Technology and acknowledgements

Stack

Layer	Stack
Services and API	Python 3.11, FastAPI, Uvicorn
Console	Static HTML, CSS and JavaScript served by Aegle, WebGL reference anatomy, local 3Dmol molecular viewer
Numerical biology	NumPy, SciPy (LSODA), Myokit with SUNDIALS CVODE, libRoadRunner, libSBML, libCellML, COPASI/BasiCO
Genome-scale metabolism	Human-GEM 2.0, COBRApy, GLPK (isolated worker)
Knowledge	NetworkX property graph, TF-IDF retrieval, optional Neo4j export with explicit credentials
Analysis	JupyterLab, pandas, Matplotlib, nbformat/nbclient
Verification	pytest (about 6,500 tests shipped in the archive), Node.js and Playwright console checks
Packaging	Hash-locked requirements, checksum-verified release archive, Docker Compose

Published science and software

Livemore Bio stands on openly published science and software. Each source keeps its own license and attribution terms.

Human-GEM / Human2 v2.0.0, SysBioChalmers (CC BY 4.0), pinned at commit 635f533. Its citation.cff is retained with the installed model.
O'Hara–Rudy human ventricular myocyte model, CiPA 2017 variant, executed from its CellML source.
Hovorka et al., Physiol Meas 2004;25:905–920, and Wilinska et al., J Diabetes Sci Technol 2010;4(1):132–144, for the exogenous-insulin model.
Bergman et al., Am J Physiol 1979 and J Clin Invest 1981, for the glucose–insulin minimal model.
BodyParts3D, © The Database Center for Life Science (CC BY-SA 2.1 JP), and the Human Reference Atlas for reference anatomy.
NHANES 2021–2023 and the published Diabetes Prevention Program baseline (PMID 11092283) for population anchors.
3Dmol.js, Myokit, SUNDIALS, COBRApy, GLPK, libRoadRunner, libSBML, libCellML, COPASI/BasiCO, FastAPI and the scientific Python and Jupyter ecosystem.

Citing Livemore Bio

@software{livemorebio_2026,
  author    = {{Livemore Health \& Biosciences}},
  title     = {Livemore Bio: computational human-biology infrastructure},
  year      = {2026},
  version   = {stable 658870775e581c044a8832fd107e4097f7a30959},
  url       = {https://github.com/MannyAmah/livemorebio-dist}
}

When you publish work derived from a run, also cite the underlying models listed above. Each run records its sources in its provenance.

Technology and acknowledgements

Stack

Published science and software

Citing Livemore Bio

License