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These are the public notes for the JuliaHealth Community. Notes are published publicly here and are available for comments and review on the public HackMD. Additionally, the notes are hosted publicly on the GitHub and are open for PRs or edits as needed

February 29 2024

Meeting Summary (Americas/Europe/Africa Specific)

In Attendance: Jacob Zelko, Anshul Singhvi, Adam Wysokiński, Aurora Rossi, Dan Getz, Luna Fazio, Jay Landge, Edwin Mkwanazi, Alice Piller, Thembi Ndimande, Siyabonga Nxumalo, Hlengiwe, Muhammad Mahmoud, Jan Zubik, Sfundo Khumalo, Carlos Castillo Passi, Ram Samarth, Dina Khalid

Location: Virtual (Northeastern University Zoom)

Summary: Introducing new JuliaHealth projects, JuliaHealth blog, Google Summer of Code, and planning a JuliaHealth Day

Keywords: #juliahealth #meeting #americas #africa #europe #neuro #imaging #gsoc #planning

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

  1. Announcements:

    • Meeting recording logistics

  2. New member introductions

    • Luna Fazio

      • Statistics PhD

      • Coming back to epidemiology

      • Coming back to health roots

    • Adam Wysokiński

      • Creator of NeuroAnalyzer.jl

      • Psychiatrist

      • Many different modalities of research

    • Aurora Rossi

      • Functional MRI

      • PhD student

    • Alice Piller

      • Applying Julia in bioinformatics

    • Edwin Mkwanazi

      • Julia in clinical trials

      • Learn more about how to implement more in Julia

    • Carlos Castillo

      • Creator of KomaMRI

      • PhD student

  3. New contributor round-up!

    • KomaMRI

    • NeuroAnalyzer Adam Wysokinski

  4. JuliaHealth News

    • Northeastern University RISE Conference

    • A JuliaHealth Blog?!?!?

  5. Task Follow-ups

    • Jacob follows up with Carlos and Boris about synthetic MRI generation

  6. GSoC + JuliaHealth

    • Projects

    • Important dates

    • Open discussion

  7. Brainstorming a JuliaHealth Day

    • JuliaHealth is growing rapidly!!!

    • Might be confusing about where to go/get started

      • Three core ares

    • Luna

      • Had a mixture of working with different data

      • Public health approach

      • I as a doctor want to predict for patients

      • Perhaps it would be interesting to see what problems they have

        • Possible approaches

    • Jan

      • More about pipelines

      • What's their strength in practice

      • Seeing pipelines in action

    • Ram

      • How is Julia being used in health already?

  8. Glass Notebooks

    • Created by Dale Black

    • Link: https://glassnotebook.io

  9. Upcoming and ongoing research opportunities

    • Observational Health Research at Northeastern Uni

  10. Upcoming Events

    • JuliaCon 2024

  11. Open Discussion

January 25 2024

Meeting Summary (Americas/Europe/Africa Specific)

In Attendance: Jay Sanjay, Abhirath Anand, Carlos Castillo, Boris Enrique, Jacob Zelko

Location: Virtual (JuliaHealth Google Meet)

Summary: Medical imagining, fairness and health equity in observational health, and dashboards!

Keywords: #juliahealth #meeting #americas #africa #europe #fairness #koma #fairness #dashboards

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

  1. New member introductions

    • Carlos Castillo

      • King's College London

- PhD student

  1. Announcements:

    • New meeting times

      • Last Thursday of every month at 12PM EST

    • Why two separate meetings?

      • One for Asia/Oceania

        • Thanks Jay Sanjay for running this!!!

      • One for Americas/Africa/Europe

      • Trying to improve accessibility and inclusion

  1. New contributor round-up!

    • Nothing this meeting

  2. Running tasks follow-ups:

    • Nothing this meeting

  3. Presentation by Carlos Castillo Passi on GSoC projects on medical imaging.

  1. Fairness and health equity within Observational Health Research

    • Assessing phenotype fairness

    • Forthcoming package

    • Work done so far

    • Paper reference: https://arxiv.org/pdf/2203.05174.pdf

  2. Creating dashboards for JuliaHealth

    • Announcement from Genie.jl

    • Custom dashboard components

    • Question: What would this look like for JuliaHealth?

      • Create a standard interface across JuliaHealth packages

      • Can interface with a JuliaHealthDashboards package

        • HealthDashboard.jl?

