Lutetium-
Transcript for Open Hardware for Science Part 2
05/11/2018 at 19:54 • 0 commentsThey just check for the proper Hardware and software licenses and make sure they are properly documented, I would imagine enforcing them would be a totally different ball game
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@Sophi Kravitz I was asking this having the reliability aspect in mind (which was answered before) - in the sense that building trust and quality feeling with your users may be difficult.. but it is essential.![]()
do any of you feel @Lex Kravitz @Ashwin K Whitchurch @Laura Cox @Sanworks that reliablity is more questioned because your product is open source or because you're doing research with open source hardware?![]()
@kelu124 I agree completely! I think it's going to be difficult for a 3rd party to certify that a device works as it should or produces reliable data. I've found that kind of feedback comes from users trying the devices![]()
I feel, after my discussion with a few people in science, they're unable to visualize how a $20000 pieces of equipment can be replaced with something that costs $200![]()
maybe you should put a higher price tag on it @Ashwin K Whitchurch ?![]()
@Sophi Kravitz That would definitely work !![]()
@Laura Cox by chance, is the low-level communication to the lab-bots' positioning systems in standard g-code?![]()
LOL!![]()
@Sophi Kravitz I have met people who just won't use anything that's not one specific brand, because they are stuck in their ways. There is a lot of this in science, but I haven't met people who criticize something for being open-source, or hand-made![]()
Next question is from @Shah Selbe : Curious about any mechanisms or ideas around bringing open science hardware and citizen science into more mainstream science and get rid of the stigma associated with it. Particularly around calibration and data verification/validation...![]()
Seems like everyone is interested in calibration!![]()
@Ashwin K Whitchurch I have the same issue with pricing.. even when lab suppliers sell something in 1000s$, and you come up with something in 100s, they wonder about reliability..![]()
@kelu124 yes, but i may be generalizing the problem too much, but this is true of most research labs![]()
I guess the reliability, calibration, price and patents issues are all related![]()
@Lex Kravitz thought re sterilization... what about using materials that are oligodynamic, that self-sterilize their surfaces by e.g. silver or copper ions? (also, how to assess the effect of such materials, e.g. brass- or copper-filled printing filament?)![]()
@Shah Selbe I think websites like this, Github, etc are doing a lot to remove the stigma around citizen science. I find scientific journals to be inadequate for documenting and disseminating hardware - it's just not a great format for describing code and devices. So we're using Hackaday.io to document projects. I think this becomes a mechanism for driving interaction between communities that otherwise don't interact much. It would be great to think of ways to foster/engineer more formal interactions too.![]()
Good question! @Sophi Kravitz We basically utilize data to show reliability like any other company. For our pipetting robot we have extensively tested our hardware and found it to have a lifetime of heavy use to be ~ 4 years without needing extensive maintenance. Our positioning system's accuracy can be seen both by the hardware we use (which is opensource) and users can re-calibrate any time they would like very easily. As for our pipettes, we created a whitepaper so users can see the accuracy as well as test out the exact same protocol on their own.![]()
Sophi Kravitz: Thanks for all the great responses so far!![]()
Next question is from @Andre Maia Chagas :Do you think, with all the open science efforts going on, that we need to make grant committees and other institutions give more attention to hardware? (I think science will only be truly open once people can actually do experiments everywhere ) It never gets mentioned by open science people![]()
...indeed. sci journals articles are often rather skimpy about the equipment, even the one the researchers made and are writing about. and then the journals would want tens of bucks to just access the tell-you-nothing article. thank gods for sci-hub!![]()
Similar to @Ashwin K Whitchurch we mainly find that people question our reliability because of the price tag as compared with other automated liquid handling devices![]()
@Thomas Shaddack That's a cool idea, but I doubt the vets would find it useful. They are a bit more "checklist" about these things, but luckily there are approved protocols for sterilizing items that come in contact with mice that can't be autoclaved. So we got approval just to wipe them down with ethanol. We also can do gas sterilization if they made us do that but it's annoying so I'd much rather just wipe them down!![]()
what about sterilization with 30% hydrogen peroxide mist? (could the ultrasound misters be useful here?)![]()
@Laura Cox Are these people convinced by your data?@Lex Kravitz also, could there be some materials that'd indicate by e.g. color change the presence of microorganisms? some indicator dye bound to the polymer and sensitive to some markers of their metabolism?
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@Thomas Shaddack There are established gas sterilization methods - Ethylene Oxide is common in hospitals. I'm not sure if hydrogen peroxide would work.![]()
I believe so. We certainly haven't had it negatively impact us :) We also highly encourage our customers to try out the experiment we used ourselves (photometric and gravimetric testing)![]()
@Thomas Shaddack and @Lex Kravitz : this is very interesting indeed, researchers need to get out of the tower and due proper interaction/collaboration with non-academics. But at the same time, one needs to keep playing the publish or perish game... (until we can finally get rid of it...)Some resources for spreading hardware in the academic setting (which you probably already know):
https://channels.plos.org/open-source-toolkit
https://openhardware.metajnl.com/about/
https://www.journals.elsevier.com/hardwarex
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@Laura Cox That's great! Yeah I find many scientists can be rigid about specific brands, but ultimately they respect data. If not you probably don't want to work with them too....![]()
ethylene oxide is... a bit too explosive for my tastes. i heard about the 30% hp as an alternative method somewhere.Sophi Kravitz: Our last question for today is about community and is from @Mark Sporleder : I'm currently in development of an environmental iot sensor device network with market towards scientific community. Am weighing options of having devices open source hardware/software or licensed. Will likely be kits requiring assembly at lower cost and open source to a degree. Looking to build an online community for sensor data sharing while making this into a profitable small business. Any suggestions?
