# Cancelled ~~Health Data Science Hangout~~

### Every Wednesday @ 12PM (Arizona time) on [zoom] join a community conversation to discuss computing workflows and methods

###### tags: `best practices` `data science` `human subjects` `health data`

> Log in (upper right hand corner) and use the icons (in the upper left hand corner) to edit

:::info
:+1: Creating a community meetup that fosters learning through diverse mechanisms

:-1: Creating another learning resource that ends up out of date, unorganized, and unmaintained
:::

## :spiral_note_pad: Weekly Meetup Agenda

I. Introductions
- Name
- Position & Affiliation
- How you interact with data

II. Learning Activity
- Save room for Q&A

III. Announcements
- Upcoming events
- Reminder for next week's meetup

## :calendar: Meeting Schedule / Signup!

- Aug. 24 :school_satchel: **w/ Sarah Y**
- Aug. 31 :link: **w/ Brandon J**
- Sept. 7 :film_projector:
- Sept. 14 :newspaper:
- Sept. 21 :school_satchel: **w/ Brandon J**
- Sept. 28 :link:
- Oct. 5 :film_projector: w/ Zhiyang
- Oct. 12 :x:

#### Event Tags Legend
:film_projector: Scheduled speaker
:school_satchel: BYOD - Bring your own data
:link: community `discussions`
:newspaper: journal club
:notebook_with_decorative_cover:`debrief` and re-organize meetings, bring your questions, comments, feedback and concerns
:x: Meetings Cancelled

#### Topics Tags Legend
:black_left_pointing_double_triangle_with_vertical_bar: `version control` `git` `github`
:page_with_curl: `literate programming` `jupyter` `rmarkdown`
:computer: Code-along `workshops` or live coding demonstrations

:::success
### Living Sign in :wave:
Sign in here, update whenever!

+ Emoji
+ **Name**
+ UArizona Affiliation
+ How you interact with data
+ `tags`

:avocado: [**Heidi Steiner**]([e-mail]), Data Science Educator @ Data Science Institute, human genome and gut microbiome research, `R` `genomics` `NGS`

:cloud: [**Shashank Yadav**]([e-mail]), 1st Year PhD Student, Biomedical Engineering. Previous research: DNA and Protein Language Models and Drug Discovery. Future: Bioimaging, ML stuff.

:octopus: [**Brandon Jernigan**]([e-mail]), IT @ Health Sciences Biobank

:space_invader: [**Nicole Jimenez**]([e-mail]),Postdoctoral Fellow/Data Science Fellow @ UA-CoM-P , Human microbiome in Womxn's Reproductive Health Research

:sunflower: [**Sarah Yates**]([e-mail]), Data Manager, Petersen HIV Clinics, CTS MSc candidate. Lots of clinical trial data management experience + health programs metrics and monitoring.
:::

:::warning
### Future topic request zone :pushpin:

Or submit confidential feedback, [here](https://uarizona.co1.qualtrics.com/jfe/form/SV_0qsYrSg9sQuHNVc)!
- [ ] [UA Soteria](https://datascience.arizona.edu/analytics-powerhouse/ua-soteria)
- [ ] Using git/github
- [ ] Stata
- [ ] Data planning
- [ ] [All of Us](https://www.researchallofus.org/data-tools/workbench/)
- [ ] image analysis
- [ ] shiny, reactive programming
- [ ] proper de-identification techniques
- [ ] HPC
:::

## Meeting Notes

### Oct.12 :newspaper:
I. Introductions (green box above)
II. Journal club
- Review https://doi.org/10.1093/jamia/ocy154
- Discuss as a group

III. Announcements

-

### Oct. 5 :film_projector:
I. Introductions (green box above)
II. Group Activity
- Lecture with Data Science Fellow, Dr. Zhiyang Fu
- dedicated breast CT via sinogram inpainting
- [Learn PyTorch for Deep Learning](https://datascience.arizona.edu/events/learn-pytorch-deep-learning-scratch) with Zhiyang

