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Next Steps

After you have read the overview and completed either a local simulation or a federated deployment setup, use the rest of the documentation based on what you want to do next.

Configure a study​

Use the User Guide when you are preparing your own data, adjusting runtime settings, or operating FedGWAS beyond the first quick run.

  • Configuration: center YAML files, input data paths, thresholds, output directories, and Flower settings.
  • Simulation Mode: repository-level local simulation behavior, Flower run config, scenario layout, and output locations.
  • Installation and Overview: federated roles, ports, and checks.
  • CLI Deployment and Script Deployment: the two ways to start SuperLink, SuperNodes, and flwr run.
  • fedgwas-sim CLI: full command reference for local simulation projects, presets, checks, evaluation, and result collection.
  • Troubleshooting: common setup, data, PLINK, and runtime issues.

Run examples​

Use Examples when you want a known scenario before moving to your own study.

Understand the design​

Use Design when you need to understand why the pipeline is structured the way it is, or when you are reviewing the protocol before extending the code.

  • Architecture: major components and how Flower, clients, server strategy, PLINK, and output directories fit together.
  • Workflow: four conceptual screening stages and the federated rounds from initialization through association screening.
  • Privacy masking: encryption, shuffling, anonymization, lightweight secret-sharing, and the server’s relay role.

Reference APIs and outputs​

Use API Reference when you need exact runtime fields, module responsibilities, or output file expectations.

  • API Reference: Flower run config, server and center configuration fields, and main Python entry points.
  • Output files: result directories and generated artifacts.
  • Module Reference: client, server, quality control, kinship, and association modules.