        • Custom components for the general JuliaHealth ecosystem could be housed in package

      • Researchers can easily build together commonly used health dashboards

  3. Event Reminders

    • Google Summer of Code

    • JuliaCon 2024

  4. Upcoming and ongoing research opportunities

    • Observational Health Research at Northeastern Uni

    • Glass Notebooks from Dale Black (Not Discussed; saved for next month)

January 20 2024

Meeting Summary (Oceania/Asia specific)

In Attendance: Jay Sanjay, Abhirath Anand, Jacob Zelko

Location: Virtual (JuliaHealth Google Meet)

Summary: Overview of the Oceania/Asia specific JuliaHealth monthly meeting

Keywords: #juliahealth #meeting #asia #oceania #llms #beginner

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Meeting Notes

December 15 2023

In Attendance: Jacob Zelko, Jay Sanjay, Jakub Mitura, Zach Christensen, Divital coder

Location: Virtual (JuliaHealth Google Meet)

Summary: JuliaHealth full year review, Dicsussions on the upcoming GSoC projects in JuliaHealth.

Keywords: #medical #imaging #gsoc #ohdsi #newyear #observationalHealth

Agenda

  1. New member introductions

  2. New contributor round-up!

  3. Running tasks follow-ups:

  4. State of the JuliaHealth community discussion

    • Talking about the different aspects of the JuliaHealth community

      • Mapping the JuliaHealth community

    • Accomplishments throughout the year

      • JuliaCon 2023

      • GSoC

      • Publications/etc.

    • Open Problems and ongoing work

      • Technical problems

      • Making JuliaHealth more accessible for all

    • Future goals for the JuliaHealth ecosystem

    • Open discussion

  5. JuliaCon 2024!

  6. Google Summer of Code Discussion

    • What it is

    • Proposed projects and ideas

    • Open discussion

  7. Calls for collaboration

  8. Open discussion

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

  1. Introductions

    • Divital coder

      • Aspiring contributor for the 2024 Julia Organization.

  2. Contributor Round-Up

    • Shout outs to Farreeda for working on JuliaHealth Observational Health Sub-ecosystem Juliacon proceddings paper.

    • Shout outs to Jay-Sanjay for tagging new release of OMOPCDMCohortCreator.

  3. State of the JuliaHealth community discussion

    • Talking about the different aspects of the JuliaHealth community

      • Mapping the JuliaHealth community

    • Accomplishments throughout the year

      • JuliaCon 2023

        • Birds of Feather: Julia for Health and Medicine – Dilum Aluthge, Jacob Zelko

        • 100 Million Patients: Julia for international Health studies

      • First ever JuliaHealth GSoC fellow - Fareeda Abdelazeez

      • ODHSI Global Symposium 2023

    • Open Problems and ongoing work

      • Technical problems

      • Making JuliaHealth more accessible for all

      • Future goals for the JuliaHealth ecosystem

      • Expanding the OMOPCDM for hospital price transparency and transparency coverage.

    • Open discussion

      • Open discussion on standards across JuliaHealth

      • Zach happy to support and think around this

      • Schedule one-off discussion

      • Making juliahealth calls more Europe+asia/pacific friendly. Suggestions to have a one meet each for american time zone separate and one for asia/pacific time zone

  4. JuliaCon 2024!

    • Proposal-a-thon

  5. Google Summer of Code Discussion

    • What is GSoC/JSoC ?

    • Proposed projects and ideas

    • MedPipe3D

      • Loading medical imaging data

      • Modeling perspective most generally developed

      • Super-voxels image mapping

      • Edge matching; can make this code within Julia vs. Cpp

      • Display borders of images

      • Integrate segmentation like rotations recalling gamma.

      • Add basic post-processing like largest corrected components.

      • Add patch based data loading with probabilistic oversampling.

    • Open discussion

  6. Calls for collaboration

  7. Open discussion

    • JuliaCon 2024 and Proposal-a-thon

    • Addressing the “Paradox of Composition”

October 27 2023

In Attendance: Jakub Mitura, Phil Vernes, Jay Sanjay

Location: Virtual (JuliaHealth Google Meet)

Summary: Jakub Mitura presented on his work for MedEval3D, discussion on medical imaging, debrief from the OHDSI Symposium, and some initial conversation about GSoC

Keywords: #medical #imaging #gsoc #ohdsi

Agenda

  1. New member introductions

  2. New contributor round-up!

  3. Running tasks follow-ups:

  1. Presentation by Jakub Mitura on sub-ecosystem he created for working with CT, PET, and other medical imaging types of data.

