Leaving Stanford

This page has information on how to prepare your SCG account when you depart from Stanford. For best results, you should start planning about 12-24 weeks (one-two quarters) before your expected departure date.

Preparing to Leave

Once you know you will be leaving Stanford, you should start to plan for someone to be able to access your SCG data after your departure. We recommend the following actions, in order:

Make a Plan

One or two quarters before your expected departure date, have a meeting with your PI that is focused exclusively on planning for your departure. Using this guide as a reference, make a plan for how you will organize your space and how your data will transition. If you will be accessing SCG after you leave, discuss the terms of that access and when it is likely to end. Once the plan is agreed-upon, document the plan and get your PI’s email sign-off.

(The Techsource Before you Graduate guide provides resources for planning the non-SCG parts of your departure.)

Organize Your Data

If your lab already has a method for organizing data, check all files that you own and all files related to other work where you are involved are organized according to your lab’s standards.

If you do not have a standard for how to organize your data, decide upon one and implement it now. In general, you should keep each project in a separate directory, keep software separate from data, and keep personal files separate from lab project files. Your home directory should only contain personal items that nobody else will ever need, and that you do not need access to when your SUNetID expires.

If you re-organize data related to a project that is being actively worked on, keep others informed: Let your labmates know what you are going to do before you do it and let them know when the work is done. Once your data are re-organized, check if scripts might need paths updated and if Globus Guest Collections may need to be re-created under new paths.

Label Your Data

At this point—even if you are following a standard for organization—you may be the only person who understands your data and how it is organized. You must ensure this information is made available to your PI, to the rest of your lab, and to future researchers (including you — we all forget things over time!).

In each directory you own, create a file named README.txt. This text file should explain what is in this directory in enough detail that another lab member should be able to understand it. Explain how files are named. Note if any of the following are true:

  • The directory is associated with a particular project
  • The directory contains data that is High Risk
  • The directory contains PHI, NIH Controlled-Access Data (e.g., dbGaP), or is restricted in some other way.

Your READMEs will be read by many people. Labmates working on the same project will use your README to find data. PIs will use your README when determining what data to publish and what to archive. You may even use the README in the future, if you come back to Stanford or continue the same line of research elsewhere. Write with these possibilities in mind.

Check Permissions and Ownerships

With your data organized and labelled, you should now decide on who should own the files & directories after you leave. Make a high-level list of who should own what and get it approved by your PI. Keep a copy of the approval in email.

Make sure permissions are set to what you want. For files & directories which are accessible to the entire lab, you can transfer ownership as soon as the new owner is identified. For files & directories that are access-restricted or private, decide with your PI when ownership should transfer.

When you are ready for an ownership transfer, let us know: Tell us the paths to change, who the new owner should be, and attach a copy of the approval email (or CC the PI for them to approve via email).

Update Workflows

When your SUNetID expires, things which have been acting automatically on your behalf will stop working.

If you have any recurring compute jobs (scrontab jobs and jobs which resubmit themselves), you should stop scheduling/running those jobs. Afterwards, a labmate should start running those jobs. Once the jobs transition, check that they are running correctly under the new custodianship.

If you host any Guest Collections using Globus, those will stop working when your SUNetID expires. Unfortunately, Globus Guest Collections themselves cannot be transferred; a labmate will need to create a new Guest Collection and all workflows/documentation related to the old Guest Collection should be updated. The Leaving Stanford page on the Globus @ Stanford web site has more information about Globus in general.

If you have a web site hosted in /public, you will need to move the content to an alternative location. Content hosted for the UCSC Genome Browser should move to a labmates’ public directory or to a Globus Guest Collection. Lab content should move to an appropriate Stanford web-hosting option. Personal content should move to a third-party static web-site provider.

Contact Us

The SCG admin staff can help you with all the issues described above. Issues that are likely to need administrative intervention include:

  • file ownership and group changes
  • deletions of Globus Guest Collections
  • automated workflows

To ensure we can reach you, please update your email address in StanfordYou before you leave.

Do you need to access SCG after you leave?

If your PI will need you (or allow you) to continue to access SCG after you leave, you will need to maintain a sponsored SUnetID after your departure.

Faculty, Postdocs, and Students keep their Full SUNetIDs for 120 days after graduation or end of appointment. Students then receive an additional five years of Base SUNetID access. Staff and Affiliate SUNetIDs expire on the last day of employment or sponsorship.

Full details on SUNetID validity are available on the UIT web pages for Students/Postdocs and for Faculty/Staff. Students should also read the Techsource Before you Graduate information guide.

Extending A SUNetID

If you will need access after your SUNetID expires, your PI—or another authorized person, such as a lab manager—can sponsor your SUNetID. For more information, read the guides on Who can Access Sponsorship Manager and How to Sponsor a Person. The GBSC does not sponsor SUNetIDs, except in limited cases related to active BaaS consultations.

A Base SUNetID is free and is enough to maintain access to SCG, although it does not include access to services like Stanford email or Google Cloud. Read about which services are available by SUNetID level.

We wish you luck in your future endeavors!