Interest on Starting a JuliaHealth Workgroup?

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Hi folks,

I am really interested in starting a working group around JuliaHealth similar to the Julia HPC, Julia ML, and other workgroups here within the Julia community. In a nutshell, I am imagining the group could meet virtually once or twice a month and for some starter discussion points, here is what I have written up:

  1. Introductions
  2. Purposes of the working group
  3. Recap on current state of the JuliaHealth ecosystem
    1. Tools for standards (FHIR, SMART, DICOM, etc.)
    2. Observational Health Tools
    3. Medical imaging tools
    4. Misc
  4. Ongoing Projects
  5. Interfaces
    1. Common interfaces for the JuliaHealth ecosystem
      1. Representation of clinical concepts (ICD9/10, SNOMED, other
        ontologies) fundamentally
      2. Definitions of disease
      3. Definition of patient populations
      4. Definitions of phenotype definitions
    2. Interoperability with JuliaData and Julia ML ecosystems
  6. Dreams for the ecosystem

Obviously this does not cover all of what JuliaHealth (and health informatics for that matter) could address, but these are just some ideas. I feel like we are slowly reaching critical mass where some really exciting things can take off in the Julia ecosystem for health informatics.

If you are interested, please vote in this poll:

  • Yes
  • No

0 voters

Also, for those who vote yes, could you please share if you could attend, tentative times that could work for you to attend, and topics that you would be interested in discussing?

Thanks!

~ tcp :deciduous_tree:

P.S. Also, I am going to CC some folks in case this idea may overlap with ongoing initiatives that I am unaware of (sorry for the pings): @ChrisRackauckas @dilumaluthge @jakobnissen @InPhyT @kevbonham @ScottPJones @tim.holy @cce @Adam_Black

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One issue with naming:

Some of these tools will overlap with pre-clinical research, that are not really related to “health” per se.

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Yea, I fully anticipate that. I figure as time progresses with the group, other ideas/groups could spin out to host packages that better fit what you are thinking of (for example, JuliaNeuro for more neuroscience related research could host tools for analyzing BIDS type data).

Also, would you actually mind sharing what you think would be overlaps or what have you at the moment?

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I’m interested. This last year has been a bit of a whirlwind making up for two years of no subject data so my participation with Julia has dipped. However it might be good to get a collective dialogue together instead of trying to keep pushing random things periodically from my end.

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So awesome to hear from you! I am glad we are somewhat crossing paths again after a couple years – hope you have been well! Depending on the situations, I hope JuliaHealth could assist with subject data side of things potentially. :slight_smile:

And I fully agree – have a collective dialogue would be useful as I know you have been contributing all acros the ecosystem. Would be good to see if there could be mutual overlaps to draw attention where appropriate for various endeavors

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I can add from me that there is some small intrest from industry i got a proposition of monetization of julia solutions for medical imaging ; i needed to reject it as i have now quite demanding research role, very little time , and they wanted big results in 6 months. Still there is some intrest in Julia for medical imaging.

If somebody would have time to help me maintain the medical imaging packages I would guide you in a matter, but frankly I am not able to actively maintain it currently on my own.

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It will continue to take a lot of collaborative work across disciplines but Julias ability to succeed in that field is going to depend on robust interfaces that play seamlessly with high performance mathematical computing in other Julia ecosystems.

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Continuing on the medical imaging theme … we have some geophysical imaging codes which work basically on the same principles as medical MRI but using the earth’s magnetic field as the main field … see here https://github.com/richardt94/SMRPInversion.jl

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That’s probably the same basic idea as what we need to do. Neuroimaging specifically is a lot messier than geophysical systems at the moment. Despite our best efforts, standardizing metadata even through BIDS is difficult. Working around these issues may be worth discussing as group elsewhere, but this compounds the complexity of getting all the tools in Julia up to speed too.

We have recently made some progress on getting a minimal metadata interface into DataAPI.jl but things like a lack of consensus on geometric (GeometryBasics.jl or Meshes.jl) and coordinate system interfaces CoordinateTransformations.jl or ReferenceFrameRotations.jl) make it very difficult to push certain things forward.

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I would be interested in attending. I am in GMT+2. Particular topics of interested to me would be:

  • tools for standards, such as FHIR, HL7, etc.
  • Representation of clinical concepts.

I am not sure how much I can contribute to these topics currently, as I don’t have any specifics needs or gaps that need to be filled, but I can imagine that long term I would benefit a lot from these initiative.

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Been waiting for this call for a while :smiley:
There will be alot of interesting topics around JuliaHealth, following @Ashwani_Rathee ML and DL applications can be initial idea to talk about, then I think this will drive us to different topics.

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@TheCedarPrince Any updates on this?

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Hi folks,

Sorry for the delay in response here! Been busy with transitioning back
to student-mode and wrapping up my last job. That said, definitely some
thoughts to share here!

I think it would be very good to get the ball rolling on this front
and start having a JuliaHealth interest group meeting. I propose that
to start with, we can meet once a month. For a first agenda of
topics, here is what I am thinking we could discuss:

  1. Introductions
  2. What people are using Julia for in health research
  3. Selected topics and state within the Julia ecosystem:
  4. Observational Health
  5. Medical Imaging
  6. Machine Learning and Health
  7. Interoperability Standards
  8. Standard Interfaces

I think we could have this first meeting last for about an hour and
then from there see what happens next.
Let’s schedule our first call for May 26th from 10 - 11 AM EST.

Let me know what you all think and let’s make this happen!

~ tcp

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Hey folks! Just a reminder that our first kick-off meeting for JuliaHealth will be this Friday from 10 - 11AM EST! Link to join the call is here:

JuliaHealth Monthly Call
Friday, May 26 · 10:00 – 11:00
Time zone: America/New_York
Google Meet joining info
Video call link: https://meet.google.com/wgf-jukg-yrx

I’ll look to see about getting something a bit more permanent set-up for the future about regularly recurring meetings. Thanks all and hope to see you there!

~ tcp :deciduous_tree:

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Does drug discovery count?

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I’m not leading this effort but I can personally say I’d be interested if your drug discovery process incorporates experimental biomedical data or outcomes in some way.

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Hi folks!

I can definitely say that “counts”! I’ll add it to the discussion
agenda for tomorrow.

~ tcp

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Btw, 10-11 is morning or evening your time @TheCedarPrince? I’ll come by

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Ah sorry if it wasn’t clear. 10 - 11 AM EST! See you then! :smile:

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Thanks everyone so much for joining the inaugural JuliaHealth discussion today! We had a nice turn out with nearly ~8 - 10 people (hard to see while taking notes!) and a nice discussion! Here were some high level take aways:

  • Additionally, I’d love to hear feedback! Let me know:

    • Was this useful in learning more about the JuliaHealth ecosytem?
    • What more you’d like to discuss?
    • What would be a good focus for future discussions?
    • Other ideas?

In terms of next steps,

  • I will set-up a more permanent place for the JuliaHealth notes/space
  • I will organize with Logan Kilpatrick about getting our group added to the Julia Community calendar for monthly calls
  • If you are coming to JuliaCon, please come to the JuliaHealth Birds of a Feather!!! July 28th on Friday at 4pm EST

Thanks so much for joining today! Next call will tentatively be on the last Friday of next month! If you want to keep in touch, feel free to DM me here and Slack/Zulip (I am TheCedarPrince). Join the JuliaHealth Slack channel as well being: #health-and-medicine!

Thanks all!

~ tcp :deciduous_tree:

P.S. Sorry for the abrupt end to that call – didn’t realize Google would just kick us off Meet in exactly an hour!

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