions you have!
Tito
Founder, Pearl Biotech
On Mon, Oct 26, 2009 at 10:51 AM, Justin Sovine <xi...@hive13.org>
wrote:
>
> To whom it may concern,
>
> We here at the cincinnati hackerspace Hive13 (hive13.org / wiki.hive13.org), are setting up a basic biology lab and have been interested in the possibility of building a gel electrophoresis system, among other things. When I stumbled upon your site I was immediately enthused. Is there a price drop for the unassembled kit, as opposed to the normally assembled version?
>
> Also, are there any other sites promoting open source biohacking that you could recommend as we are definitely interested in being a part of a larger open source DIY community.
>
> Thank you for your time!
>
> Justin (XiO2)
> Hive13 Labs
> Alternate Energies / Biology
----------------------------------------------------------------------------------------------------------------------
XiO2
Oct 26, 2009, 8:56:52 PM10/26/09
to The Cincinnati Hackerspace Project
This can also tie in with the custom inkjet printer apparatus,
possibly in being a decent gene sequencer once modified properly:
http://www.physorg.com/news173950754.html
Justin (XiO2)
On Oct 26, 8:54 pm, XiO2 <voxcrys...@gmail.com> wrote:
> Please see the email correspondence I had with a certain Tito
> Jankowski, founder of Pearl Biotech at the bottom of this message for
> more information. Sorry this is so jumbled, I'm still working out my
> plan. Feel free to add to this
> ------------------------------------------------------------------------------------------------
>
> For the future Hive13 Research Labs - Biology Division:
>
> Open Source Gel Electrophoresis Kit
> Assembled: $200
> UnAssembled: $125 (Of course I'll be getting this one)http://www.pearlbiotech.com/
possibly in being a decent gene sequencer once modified properly:
http://www.physorg.com/news173950754.html
Justin (XiO2)
On Oct 26, 8:54 pm, XiO2 <voxcrys...@gmail.com> wrote:
> Please see the email correspondence I had with a certain Tito
> Jankowski, founder of Pearl Biotech at the bottom of this message for
> more information. Sorry this is so jumbled, I'm still working out my
> plan. Feel free to add to this
> ------------------------------------------------------------------------------------------------
>
> For the future Hive13 Research Labs - Biology Division:
>
> Open Source Gel Electrophoresis Kit
> Assembled: $200
>
> This, among other things like a good microscope with nice camera
> functionality for use with a PC, a PCR Thermal Cycler (this can be
> built), and more equipment that can surely be built DIY style
> (Biohacking is the proper term I suppose).
>
> My first set of goals was to splice GFP (Glowing Fluorescent Protein)
> with some form of vegetation, making it naturally fluoresce. This can
> be useful for detecting the activation or status of various genes, and
> also the presence of any number of chemicals (please forgive my
> nonstandard vernacular, I'm still picking up the lingo).
>
> This equipment will be useful for any of the algae experiments I know
> people have expressed interest in. The photo-bio-reactor being one of
> them. Perhaps we could increase lipid production or alter the type of
> lipid it produces, or even what it produces altogether. Perhaps
> altering basic bacterial structures as well, I know ecoli has been
> sequenced heavily, having only around 5000 base pairs. A lot of this
> stuff has been done in garages for years, and I know there is a lot of
> info out there now. I'm reading and listening to basic biology
> lectures to get up to snuff on everything before I/we invest any
> funding.
>
> Let me know if anyone is interested, and forward this on to anyone in
> the group who might have any interest in possibly going in on any
> equipment or parts for eventual DIY equipment. I'll be creating a more
> detailed wiki page with some of my suggested goals.
>
> Some Links:http://diybio.org/- DIYbio is an organization dedicated to making
> This, among other things like a good microscope with nice camera
> functionality for use with a PC, a PCR Thermal Cycler (this can be
> built), and more equipment that can surely be built DIY style
> (Biohacking is the proper term I suppose).
>
> My first set of goals was to splice GFP (Glowing Fluorescent Protein)
> with some form of vegetation, making it naturally fluoresce. This can
> be useful for detecting the activation or status of various genes, and
> also the presence of any number of chemicals (please forgive my
> nonstandard vernacular, I'm still picking up the lingo).
