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.
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
New member introductions
Misc Announcements
CalciumScoring.jl – Dale Black
Survival Analyses – Arin Basu
Google Summer of Code Fellowship wrapping up
We are on the Julia Community Calendar!
Small updates to the JuliaHealth website
Running tasks follow-ups:
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
@Dilum finds out how to live stream JuliaHealth BoF
Long-term task follow-ups:
Creating a template repository
Debrief from JuliaCon
Interoperability of Julia with health research ecosystems (R )
Develop and document tutorials showcasing compositional solutions to JuliaHealth ecosystem problems
Coordinate with bigger Julia Blog to bridge between communities even better
Databases and JuliaHealth
Jon Starr and NumFOCUS's OSSci Program
Open discussion on next steps for the JuliaHealth community
@Jacob follow-up with Jonathan about JuliaHealth + OSSci
@Edmund let Jacob know about blog posts solving problems
Support OSSci about JuliaHealth
Introductions
Clark C. Evans
Master cobbler of YAML
Used to work at Prometheus Research
Sold to IQVIA
Worked under MechanicalRabbit Umbrella
Developed FunSQL.jl with Kirill
Database characterization
Joined Tufts University CTSA
Helping with data warehousing
Objects to query OHDSI databases and EPIC Clarity
Getting Pluto working
Jonathan
Manager for OSSci for NumFOCUS
Goal: Mapping open source science ecosystem
Work with Distributed Computing
Berkeley technology
Blocks and chains!
Using Open Source and Science to drive research
Edmund
PhD Candidate at Texas Dallas
Molecular and Cell Biology
Functional Genomics
Coming from JuliaCon
Excited about Health stuff
Interoperability of Julia with health research ecosystems (R )
Easiest way to interoperate is to call them directly from the command line
Build your own executables
Most reliable/easiest
Database approach:
Build table in one language
Ingest in another
Combining executables in one location – use Docker?
Can run on several different machines
Building R packages with Julia backends is possible
Develop and document tutorials showcasing compositional solutions to JuliaHealth ecosystem problems
Competing Julia with other tutorials?
Switching over to Julia from what?
Why are people still not switching?
Demonstrating the use is one way
Obviously, one could write more posts
But there seems to be a lot of content already – what is missing?
Does seem like there is two different levels of documentation
Beginner
Advanced
Where are the practical means of solving problems in Julia?
Databases and JuliaHealth
Show how to do the basics
Common database errors
How to address them
Unclear on how to solve it; more people working in this space?
Not really a problem within ecosystem
Look at drivers across all packages to see how things work in Julia ecosystem
See how we can address issues across ecosystem
Jonathan Starr and NumFOCUS's OSSci Program
Getting to deep diving within Julia ecosystem
Researchers who want to find a package that they can use and develop
Mapping projects and people to a given tool
Can look at map to see where packages are needed for a particular ecosystem
Can click on and connect with researchers
Highlighting of credit for researchers
Starting with NumFOCUS projects
Building out knowledge of all ongoing projects/software
Julia is little represented right now
How to show to funders/orgs what projects to support
How to build support across or collaboration between groups
Trying to stop abandonware from happening
Attempting to build social infrastructure
Q&A
Tufts doing something very similar – happy to collaborate
How can JuliaHealth get started and involved?
Jonathan: Send me reference page and we can get this started!
Links:
About: https://numfocus.org/open-source-science-initiative-ossci
How To Join: https://opensource.science
Map of Open Source Science (MOSS)
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
Introductions and what people in the community are using Julia for in health research
What is missing of painful in Julia that is needed to drive health research forward
Thoughts on how to address some of these problems
Open discussion and next steps for JuliaHealth
Not Available
ACTION: Develop and document tutorials showcasing compositional solutions to JuliaHealth ecosystem problems.
ACTION: Establish cohesive and organized Julia Blog to guide users and highlight official blogs.
Attendee interests and background
Here to learn
From EHR development and background
Genie folks here to support JuliaHealth endeavors
Genomics research and prevention
Quebec Heart and Lung Institute
Representing PumasAI
Consulting group
Developing health research in Michigan area
Aggregating claims data
To learn what is going on in the community
Creator of MetaAnalysis.jl
Involved with backend of healthcare IT
Working on JuliaHub
Learning about packages that are out there
Here to support JuliaHealth members
New Zealand longitudinal child health
Have own secure system
Post-COVID syndrome
Computational biology
Sickle Cell
Applying some ML
Problems within the Julia ecosystem
Julia needs more database connectivity to more easily do operations research
Databases are a pain point and composing with other aspects of the ecosystem
Interoperability within Julia and other sorts of resources
I end up doing the bare minimum in SQL
Do we have RAM?
Can we pull this into the Julia ecosystem?
