Aspen FAQs

How to use Aspen

How do I login?

Navigate to aspen.cziscience.com and click on the “Sign In” button in the center of the page. You should be redirected to a login screen where you can enter your email address and password. Note: you can login to Aspen using the same credentials that you used to login to the COVID Tracker app. If you forget your password, click the “Forgot password?” link on the login screen. You will receive an email with instructions for resetting your password.

How do I upload samples?

Until we conclude SARS-CoV-2 genomic sequencing-as-a-service in June 2021, we will continue to upload any consensus genomes created at the Biohub directly to Aspen.

If you are generating your own SARS-CoV-2 consensus genomes, please continue to upload these to GISAID. We will pull new genomes uploaded to GISAID once per day. After we pull from GISAID, you should see your genomes in Aspen within 1 day.

In June, we will be adding the ability for you to upload consensus genomes directly to Aspen, making the entire process of getting your data into Aspen smoother and faster. Stay tuned for this update!

How do I generate trees?

Every night, Aspen will generate a new Nextstrain build with all of your samples. You can find these new phylogenetic trees by clicking on the “Phylogenetic Trees” tab. The trees are sorted by “Upload Date” so your newest builds will be at the top of the list. For now, these builds will automatically include all of the samples your DPH has uploaded to Aspen. In the very near future, you will have the ability to kick off your own tree builds, allowing you to select only the set of samples you are interested in.

How do I securely overlay my PHI / PII metadata?

For each tree in the “Phylogenetic Trees” tab of Aspen, you can download a TSV template that can be used to collect any other metadata that you would like to visualize alongside your genomic data.

Once completed, you can drag and drop this TSV file onto your tree visualizations in Nextstrain. Your private metadata spreadsheet will never leave your computer; see here for more details.

We’re also hard at work thinking of new ways to enable you to securely overlay PHI / PII directly in Aspen. If you have ideas or requests, please let us know at helloaspen@chanzuckerberg.com!

How can I get support or make a feature request?

Our team is here to support you! Please reach out to us anytime at helloaspen@chanzuckerberg.com. We regularly monitor that inbox for support requests, bug reports, and feature requests. Aspen is still in its early stages, and we work closely with our users to improve the experience -- we read and discuss every bit of feedback. We want to make sure that we are building a tool that satisfies the most pressing needs of the public health communities.

How can I delete my data?

Please reach out to our team at helloaspen@chanzuckerberg.com with your deletion requests and we will handle it within 60 days. When we delete your data, we remove it from our database and any file storage we have. In a future version of Aspen, you will have the ability to delete your own data from within the app.

COVID Tracker Program

Where can I find links to the COVID Tracker Seminar Series?

You can find links to recordings of all previous seminars at https://covidtracker.czbiohub.org/resources. If you would like to be added to the calendar invitation for any future seminars please email Alli Black.

Where can I find aggregate statistics on genomes sequenced by the Biohub?

Aggregate statistics on genomes sequenced by the Biohub can be found at https://covidtracker.czbiohub.org/statistics. This page is available to the public.

Privacy and data sharing

Where can I view the Privacy Policy & ToS?

You can find our Privacy Policy at: https://aspen.cziscience.com/privacy

You can find our Terms of Service at: https://aspen.cziscience.com/terms

A summary of key things to know:

  • You always own and control the data you upload.
  • Only other members of your group can see your data. CDPH can see samples, but not your private, internal identifiers.
  • New sequences will be automatically submitted to GISAID two weeks after upload, unless marked "private."
  • You can mark a sample as "private" anytime during the first two weeks after upload. "Private" samples are not shared with CDPH or GISAID, but are visible to your group. (For now, please send us a quick email to mark samples as "private.")
  • Aspen does not support protected health information.
  • We utilize industry standard best practices in information security to protect your data.

Who else can see my sample data?

Your group (i.e., your Department of Public Health / "DPH" in many cases) can see all of the consensus genomes, metadata and trees that are uploaded or created by other members of the group to facilitate seamless communication and reporting.

When you upload new samples (or send a new sample to CZBiohub for sequencing), you can choose to mark it as "Private." These samples will still be visible to other members of your group, but will never be shared beyond your group.

For new samples that you do not choose to mark "private," we share this data in two ways:

  • Consistent with the prior COVID Tracker program’s policies, the California Department of Public Health (CDPH) will be able to see non-private samples, but with your internal, private identifiers redacted.

We are also working on new features to give you granular control over how you share data with other groups (e.g., CDPH, or other local DPHs).

Which service providers do you use?

We rely on service providers to help us provide and improve Aspen, specifically:

  • Our technology partner, Chan Zuckerberg Initiative, LLC, who helps us operate and secure our technical infrastructure
  • Amazon Web Services, which hosts our database and pipelines.

In our work with any service provider, we always prioritize the security of your data and preventing unauthorized access (e.g., by encrypting your data at rest and in transit). All service providers are bound by Aspen’s Terms of Service and Privacy Policy, and are only permitted to use your data to provide the relevant services that we rely on in order to offer Aspen to you.

How do I share my data with CDPH?

Please see “Who else can see my sample data” above.

How do I access pathogen genomic data stored in Terra?

We’re partnering with CDPH and Terra to make it seamless for data to be accessed from CDPH very soon. Stay tuned for updates!