Home - HealthRex/CDSS GitHub Wiki

Collaborative Work Tools

  • Github.com/HealthRex Get access here to the codebase, project and issue tracking tools, and shared Wiki
  • HealthRex.Slack.com Get onboard here to facilitate intragroup communication
    • group-meeting: Channel to subscribe to if you will be attending group meetings (time/place/subject announcements)
    • weekly-update: Channel for posting your weekly updates
  • Group Calendar: Publicly accessible to track group meetings, events, log when you will be out-of-town, etc. [email protected]
  • Box (Stanford Medicine) Sharing mechanism for most clinical data files
  • Google BigQuery Converging here for database hosting

Expectations

  • Regular check-in (phone or in person) with Jonathan (generally every 1-2 weeks). Even if my meeting calendar looks full, you can request and I'll make extra time if you need support. This is much better than not asking for help, and then flailing afterwards.

  • If you're unclear what the expectations are, work together to clarify. If we have different ideas of what the expectations are, or if you know what they are and decide not to follow through with them, expect disaster.

  • Weekly (Monday) updates to Slack on your personal Goals, Accomplishments, Objectives, Issues, and Miscellania

    • Goals: Months to years. Often helpful to frame these as a paper or conference submission, with a due date to aim for.
    • Accomplishments: What did you get done in the past week?
    • Objectives: What do you plan to get done in the next week? Even better to schedule milestones for the next 10 weeks.
    • Issues: What challenges are you facing that you may want some support for?
  • Regular attendance to group meetings -> Be prepared to present / facilitate ~once per quarter. Send a reminder message to the Slack channel about it 1-2 days prior. Usually review what you've been working on and want feedback on, but can also be discussing a technique or paper / conference / topic you think the group will be interested in. Don't just show us something, teach us something. Interactive workshop, even better. Highly recommend you NOT plan to talk for more than half the allotted time, as much of the value comes from engaged discussion, not an information relaying presentation.

In a post-pandemic world, we have Zoom/hybrid option, but I highly encourage in-person attendance and presence on group meeting (and BMIR Thursday colloquia) days to engage with other team members without requiring an appointment. This allows you to learn from others and others to learn from you. Given that other settings would expect you to be in a seat 40+ hours a week, I think it is more than reasonable to expect people to make an effort to be present for at least a couple hours per week. I'm not enforcing in-person attendance at this point, but realize that while purely remote connection feels convenient, you're much less likely to mutually benefit from mentorship, collaboration, networking, sponsorship, and general life satisfaction if the only way people can interact with you is through a Zoom appointment. Much of this will be unintentional. If poeple never see you in person, they may just forget that you exist. Respectively, they will not think to suggest, recommend, or otherwise connect you to opportunities as they arise.

  • If you want course credit, you can signup under BIOMEDIN 299. Remind me if you did this at the beginning of the quarter. Simpler to sign up for Credit/No Credit. If you sign up for a letter grade, then we'll need to work out grading criteria (e.g., A if you produce something ready to submit as a (conference) paper).

  • Unit testing framework: For any non-trivial code / application development, I expect respective unit tests to validate the function and programming interface for your code. Before doing any initial development or committing new changes to central source control repository, run the full suite of unit tests to verify everything still works as expected and you didn't accidentally break something else.

  • Most data files will be shared through a common database infrastructure or Stanford Medicine's Box system that is considered safe for PHI (Protected Health Information). Make sure you do not release this data beyond our own encrypted hardware. If you do not already have access, you may need to "opt-in" here to access to Stanford Medicine's Box system. Complete the respective Data Usage and Training Agreements as needed first https://github.com/HealthRex/CDSS/wiki/Data-usage-training-and-agreements

  • Time Off: High quality scientific work requires intensive and sustained effort. Yet I also subscribe to the principle that (creative) work such as scientific thinking, writing, and coding are not effective if you push overtime for more than two weeks. Respectively, okay to take all normal University breaks between "school in session" times off (e.g., Spring Break, Winter Break). I'll still usually be working, so you can reach out and connect if it helps you, but not obligated to any of our usual 1-on-1 meetings and we'll defer group meetings. Decompress and recharge as needed, though these are often some of the best times to catch up and make progress on work that require focus time without the distraction of meetings, seminars, and classes.

Outside of University break times, if you want to take some time off / vacation / travel, etc. All should be doable within reason. As long as your work is getting done and you are making good progress on your projects (crudely measured as peer-reviewed publications), that is what will matter to your career. If you take a long weekend, it's unlikely I will know or care. If you're out of town and offline for a week or more, you should likely let me know a month+ in advance. It should be fine, but we just need to plan project work around such gaps. If you're planning to be out of town for some weeks to visit family, but will still be working remotely, this could be fine and maybe even encouraged to stay connected with your families. If you're planning to be out of town and offline (not responding or doing remote work) for more than 2 weeks, you probably shouldn't be.

  • Gari Clifford's lab site has a detailed and thoughtful perspective on academic (computational) work. E.g., What to expect for authorship, letters of reference, code sharing, etc. Most of it shouldn't be an issue, yet each point was written because it came up with someone before.
  • Another nice lab manual. More for a biology lab, so discussion on reagents don't apply, but general principles on roles and expectations are good.