  2. Debrief from OHDSI Symposium (Observational Health research venue)

  3. Google Summer of Code Project Discussion

  1. Upcoming and ongoing research opportunities

  1. Medical Imaging Extension for Real World Evidence exploration

  2. Open discussion

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

September 29 2023

In Attendance: Tiem van der Deure, Scott Jones, dx/dt

Location: Virtual (JuliaHealth Google Meet)

Summary: Discussion on viral load found in wastewater, GSoD for this fall/GSoC for next summer, and upcoming research opportunities and events

Keywords: #databases #wastewater #interfaces #gsoc #ohdsi

Agenda

  1. New member introductions

  2. Running tasks follow-ups:

a. Short-term task follow-ups:

b. Long-term task follow-ups:

i. Creating a template repository

  1. Infectious Disease load for various sewage water data

  2. Upcoming research opportunities and events

a. Not too early to start thinking about GSoC

b. Julia and OHDSI Symposium

  1. Open discussion

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

September 29 2023

In Attendance: Tiem van der Deure, Scott Jones, dx/dt

Location: Virtual (JuliaHealth Google Meet)

Summary: Discussion on viral load found in wastewater, GSoD for this fall/GSoC for next summer, and upcoming research opportunities and events

Keywords: #databases #wastewater #interfaces #gsoc #ohdsi

Agenda

  1. New member introductions

  2. Running tasks follow-ups:

    1. Short-term task follow-ups:

    2. Long-term task follow-ups:

      • Creating a template repository

  3. Upcoming research opportunities and events

    1. Not too early to start thinking about GSoC

    2. Julia and OHDSI Symposium

  4. Infectious Disease load for various sewage water data

  5. Open discussion

Meeting Outcomes

Short-Term Outcomes

Notes

August 25 2023

In Attendance: Edmund Miller, Jonathan Starr, Clark Evans, Kirill Simonov, Jacob Zelko

Location: Virtual (JuliaHealth Google Meet)

Summary: Recap of events from the JuliaHealth BoF at JuliaCon and introduction to the NumFOCUS OSSci project

Keywords: #numfocus #ossci #juliacon #bof #interoperability #databases #documentation

Agenda

  1. New member introductions

  2. Misc Announcements

    1. CalciumScoring.jl – Dale Black

    2. Survival Analyses – Arin Basu

    3. Google Summer of Code Fellowship wrapping up

  1. We are on the Julia Community Calendar!

  1. Small updates to the JuliaHealth website

  2. Running tasks follow-ups:

  3. Short-term task follow-ups:

    • @Jacob Set-up HackMD to take notes going forward

      • Copy and paste meeting minutes over to JuliaHealth PR to update at end of meetings

  4. @Dilum finds out how to live stream JuliaHealth BoF

    • Long-term task follow-ups:

  5. Creating a template repository 

  6. Debrief from JuliaCon

  7. Interoperability of Julia with health research ecosystems (R )

  8. Develop and document tutorials showcasing compositional solutions to JuliaHealth ecosystem problems

  9. Coordinate with bigger Julia Blog to bridge between communities even better

  10. Databases and JuliaHealth

  11. Jon Starr and NumFOCUS's OSSci Program

  12. Open discussion on next steps for the JuliaHealth community

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

July 28 2023

In Attendance: [Attendance Waived for In-Person Meeting

Location: JuliaCon 2023 JuliaHealth Birds of a Feather

Summary: New member backgrounds, problems within the Julia ecosystem related to healthcare, thoughts on addressing issues within a JuliaHealth context, and learning resources for Julia within the context of health.

Keywords: #ehr #genomics #biology #interoperability #database #sql #outreach

Agenda

  1. Introductions and what people in the community are using Julia for in health research

  2. What is missing of painful in Julia that is needed to drive health research forward

  3. Thoughts on how to address some of these problems

  4. Open discussion and next steps for JuliaHealth

Short-Term Outcomes

Not Available

Long-Term Outcomes

Meeting Notes

June 30 2023

Meeting Summary

In Attendance: Jacob Zelko, Fareeda Abdelazeez, Zachary Christensen

Location: Virtual

Summary: Discussed new members, upcoming JuliaCon, JuliaHealth Birds of a Feather discussion on topics like neural decoding and OMOP tooling, managing logistics for Julia organizations, and JuliaHealth PR reviews.

