Sophi Kravitz
Hi! Let’s get started! I’m Lex Kravitz, I run a research group at the National Institutes of Health (https://irp.nih.gov/pi/alexxai-kravitz). We study the neuroscience of obesity in mice, and have made a few devices to assist us in our research (https://hackaday.io/projects/hacker/294140). I also co-founded a website for disseminating information on open source tools for behavioral research (http://openbehavior.com/). I have moderate experience in engineering, but am really a biologist/neuroscientist. Happy to take questions!
ok I'm taking questions from here https://hackaday.io/event/157820-open-hardware-for-science
our first question is from @Craig Watson:
As a PhD student in a small and new lab, I have to make a lot of things myself. Often the goal is to get whatever new piece of DIY equipment ready to run experiments as soon as possible -- not to make a great product or open source ressource. And so as soon as something is functional, I can't necessarily spend the time to polish it, improve the design or even document it fully. I believe this is a common problem facing researchers working on open source hardware. So my question is, how do you balance the need for conducting research with the time required to finish non-essential parts of a project?
This is a really important question, and I have direct experience with this. It's often very difficult and time consuming to document equipment. However, over the years I've found that documenting projects as you go *saves* time in the long run - you may want to share the design, publish it as part of a paper, or even re-build it yourself and find you forgot how it was made. Having good documentation can save your future self a lot of time.
any tips for better documenting? do you film yourself working?
The emergence of websites like Github or Hackaday.io has made it much easier to document as you go as well... I've never been great at keeping track of written lab notebooks
I take a lot of photos as I go, not much video. But I take photos of every step and try to take the time to organize them into instructions that I can follow later. Our lab has recently started using Hackaday.io for documenting them as we go as well, I hope to have ~5 more projects up soon!
nice!
next question: Do you or other scientists consider hand-made "open source" tools as reliable as commercial ones?
This is also a question I'm concerned about
This is often a worry, but in my experience it's unfounded. There is a rich history in “home-made” science hardware – often in papers people provide calibration data anyway. So I haven't experienced any issues with publishing "home-made" equipment
but what about reliabililty and how its perceived?
It can be reassuring if someone is using a commercial device/equipment that has a lot of precedent, but as long as the reliability is documented and calibrated I think it's perceived the same as a commercial device
...also, with all the documentation in-house and on-hand, the repairs and ad-hoc mods are much easier and the turnaround times are shorter than when big-name vedors are involved.
thanks!
well that leads into the next question: Do you use any open source projects in your research?
I'll mention that human research is a whole other can of worms with might stricter standards... @Ashwin K Whitchurch I noticed you're making a heart rate monitor?
remember that because of the nature of science, researchers have to make "home made solutions all the time!
*much
history is full of examples, where discoveries were only made because someone "hacked" something together in the lab
@Lex Kravitz yes, but in the case of humans, they decide whether to use it or not, in the version for mice, we're seeing more issues, I've posted a question also about that
everything was a prototype once. the universe itself still is, and it shows.
I'll jump to that question Ashwin
@Andre Maia Chagas Couldn't agree more. I love seeing historical science exhibits - there's one at my job now on artificial heart valves. The first ones they made (and used...) look very hand-made
@Lex Kravitz When I looked at your page, it seems like you're using open source for mice experiments. What would be the view of the research ethics committee about putting something open source on the animal? Would that raise reliability issues? The reason I ask is because we're currently working with a lab to make a version of our HeartyPatch project (https://hackaday.io/project/21046-heartypatch-a-single-lead-ecg-hr-patch-with-esp32) for mice
About documentation, I would like to add two resources:
and
http://www.dozuki.com/ (not open source itself, but free for education. It is the system from Ifixit)
...is it really so big problem if a mouse croaks? i mean, we're trapping and poisoning them by tons.
@Ashwin K Whitchurch There are a couple issues - 1) Regulatory issues. The regulations on devices for use with humans are very strict, so the standard for proving safety can be very high. For mice there are still regulatory bodies but the standards are lower than for human use. Usually this will depend on the animal committee and veterinarians. We have had no issues with putting our home-made devices in mouse cages. The vets were initially concerned about whether the plastics were toxic (PLA is not), and our ability to sterilize them. We wipe them down with ethanol, which is an acceptable form of sterilization for other electronics that come in contact with mice that cannot be autoclaved. So this worked out fine for our vets. Of course this will depend on the specific vets at each place…
I think there is a difference between active and passive devices. For passive devices taking measurements I wouldn't think there would be an issue. It's when you go to active like controlling the brain etc you run into issues. I could be wrong.
I do not have any experience working with mice or animal experiments, but looking at our Hackaday page, we got a message from some scientists wanting to make "wearable" devices for mice HRV, so we went ahead and made (just because we can :))
Ashwin, where are these being used ? (if you can say)
@Thomas Shaddack Untill recently I was working in Germany and ethical regulations for animal use in research are super strict. One has to take courses, takes tests before even looking at a mouse with experimental eyes...
2) Ethical issues. As long as they are safe, I don't think there's an ethical issue with exposing mice to potentially unreliable devices. If there's any chance of high current or anything like that I would hope the animal regulatory body (usually called ACUC) would investigate that
There have been questions about IACUC and whether they have approved it
and IACUC seems to even more strict than asking people to try it
even for passive devices i thought you have to be very careful in the design? like isolation i think?
These committees are independent at each institution, and some can be much more strict than others. I've heard that European IACUC are generally stricter than American
...the advantages of not being in an institution. no committees to worry about.
@Lex Kravitz @Ashwin K Whitchurch can I move on to the next question?
