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Operations and Management


All CEDAR software is stored in GitHub repositories. We created a GitHub organization called metadatacenter to manage access to the software. Since all CEDAR software is open source, we provide read access to all GitHub users.

We make all our software freely and publicly available under the 2-Clause BSD open-source license, which allows the dissemination and commercialization of derivative products by everyone. We have used this license in our CEDAR, Protégé, and NCBO projects. The CEDAR Web site facilitates browsing and downloading of all tools and knowledge resources in the project.

Issue Tracking

CEDAR uses a GitHub-based project issue tracking board to track features and bug fixes. This board is integrated with GitHub so feature requests and bug reports made by GitHub users can be automatically tracked. We also have a dedicated mailing list.


We continuously monitor system uptime using the third-party StatusCake system. Any outages are immediately routed to core developers via email and Slack channels. Since its release in 2017, the system has had only a dozen hours or so per year of outages.


The CEDAR software team adopts an agile software development methodology with frequent releases that focus on adding new system features.

The software development team uses the Git Flow branching model to control the addition of features to each release. Minor releases are usually made approximately every month, with major releases every year or so. The first major 1.0.0 release was made in February 2017. Releases are tagged using standard Git-based version tagging and all releases are publicly available on GitHub. We generate a comprehensive release documentation on each numbered release that identifies the new features provided in the release in addition to any bug fixes. We also produce a Web-based newsletter that describes the features contained in major releases.

We use standard test-driven strategies for developing our REST-based services and also have developed an array of tests for CEDAR’s front end components. All CEDAR components have a set of tests that are executed automatically using the Travis continuous integration system. All developers are immediately notified via Slack when tests fail so that issues can be quickly addressed.

Backup Schedule

All CEDAR servers that contain persistent data are backed up nightly. The servers that host CEDAR’s main production and staging services are also backed up nightly, with incremental backups every hour.

Incident Management

We define incidents as problems in production. Incidents may or may not be customer facing. Incidents are categorized as:

  • Blocker Major failure for a user or failure that affects the entire system or multiple modules of the system. This failure prevents a person from using the system.
  • Critical Major functionality is impaired in one or more common scenarios. A temporary workaround is available.
  • Minor A core function or feature is failing in rare or difficult-to-reproduce scenarios for a user.

Incidents may be caught through automated monitoring and alerting (e.g., StatusCake, Slack) or manually (user-reported, reported by developers or UI teams).

We aim to address blocker incidents immediately and, ideally, to fix them within minutes. Critical issues are also addressed immediately with the goal of fixing the underlying issue within 24 hours. For minor issues we create a GitHub issue and decide if it is serious enough to be incorporated into the next sprint or it can wait for subsequent sprints.

Access and Security

New developers added to the CEDAR codebase complete an internal onboarding process that includes access to various internal groups. Highly granular repository-level modification access is provided through standard GitHub access control mechanisms. Security related onboarding includes completion of the following:

  • HIPAA and Health Information Security training
  • Application Security Training

CEDAR servers are deployed using an in-house server hosting infrastructure. Access to deployment machines is governed by Stanford security and access control mechanisms. Access is mediated through each user’s Stanford SUNetID account credentials.

In addition to this, Stanford hires are required to complete a background check. Once these procedures have been completed, developers are then considered suitable for code deployment and on-call operations.