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Yes definitely @Lex Kravitz that's why open-sourced devices and software are so important because it makes recreating experiments easier![]()
Andre Maia Chagas: Hi @Tobias Wenzel ! Nice to see you here too!@Mark Sporleder Wow that sounds extremely useful. I have a lot of experience in this actually as my lab has also been developing an environmental IoT device (raise your hand if you are too!). There are many pieces of commercial IoT hardware that do this sort of thing, and so I think that aspect of a system like this is solved many times over and may not need more innovation. The challenge is sharing data and getting the online community engagement. Unfortunately I don't have any advice on how to be profitable :)
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Hi @Andre Maia Chagas, same here! Better late then never. I try to join #GOSH activities where I can to promote good Open Hardware documentation and publication ;-)![]()
If you're just coming in now (hi @Tobias Wenzel !) you can catch up via transcript: https://hackaday.io/event/157820-open-hardware-for-science@Mark Sporleder Some info on our project here, we plan to release more documentation very soon, just working on a new PCB design: https://www.niddk.nih.gov/research-funding/technology-advancement-transfer/research-materials-licensing/mios-better-animal-care-better-research
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Am aiming specificily to underwater in similar fashion to how openrov has built a large community with like device.![]()
By open source am considering building kit and enclosures but having documentation so that additional sensors could be networked or wired to existing system.![]()
In my opinion, I would put your efforts into building the community, and finding out what's missing from the commercial solutions for your target audience. I think the challenges will be in data sharing and community engagement/support, more so than building the actual devices.![]()
I haven't heard of many underwater solutions so you may be able to provide something novel to people who need that![]()
Would publications from institutions whom have worked with this device be a strong point for additional users or institutions to want to buy it?Thanks @Sophi Kravitz, I am trying to do just that. Short intro: I am editor in chief of the Open Access Journal 'Journal of Open Hardware' https://openhardware.metajnl.com/articles/10.5334/joh.3/ and co-founder of DocuBricks http://docubricks.com/search.jsp. I am also a scientist and build many open projects myself.
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nice to meet you!![]()
I believe so - scientists like to see peer reviewed publications, so it can be a boost if your device is being used in these![]()
This taps into the community engagement as well - if you create something and someone learns something useful with it, it's likely that others may want to replicate their work or use the device for other experiments.![]()
hi @Tobias Wenzel, glad to see you there. Would be good to see some hackaday science projects in the Journal of Open Hardware!![]()
@Tobias Wenzel Hi! Nice to meet you!![]()
This chat is officially over in a few minutes, everyone should hang out and keep talking though! To catch up if you're just getting here, there's a transcript posted: https://hackaday.io/event/157820-open-hardware-for-science![]()
@Lex Kravitz - I confirm that peer review publication helps with sharing open science projects, thanks to @Tobias Wenzel that help for a ultrasound module kit.![]()
Hackaday has just launched a Journal as well: https://hackaday.io/project/28128-hackaday-journal-of-what-you-dont-know![]()
@Mark Sporleder and @Lex Kravitz I would also suggest to look for people who are already doing IoT, environment and sensors, even if its not underwater, join forces, you bring a new environment, they bring the community, everyone wins because it is another good open source tool.![]()
has anyone worked with patenting their device before publicly releasing it?![]()
you have to do it, once it is publicly out, you cannot patent it anymore.![]()
Absolutely. There are a few Hackaday projects preparing manuscripts or currently submitting to the Journal of Open Hardware. I have already seen some really awesome drafts. But we would like to see much more. Why not take academic credit for the amazing work that is being done on instrumentation and models. We review the documentations also to make sure it is really actionable for other readers/scientists.plus, maybe this is the wrong audience to ask? considering the whole "open hardware for science motto"? :P
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@Andre Maia Chagas Good point. Have very long list of contacts am looking towards networking and joining forces with.![]()
@mark spor![]()
@Tobias Wenzel can we connect on email? sophi@hackaday.com![]()
@Mark Sporleder Publications are an alternative route to protect intellectual property (instead of patents). Publications are assumed public knowledge and no one else can prevent you from working and selling this published information.![]()
@Mark Sporleder Probably you already know, but make sure to check public lab, and safecast![]()
@Tobias Wenzel Would you consider setting up a way to submit directly from Hackaday? Like BioRXIV is doing with many journals? One challenge with publishing is that it's a lot of work to prepare a manuscript for an uncertain reward. If there was a way to know that, given sufficient quality of presentation, etc, etc, the work would be published in your journal that may drive people to submit![]()
@Tobias Wenzel thought. perhaps as important as open hardware, or sometimes even more, could be protocols. step by step methods for testing procedures, e.g. for measuring material properties (strength, electrical properties, biocompatibility...), with easily available materials/tools.![]()
I have to jump off. Thank you @Lex Kravitz for hosting a great chat!![]()
@Tobias Wenzel but at the same time they don't prevent others from doing the same with the data in your publication (which I'm guessing is what Mark is looking for? some kind of protection?)An interesting read for alternative models of business are in https://www.sparkfun.com/products/13220 which is super good read
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Transcript for Open Hardware for Science
05/11/2018 at 19:16 • 0 commentsHi! 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!
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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?![]()
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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)
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...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?
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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
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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
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@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
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We got most of our boards OSHWA certified, not sure how much it helps though![]()
Open Hardware for Science
In this chat we'll look at some of the ways that open hardware has made science equipment more accessible
do any of you feel 
