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Open Hardware for Science

In this chat we'll look at some of the ways that open hardware has made science equipment more accessible

Friday, May 11, 2018 12:00 pm PDT Local time zone:
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______________________________________________________________________________

Lex Kravitz will be hosting this week's Hack Chat. 

This Hack Chat is at noon Pacific time on Friday, May 11th. 

Time Zones got you down? Here's a handy count down timer!

Scientific equipment is expensive, costing many hundreds of thousands of dollars to set up a lab. The costs of machines can be prohibitive to scientists and citizen scientists who wish to do research. In this chat, we'll be talking about open source equipment, hardware, and modular electronics that has been created to mitigate this problem.

Dr. Alexxai Kravitz obtained his PhD in Neuroscience from the University of Pennsylvania in 2009 and subsequently completed a postdoc at the Gladstone Institutes in San Francisco, CA. Dr. Kravitz joined the NIDDK in December of 2012. His research focuses on understanding reward circuitry in the brain. The lab uses a variety of approaches to examine this, including behavioral testing, in vivo electrophysiology, and optogenetics.

TL:DR

In this chat, we'll discuss:

  • What open source science equipment is used today
  • The initiatives behind open source hardware for science applications
  • Science applications that could benefit from open hardware

  • Transcript for Open Hardware for Science Part 2

    Sophi Kravitz • 05/11/2018 at 19:54 • 0 comments

    Ashwin K Whitchurch3:40 PM
    They 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

    kelu1243:41 PM
    @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?

    Lex Kravitz3:42 PM
    @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

    Ashwin K Whitchurch3:43 PM
    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 ?

    Ashwin K Whitchurch3:44 PM
    @Sophi Kravitz  That would definitely work !

    Thomas Shaddack3:44 PM
    @Laura Cox by chance, is the low-level communication to the lab-bots' positioning systems in standard g-code?

    LOL!

    Lex Kravitz3:44 PM
    @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!

    kelu1243:46 PM
    @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..

    Ashwin K Whitchurch3:47 PM
    @kelu124 yes, but i may be generalizing the problem too much, but this is true of most research labs

    Ashwin K Whitchurch3:48 PM
    I guess the reliability, calibration, price and patents issues are all related

    Thomas Shaddack3:48 PM
    @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?)

    Lex Kravitz3:48 PM
    @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.

    Laura Cox3:48 PM
    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...

    Read more »

  • Transcript for Open Hardware for Science

    Sophi Kravitz • 05/11/2018 at 19:16 • 0 comments

    Lex Kravitz3:07 PM
    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?

    Lex Kravitz3:08 PM
    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?

    Lex Kravitz3:09 PM
    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

    Lex Kravitz3:10 PM
    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?

    Ashwin K Whitchurch3:11 PM
    This is also a question I'm concerned about

    Lex Kravitz3:12 PM
    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?

    Lex Kravitz3:12 PM
    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

    Thomas Shaddack3:13 PM
    ...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?

    Lex Kravitz3:13 PM
    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?

    Andre Maia Chagas3:13 PM
    remember that because of the nature of science, researchers have to make "home made solutions all...

    Read more »

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Mark Sporleder wrote 05/11/2018 at 19:33 • point

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?

  Are you sure? yes | no

Andre Maia Chagas wrote 05/11/2018 at 19:28 • point

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

  Are you sure? yes | no

Ashwin K Whitchurch wrote 05/11/2018 at 18:53 • point

@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

  Are you sure? yes | no

Shah Selbe wrote 05/11/2018 at 18:52 • point

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...

  Are you sure? yes | no

Sophi Kravitz wrote 05/11/2018 at 18:59 • point

there's a comment on Hackaday.com about calibration: https://hackaday.com/2018/05/09/friday-hack-chat-open-hardware-for-science/#comments

Alan says:

The next problem is: reproducibility. Which means, before you gather results, your gear needs to be CALIBRATED.

I’ve seen professional gear ripped out of racks, to be sent for annual calibration. Open hardware, depending on where / how it is deployed, may not have that luxury. You’re going to have to calibrate it yourself, in situ. If “calibration” isn’t a major part of your hardware documentation (along with how often, tools &environment required, etc.) every reading you make will be called into question.

  Are you sure? yes | no

kelu124 wrote 05/11/2018 at 18:51 • point

What do you think of the idea of certifying open-source equipment ( such as http://certificate.oshwa.org/ ) ?

  Are you sure? yes | no

Thomas Shaddack wrote 05/11/2018 at 16:55 • point

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?

  Are you sure? yes | no

Mark Sporleder wrote 05/11/2018 at 15:20 • point

Will this be webinar or just group chat? Would love to attend but unsure if can make it. If is webinar will it be recorded for later viewing?

  Are you sure? yes | no

Sophi Kravitz wrote 05/11/2018 at 18:45 • point

hi @darkmoon3d this is a text-based chat, and we'll post a transcript on this page afterwards

  Are you sure? yes | no

K.C. Lee wrote 05/10/2018 at 20:12 • point

Some cases you might not have much of a say.  Some grants come from commercial backing or that the University like to patent and own your work because you are using the facilities and equipment.

  Are you sure? yes | no

Sophi Kravitz wrote 05/10/2018 at 19:47 • point

A popular question will be 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?

  Are you sure? yes | no

like wrote 05/10/2018 at 19:46 • point

Do you use any open source projects in your research?

  Are you sure? yes | no

like wrote 05/10/2018 at 19:45 • point

Do you or other scientists consider hand-made "open source" tools as reliable as commercial ones?

  Are you sure? yes | no

Lex Kravitz wrote 05/10/2018 at 19:23 • point

Great question!  This is an important issue... I have built many things for research purposes and experienced exactly what you're talking about.  However, over the years I've found that documenting projects as you go actually *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.  

Especially for sharing, when people ask me for something I made I can share my documentation instead of building it for them...

  Are you sure? yes | no

Craig Watson wrote 05/10/2018 at 14:18 • point

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?

  Are you sure? yes | no

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