05_CallDigest [ 2023-fred-hutch ]

[stefaniebutland]

Hi @Openscapes/2023-fred-hutch-cohort

Thank you all for our final session last week! It was really inspiring to see you find common themes with your colleagues across Fred Hutch labs, share about where you’d like to improve your workflows, and identify new ways to connect around open science. It’s so great to hear that DaSL will continue with Lakeside Chats. This is just the beginning! Below is a brief digest of Call 5.

We look forward to watching you advance on your journeys! We’ve got several ways to stay in touch.

• If you can make it, please join us for a 3 month checkin in the new year. We’ll send a calendar invite.
• Join Openscapes Slack (if you haven’t already) where your colleagues and other friendly Openscapes Champions and Mentors are. Email stefanie@openscapes.org if you’d like an invitation or some orientation.

Increasing the visibility and value of the work you’re doing is important. You can add Openscapes to your CV: “Professional Development: Openscapes Champions Program, August - October, 2023 DOI: 10.5281/zenodo.7407247”. You will find your Completion Certificates in our Cohort Folder, Openscapes_CohortCalls [ 2023-fred-hutch ]. Look for a summary post on the Openscapes blog in November and share it with your colleagues. Would someone from each team please give Stef a physical address where we can send stickers for you to distribute within your team?

Openscapes would love your feedback so we can improve and support future cohorts; please fill out this survey by November 16th.

In the meantime, use our Openscapes Spotify Playlist for inspiration - updated with your tunes! 🎶

Happy Open-Sciencing!

Stef, Julie, Sean, Monica, Liz

Digest: Cohort Call 05 [ 2023-fred-hutch ]

Openscapes_CohortCalls [ 2023-fred-hutch ] Google folder - contains agendas, recordings, pathways
https://openscapes.github.io/2023-fred-hutch - Cohort website

Goals: Teams shared their Pathways and we discussed next steps going forward.
Teams' Pathways
Most work and links shared in Pathway presentations are private to Fred Hutch so we’re not linking them here. Thanks to folks for adding them to our collaborative Agenda doc!

Openscapes Team (slides). Stef shared how we use the Kyber R package to automate some processes we need to repeat many times, like creating Cohort Call Agendas. She noted the impact of participating in open communities on getting critical R help to learn to make Openscapes Certificates of Completion for everyone by combining Google Sheets, a create_certificate.R script and a certificate.Rmd.

Berger Lab. Alice talked through the team’s Pathway sheet (linked in the doc). Sita put an example analysis in a GitHub repo shared with the lab for the first time. She’s done this so others can reuse or adapt the code and have an example to follow for more open practice. Open doesn’t have to mean fully public; it can be private to Fred Hutch, or even just your lab. Daniel was inspired to use GitHub Issues and screenshared a checklist for the week with people’s replies. This led to a discussion of Issue templates and other recurrent processes they could use a checklist or template for. Monica shared a package she made with basic analysis templates for different immunoassays and she’s working on more of these for DaSL’s work.

Setty Lab. ‎Cailin and Sarah co-presented to share their plans in categories: Lab wish list; Community involvement; Data sharing; Promote DEI, identified next steps in each and how they’re making progress. They’d like to switch to VS Code as it has better integration with GitHub and they want to use Copilot. Sarah wrote a script to make setting it up smooth for people. They plan to start a once a month meet up to do something that’s related to work but that’s not the usual data science discussion. Examples are listening to a podcast and discussing, or learning about techniques for giving feedback. They prompted a good discussion of using Notion that revealed expertise and willingness to share across the labs and DaSL.

Ha Lab. Thomas raised the challenges of version control and code sharing when changes made downstream are not pushed back to the main GitHub repo. Monica noted that slowing down to speed up is key here; behavior change takes time and care but the benefits are huge. Patty screenshared her use of the project management tool Jira (supported by Fred Hutch). It requires upfront infrastructure development, but it’s worth it. She is piloting Starfish, a software application for unstructured data management, for viewing all your files, tagging them with metadata or actions like ‘moved to S3, and for visualizations of file sizes and counts. Adil brought up something that the other groups see as a common need: how to keep track of papers with useful looking data and then find them later when you actually need them.

DaSL. Sean wants people to stay in touch! With each other and with DaSL. He shared many ways to continue to connect with DaSL. The newsletter is where they post all educational offerings like this one. He shared links for bookable Data House Calls for code, GitHub, and data management questions or issues, and Monica holds Data Analysis/Stats and Clinical Data House Calls. Sean even offered 1:1 coworking time to folks in this Cohort! Such rich opportunities to get direct engaged support. Links for booking are in our Agenda doc. Monica has started hosting Lakeside Chats for discussions and coworking! She’s been forking Openscapes practices for the win - like reusing our agenda doc structure and collaborative note taking. In response to the interest in Notion, Monica screenshared how she uses it for Agendas and Notes for Our Connections Points. She’s got templates for different meeting types to save time and minimize errors that can come from manual re-typing.

A few lines from shared notes in the Agenda doc

• ‎I think continuing seaside chats and coworking could be an effective means of group communication for the lab, for data practices and lab work in general+1 +1+1
• Will there ever be a semi-holy-grail for the good practices with lots of data?
• Perhaps most interesting to me is the number of methods there are to achieve relatively similar goals (organization of code/documentation, project management, etc.). Overall, I think the current need I feel most acutely is a better understanding of which tools achieve these objectives with the least effort, …
• I think that we could use support from DaSL on some specific parts of our wish list (ex data management). I think the seaside/lakeside chat format fits in well with the non-traditional lab meetings we’re thinking of doing and we can merge those two concepts together for some structure at least at the start +1.
• Coworking and quiet working spaces (with good internet connection!) would be a great tool to support computational work for those of us doing hybrid wet/dry work.
• When to automate? When I do this on average π times per month or know that π people will use this
• Opened my eyes to a lot of possibilities and got a lot out of this program. Implementation and changing current practices feels challenging.
• The Dream is this Openscapes Cohort and way of working is the on-ramp. This is not the end! (If you don’t want it to be)

Thank you all so much for your participation! Please reuse/remix resources and stay in touch.

• openscapes.org
• /series: Champions program lesson series
• /media: slide decks, publications, media
• /blog: stories from the community
• github: @openscapes
• how_we_work, seaside-chats: Examples from previous cohorts
• Mastodon: fosstodon.org/@openscapes
• artwork: by the amazing Allison Horst