CAphase2

CAphase2 is a modular software framework designed to support the second phase of computational analysis workflows in research settings, especially where data fusion, rigorous modeling, and decision support are needed. Built as the successor to CAphase1, CAphase2 expands statistical modeling capabilities, supports adaptive analysis designs, and provides tools for simulation and visualization.

The project uses a plugin-based architecture that allows researchers to plug in data adapters, models, and reports. It supports Python and R interfaces and can connect to common data sources such as CSV files and SQL databases, as well as clinical data standards like HL7 FHIR. It includes a workflow layer to orchestrate steps and aims to ensure reproducibility with versioned pipelines, complemented by visualization dashboards for result interpretation.

Its features include data integration and cleaning, exploratory analysis modules, Bayesian and frequentist modeling options, dose–response and time-to-event analyses, adaptive design simulations, reporting templates, and audit trails. CAphase2 is designed to support transparent and auditable analysis processes across collaborative teams.

Development and governance are managed by the CAphase Collective, with contributions from academic laboratories and industry partners. The project is released as open-source software under a permissive license, and its repository provides issue tracking, contributor guidelines, and release notes.

Usage of CAphase2 spans phase II research contexts such as oncology and pharmacology, where it is employed to analyze trial data, run simulations to evaluate design choices, and generate standardized reports for stakeholders. History-wise, CAphase2 emerged from CAphase1 to address needs in second-phase analysis, with the first public release in the 2020s and ongoing development since then.