2019 Digital Biology community gathering, Toronto, Canada


#1

Just starting to plan for an upcoming Digital Biology gathering in Toronto, Canada for summer 2019. Details still coming together, but one thing I have secured is the donation of one of the (now discontinued) Mondrian systems + chips courtesy of the Wheeler lab at the University of Toronto, ready for a teardown. I figure this should get @gaudi excited :wink:

Another idea that has been percolating for a while is the community implementation of a full water testing workflow (i.e., sample to cloud) using the OpenDrop and DropBot. We plan to take spectroscopy readings using the the Hamamatsu Micro-spectrometer prototype that @bengtsjolen and I integrated with the OpenDrop last June in Lucerne. There’s still a lot of work to do tidying up this setup and making an analogous sensor “shield” for the DropBot.

image

I’ve also started a forum thread based on suggestions by @juanmagararc asking people to contribute different commercially available water test kits that we can hopefully implement on both platforms, and then upload test results to @gbathree’s http://our-sci.net platform.

I am super excited to see all of these projects coming together to solve a real world problem. If anyone has any other ideas, suggestions or wants to get involved, let us know in the comments!


GOSH Nodes / GROLScH / Collaborative Production Events: Full Proposal
#2

Sure, I missed dumpster diving in China.
With the good time we had hacking in the lab at OpenFIESTA I was thinking of doing GOSH-Labs or LabGOSH. Maybe Toronto can be in that series of more lab / hand’s on / project oriented GOSHLab - Global Open Source Hardware Lab…

Urs


#3

yesssssssssssss to all the things!!!

Sorry, not productive. I think anyone interested in organizing the NA-GOSH event should find a time to meet - then we can start nailing things down. I’m happy to bring the main GOSH process and values to the discussion, which is something I know @shannond is working on putting together for this year.

I actually really want to see if I can connect to Open Trons hardware as well, and maybe slap a spec on it to also collect spectral data. I know this is way less efficient than a 96 well plate reader, but a 96 well plate reader can’t ever be very comparable to field-based methods which is a big pet peeve of mine. I want field-based and lab-based methods to be comparable, which means some give and take from both sides.

I also want to do what ryan said, and try to integrate with dropbot, but need more details to see if we need to adjust our design to make that possible. Actually… I’m wondering if we stuck a dropbot inside a Open Trons, you could use Open Trons’ XY system to move the spec over the appropriate blob. That’s a bit frankenstien-ish, but in theory possible.


#4

Yes, definitely appreciate you and @shannond bringing your GOSH process/values/facilitation superpowers to this.

Re: integration with OpenTrons, this is an idea that’s been floating around for a while now:

Or similarly, @gaudi’s BioServer:

Essentially, I think there is value in supporting two different workflows:

  1. in-the-field, sample-to-answer measurements (usually referred to as point-of-care in the health diagnostics context, but I’m sure there’s a similar phrase for environmental testing?)
  2. bulk sample collection followed by batch processing back in the lab.

For option 2, another thing to consider would be something like this Discrete Analyzer introduced to me by @nanocastro. It looks analagous to the way diagnostic tests are performed in centralized lab facilities by automated analyzers:


#5

hello - this is Chiu from Opentronsdo you want to use opentrons to transfer the drop ? for the readout - maybe a simple LED/ filter readout ?


#6

Well, maybe though that’s more a question for @ryanfobel, I was thinking more about using the XY axis to aim a spectrometer (probably a fiber optic) on a specific drop on the dropbot. Dropbot’s issue now is that it can do chemistry on a small scale, but it has a hard time producing quantifiable results from that chemistry. Measuring color changes is a common way to investigate chemical reactions… so it would open up dropbot to a wider range of applications.


#7

Hi,

I’m kind of late to the party. But I look forward to working with you this summer. I’ve been working on a flow based mifcrofluidics system for the past year that I think would work well with this project. I’ve also played around with building some simple photodiode based absorbance meters with synchronous detection which could also be fun to play with.

Kam