A computer-implemented method performed at a health study management system collects health-related data from data sources, including sensors monitoring system users. A modular data ingestion subsystem includes interface modules adapted to receive health-related data from a respective type of data source. A modular data processing subsystem includes processing modules, processing health-related data to determine derived health indicators. The system receives configuration information for a health study using the health study management system, the configuration information specifying data collection activities, for collecting respective health-related data. The data collection activities include sensor-based data collection activities associated with a sensor type for collecting sensor data, and processing collected sensor data. The data ingestion subsystem and data processing subsystem are configured for the health study. Health-related data is collected from the data sources via the configured data ingestion subsystem and processed using the configured data processing subsystem. A study dataset is generated and output.