What are you working on?

[Michael Flynn]

I read a lot of the topics on this board, a lot of questions of how to do this, how to fix that. I was wondering what everyone was trying to do with these cool DIYBio projects. So what are you working on?

[John Griessen]

On 08/17/2016 06:54 AM, Michael Flynn wrote:
> So what are you working on?

Developing an electroporator to sell for $125 or so as a kit that allows programmable
high voltage profiles for transformation of solutions that measure 30k Ohms or more
for the whole cuvette or well or dish used. More on that soon.

[Sebastian S Cocioba]

A couple projects on the burner at the moment:

True Blue Rose - working at the School of Visual Arts in NYC with genes from a tropical clam to express a brilliant blue protein in white rose using petal promoters of other rosid family organisms. 

Bacterial Metabolism Paper for PLoS - working for a year now in my home lab on a research paper we (me and my research buddy) plan to submit to the public library of science for review and hopeful publication. Using a nifty DIY turbidity meter we found some interesting new data never before seen in EColi and we wish to investigate this phenomenon as a function of media. Device will be open source and we will be working with charter schools (middle and high school) to develop open ended curricula using our devices so students can have a chance to conduct actual research and be given DOI numbers as a means of attribution to said work. We formed an education non-profit company, Binomica Labs, to push this idea further. 

Open Oxalis Project - a crowd sourced genome sequencing attempt using the cosmopolitan weed Oxalis stricta. Each biohacker and/or bio-hackerspace would isolate the chloroplast DNA from this plant using simple chemicals, then barcoding primers are run at various expected sites along the chloroplast genome and the resulting sequences are saved to a GitHub account. Then the next hacker would use the data generated from the pilot run to design primers and continue "walking" the genome until the entire 150kbp plastome is sequenced at least 10x. It would allow hackerspaces to educate folks on the entire process of DNA barcoding using a tried and true, albeit slow and hands-on method of Sanger sequencing. Potentially the worlds first entirely crowdsourced plant genome. 

A couple other side side projects but these are top priority.

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

On Aug 17, 2016, at 9:54 PM, Michael Flynn <mfly...@gmail.com> wrote:

I read a lot of the topics on this board, a lot of questions of how to do this, how to fix that. I was wondering what everyone was trying to do with these cool DIYBio projects. So what are you working on?

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[Gordana Ostojic]

Capillary electrophoresis for everyday use for ordinary people to track biochemicals in urine. I am still in troubleshooting mode but it's fun to do experiments. 

Next, I would like to do drug-carriers that could be remotely opened at a precise position in the body, but of course, no way I could do that at home. 

[Nathan McCorkle]

Microfluidic production using open-source software and tools. Lately
not much progress, but I was last working on a way to easily describe
the connectivity of lab-on-a-chip components easily through Python
code, which in turn talks to BRL-CAD to generate physical models,
which can then be exported to STL files (think 3d printer software) or
g-code (think CNC machines, laser etcher/exposers) or Bitmap files
(think lithography masks, stencils, images for projection using DLP
projector).

Specifically the last thing I was working on was an API for connecting
CAD 'objects' using fluidic ports, such as the center points of each
of the 5 connections on this peristaltic pump:
https://github.com/nmz787/python-brlcad-tcl/blob/master/examples/output/microfluidic_pump.stl

(3 pneumatic connections, 2 fluidic) (notice the pneumatic connections
can come from either side, so maybe there are actually 6 options for
pneumatic connection points)

I've also been investigating how to command the NIRT tool, to take the
BRL-CAD model and generate g-code from the layers/slices of the model.
Then I can take that g-code and throw it into my laser etcher,
exposing some photoresist, repeat with new photoresist slide for each
layer, then combine layers (back to back) (or, pour silicone on, later
peel it off, then make a sandwich between glass plates).

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-Nathan

[d wright]

CRISPR knockout of the arabidopisis flowering gene. I am at the ligation step.

Dan

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[Koeng]

A couple main things-

Developing open source plasmid vectors and easy cloning methods. This has taken a massive amount of time, far longer than I expected, because I've been a perfectionist with base plasmid design, although I've gotten some great data lately on my cloning methods. Right now I'm in the process of finishing a few of the base plasmids, characterizing phage packaging, and Vibrio natriegens transformation.

Protein-primed replication in bacteria

I work in a lab based on this technology and I want it working in bacteria. It is based on pBClin15 and hypothetically I may be able to get an orthogonally replicating plasmid (though I have doubts on true orthogonality)

-Koeng

[Michael Flynn]

What is "transformation of solutions"?

[Michael Flynn]

CRISPR knockout of the arabidopisis flowering gene. I am at the ligation step.

What is "knockout"? 

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-Nathan

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[djwr...@gmail.com]

Knockout in a CRISPR experiment usually means cutting the promoter of the gene so when it repairs itself thru what is called non homologous end joining, the gene doesn't work because the promoter is replaced by random nucleotides or the ends join together which results in gibberish instead of a promoter. The long term goal is to do this in oncogenes as a treatment for cancer.

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[Nathan McCorkle]

On Aug 18, 2016 10:20 AM, "Michael Flynn" <mfly...@gmail.com> wrote:
>
> What is "transformation of solutions"?
>

Somehow shoving molecules into a cell... when the molecules are nucleic acids it can 'transform the genotype or phenotype' of the cell... i.e. the DNA or RNA changes, and maybe a protein is produced (etc...)

[Nathan McCorkle]

On Wed, Aug 17, 2016 at 2:00 PM, Nathan McCorkle <nmz...@gmail.com> wrote:

> Microfluidic production using open-source software and tools. Lately
> not much progress, but I was last working on a way to easily describe
> the connectivity of lab-on-a-chip components easily through Python
> code, which in turn talks to BRL-CAD to generate physical models,
> which can then be exported to STL files (think 3d printer software) or
> g-code (think CNC machines, laser etcher/exposers) or Bitmap files
> (think lithography masks, stencils, images for projection using DLP
> projector).
>
> Specifically the last thing I was working on was an API for connecting
> CAD 'objects' using fluidic ports, such as the center points of each
> of the 5 connections on this peristaltic pump:
> https://github.com/nmz787/python-brlcad-tcl/blob/master/examples/output/microfluidic_pump.stl
>
> (3 pneumatic connections, 2 fluidic)

Well I made some progress even if it is only for faces of a cube-like shape:
https://github.com/nmz787/python-brlcad-tcl/commit/5e57bef2f8acac4e5609e526759c5503ec129088

I think in the coming evenings I will work on g-code export, so I can
actually try making some things.

[Nathan McCorkle]

On Fri, Aug 19, 2016 at 1:28 AM, Nathan McCorkle <nmz...@gmail.com> wrote:
>> Specifically the last thing I was working on was an API for connecting
>> CAD 'objects' using fluidic ports, such as the center points of each
>> of the 5 connections on this peristaltic pump:
>> https://github.com/nmz787/python-brlcad-tcl/blob/master/examples/output/microfluidic_pump.stl
>>
>> (3 pneumatic connections, 2 fluidic)
>
> Well I made some progress even if it is only for faces of a cube-like shape:
> https://github.com/nmz787/python-brlcad-tcl/commit/5e57bef2f8acac4e5609e526759c5503ec129088

P.S. the point of this aiming to enable some sort of easy-to-use GUI
for designing microfluidics... so in that sense, a connection point
would be the point at which your mouse hovering and clicking
near-enough would 'snap to' and start connecting this pump to i.e. a
pipe shape to route connections to other parts/components.