the platform for direct-to-participant research studies

View the Project on GitHub broadinstitute/pepper

What’s Pepper?

Pepper is an open-source platform for building high quality, scalable, cross-platform, and secure direct-to-participant studies for human subjects research. Pepper is the software foundation of a growing number of patient-partnered research studies operating at the Broad Institute and beyond.

We encourage you to use our deployed instance of pepper to host your studies, but if you would like to spin up your own instance of Pepper, you are welcome to do so. We feel that in the interests of democratizing access to patient partnered research, sharing our code is the right thing to do, even though we do not currently offer support for standing up your own instance.

We are also happy to look at pull requests, although our ability to do so is limited at this time. Please adhere to our code of conduct at all times.

Pepper is a team effort, and we are grateful to the many wonderful people who have contributed to it over the years, in particular:


We believe in loose coupling and the ability to innovate, so rather than bundling everything together, we have backend APIs and SDKs. Hopefully you find the SDKs helpful, but if they are too constraining, you can always drop back to the APIs directly.

Study Server

The study server is where participant-reported information is stored and managed using our APIs. The study server also manages participant-facing workflows and reminders.

Study Manager

Study staff interact with the study manager to review the status of participants and keep track of logistics such as form completion, medical records and kit logistics, abstraction, and review participant-reported data.

SDKs: Angular, iOS, and Android

Pepper’s SDKs provide more fluent ways to interact with the backend, and provide glue between backend APIs and Angular web apps, native iOS, and native Android.


We rely on docker and are in the process of moving towards google app engine to simplify deployment, compliance, and reduce operational costs. The Study Manager and Study Server communicate with one another directly, as well as through Elastic. Participant-facing applications primarily interact with the study server, while study staff primarily interact with the study manager. The backend of Pepper is written in Java and uses relational storage for well-structured data such as patient-reported information and abstracted medical records. Bucket-based storage is used for pretty much everything else.


Our bandwidth to assist with building the entire platform outside of its current home is extremely limited. Each repository should have sufficient build instructions for local builds. However, there are a number of dependencies that we know are challenging to stand up outside of the due to logistical constraints. Our primary deployment at is where we focus our efforts, so the investment we have made in making the platform easy to build and deploy outside of its current home is minimal. In general, we would prefer to see code contributions and use of the multitenant instance as it is routinely monitored both for uptime as well as security, and using a shared instance will be less expensive to operate than deploying your own. That said, PRs that streamline builds and deploys are very welcome!


We use vault to store build secrets. Our build scripts hardcode vault paths, and tools expect that whoever runs the scripts has sufficient access to vault. Take a look at *.conf.ctmpl files to get a sense of what these values are. We do not provide rendered example configuration files.


Auth0 is the backbone for identity management. In order to deploy a running backend instance, you will need at least one auth0 tenant. Auth0 has some terrific free options.

Sendgrid (Twilio)

Emails from Pepper are sent via Sendgrid. Sendgrid has great free options.


We use EasyPost as a shipping aggregator for studies that ship sample collection kits to participants. You can setup a test account with EasyPost.