
Open-sourcing bioinstruments - homarp
https://liorpachter.wordpress.com/2019/01/18/open-sourcing-bioinstruments/
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sinab
My name is Sina Booeshaghi a second year PhD student at Caltech and I built
and designed the poseidon system (with the help of Eduardo Beltrame, Jase
Gehring, Dylan Bannon, and Lior Pachter) in the Pachter Lab.

If you have any questions I'm happy to answer them!

~~~
sbr464
I was needing a fully digital (controlled) microscope stage and stand
recently. I was suprised to find a lack of motorized stages compared to other
items. It would be nice to have a modular stage so it could be used with
different stands. Rotation and height adjustment would be nice as well.

Have you came across anything similar? It seems like it would be trivial to
build similar to your other designs.

~~~
munfred
I have been thinking about this problem for a while. I would like a cheap,
open source, commercially available kit for xyz gantry systems. That's
essentially what desktop CNC machines and 3D printers are and people hack them
for all kinds of purposes.

Unfortunately my current conclusion is that there is no solution that
satisfies all 3 at the moment. Your best bet for building such a system is
looking at cheap 3D printers and CNC machines, but it'll always be a little
bit of a hack and extra work because you'll have to remove parts (hot end,
drill bit..) and adapt something that was not designed with the intent of
being entirely re-purposed.

If anyone here knows of a xyz gantry system kit that satisfies all 3 (cheap,
open source, commercially available) please let me know.

~~~
Ccecil
It would be fairly trivial to build. Basically, it is just a CoreXY 3d printer
without the head.

I have modified a small CNC mill/router to be used as a "paste printer" for
printing frosting/ceramic
([https://youtu.be/XwjnVzfl0wA](https://youtu.be/XwjnVzfl0wA)). Many people in
the 3d printing community have done similar things with their printers.

I would recommend something without a bed that moves in the XY direction.
CoreXY designs would be great but there may be limitations on the carriage
weight. In that case a gantry style cartesian printer would be suitable but
with 2 Y motors to carry the X stage without skipping.

Edit: Also, See Openbuilds.com there are many machines that fit what you are
looking for.

~~~
munfred
Looking at openbuilds.com, in terms of functionality it definitely fits the
bill, I'll look at the designs with care.

I'd like to have a generic open source xyz gantry platform that I could just
order on amazon for <$200 and tinker around with.

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AndrewGYork
A different target audience, but in the same spirit, here's an open source
microscopy project from our lab:
[https://andrewgyork.github.io/remote_refocus/](https://andrewgyork.github.io/remote_refocus/)

My friend André Maia Chagas is doing some inspiring work in open hardware too:
[https://mobile.twitter.com/chagas_am](https://mobile.twitter.com/chagas_am)

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kemitchell
The BioBricks Foundation, an organization bringing the spirit of open source
to genetic programming, engaged me to develop Public Domain Chronicle, a fast,
easy, and free way to secure scientific methods and findings for the public
domain.

[https://publicdomainchronicle.org/](https://publicdomainchronicle.org/)

Public Domain Chronicle combines elements of defensive publication, open-
access scholarship, and commons licensing to make public domain advocates the
fastest runners in the race to publish, preventing others from patenting their
findings.

PDC's disclosure form for findings in biology is shorter and easier than any
standard corporate or academic invention-disclosure process, and produces an
immediate, public, republishable prior art record.

[https://pdc.biobricks.org/publish](https://pdc.biobricks.org/publish)

It's early days for the project, and we're seeking out as many potential
researcher-contributors as possible. We're particularly keen to hear from
academic scientists and folks in corporate tech transfer offices who may
prefer PDC to expensive defensive publication services.

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neltnerb
Oh, this is awesome. I build a lot of random equipment, how do I help? This
kind of thing could kickstart a lot of novel systems that'd take forever to
design or cost a ton otherwise.

~~~
sinab
I love your enthusiasm! Why don't you shoot me an email and we can chat some
point next week.. It would be really cool to get a great community around the
project, extending capabilities and adapting the core technology to random
equipment.

My email should be in my profile.

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amelius
Some critical questions: who is the target audience for these instruments?
Aren't academic budgets sufficient to provide for a lab with proper basic
instruments? Are these kind of instruments a financial bottleneck when setting
up a lab? And do we want biology PhD students and postdocs to spend time on
instrument-making (and publish papers on that) rather than on biology?

~~~
sinab
Hey amelius!

Great questions. The target audience for these instruments are scientists and
hobbyists who don't want to spend a ton of money on similar commercial
systems, and want the flexibility to modify their operation (e.g., poseidon
can run custom flow profiles per experiment whereas off-the-shelf commercial
systems typically only run one flow rate per experiment). The purpose of
poseidon is to show that open source biological instruments can be developed
and used by a community, similarly to how open source software tools in
biology are developed and used.

Academic budgets vary from institution to institution and are sometimes
determined by exogenous forces beyond the lab's control.

A complete commercial system to do single-cell RNA sequencing costs tens of
thousands of dollars! Using alternatives such as the Harvard Apparatus syringe
pumps and DropSeq [0] to run the same experiment will still cost you into the
thousands of dollars. With the poseidon system, we greatly reduce these costs.
Users can build the instruments to run these experiments for less than $400
and are not restricted to additional costs and tedious firmware upgrades to
expand the system.

In response to your point on time management and instrument-making, I think
that if there exists a need to develop these systems such that they will
advance biological experiments then it's totally cool to have academics work
on these sorts of projects! Biologists and bioengineers have always developed
tools alongside discovery and this is no different from developing
bioinformatics tools.

[0]
[https://www.cell.com/abstract/S0092-8674(15)00549-8](https://www.cell.com/abstract/S0092-8674\(15\)00549-8)

~~~
amelius
Thanks for these great answers. The only point where I would disagree is your
comparison with bioinformatics software. The difference there is that
installing a bioinformatics package and learning to use it takes far less time
than crafting an instrument, especially considering tasks like finding the
right suppliers of components, and calibrating and testing the device (for
which you might need other instruments). But on the other hand, perhaps
building these self-made instruments can become a task for specialized,
facilitating instrument-makers that are already part of many institutions.

~~~
munfred
Note: I also helped develop poseidon

The poseidon system was explicitly designed with ease of assembly in mind. If
you look at the build videos [1] you'll see that assembly of the entire system
(3 pumps + microscope station) takes less than an hour and requires just
pliers and screwdrivers.

The importance of ease of assembly was a lesson that we took from assembling
the miniDrops microfluidics station [2] developed specifically for one kind of
experiment (dropSeq) [3]. The miniDrops is very good at what it does but
assembly was somewhat cumbersome: it required ordering a custom PCB,
specialized parts only available from one vendor (whom I had to nag over the
phone to send me a quote!) and assembly of the device itself took 10-20h.

Not every kind of equipment can be made as easy to source and assemble as we
did with poseidon, but we really think that keeping this at the front of your
mind can make or break the adoption of a piece of open source hardware. This
is especially true in the context of biology laboratories, where many people
are not what you could call "hackers" or "makers" and will be immediately put
off by a daunting assembly process.

[1]
[https://pachterlab.github.io/poseidon/hardware](https://pachterlab.github.io/poseidon/hardware)

[2]
[https://metafluidics.org/devices/minidrops/](https://metafluidics.org/devices/minidrops/)

[3]
[https://www.nature.com/articles/s41467-017-0265](https://www.nature.com/articles/s41467-017-0265)

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GautamGoel
I work with Lior at Caltech. He's an amazing guy, probably the only person I
know who is capable of doing first-rate work in both biology and mathematics.