>
> This equipment will be useful for any of the algae experiments I know
> people have expressed interest in. The photo-bio-reactor being one of
> them. Perhaps we could increase lipid production or alter the type of
> lipid it produces, or even what it produces altogether. Perhaps
> altering basic bacterial structures as well, I know ecoli has been
> sequenced heavily, having only around 5000 base pairs. A lot of this
> stuff has been done in garages for years, and I know there is a lot of
> info out there now. I'm reading and listening to basic biology
> lectures to get up to snuff on everything before I/we invest any
> funding.
>
> Let me know if anyone is interested, and forward this on to anyone in
> the group who might have any interest in possibly going in on any
> equipment or parts for eventual DIY equipment. I'll be creating a more
> detailed wiki page with some of my suggested goals.
>
> biology an accessible pursuit for citizen scientists, amateur
> biologists, and DIY biological engineers who value openness and
> safety.
>
> http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/- DIYbio at
> biologists, and DIY biological engineers who value openness and
> safety.
>
> Noisebridge hackerspace in San Fransisco
>
> EMAIL CORRESPONDENCE
> ------------------------------------------------------------------------------------------------------------------
> Hey Justin,
> Great to hear from you, I'm happy to see that hackerspaces are
> springing up all across the world!
>
> A Pearl Gel box kit that puts your soldering iron and some silicone
> glue to work is $125, and the assembled box is $199 - Paypal link. The
> gluing and soldering steps are fun and teach the user about how a gel
> box works, and will take a new builder about 2 hours to finish.
>
> Let me know what other questions you have!
>
> Tito
> Founder, Pearl Biotech
>
> On Mon, Oct 26, 2009 at 10:51 AM, Justin Sovine <x...@hive13.org>
>
> EMAIL CORRESPONDENCE
> ------------------------------------------------------------------------------------------------------------------
> Hey Justin,
> Great to hear from you, I'm happy to see that hackerspaces are
> springing up all across the world!
>
> A Pearl Gel box kit that puts your soldering iron and some silicone
> glue to work is $125, and the assembled box is $199 - Paypal link. The
> gluing and soldering steps are fun and teach the user about how a gel
> box works, and will take a new builder about 2 hours to finish.
>
> Let me know what other questions you have!
>
> Tito
> Founder, Pearl Biotech
>
XiO2
Oct 26, 2009, 8:58:34 PM10/26/09
to The Cincinnati Hackerspace Project
Also,
http://2009.igem.org/About
The International Genetically Engineered Machine competition (iGEM) is
the premiere undergraduate Synthetic Biology competition. Student
teams are given a kit of biological parts at the beginning of the
summer from the Registry of Standard Biological Parts. Working at
their own schools over the summer, they use these parts and new parts
of their own design to build biological systems and operate them in
living cells. This project design and competition format is an
exceptionally motivating and effective teaching method.
Justin (XiO2)
> > Some Links:http://diybio.org/-DIYbio is an organization dedicated to making
http://2009.igem.org/About
The International Genetically Engineered Machine competition (iGEM) is
the premiere undergraduate Synthetic Biology competition. Student
teams are given a kit of biological parts at the beginning of the
summer from the Registry of Standard Biological Parts. Working at
their own schools over the summer, they use these parts and new parts
of their own design to build biological systems and operate them in
living cells. This project design and competition format is an
exceptionally motivating and effective teaching method.
Justin (XiO2)
> > biology an accessible pursuit for citizen scientists, amateur
> > biologists, and DIY biological engineers who value openness and
> > safety.
>
> >http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/-DIYbio at
> > biologists, and DIY biological engineers who value openness and
> > safety.
>
Karl Wilbur
Oct 27, 2009, 1:13:36 AM10/27/09
to cincihac...@googlegroups.com
Chris Anderson
Oct 27, 2009, 8:59:51 AM10/27/09
to cincihac...@googlegroups.com
wow, this is really cool.
not sure how i can help, but you have my sword.--
~chris
kil...@hobbiton.org
http://kill-9.hobbiton.org
I tried to break down the essential position for him. "You're arguing for a universe with fewer waffles in it," I said. "I'm prepared to call that cowardice." --Tycho Brahe, Penny Arcade
not sure how i can help, but you have my sword.