III. Announcements
- Find me at the CoM-P Resource Fair thursday October 6!

### Sept. 28 :link:
I. Introductions (green box above)
II. Group Activity
- Journal club in 2 weeks
- Advertising this meetup
- Data Science Ambassador is going to survey CoM
- possibly a Q&A session? or BYOD thing
- paper fliers on north campus
- Intro to problem: Health Data Science Community
- [Collaborative Brainstorming/Mind Mapping](https://app.diagrams.net/#G1R_s7yLHexAV88Py0wJV646ZEZAxefufL)
- [List Serv site](https://list.arizona.edu/sympa/)
- Code Commons Wednesdays 2-6 PM at the CATalyst Data Studio in UA Main Library

III. Announcements
- [Data Management on HPC](https://datascience.arizona.edu/events/data-management-hpc)
- [QIIME2 workshop](https://datascience.arizona.edu/events/microbial-community-analysis-16s-rrna-amplicons-using-qiime2-hpc) tomorrow

### Sept. 21 :school_satchel:
I. Introductions (green box above)
II. Learning Activity w/ Brandon
- [OMOP Data Model](https://ohdsi.github.io/CommonDataModel/)
- [Book of OHDSI](https://ohdsi.github.io/TheBookOfOhdsi/index.html)
- ETL (extract, transform, load)
- like data wrangling but more serious
- never edit raw data, make a copy
- [Athena: Search OMOP](https://athena.ohdsi.org/search-terms/start)
- [ATLAS: collect concepts](https://atlas-demo.ohdsi.org/#/search)
- [Online Training](https://academy.ehden.eu/my/)
III. Announcements
- [Quarto lecture - no installations](https://datascience.arizona.edu/events/reproducible-reporting-quarto), [DSI Drop in Hours](https://datascience.arizona.edu/events/data-science-drop-hours), [Intro to Python](https://datascience.arizona.edu/events/introduction-data-analysis-visualization-python-0)
- [APIs for Researchers](https://datascience.arizona.edu/events/demystifying-apis-researchers)

### Sept. 14 :newspaper:
I. Introductions (green box above)
II. journal club discussion
III. Announcements
- Do we need a volunteer for next week? - Brandon! :school_satchel:
- [Data Science Institute Events](https://datascience.arizona.edu/calendar)

### Sept. 7 :x:

- cancelled!

### Aug. 31 :link:
I. Introductions (green box above)
II. Group Activity w/ Brandon
- Intro to problem: Health Data Science Community
- [Collaborative Brainstorming/Mind Mapping](https://app.diagrams.net/#G1R_s7yLHexAV88Py0wJV646ZEZAxefufL)

III. Announcements

### Aug. 24 :school_satchel:
I. Introductions (green box above)
II. Learning Activity w/ Sarah

- Summary: The HIV Care Cascade (Care Contiuum) is a national/international way to measure HIV health programs outcomes. The Petersen Clinics pull data from Cerner/Banner and REDCap to identify patient's meeting specific criteria. Metrics are performed in Stata and Excel, but could benefit from any suggestions to make the information more engaging to health care providers.

- MRN mismatch: mrns can't always be used reliably to merge patient data
- regrex ?
- Cerner personID
- Future of data
- it's an ML problem! ML to the rescue!
- You could automate your .ppt reports with the code chunks included?
- Could [this] (the cascade charts) be done as a survival analysis? (I think this is a good idea - Shashank) (i think i was starting to work on this idea and will try it again)
- I can help with ML based survival analysis. (https://tinyurl.com/mwpundxz) (https://github.com/xinformatics/coxnnet_py3)
- Sankey diagrams could be helpful here to show how many patients enroll and reach to the stage where you get their viral load. (ooo- that sounds interesting! bonus: can be done in Excel!)
- note: i find the cascade to be non-specific, you could have an ART Rx but no visit, so be "linked" to care but never see a clinician. the Sankey diagram can show the pts compliant with ALL benchmarks (a much smaller group), and also highlight the commonalities of those not accessing all types of care.

III. Announcements

- Upcoming events
- [Reproducible Reporting with Quarto](https://datascience.arizona.edu/events/reproducible-reporting-quarto)
- [Data Science Institute Office Hours](https://datascience.arizona.edu/events/data-science-drop-hours)
- [Data & Viz Drop In](https://datascience.arizona.edu/events/data-viz-drop)
- [ResBazAZ Events](https://www.meetup.com/ResBazAZ/)

</br>

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#### Your feedback is encouraged ^^

---

### Archived Notes
:seedling: [Spring 2022](https://hackmd.io/Zu4XLBwETCS1hAWwwFQAhQ)