04 Call Digest [ 2023-fred-hutch ]

[stefaniebutland]

Hi @Openscapes/2023-fred-hutch-cohort,

Y'all are Champions of sharing your thoughts and questions in our collaborative Google doc! Below is a light digest of Call 04 with a reminder of your task for next time.

Sean added copious responses to people's Coding Strategies comments and questions and he invites you to book a House Call to get help (this is rare and wonderful). Consider screensharing and recording as you do this and share back to your Fred Hutch community; your strategy and solution might be what someone else is looking for!

• https://calendly.com/data-house-calls 
• https://calendly.com/data-house-calls/code 

Note DaSL has great relationships with Scientific Computing. For specific questions like GPU driver versions etc, it's ok to email them: [email protected]

In our final Cohort Call, Teams or individuals are invited to share their Pathway. Come to final Coworking Thursday, October 19, 10:00 - 11:00 am to think through that with your peers, or to get your own work done.

Here's Zoomie2 that includes Sean and your new DaSL colleague @sckott

Happy Open-Sciencing!

Stef, Julie, Sean, Monica, Liz

Digest: Cohort Call 04 [ 2023-fred-hutch ]

Openscapes_CohortCalls [ 2023-fred-hutch ] Google folder - contains agendas, recordings, pathways 

https://openscapes.github.io/2023-fred-hutch - Cohort website

Goals: We discussed open communities and coding strategies for future us.

Tasks: please see the Agenda doc (under Closing) for details and links.

• Prepare to present your Pathway work-in-progress on our final call. Each group has 5 minutes to share their pathway: (3 min present + 2 min Qs). See Champions Series - Pathways Chapter for more details and examples

Slide Decks:

• Open communities (slides)

• Coding strategies for Future Us (slides) 

A few lines from shared notes in the Agenda doc

• If you had 2 hours a week to prioritize learning/implementing something you've seen through Openscapes, how would you spend those 2 hours?

  • Getting a better understanding of our various workflows (different for each person on the team)

  •  Improving our data management. It's something I think we all want to do in the lab but at this stage it feels like it would be a ton of work.+++

  •  Organize my github repos, so it's easy for me and other people to find things that they need. Take time to write good README.md files. +1 +1

  • No question it would be documentation, I would likely split he time between just doing the documentation work that I wish existed for an hour, and then spend the next hour building tools to better helps folks do their own documentation work. The "building" work might include just making better guidance/ guidance in multiple formats for doing documentation.

• Strategies for protecting time / advocating for time. What do you need?

  • Goal of mine: add protected time to my outlook calendar for specific tasks or even brainstorming time  +1 +1+1

  • I wear a few different hats as a trainee / technician and often find myself with hands in multiple pots. Some focused time where I can collaborate with my colleagues in the lab on different computational projects specifically, whether virtually or in person, would be helpful +1+1

  • I hike/walk to think. That's work time, doesn't have to be at my computer +1

  • DaSL group code review hour or protected coding time would be good. Time protected for DaSL common needs.

• Open communities

  • Posit data science hangouts (online) are really fun!

  • Common theme: didn't know open communities existed until were invited to one

  • Geographically local communities too, not only online

  • CascadiaR conf was fun, especially being in an envt where ppl were excited about talking about scientific code, with low stakes, not about achievements

• Coding strategies for Future Us - Look in the doc for MANY replies from Sean Kross!

  • How do these coding strategies resonate with you / in your work?

  • I definitely fall prey to setting brittle file paths, which has come back to haunt me in old notebooks! I knew that there should be a better way, and now it seems obvious that you should set the working directory to the highest file path for the project.

  •  Love the idea of having project specific folders, but I find myself duplicating data files to be used for multiple projects 

  • We are developing a lab wiki and it would be amazing if team members could just put in URLs for their working notebooks to share their most updated work or to document past work. +1

  • What do you need to better strengthen the consistency of your scientific workflow (quality, reproducibility, utility, collaboration)? How can DaSL help?

  • ‎I think I need a singular code-sharing space on github etc. to allow myself to be open to a more collaborative coding experience

  • Additional support for onboarding, Github, etc. - Our lab ran out of seats in our Github organization so the fellow I was working with this summer couldn't access any of our internal documentation and I had to send it all to her manually. It also limits my ability to share repos with collaborators even within the Hutch - there must be a better way around this.

    • My summer mentees weren't able to document their projects as well as we could have wanted because of this

  • Everything is specific to jupyter notebooks at the moment, and I am considering switching to VS code. A little worried I'll have to remake all my environments.

  • How we can keep version control of large file data

  • When someone new joins your group, how do standardized workflows, automated workflows, and code fit into the mix?

  • Developing a Lab Atlassian Wiki that will have some onboarding elements (and hopefully workflows) through https://wiki.fhcrc.org/ , but it is in it's very early stages (Ha Lab)

  • We have a wiki and standard base workflows for common tasks/analyses which work for most cases and can be adjusted to a specific task if needed.