# :warning: This is an archive, [visit current](https://hackmd.io/6iddVJbuTQujG--cOgLfxQ?both)
## [Hitchhikers Guide to Biomedical Scientific Computing](https://datascience.arizona.edu/events/hitchhikers-guide-biomedical-scientific-computing)

:::success
### Living Sign in :wave:

Sign in here, update whenever!

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

:couch_and_lamp: [**Heidi Steiner**]([e-mail]), Data Science Educator @ Data Science Institute, human genome and gut microbiome research `R`
:love_letter: **Sarah Yates**, Sr. Data Specialist @ Petersen HIV Clinics, patient population metrics and quality improvement programs `stata`
:female-scientist: **Juvie Farol**, PhD Student @ CoM-T, pharmacogenomics
:baby_chick: **Nicole Jimenez**, Post-doctoral researcher @ CoM-P, vaginal microbiome and gynecological phenotypes `microbiome`
:octopus: **Brandon Jernigan**, Biobank Research Specialist @ UAHS, Biorepository quality and IT `EHR` `communications`
:scissors: **Michael Plank**, Post-doctoral Researcher @ Department of Molecular and Cellular Biology, large scale network `omics` `R` `perl` `systems biology`
:coffee: **Angie**, Post-doctoral Researcher @ Department of Molecular Cellular Medicine
:sunny: **Marjan Aghajani**, Post-doctoral Researcher, @ CoM-P, Translational Cardiovascular Research `proteomics` `metabolomics`
:cloud: [**Shashank Yadav**](xinformatics.github.io), 1st year PhD student, Department of Biomedical Engineering `dna` `protein` `biomedical imaging`

:::

## :scroll: Meeting Notes

### June 16, 2022 :speech_balloon:

- Heidi, Sarah, Juvie
- Heidi is teaching on [Data Visualization](https://datascience.arizona.edu/events/power-data-visualization) tomorrow at 1pm
- [New Data Sharing Management Plan video series](https://arizona.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0badb55c-2a53-48c5-a491-aeb401522714&start=0)

### June 23, 2022 :film_projector: :black_left_pointing_double_triangle_with_vertical_bar:

- Heidi, Nicole, Juvie, Sarah, Brandon
- [Slides](https://datasciencebox.org/course-materials/_slides/u1-d03-toolkit-git/u1-d03-toolkit-git.html#1)
- More follow-up information [here](https://the-turing-way.netlify.app/reproducible-research/vcs.html)
- Kristina Riemer and Jessica Guo are teaching [Principles of Tidy Data & Data Management](https://datascience.cals.arizona.edu/services-overview/workshops?_gl=1*1340o5q*_ga*MTUyMzQ2NDExMC4xNjUxMDAxNjgx*_ga_7PV3540XS3*MTY1NjAyMDk5My4xMTUuMS4xNjU2MDIxMDI3LjI2). [Register here!](https://arizona.zoom.us/meeting/register/tZYkd-uoqj0oH9FPnVZws-6ziybvI9Vc_5Pr)

### June 30, 2022 :computer: :book:
- Heidi, Sarah, Juvie, Brandon, Nicole
- [Installing](https://jupyter.org/install) `jupyter lab` and `jupyter notebook`
- on Mac this looked like `brew install jupyterlab`
- on PC you'll need `pip` or another installer to run `pip install jupyterlab`
- Clearing up some of the [jargon](https://docs.jupyter.org/en/latest/projects/architecture/content-architecture.html)
- [Try this notebook](https://training.galaxyproject.org/archive/2021-12-01//topics/data-science/tutorials/r-dplyr/tutorial.html)
- [Reproduce this `jupyter notebook` pipeline](https://github.com/tomszar/HGDP_1000G_Merge/blob/master/Code/2018-05-MergeGenotypes.ipynb)
- Similar but different, slides from [Quarto for Reproducible Reporting](https://hidyverse.github.io/resbaz22/#1)
- ResBazAZ [meetups](https://www.meetup.com/ResBazAZ/)

### July 7, 2022 :computer: :book:

- Heidi, Juvie, Brandon, Michael
- Brandon is walking through a jupyter tutorial!
- Another great [example notebook](https://github.com/clizarraga-UAD7/Notebooks/blob/main/ExploratoryDataAnalysisExample.ipynb)
- [UK Biobank in RStudio](https://dnanexus.zoom.us/webinar/register/2716545396117/WN_b_D0T3bPTzyEy9l7fWbYgQ)
- NIH Data Sharing and Re-use [seminar series](https://datascience.nih.gov/data-sharing-and-reuse-seminar-series)
- Aegis Bioinformatics seminar series (Hybrid, Monday at 3P)

### July 14, 2022 :x:

- Meeting cancelled

### July 21, 2022 :speech_balloon:

- Heidi, Brandon, Michael, Angie
- Map/Pool of resources
- HPC and where to get training
- Collaborations, who does what
- edge, linkedin learnings trainings
- Fantastic CI and where to find them
- Brandon's [Notion](https://ua-data-science.notion.site/c0bc65982aff4a5dae913fa64aee6cc4?v=7a597a72dc274e8893c8c971c5687750)
- [Data Methods](https://discourse.datamethods.org/)
- Slack Channel?