~chris
kil...@hobbiton.org
http://kill-9.hobbiton.org
I tried to break down the essential position for him. "You're arguing for a universe with fewer waffles in it," I said. "I'm prepared to call that cowardice." --Tycho Brahe, Penny Arcade
XiO2
Oct 27, 2009, 10:56:24 AM10/27/09
to The Cincinnati Hackerspace Project
A few links to whole courses worth of video lectures I found. Amazing
what is available for free nowadays. If I'm not mistaken, a lot of
what goes on at Berkely is available online even if you don't take the
class.
http://www.learnerstv.com/course.php?cat=Biology
http://freescienceonline.blogspot.com/2006/08/chemistry-biology-and-life-sciences.html
http://webcast.berkeley.edu/courses.php
More updates as I come up w/ them
On Oct 27, 8:59 am, Chris Anderson <deth...@gmail.com> wrote:
> wow, this is really cool.
>
> not sure how i can help, but you have my sword.
>
>
>
> On Tue, Oct 27, 2009 at 1:13 AM, Karl Wilbur <k...@karlwilbur.net> wrote:
> > I am interested.
>
> >>http://diybio.org/- DIYbio is an organization dedicated to making
>
> --
> ~chris
> kil...@hobbiton.orghttp://kill-9.hobbiton.org
what is available for free nowadays. If I'm not mistaken, a lot of
what goes on at Berkely is available online even if you don't take the
class.
http://www.learnerstv.com/course.php?cat=Biology
http://freescienceonline.blogspot.com/2006/08/chemistry-biology-and-life-sciences.html
http://webcast.berkeley.edu/courses.php
More updates as I come up w/ them
On Oct 27, 8:59 am, Chris Anderson <deth...@gmail.com> wrote:
> wow, this is really cool.
>
> not sure how i can help, but you have my sword.
>
>
>
> On Tue, Oct 27, 2009 at 1:13 AM, Karl Wilbur <k...@karlwilbur.net> wrote:
> > I am interested.
>
> >> biology an accessible pursuit for citizen scientists, amateur
> >> biologists, and DIY biological engineers who value openness and
> >> safety.
>
> >>http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/- DIYbio at
> >> biologists, and DIY biological engineers who value openness and
> >> safety.
>
> >> Noisebridge hackerspace in San Fransisco
>
> >> EMAIL CORRESPONDENCE
>
> >> ------------------------------------------------------------------------------------------------------------------
> >> Hey Justin,
> >> Great to hear from you, I'm happy to see that hackerspaces are
> >> springing up all across the world!
>
> >> A Pearl Gel box kit that puts your soldering iron and some silicone
> >> glue to work is $125, and the assembled box is $199 - Paypal link. The
> >> gluing and soldering steps are fun and teach the user about how a gel
> >> box works, and will take a new builder about 2 hours to finish.
>
> >> Let me know what other questions you have!
>
> >> Tito
> >> Founder, Pearl Biotech
>
> >> On Mon, Oct 26, 2009 at 10:51 AM, Justin Sovine <x...@hive13.org>
>
> >> EMAIL CORRESPONDENCE
>
> >> ------------------------------------------------------------------------------------------------------------------
> >> Hey Justin,
> >> Great to hear from you, I'm happy to see that hackerspaces are
> >> springing up all across the world!
>
> >> A Pearl Gel box kit that puts your soldering iron and some silicone
> >> glue to work is $125, and the assembled box is $199 - Paypal link. The
> >> gluing and soldering steps are fun and teach the user about how a gel
> >> box works, and will take a new builder about 2 hours to finish.
>
> >> Let me know what other questions you have!
>
> >> Tito
> >> Founder, Pearl Biotech
>
> >> wrote:
>
> >> > To whom it may concern,
>
> >> > We here at the cincinnati hackerspace Hive13 (hive13.org /
> >> wiki.hive13.org), are setting up a basic biology lab and have been
> >> interested in the possibility of building a gel electrophoresis system,
> >> among other things. When I stumbled upon your site I was immediately
> >> enthused. Is there a price drop for the unassembled kit, as opposed to the
> >> normally assembled version?
>
> >> > Also, are there any other sites promoting open source biohacking that
> >> you could recommend as we are definitely interested in being a part of a
> >> larger open source DIY community.
>
> >> > Thank you for your time!