Keywords: #brain #imaging #neural #decoding #collaboration #community #engagement

Agenda

  1. New member welcomes!

  2. Planning JuliaHealth Birds of a Feather

    1. Topics?

    2. Facilitators?

    3. Creating actionable outcomes?

  3. Open discussion on Julia Orgs, How Do You Manage Logistics?

  4. Misc topics

  5. Julia for Health Informatics Research & Bridging community organizations

    1. Open Discussion on The Graphs Ecosystem

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Meeting Notes

May 26 2023

Meeting Summary

In Attendance: Jacob Zelko, Dilum Aluthge, Asher Wasserman, Fareeda Abdelazeez, Kyle Beggs

Location: Virtual

Summary: First JuliaHealth community call to meet other Julians, learn how we can galvanize the Juliahealth Community, and open discussion on paths forward

Keywords: #data #analysis #hemodynamics #omop #machine #learning

Agenda

  1. Introductions

  2. What people are using Julia for in health research

  3. Selected topics and state within the Julia ecosystem:

    1. Observational Health

    2. Medical Imaging

    3. Machine Learning and Health

    4. Interoperability Standards

    5. Drug Discovery

  4. Standard Interfaces

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Meeting Notes

  1. Introductions

    1. Dilum Aluthge – MD/PhD Student Brown University (BCBI), PumasAI

      1. Julia Community Involvement

        1. Pkg

        2. General Registry

        3. Continuous Integration

      2. JuliaHealth and beyond

        1. Originally created JuliaHealth to bring people together in health

        2. BioJulia folks are a great source of inspiration for packages!

      3. Birds of a Feather!!! COME VISIT! – Friday July 28th, 4PM EST in Boston, MA!

    2. Asher Wasserman – Astronomy PhD, Data Scientist in BioTech

      1. Julia Community Involvement

        1. Differential Equations

        2. One off deployments

    3. Fareeda Abdelazeez – GSoC JuliaHealth (First GSoC Student!!!!!)

      1. Julia Community Involvement

        1. Observational Health tooling JuliaHealth!

    4. Kyle Beggs – Software Engineer in small Optics company, Finishing PhD in MechE

      1. Julia Community Involvement

        1. PDEs

        2. Hemodynamics research focus

        3. Take advantage of these tools for imaging, segmentation

  2. What people are using Julia for in health research

    1. Asher: Cancer patient data

      1. PDFs and other data formats 

        1. CDA documents

      2. How to structure this ad hoc type of data into common data model

      3. Developing processes to automatically make these documents useful

      4. How do we clean the data to match actual reality

      5. How do we make this data actionable/useful

      6. Could match towards goals of OHDSI/observational health

        1. Analyses at population level?

        2. Outcome propensity scores?

        3. Patient phenotype development?

      7. Role of Julia:

        1. Mainly as a scripting language

        2. Supplement to a lot of SQL scripting (FunSQL discovered)

        3. Python is generally being deployed because of software devs

          1. How to not crash AWS, etc.

        4. Julia deployment for risk (?)

        5. Survival Analysis in Julia; lifelines in Python otherwise

    2. Kyle: Vascular Surgical Planning

      1. Unobvious on where to place graft, etc – educated guesses

      2. Creating a tool to simulate operations

      3. Why Julia?

        1. Existing tools are open source but really GUI-driven

        2. Integration across ecosystem would be even better for hemodynamics in Julia

        3. Give a base to simulate the mechanics involved with this

          1. JuliaFEM, etc. 

      4. Mesh list methods

        1. Point clouds

        2. Main application is within hemodynamics

    3. Fareeda: JuliaHealth GSoC Student

      1. Working on OMOP Common Data Model

      2. Standard model for observational health patient data

      3. Develop infrastructure of JuliaHealth to work with OMOP CDM data

        1. Improve DBConnector

        2. OMOPCDMCohortCreator.jl – add tooling

        3. OHDSIAPI.jl – creating interfaces for ATHENA/ATLAS

      4. Patient Level Prediction tooling

        1. Using MLJ algorithms

        2. Attempting to solve a research question

          1. Evaluate success of package

      5. Stretch goals:

        1. Cohort Quality and underlying data is “good”

        2. Build support for OBDC connections

    4. Overlap with other organizations

      1. Doesn’t happen in a vacuum

      2. Serving as a bridge between a bridge and a community between other groups

      3. What should be JuliaHealth?

        1. Bringing together people 

  3. Selected topics and state within the Julia ecosystem:

    1. Observational Health

    2. Medical Imaging

    3. Machine Learning and Health

    4. Interoperability Standards

    5. Drug Discovery

  4. Standard Interfaces

June 30th, 2023

Attending:

Agenda:

  1. New member welcomes!

  2. Planning JuliaHealth Birds of a Feather

    1. Topics?

    2. Facilitators?

    3. Creating actionable outcomes?

  3. Open discussion on Julia Orgs, How Do You Manage Logistics?

  4. Misc topics

    1. Julia for Health Informatics Research & Bridging community organizations

      1. Open Discussion on The Graphs Ecosystem

Notes: 

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