Portable Encapsulated Projects

An open structure and toolkit for organizing large-scale, sample-intensive biological research projects.

Quick start

What is a PEP?

PEP, or Portable Encapsulated Projects, is a community effort to make sample metadata reusable. PEPs decouple metadata from analysis by providing:

  1. a standardized metadata structure;
  2. a metadata validation framework; and
  3. programmatic metadata modifiers.
A PEP is written using a familiar yaml + csv format that can be read by our R and Python packages, and well as by workflow frameworks. PEP is your metadata solution for sample-intensive research projects. The PEPkit suite is a set of modular tools that work to help you use PEP in practical applications.



Validation framework

A PEP can be validated using a generic JSON schema, or you can define your own custom schema for a more specific analysis.
JSON-Schema

Workflow systems

A PEP description can be a starting point for many workflow systems, with more on the way!

Data analysts

Start by writing your metadata in PEP format, and immediately benefit from metadata organization tools written in R and Python.

Software developers

Handle input sample metadata formatting, parsing, and validation with our R or Python APIs, making your tool able to process PEP-compliant projects.

PEPkit: the bio data management toolkit