>
> >> > Justin (XiO2)
> >> > Hive13 Labs
> >> > Alternate Energies / Biology
>
> >> ----------------------------------------------------------------------------------------------------------------------
>
> > --
> > Karl Wilbur
> > 513-322-2481
> > k...@karlwilbur.net
>
> >> > To whom it may concern,
>
> >> > We here at the cincinnati hackerspace Hive13 (hive13.org /
> >> wiki.hive13.org), are setting up a basic biology lab and have been
> >> interested in the possibility of building a gel electrophoresis system,
> >> among other things. When I stumbled upon your site I was immediately
> >> enthused. Is there a price drop for the unassembled kit, as opposed to the
> >> normally assembled version?
>
> >> > Also, are there any other sites promoting open source biohacking that
> >> you could recommend as we are definitely interested in being a part of a
> >> larger open source DIY community.
>
> >> > Thank you for your time!
>
> >> > Justin (XiO2)
> >> > Hive13 Labs
> >> > Alternate Energies / Biology
>
> >> ----------------------------------------------------------------------------------------------------------------------
>
> > --
> > Karl Wilbur
> > 513-322-2481
>
> --
> ~chris
> kil...@hobbiton.orghttp://kill-9.hobbiton.org
Craig
Oct 27, 2009, 11:07:11 AM10/27/09
to cincihac...@googlegroups.com
So will we be able to make glowing puppies?
(Reference: http://www.newscientist.com/article/dn17003-fluorescent-puppy-is-worlds-first-transgenic-dog.html)
hehe
:D
(Reference: http://www.newscientist.com/article/dn17003-fluorescent-puppy-is-worlds-first-transgenic-dog.html)
hehe
:D
Avishaan Sethi
Oct 27, 2009, 1:42:57 PM10/27/09
to The Cincinnati Hackerspace Project
Wow, really interesting stuff. Count me in. When are you getting the
Gel electrophoresis kit?
On Oct 27, 11:07 am, Craig <agent.cr...@gmail.com> wrote:
> So will we be able to make glowing puppies?
>
> (Reference:http://www.newscientist.com/article/dn17003-fluorescent-puppy-is-worl...)
>
> hehe
>
> :D
> >> >>http://diybio.org/-DIYbio is an organization dedicated to making
Gel electrophoresis kit?
On Oct 27, 11:07 am, Craig <agent.cr...@gmail.com> wrote:
> So will we be able to make glowing puppies?
>
>
> hehe
>
> :D
>
> On Tue, Oct 27, 2009 at 10:56 AM, XiO2 <voxcrys...@gmail.com> wrote:
>
> > A few links to whole courses worth of video lectures I found. Amazing
> > what is available for free nowadays. If I'm not mistaken, a lot of
> > what goes on at Berkely is available online even if you don't take the
> > class.
>
> >http://www.learnerstv.com/course.php?cat=Biology
> >http://freescienceonline.blogspot.com/2006/08/chemistry-biology-and-l...
> On Tue, Oct 27, 2009 at 10:56 AM, XiO2 <voxcrys...@gmail.com> wrote:
>
> > A few links to whole courses worth of video lectures I found. Amazing
> > what is available for free nowadays. If I'm not mistaken, a lot of
> > what goes on at Berkely is available online even if you don't take the
> > class.
>
> >http://www.learnerstv.com/course.php?cat=Biology
> >> >> biology an accessible pursuit for citizen scientists, amateur
> >> >> biologists, and DIY biological engineers who value openness and
> >> >> safety.
>
> >> >>http://diybio.org/2009/05/03/diybio-salon-at-noisebridge/-DIYbio at
> >> >> biologists, and DIY biological engineers who value openness and
> >> >> safety.
>
Dave Menninger
Oct 27, 2009, 3:22:30 PM10/27/09
to cincihac...@googlegroups.com
We could try to make this one that's up on thingiverse.com using the MakerBot:
http://www.thingiverse.com/thing:985
See also: http://www.shapeways.com/shops/labsfromfabs and
http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/
~Dave
http://www.thingiverse.com/thing:985
See also: http://www.shapeways.com/shops/labsfromfabs and
http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/
~Dave
XiO2
Oct 27, 2009, 10:02:28 PM10/27/09
to The Cincinnati Hackerspace Project
That would be the win, definitely a sweet idea. But look at the shiny!
http://www.pearlbiotech.com/wp-content/uploads/2009/10/gel_box1.jpg
-Justin
P.S. Wonder if we could do that with this and other equipment? If only
temporarily :D. How big of an object can we make again?