In fact, we had so much trouble to test the device, because I don't have access to animals
@Sophi Kravitz yes
I am at a rigorous/strict Institution in the US (National Institutes of Health) and fortunately our IACUC committee is reasonable, as in, I can talk to them in person, show them the devices, explain how we're making and cleaning them, etc.
Next question: Why would you release something as open-source instead of patenting/commercializing it? Especially if the product is worth a lot of money and took years to develop?
@Ashwin K Whitchurch Perhaps we can test your devices here? The heart rate monitoring seems very interesting!
@Lex Kravitz excellent !!, I will keep in touch with you
@anfractuosity True. I guess you design as if it's going into a human and do your due diligence with thought of safety for operator and wearer of the device.
public money! it is all funded with public money! should be open for the common good! :)
Great question - First, as I saw KC Lee mentioned in the comments, you don’t always have a choice. You may work for a company or research institute that does not allow things to be released as open source – I’ve heard of this happening. Fortunately my job allows/encourages open-source projects.
Couldn't agree more @Andre Maia Chagas =)
But beyond this, it depends a lot on your goal – do you want to start a business? Commercializing something is not easy, nor without risk. It can cost a lot of time/money to patent something, try to defend the patent, etc. If you sell it you also need to support it or you’re going to piss people off. You could consider licensing it, but that can be difficult too...
@Andre Maia Chagas absolutely
plus, you can still make money having an open source business model
I can speak a little to that question as well @Sophi Kravitz
hey @Laura Cox !
please do!
I work at an open-sourced hardware/software company called opentrons! (http://opentrons.com/)
To quickly summarize before @Laura Cox jumps in, my motivation for doing things open source is that I’m a scientist and am not necessarily interested in running a company. I like to make things open source because it seems efficient... why have someone else go through the same efforts we're going through. As an NIH employee I'm also not allowed to start a company, but I do get some scientific "cred" for doing open source things.
I did not know that the NIH liked open source, that's very encouraging !
@Laura Cox That is fantastic stuff! didn't know your were here as well! you people are doing amazing!
Speaking from the business side of things, we try to build a business around the opensource community. We encourage our users to hack their own stuff from software to hardware. All of this can be found on our github at https://github.com/OpenTrons
@Laura Cox Indeed! a wonder what a simple-in-principle xyz positioner can do, how much work it can save.
Our main goal is to give a low-cost solution to users to allow more reproducible results and help science move faster!
Next question is from @Thomas Shaddack : What kinds of such equipment would you consider the most important to be available as DIY? What ones are already available and what has to be developed?
@Ashwin K Whitchurch NIH is very supportive of open-source! The mission at NIH is to advance health, not make $$. So that's an important distinction. Sometimes the best way to disseminate something is to commercialize or license it, but unless it's a groundbreaking new drug or something, open-sourcing it usually a good way to achieve that.
(also, thanks @Laura Cox ! perhaps you'd like to host one of these chats in the future?)
Yes we would definitely love to! Wanted to see what other people are up to in the community. We just recently discovered hackday.io :)
@Lex Kravitz thanks, great to know that
in case this got lost:
Next question is from @Thomas Shaddack : What kinds of such equipment would you consider the most important to be available as DIY? What ones are already available and what has to be developed?
Quick note on what @Laura Cox said - and to connect to a prior question about reliability, it's also a mistake to think that commercial equipment is inherently more reliable/reproducible than open source... if you can see the code, tinker with it, calibrate it, etc, you can be extremely certain of the reliability of the equipment
agree!
Ditto!
oh, speaking of communities, @Sophi Kravitz , is anyone from hackaday in contact with the people from the gosh community? https://forum.openhardware.science/
People from all over trying to make open science hardware ubiquitous by 2020
That's where designing with flexibility where most mods can be in code helps.
yes, we spoke with Gosh a couple of years ago.... we wanted to synch up with them at CERN
i'd take exception to "extremely certain" as it is a Murphy-bait. if it is technology it will have quirks and they will appear in unexpected times. but with all docs on hand they are way easier to handle.
actually I think @Lex Kravitz spoke with them
as well
@Andre Maia Chagas I'm just getting familiar with GOSH and it seems amazing
@Lex Kravitz : a question that I always like to ask people: what was the last time you calibrated your fancy commercial scale/pcr machine/pipette? responses range from last week to never (for equipment at least 3-5 years old)
@Thomas Shaddack I think there's a balance between cost and ease of manufacture. Ideally new open source projects are going to save $$ and time, not the opposite. So I don't know what specific hardware is needed in different fields, but in my field some successful projects are:
http://miniscope.org/index.php/Main_Page
@Sophi Kravitz , @Lex Kravitz @Ashwin K Whitchurch fantastic, we should try to figure out some sort of merge! Also Hackaday could join this year's meeting in shenzen https://forum.openhardware.science/t/gosh-2018-in-shenzhen-china/684
and maybe sponsor some? ;)
The bar for manufacturing complex equipment has really come down though. I think those projects above would have been very difficult for an individual to manufacture ~5 years ago. But with modern prototyping services they are all very do-able today.
As a reference on price, each of those three links is ~10-20x cheaper than commercial solutions for the application, and they are pushing the functionality beyond what's offered commercially as well
@Andre Maia Chagas Shenzhen sounds, i'm gonna plan to be there
@Ashwin K Whitchurch +1 yeah
indeed. a lot of "complex" things aren't so complex anymore when they can be 3d printed or lasercut in hours to minutes.
I think @Sanworks is in here if anyone wants to ask him about starting an open source company too
hey @Sanworks welcome!
next question: What do you think of the idea of certifying open-source equipment ( such as http://certificate.oshwa.org/ ) ?
I may punt this to someone who knows more about it as this concept is actually new to me, but it seems like a great idea
We got most of our boards OSHWA certified, not sure how much it helps though
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