Loggene

Loggene is a software framework designed to log, organize, and audit gene-related experimental data and analyses. It provides a structured data model for projects, samples, experiments, sequencing runs, analyses, and results, with the aim of improving reproducibility and provenance in genomic research. The framework supports versioned records, time stamps, and immutable entries, enabling researchers to trace the lineage of data from collection through processing to interpretation.

The project emerged in the 2010s from a community of researchers and software engineers seeking a unified approach to data provenance in biology. Loggene uses a modular architecture consisting of a core API and a suite of plug-ins that connect laboratory instruments, sequencing platforms, and analysis pipelines. The data model centers on entities such as Project, Sample, Experiment, Run, and Analysis, and tracks metadata, access permissions, and software versions. It supports export in JSON and CSV, and provides audit-friendly views of data history.

Adoption and reception have grown in university labs and smaller data repositories to improve traceability and collaboration. It integrates with common workflow systems and laboratory information management practices, offering interoperability with related standards in data provenance and bioinformatics. Some users note a learning curve and overhead for very small projects, while others highlight its value for ensuring reproducibility and accountability across complex experimental pipelines.