On Oct 27, 3:22 pm, Dave Menninger <dave.mennin...@gmail.com> wrote:
> We could try to make this one that's up on thingiverse.com using the MakerBot:
>
> http://www.thingiverse.com/thing:985
>
> See also:http://www.shapeways.com/shops/labsfromfabs andhttp://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and...
> >> >> >>http://diybio.org/-DIYbiois an organization dedicated to making
http://www.pearlbiotech.com/wp-content/uploads/2009/10/gel_box1.jpg
-Justin
P.S. Wonder if we could do that with this and other equipment? If only
temporarily :D. How big of an object can we make again?
On Oct 27, 3:22 pm, Dave Menninger <dave.mennin...@gmail.com> wrote:
> We could try to make this one that's up on thingiverse.com using the MakerBot:
>
> http://www.thingiverse.com/thing:985
>
>
> ~Dave
>
> On Tue, Oct 27, 2009 at 1:42 PM, Avishaan Sethi
>
> ~Dave
>
> On Tue, Oct 27, 2009 at 1:42 PM, Avishaan Sethi
>
XiO2
Oct 27, 2009, 10:08:42 PM10/27/09
to The Cincinnati Hackerspace Project
Not sure when I plan on getting much equipment, I was hoping that if
enough people got interested we could take up a donations thing on
that one site (it is escaping me atm), at least until the next month
or so. It would of course then be property of the hive.
We need a lot of basic stuff too, like a nice microscope w/ camera
capability, and various other basic equipment (gloves, chemicals, pvr
thermal cycler, spectrometer). Not that we necessarily need it all to
begin working on something cool. Algae strains and various bacteria
would be cool to start working with. Maybe watching a few lectures on
the projector for those interested. I only recently started
accumulating data, maybe we should start a wiki w/ interested members
listed so we know who to keep in the circle?
-Justin
> > >> >>http://diybio.org/-DIYbiois an organization dedicated to making
enough people got interested we could take up a donations thing on
that one site (it is escaping me atm), at least until the next month
or so. It would of course then be property of the hive.
We need a lot of basic stuff too, like a nice microscope w/ camera
capability, and various other basic equipment (gloves, chemicals, pvr
thermal cycler, spectrometer). Not that we necessarily need it all to
begin working on something cool. Algae strains and various bacteria
would be cool to start working with. Maybe watching a few lectures on
the projector for those interested. I only recently started
accumulating data, maybe we should start a wiki w/ interested members
listed so we know who to keep in the circle?
-Justin
Paul
Oct 28, 2009, 12:45:28 AM10/28/09
to cincihac...@googlegroups.com
I have a cool looking microscope, it may need some work. I think we picked it up at a school auction some years ago... I can bring it into the hive.
This week and next are going to be pretty much hell for me, midterms, projects, homework and quizes all coming due in the same two weeks... I will see if I can take a picture of it and upload, I might ahve time tonight.
This week and next are going to be pretty much hell for me, midterms, projects, homework and quizes all coming due in the same two weeks... I will see if I can take a picture of it and upload, I might ahve time tonight.
XiO2
Oct 28, 2009, 9:57:17 AM10/28/09
to The Cincinnati Hackerspace Project
That would be excellent!
On Oct 28, 12:45 am, Paul <pvi...@gmail.com> wrote:
> I have a cool looking microscope, it may need some work. I think we picked
> it up at a school auction some years ago... I can bring it into the hive.
>
> This week and next are going to be pretty much hell for me, midterms,
> projects, homework and quizes all coming due in the same two weeks... I
> will see if I can take a picture of it and upload, I might ahve time
> tonight.
>
> > > > >> >>http://diybio.org/-DIYbioisan organization dedicated to making
On Oct 28, 12:45 am, Paul <pvi...@gmail.com> wrote:
> I have a cool looking microscope, it may need some work. I think we picked
> it up at a school auction some years ago... I can bring it into the hive.
>
> This week and next are going to be pretty much hell for me, midterms,
> projects, homework and quizes all coming due in the same two weeks... I
> will see if I can take a picture of it and upload, I might ahve time
> tonight.
>
Paul
Oct 28, 2009, 10:29:50 AM10/28/09
to cincihac...@googlegroups.com
I should say from what I recall it might have some issues with the higher zoom lenses (maybe they need to be cleaned?) and the platform is set up to allow for X, Y panning, but it is missing the X part of the platform (could be replaced with some cut acrylic probably). I have not used or looked at it in years so it is also a bit dusty. In any case, it is something to look at and try. I just wanted everyone to be aware that it might not be the ideal option.
