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Research Areas

Computational BiologySingle-cell, bulk RNA-seq, spatial, and biomarkers
CardiologyCardiovascular signals, cohorts, and interpretationImmunologyImmune cell states, signaling networks, and repertoire dynamicsNeurologyBrain connectivity, functional imaging, and electrophysiologyOncologyTumor microenvironment, immune response, mutations, and survivalPathologyWhole-slide imaging, tissue quantification, and spatial pathology

Application

Documentation

Documentation

Back to studies

Runs and reproducibility

Every oncology analysis step is a versioned pipeline run suitable for methods sections and audit trails.

Finding runs

LocationWhat you see
Study overview — Run historyAll pipeline runs for the study
Workflow pagesLatest completed run per pipeline type
Job poll responseFull result JSON with summary statistics and artifact paths

Run record

Each run stores:

  • Pipeline type (cell_communication, immune_profile, mutation_landscape, survival, interpret)
  • Status, timestamps, and run_id
  • Parameter JSON and pipeline version
  • Result summary (TMB, interaction counts, KM groups, etc.)
  • Artifact path under data/oncology/artifacts/{run_id}/

Provenance chains

Common chains:

interpret → mutation_landscape / immune_profile / cell_communication / survival
survival → clinical endpoints + optional feature matrix from immune or mutation runs
mutation_landscape → registered MAF dataset
cell_communication → expression CSV + metadata CSV
immune_profile → expression CSV (+ optional repertoire CSV)

Interpretation requires completed source runs with artifacts on disk.

Artifacts

Pipeline outputs live under:

data/oncology/artifacts/{run_id}/result.json

Poll job status to retrieve the full result:

curl http://localhost:8001/oncology/jobs/{run_id}

Completed runs are also listed via the metadata API:

curl http://localhost:8000/oncology/studies/{study_id}/runs

Failed runs

Failed jobs retain error messages in the job poll response. Common causes:

  • Missing required file path parameters (mutation_path, clinical_path, expression_path)
  • Expression/metadata CSV column mismatches for communication pipelines
  • Empty or malformed MAF files
  • Missing source run artifacts for interpretation

Fix the underlying issue and re-run from the workflow page or API.

Versioning

Every run records pipeline_version (currently 0.1.0 for oncology pipelines). Include run IDs and versions in methods sections for reproducibility.

Re-running pipelines

Launch the same pipeline again with identical or updated parameters. A new run is created; the UI displays results from the latest completed run per pipeline type.