Crank up the RAM! But only so much scaling
Minimal SQL writing
Searchlight.jl: Julia ORM layer within
Is Genie like a shiny?
No, more of a full-stack
Goes beyond just visualization dashboards
Sequencing data
Equally data
Everyone uploads data in slightly different ways
Make simple ways to pull that data
R Conductor –> JuliaConductor?
Would make genomic pipelines within Julia pipelines a lot easier
We need to understand the underlying structures
One of the big pain points
Often to have roll your own
EpiR –> EpiJ?
Power calculators
Co-founder of start-up
Found unmet need for remote monitoring for neuotropenia
Non-invasive screen for neutropenia
Device runs Julia
Pain points:
Testability of hardware
LOTS of CI – bit of a pain
How much repetition happens in CI
Part of the problem for these problems:
There are still going to be folks who use the same organizations
Overcoming inertia to do the same or similar things in Julia
Wrapping around Julia?
Bringing it into the R ecosystem
Leading to big impacts for callable things from R by having smaller static binaries
Wrapping Julia packages in R
N3C – National COVID Cohort Collaborative
Went to many healthcare systems across the US to get COVID data
Shelled out to Palantir
Open source tools within the ecosystem
JuliaHub has Boeing board member
Trusted within security community
Could help in this situation
Thoughts on how to address some of these problems
Using other packages outside of Julia
If you have some way to wrap around it
Getting support
PythonCall.jl or RCall.jl
Not clear how to make this compositional
The paradox of compositionality
Blog posts go a huge ways to solving problems
Tutorials showing how things can be combined together
Promotional type material
Nice docs are nice
The Julia Blog itself
Mentions JuliaBloggers but doesn't help with guiding users to read
Blogs need to go on as official blogs
Julia Forem – is it maintained?
Hook into the tags from blogs
Cross-posting where appropriate
How to learn Julia within the context of health
Carpentries for learning resources
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
New member welcomes!
Planning JuliaHealth Birds of a Feather
Topics?
Facilitators?
Creating actionable outcomes?
Open discussion on Julia Orgs, How Do You Manage Logistics?
Misc topics
Julia for Health Informatics Research & Bridging community organizations
Open Discussion on The Graphs Ecosystem
@Jacob Set-up HackMD to take notes going forward
Copy and paste meeting minutes over to JuliaHealth PR to update at end of meetings
ACTION: Creating a template repository
New members:
Zachary Christensen
Neuroimaging research
MD/PhD
Trying to finish this year!!!
Lots of background work like in JuliaData
Works on making Julia interface
Announcement: JuliaCon about 1 month away!
We have our own track: biology and medicine
Many people working on different things
JuliaHealth Birds of a Feather Discussion
Possible Topics:
Neural decoding
Inspired by MATLAB: http://www.readout.info
Sister organization: https://julianeuro.github.io/packages
OMOP Tooling for Real World Data
How to start collaborations?
Maybe grant collaborations?
Getting access to datasets
Coming up with different research questions
How can we integrate across the community?
What problem can we solve?
Become a community resource to point to packages
Don’t need to keep recreating or developing new packages
Packages could be applications built on top of a specific use case
Combining old packages in new ways
Open discussion on Julia Orgs, How Do You Manage Logistics?
Have multiple persons part of the organizations
Sharing meeting documentation
Share Google Doc at the beginning or before a meeting in announcement
Publish notes on website publicly
PR to update the JuliaHealth website with new tab for meeting minutes
ACTION: Using HackMD to take notes going forward
Copy and paste meeting minutes over to JuliaHealth PR to update at end of meetings
Consistent APIs for JuliaHealth
Initial first pass with HealthBase.jl: https://github.com/JuliaHealth/HealthBase.jl
As free as possible from niche
Could become quickly overwhelming or run risk of bikeshedding
ArrayInterface is a learning example in this context
Light dependency package is great with a well-described API
How to move forward and get momentum
Without it turning into a mess
Common ontologies: http://obofoundry.org
JuliaHealth PR Reviews
PR Checklist:
Purpose
Reduce cognitive load
JuliaHealth package forks: https://github.com/JuliaCI/PkgTemplates.jl
ACTION: Creating a template repository
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
Introductions
What people are using Julia for in health research
Selected topics and state within the Julia ecosystem:
Observational Health
Medical Imaging
Machine Learning and Health
Interoperability Standards
Drug Discovery
Standard Interfaces
@Dilum finds out how to live stream JuliaHealth BoF
Introductions
Dilum Aluthge – MD/PhD Student Brown University (BCBI), PumasAI
Julia Community Involvement
Pkg
General Registry
Continuous Integration
JuliaHealth and beyond
Originally created JuliaHealth to bring people together in health
BioJulia folks are a great source of inspiration for packages!