XiO2
Oct 29, 2009, 9:03:03 PM10/29/09
to The Cincinnati Hackerspace Project
Hey, anything is helpful. Maybe this would be a good opportunity to
learn about how it operates, and fixing it might be fun. Maybe we
could use the makerbot to print missing pieces out?
-Justin
On Oct 28, 10:29 am, Paul <pvi...@gmail.com> wrote:
> I should say from what I recall it might have some issues with the higher
> zoom lenses (maybe they need to be cleaned?) and the platform is set up to
> allow for X, Y panning, but it is missing the X part of the platform (could
> be replaced with some cut acrylic probably). I have not used or looked at
> it in years so it is also a bit dusty. In any case, it is something to look
> at and try. I just wanted everyone to be aware that it might not be the
> ideal option.
>
> > > > > > >> >>http://diybio.org/-DIYbioisanorganization dedicated to
learn about how it operates, and fixing it might be fun. Maybe we
could use the makerbot to print missing pieces out?
-Justin
On Oct 28, 10:29 am, Paul <pvi...@gmail.com> wrote:
> I should say from what I recall it might have some issues with the higher
> zoom lenses (maybe they need to be cleaned?) and the platform is set up to
> allow for X, Y panning, but it is missing the X part of the platform (could
> be replaced with some cut acrylic probably). I have not used or looked at
> it in years so it is also a bit dusty. In any case, it is something to look
> at and try. I just wanted everyone to be aware that it might not be the
> ideal option.
>
XiO2
Nov 10, 2009, 11:25:56 AM11/10/09
to The Cincinnati Hackerspace Project
Updated Email correspondence:
Hi Tito and Justin -
I've got an idea for incorporating your gel box into a BioWeatherMap
protocol and for doing a distributed / collaborative research project
involving a few hackerspaces around the country.
One of my collaborators (professor at Univ. Colorado) has been
collecting a variety of environmental samples, ranging from swabs of
crosswalk buttons, doorknobs, handrails, ATM buttons, various surfaces
in public restrooms, etc...and seeing if he can get DNA to amplify in
the lab. So far, he has not been able to get DNA to amplify from
crosswalk buttons, meaning that the amounts of bacterial DNA are not
significant enough on the buttons in Boulder CO. Obviously, without
being able to amplify DNA from an environmental sample, we can't
perform DNA sequencing. So, this the "sniff test" for potential
BioWeatherMap samples.
My friend will continue to have the undergrads, grads, and post-docs
in his lab collect a diverse set of samples from different surfaces to
examine which ones will amplify, so we know what will work for the
BioWeatherMap. We're basically building a "hit list" for the
BioWeatherMap. It occurred to me that this might be an excellent
project to do on a distributed basis, leveraging hackerspaces et
cetera, and the results will be used in real life down-the-road to
help guide the BWM.
The protocol used by my collaborator is as follows: For each sample:
a. Extract DNA using the MoBio PowerSoil DNA sample extraction
kit
http://www.mobio.com/samples/powersoil-dna-isolation-kit-sample.html
b. Perform 4 independent PCRs and 1 negative control (no-
template, just water). The PCR will amplify a region (e.g. 27F-338R)
of the 16S rRNA gene
c. Combine the four replicate PCR products
d. Purify the combined PCR products with Ampure magnetic
purification beads (Agencourt)
http://www.agencourt.com/products/spri_reagents/ampure/
e. Quantify using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and
a fluorospectrometer (NanoDrop ND3300)
http://products.invitrogen.com/ivgn/product/P11496?CID=Search-Product
http://www.nanodrop.com/Productnd3300overview.aspx
The cost of a nanodrop machine might put this particular protocol out-
of-range, but perhaps step e could be replaced with running the PCR on
a gel with a ladder. (Or, perhaps we could convince Thermo Scientific
to donate nanodrop instruments)
I think it would be useful to look through this protocol or a
variation of it, through a few lenses:
(1) Biosafety: Do any of these reagents call for special waste mgmt
practices? Are they safe to work with?
(2) Do-ability: How easily could this protocol, or one like it, be
implemented by hackerspaces
(3) Cost: What would the price be for each experiment, assuming
reagents are purchased at relatively low-volumes?