### July 28, 2022 :x:

- Meeting cancelled

### August 4, 2022 :computer:

- Heidi, Brandon, Michael, Marjan
- Recap of rstudio::conf(2022) and `Pharmaverse`
- I wrote a [blog post](https://heidiesteiner.netlify.app/post/2022/rstudio-conf-2022/) with some more detail if you're interested in the conference
- some of my favorite talks:
- [How to be a pollinatoR](https://rsconnect.norc.org/rstudioconf-pollinator/presentation.html#1)
- [WTF AITA](https://wtf-aita.com/talk/)
- [Hello Quarto](https://mine.quarto.pub/hello-quarto/#/hello-quarto-title)
- [Demystifying MLOps](https://isabelizimm.github.io/rstudioconf2022-mlops/#/section)
- New-to-me health science related resources to explore:
- packages for manipulation of common data types (I think) [`healthyverse`](https://www.spsanderson.com/healthyverse/), and it's counterpart [`pharmaverse`](https://pharmaverse.org/)
- a neutral home for open source pharma software that is not tied to one company or institution, [OpenPharma](https://openpharma.github.io/#manifesto)
- a [GitHub blog post](https://www.openscapes.org/blog/2022/05/27/github-illustrated-series/) with an illustrated rock climbing theme
- Related upcoming events
- Aegis Bioinformatics Working Group
- Monday Aug 8 3-5p MST
- Health Sciences Innovation Building, Rm 642
- [Zoom](https://arizona.zoom.us/j/89781493367)
- [R/Pharma](https://rinpharma.com/post/2021-06-17-announcement/) conference
- [R/Medicine](https://events.linuxfoundation.org/r-medicine/) conference

### August 11, 2022 :speech_balloon:

- Heidi, Nicole, Brandon, Sarah
- NIH data management and sharing plan discussion
- [Workshop next week!](https://datascience.arizona.edu/events/phi-and-duas-and-irbs-oh-my-data-management-and-sharing-plans-2023-nih-requirement-0)
- Do you have all the knowledge you need to make the most of this event?
- A new fun "10 Simple Rules" paper: [Ten simple rules for maximizing the recommendations of the NIH data management and sharing plan](https://doi.org/10.1371/journal.pcbi.1007846)
- What's the difference between rule 2 and 4?
- Good resource for [standardized Informed Consent language](chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://osp.od.nih.gov/wp-content/uploads/Informed-Consent-Resource-for-Secondary-Research-with-Data-and-Biospecimens.pdf)
- :exploding_head: [Check the readability of your document](https://www.officetooltips.com/word_2016/tips/viewing_document_and_readability_statistics.html) to make sure you've written at an **8th grade level**
- remember to differentiate between **biospecimen** and **data**
- Do you **plan to share your particpant's biospecimen** with a repository?
- Do you **plan to share your participant's de-identified electronic health record data** to the world wide web?
- Upcoming learning events:
- [NIH DSMP 2023 Policy](https://datascience.arizona.edu/events/phi-and-duas-and-irbs-oh-my-data-management-and-sharing-plans-2023-nih-requirement-0)
- Next Wednesday 2pm (Arizona time)
- [Fall Reproducibility Workshop](https://datascience.arizona.edu/events/fall-2022-workshop-series-reproducibility-and-data-science-r) with Drs. Guo and Riemer
- Tuesdays from 11-1p (Arizona time)

### August 18, 2022 :notebook_with_decorative_cover:

- Heidi, Brandon, Sarah, Shashank
- - New meeting time for Fall 2022
- current time interferes with [FOSS](https://cyverse.org/foss?mc_cid=a34047b15e&mc_eid=63be86f473)
- [**New event Wednesdays @ 12pm**](https://datascience.arizona.edu/events/health-data-science-hangout)
- starts next week (Aug 24)
- consistent rotating schedule
- invited speakers series
- I invite outside people one week per month to talk about their work
- vote month before
- Team Connection working group
- creates or pushed forward the creation of resource to connect people
- bring your own issues
- sign up on a calendar?
- book club
- choose a data science book and walk through it together on a once/mo basis

- Upcoming learning events
- r/medicine
- Sarah @ ryan white conference