Birds of a Feather!!! COME VISIT! – Friday July 28th, 4PM EST in Boston, MA!
Asher Wasserman – Astronomy PhD, Data Scientist in BioTech
Julia Community Involvement
Differential Equations
One off deployments
Fareeda Abdelazeez – GSoC JuliaHealth (First GSoC Student!!!!!)
Julia Community Involvement
Observational Health tooling JuliaHealth!
Kyle Beggs – Software Engineer in small Optics company, Finishing PhD in MechE
Julia Community Involvement
PDEs
Hemodynamics research focus
Take advantage of these tools for imaging, segmentation
What people are using Julia for in health research
Asher: Cancer patient data
PDFs and other data formats
CDA documents
How to structure this ad hoc type of data into common data model
Developing processes to automatically make these documents useful
How do we clean the data to match actual reality
How do we make this data actionable/useful
Could match towards goals of OHDSI/observational health
Analyses at population level?
Outcome propensity scores?
Patient phenotype development?
Role of Julia:
Mainly as a scripting language
Supplement to a lot of SQL scripting (FunSQL discovered)
Python is generally being deployed because of software devs
How to not crash AWS, etc.
Julia deployment for risk (?)
Survival Analysis in Julia; lifelines in Python otherwise
Kyle: Vascular Surgical Planning
Unobvious on where to place graft, etc – educated guesses
Creating a tool to simulate operations
Why Julia?
Existing tools are open source but really GUI-driven
Integration across ecosystem would be even better for hemodynamics in Julia
Give a base to simulate the mechanics involved with this
JuliaFEM, etc.
Mesh list methods
Point clouds
Main application is within hemodynamics
Fareeda: JuliaHealth GSoC Student
Working on OMOP Common Data Model
Standard model for observational health patient data
Develop infrastructure of JuliaHealth to work with OMOP CDM data
Improve DBConnector
OMOPCDMCohortCreator.jl – add tooling
OHDSIAPI.jl – creating interfaces for ATHENA/ATLAS
Patient Level Prediction tooling
Using MLJ algorithms
Attempting to solve a research question
Evaluate success of package
Stretch goals:
Cohort Quality and underlying data is “good”
Build support for OBDC connections
Overlap with other organizations
Doesn’t happen in a vacuum
Serving as a bridge between a bridge and a community between other groups
What should be JuliaHealth?
Bringing together people
Selected topics and state within the Julia ecosystem:
Observational Health
Medical Imaging
Machine Learning and Health
Interoperability Standards
Drug Discovery
Standard Interfaces
June 30th, 2023
Attending:
Agenda:
New member welcomes!
Planning JuliaHealth Birds of a Feather
Topics?
Facilitators?
Creating actionable outcomes?
Open discussion on Julia Orgs, How Do You Manage Logistics?
Misc topics
Julia for Health Informatics Research & Bridging community organizations
Open Discussion on The Graphs Ecosystem
Notes:
New members:
Zachary Christensen
Neuroimaging research
MD/PhD
Trying to finish this year!!!
Lots of background work like in JuliaData
Works on making Julia interface
Announcement: JuliaCon about 1 month away!
We have our own track: biology and medicine
Many people working on different things
JuliaHealth Birds of a Feather Discussion
Possible Topics:
Neural decoding
Inspired by MATLAB: http://www.readout.info
Sister organization: https://julianeuro.github.io/packages
OMOP Tooling for Real World Data
How to start collaborations?
Maybe grant collaborations?
Getting access to datasets
Coming up with different research questions
How can we integrate across the community?
What problem can we solve?
Become a community resource to point to packages
Don’t need to keep recreating or developing new packages
Packages could be applications built on top of a specific use case
Combining old packages in new ways
Open discussion on Julia Orgs, How Do You Manage Logistics?
Have multiple persons part of the organizations
Sharing meeting documentation
Share Google Doc at the beginning or before a meeting in announcement
Publish notes on website publicly
PR to update the JuliaHealth website with new tab for meeting minutes
ACTION: Using HackMD to take notes going forward
Copy and paste meeting minutes over to JuliaHealth PR to update at end of meetings
Consistent APIs for JuliaHealth
Initial first pass with HealthBase.jl: https://github.com/JuliaHealth/HealthBase.jl
As free as possible from niche
Could become quickly overwhelming or run risk of bikeshedding
ArrayInterface is a learning example in this context
Light dependency package is great with a well-described API
How to move forward and get momentum
Without it turning into a mess
Common ontologies: http://obofoundry.org
JuliaHealth PR Reviews
PR Checklist:
Purpose
Reduce cognitive load
JuliaHealth package forks: https://github.com/JuliaCI/PkgTemplates.jl
ACTION: Creating a template repository