Thanks again,
Jason
----------------------------------------
Hey Jason, Justin,
Sounds like it has great potential for collaborative effort on a
distributed basis... Like you said, the nanodrop isn't necessary. You
can just compare it to the gel electrophoresis ladder brightness to
calculate rough approximates of DNA in the starting PCR material, if
any. In my U. Hawaii lab we are already doing traditional sequencing
with macro-algae, and environmental stream samples for cyanobacteria
as
well as eukaryotic algae. We are documenting them in Hawaiian Algal
Database (HADB).
I can get the protocols for HADB and maybe using that a gauge on
cost/material/complexity, and see if it's feasible in hackspace labs.
If it is... develop a kit that can be distributed to interested
groups.
Also PCR machines are becoming more and more affordable... this was
just
in recent blogosphere:
http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/
Cheers,
Norman
> > > > > > > >> >>http://diybio.org/-DIYbioisanorganizationdedicated to
Hi Tito and Justin -
I've got an idea for incorporating your gel box into a BioWeatherMap
protocol and for doing a distributed / collaborative research project
involving a few hackerspaces around the country.
One of my collaborators (professor at Univ. Colorado) has been
collecting a variety of environmental samples, ranging from swabs of
crosswalk buttons, doorknobs, handrails, ATM buttons, various surfaces
in public restrooms, etc...and seeing if he can get DNA to amplify in
the lab. So far, he has not been able to get DNA to amplify from
crosswalk buttons, meaning that the amounts of bacterial DNA are not
significant enough on the buttons in Boulder CO. Obviously, without
being able to amplify DNA from an environmental sample, we can't
perform DNA sequencing. So, this the "sniff test" for potential
BioWeatherMap samples.
My friend will continue to have the undergrads, grads, and post-docs
in his lab collect a diverse set of samples from different surfaces to
examine which ones will amplify, so we know what will work for the
BioWeatherMap. We're basically building a "hit list" for the
BioWeatherMap. It occurred to me that this might be an excellent
project to do on a distributed basis, leveraging hackerspaces et
cetera, and the results will be used in real life down-the-road to
help guide the BWM.
The protocol used by my collaborator is as follows: For each sample:
a. Extract DNA using the MoBio PowerSoil DNA sample extraction
kit
http://www.mobio.com/samples/powersoil-dna-isolation-kit-sample.html
b. Perform 4 independent PCRs and 1 negative control (no-
template, just water). The PCR will amplify a region (e.g. 27F-338R)
of the 16S rRNA gene
c. Combine the four replicate PCR products
d. Purify the combined PCR products with Ampure magnetic
purification beads (Agencourt)
http://www.agencourt.com/products/spri_reagents/ampure/
e. Quantify using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and
a fluorospectrometer (NanoDrop ND3300)
http://products.invitrogen.com/ivgn/product/P11496?CID=Search-Product
http://www.nanodrop.com/Productnd3300overview.aspx
The cost of a nanodrop machine might put this particular protocol out-
of-range, but perhaps step e could be replaced with running the PCR on
a gel with a ladder. (Or, perhaps we could convince Thermo Scientific
to donate nanodrop instruments)
I think it would be useful to look through this protocol or a
variation of it, through a few lenses:
(1) Biosafety: Do any of these reagents call for special waste mgmt
practices? Are they safe to work with?
(2) Do-ability: How easily could this protocol, or one like it, be
implemented by hackerspaces
(3) Cost: What would the price be for each experiment, assuming
reagents are purchased at relatively low-volumes?
Thanks again,
Jason
----------------------------------------
Hey Jason, Justin,
Sounds like it has great potential for collaborative effort on a
distributed basis... Like you said, the nanodrop isn't necessary. You
can just compare it to the gel electrophoresis ladder brightness to
calculate rough approximates of DNA in the starting PCR material, if
any. In my U. Hawaii lab we are already doing traditional sequencing
with macro-algae, and environmental stream samples for cyanobacteria
as
well as eukaryotic algae. We are documenting them in Hawaiian Algal
Database (HADB).
I can get the protocols for HADB and maybe using that a gauge on
cost/material/complexity, and see if it's feasible in hackspace labs.
If it is... develop a kit that can be distributed to interested
groups.
Also PCR machines are becoming more and more affordable... this was
just
in recent blogosphere:
http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/
Cheers,
Norman
Reply all
Reply to author
Forward
0 new messages