From 41783cee5945a16d1f5f3948250497ae799ec193 Mon Sep 17 00:00:00 2001 From: "hackmd-hub[bot]" Date: Mon, 15 Jan 2024 19:01:36 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20master=20from=20=20@=20f35208b?= =?UTF-8?q?79d2d85f59bcebfb3785cc3d1763203a9=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- Manifest.toml | 45 ++++++++++++++++++-------------- index.html | 2 +- meeting-notes/index.html | 2 +- related-organizations/index.html | 2 +- sitemap.xml | 6 ++--- 6 files changed, 32 insertions(+), 27 deletions(-) diff --git a/404.html b/404.html index 1ad5d5a..52bedbb 100644 --- a/404.html +++ b/404.html @@ -1 +1 @@ - JuliaHealth
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\ No newline at end of file diff --git a/Manifest.toml b/Manifest.toml index a953762..c1c79a8 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.4" +julia_version = "1.10.0" manifest_format = "2.0" project_hash = "7f6b3460b3f9f8414c6b163fd3b5db0c9a5b1c28" @@ -54,9 +54,9 @@ version = "1.6.0" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96" +git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.9" +version = "0.1.10" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -86,9 +86,9 @@ version = "5.9.0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "5eab648309e2e060198b45820af1a37182de3cce" +git-tree-sha1 = "abbbb9ec3afd783a7cbd82ef01dcd088ea051398" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.0" +version = "1.10.1" [[deps.IOCapture]] deps = ["Logging", "Random"] @@ -123,9 +123,14 @@ uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" @@ -136,9 +141,9 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [[deps.Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] -git-tree-sha1 = "7cf4b8ca67b6a86a2ad7526bfe514ecd00d944f9" +git-tree-sha1 = "bad26f1ccd99c553886ec0725e99a509589dcd11" uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -version = "2.16.0" +version = "2.16.1" [[deps.LiveServer]] deps = ["HTTP", "LoggingExtras", "MIMEs", "Pkg", "Sockets", "Test"] @@ -166,21 +171,21 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] -git-tree-sha1 = "f512dc13e64e96f703fd92ce617755ee6b5adf0f" +git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.8" +version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -205,20 +210,20 @@ uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" version = "3.0.12+0" [[deps.OrderedCollections]] -git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.2" +version = "1.6.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf" +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.0" +version = "2.8.1" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.2" +version = "1.10.0" [[deps.PrecompileTools]] deps = ["Preferences"] @@ -241,7 +246,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.SHA]] @@ -303,7 +308,7 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.libsodium_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -319,4 +324,4 @@ version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" diff --git a/index.html b/index.html index 4020b03..475770e 100644 --- a/index.html +++ b/index.html @@ -1 +1 @@ - JuliaHealth
JuliaHealth
JuliaHealth logo

JuliaHealth

This is the website for the JuliaHealth organization.

We use the Julia programming language to improve medicine, health care, public health, and biomedical research.

Visit us on GitHub: https://github.com/JuliaHealth

Post in the Biology, Health, and Medicine category on Discourse.

Join us in the #biology-health-and-medicine stream on Zulip.

Chat with us in the #health-and-medicine channel on Slack. (Get a Slack invite here.)

JuliaHealth packages

Here is a list of Julia packages in the JuliaHealth organization:

PackageDescription
ARules.jlJulia package for association rule learning
BioMedQuery.jlJulia utilities for interacting with biomedical databases and biomedical application programming interfaces (APIs)
CAOS.jlJulia implementation of the characteristic attribute organization system (CAOS) algorithm
CTakesParser.jlJulia package to parse the output of Apache cTAKES (clinical text analysis and knowledge extraction system)
DICOM.jlJulia package for reading and writing DICOM (Digital Imaging and Communications in Medicine) files
DICOMClient.jlJulia client for connecting to DICOM (Digital Imaging and Communications in Medicine) servers by using the DICOMweb RESTful services
DICOMTree.jlA small Julia tool for visualizing DICOM metadata.
DateShifting.jlReduce re-identification risk while preserving temporal relationships in health data sets
DiagnosisClassification.jlMappings between different systems for classifying diagnoses and problems
EHRAuthentication.jlHelper code for authenticating to various electronic health record (EHR) systems
FHIRClient.jlJulia client for connecting to FHIR (Fast Healthcare Interoperability Resources) servers and building SMART on FHIR applications
HealthBase.jlCommon namespace for functions and interfaces in the JuliaHealth ecosystem
HealthSampleData.jlSample health data for a variety of health formats and use cases
ICD_GEMs.jlICD_GEMs.jl is a Julia package that allows to translate ICD-9 codes in ICD-10 and viceversa via the General Equivalence Mappings (GEMs) of the International Classification of Diseases (ICD).
MTIWrapper.jlJulia wrapper to the Medical Text Indexer (MTI) application programming interface (API)
MedEval3D.jlSet of CUDA accelerated medical segmentation metrics.
MedEye3d.jlJulia library for visualization and annotation medical images, specialized particularly for rapid development segmentation of 3 dimensional images like CT or PET/CT scans. Has full support of nuclear medicine Data.
MedImage.jl
MedPipe3D.jl
OHDSIAPI.jlA Julia interface to a variety of OHDSI web or API-based services
OMOPCDMCohortCreator.jlCreate cohorts from databases utilizing the OMOP CDM
OMOPCDMDatabaseConnector.jlUtility package to connect to databases in the OMOP CDM format
OMOPCommonDataModel.jlPure Julia implementation of the OMOP Common Data Model (CDM)
PharmaceuticalClassification.jlMappings between different systems for classifying medications
PubChemCrawler.jlUtilities to programmatically query the PubChem database
PubMedMiner.jlJulia package for studying co-occurrences in PubMed articles
SMARTAppLaunch.jlImplementation of the SMART App Launch Framework for building SMART on FHIR applications
SMARTBackendServices.jlServer-to-server FHIR connections

BioJulia

Our colleagues in the BioJulia organization use Julia in biology, bioinformatics, and computational biology. Check out their website and visit them on GitHub.

© JuliaHealth contributors. Last updated: November 17, 2023. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file + JuliaHealth
JuliaHealth
JuliaHealth logo

JuliaHealth

This is the website for the JuliaHealth organization.

We use the Julia programming language to improve medicine, health care, public health, and biomedical research.

Visit us on GitHub: https://github.com/JuliaHealth

Post in the Biology, Health, and Medicine category on Discourse.

Join us in the #biology-health-and-medicine stream on Zulip.

Chat with us in the #health-and-medicine channel on Slack. (Get a Slack invite here.)

JuliaHealth packages

Here is a list of Julia packages in the JuliaHealth organization:

PackageDescription
ARules.jlJulia package for association rule learning
BioMedQuery.jlJulia utilities for interacting with biomedical databases and biomedical application programming interfaces (APIs)
CAOS.jlJulia implementation of the characteristic attribute organization system (CAOS) algorithm
CTakesParser.jlJulia package to parse the output of Apache cTAKES (clinical text analysis and knowledge extraction system)
DICOM.jlJulia package for reading and writing DICOM (Digital Imaging and Communications in Medicine) files
DICOMClient.jlJulia client for connecting to DICOM (Digital Imaging and Communications in Medicine) servers by using the DICOMweb RESTful services
DICOMTree.jlA small Julia tool for visualizing DICOM metadata.
DateShifting.jlReduce re-identification risk while preserving temporal relationships in health data sets
DiagnosisClassification.jlMappings between different systems for classifying diagnoses and problems
EHRAuthentication.jlHelper code for authenticating to various electronic health record (EHR) systems
FHIRClient.jlJulia client for connecting to FHIR (Fast Healthcare Interoperability Resources) servers and building SMART on FHIR applications
HealthBase.jlCommon namespace for functions and interfaces in the JuliaHealth ecosystem
HealthSampleData.jlSample health data for a variety of health formats and use cases
ICD_GEMs.jlICD_GEMs.jl is a Julia package that allows to translate ICD-9 codes in ICD-10 and viceversa via the General Equivalence Mappings (GEMs) of the International Classification of Diseases (ICD).
MTIWrapper.jlJulia wrapper to the Medical Text Indexer (MTI) application programming interface (API)
MedEval3D.jlSet of CUDA accelerated medical segmentation metrics.
MedEye3d.jlJulia library for visualization and annotation medical images, specialized particularly for rapid development segmentation of 3 dimensional images like CT or PET/CT scans. Has full support of nuclear medicine Data.
MedImage.jl
MedPipe3D.jl
OHDSIAPI.jlA Julia interface to a variety of OHDSI web or API-based services
OMOPCDMCohortCreator.jlCreate cohorts from databases utilizing the OMOP CDM
OMOPCDMDatabaseConnector.jlUtility package to connect to databases in the OMOP CDM format
OMOPCommonDataModel.jlPure Julia implementation of the OMOP Common Data Model (CDM)
PharmaceuticalClassification.jlMappings between different systems for classifying medications
PubChemCrawler.jlUtilities to programmatically query the PubChem database
PubMedMiner.jlJulia package for studying co-occurrences in PubMed articles
SMARTAppLaunch.jlImplementation of the SMART App Launch Framework for building SMART on FHIR applications
SMARTBackendServices.jlServer-to-server FHIR connections

BioJulia

Our colleagues in the BioJulia organization use Julia in biology, bioinformatics, and computational biology. Check out their website and visit them on GitHub.

© JuliaHealth contributors. Last updated: January 15, 2024. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file diff --git a/meeting-notes/index.html b/meeting-notes/index.html index ba8a3b5..779053b 100644 --- a/meeting-notes/index.html +++ b/meeting-notes/index.html @@ -1 +1 @@ - JuliaHealth - Meeting Notes
JuliaHealth
JuliaHealth logo

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.

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: 

© JuliaHealth contributors. Last updated: November 17, 2023. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file + JuliaHealth - Meeting Notes
JuliaHealth
JuliaHealth logo

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

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: 

© JuliaHealth contributors. Last updated: January 15, 2024. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file diff --git a/related-organizations/index.html b/related-organizations/index.html index 7eae516..f1397e5 100644 --- a/related-organizations/index.html +++ b/related-organizations/index.html @@ -1 +1 @@ - JuliaHealth
JuliaHealth
JuliaHealth logo

Related Organizations

This is a (not necessarily comprehensive) list of organizations that focus primarily on developing and maintaining open-source Julia packages related to the life sciences and health sciences.

If you would like to add an organization to this list, please feel free to make a pull request.

Julia community organizations

Labs and research groups

Companies

© JuliaHealth contributors. Last updated: November 17, 2023. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file + JuliaHealth
JuliaHealth
JuliaHealth logo

Related Organizations

This is a (not necessarily comprehensive) list of organizations that focus primarily on developing and maintaining open-source Julia packages related to the life sciences and health sciences.

If you would like to add an organization to this list, please feel free to make a pull request.

Julia community organizations

Labs and research groups

Companies

© JuliaHealth contributors. Last updated: January 15, 2024. Edit this page on GitHub. Website built with Franklin.jl. Powered by the Julia programming language.
\ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml index 519ff51..9ceda7b 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -3,19 +3,19 @@ https://juliahealth.org/index.html - 2023-11-17 + 2024-01-15 monthly 0.5 https://juliahealth.org/related-organizations/index.html - 2023-11-17 + 2024-01-15 monthly 0.5 https://juliahealth.org/meeting-notes/index.html - 2023-11-17 + 2024-01-15 monthly 0.5