Chan Zuckerberg GEN EPI (formerly Aspen) FAQs

How to use CZ GEN EPI

How do I login?

Navigate to czgenepi.org and click on the “Sign In” button in the upper right hand corner. You should be redirected to a login screen where you can enter your email address and password. Note: you can login to CZ GEN EPI using the same credentials that you used to login to Aspen and 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?

Once logged in, click "Upload" in the top right corner of the screen. We'll guide you through each step of the process of preparing your genomes and metadata for upload. We also pull genomes uploaded to GISAID once per day, if your genomes are on GISAID, they can be included for tree building without being uploaded to CZ GEN EPI.

How do I generate trees?

Check out our Tree Building Guide for complete information on the different tree types within CZ Gen Epi and how to build them depending on your use case.

How do I securely overlay my PHI / PII metadata?

For each tree in the “Phylogenetic Trees” tab of CZ GEN EPI, 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. Click on the “Download” button in the row of the tree that you are interested in and choose the file called “Private IDs (.tsv)”. This will download a TSV file where each row is a sample in the tree. You can add additional columns to add custom metadata.

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 CZ GEN EPI. If you have ideas or requests, please let us know at hello@czgenepi.org!

How can I get support or make a feature request?

Our team is here to support you! Please reach out to us anytime at hello@czgenepi.org. We regularly monitor that inbox for support requests, bug reports, and feature requests. CZ GEN EPI 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 hello@czgenepi.org 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 CZ GEN EPI, 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://czgenepi.org/resources

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://czgenepi.org/privacy

You can find our Terms of Service at: https://czgenepi.org/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. Other organizations that you share your data with can see your samples, but not your private, internal identifiers.
  • You can mark a sample as “private” anytime. "Private" samples are not shared with other organizations, but are visible to your group. CZ GEN EPI does not contain any personally identifiable information or protected health information.
  • We utilize industry standard best practices in information security, such as encrypting your data at rest and in transit, to ensure the security of 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, you can choose to mark them as "Private." These samples will still be visible to other members of your group, but will never be shared beyond your group.

  • We may also share your Pathogen Consensus Genomes and/or analytical outputs with third parties in accordance with the provisions of your organization’s policies and/or as required by law. For example, certain users in California currently allow the California Department of Public Health ("CDPH") to access data from their Group. Where such access is allowed by Groups, the third party can access this data through their own CZ GEN EPI accounts, and may have similar permissions as members of the uploading Group. However, they will not have access to your private, internal identifiers.
  • We are also working on new features to give you more granular control over how you share data with other groups

Which service providers do you use?

We rely on service providers to help us provide and improve CZ GEN EPI, 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 CZ GEN EPI’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 CZ GEN EPI to you.

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!