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PreprintCC BY-NCbioRxiv

Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems

  • N. Liu
  • X. Chen
  • M. Cui
  • X. Liao
  • X. Song
  • S. Pantham
  • W. Xu
  • X. Qiu1
  1. 1Stanford University
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Abstract

Scientific software is often locked in its source language, callable from others but not natively extensible or built upon. We present Bio-Babel (biobabel.stanford.edu), an autonomous framework that rebuilds software natively in target ecosystems and makes it agent-callable, shipping each package with an agent-readable contract of its usage. Reconstructing a hierarchical, interdependent R-to-Python single-cell stack, Bio-Babel reproduced the originals faithfully and revealed pancreatic differentiation dynamic defects under graded SWI/SNF loss.

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Cite

BibTeXRIS
BibTeX
@misc{liu2026biobabel,
  title = {{Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems}},
  author = {N. Liu and X. Chen and M. Cui and X. Liao and X. Song and S. Pantham and W. Xu and X. Qiu},
  howpublished = {bioRxiv},
  year = {2026},
  month = aug,
  doi = {10.64898/2026.08.30.743167},
  url = {https://www.biorxiv.org/content/10.64898/2026.08.30.743167v1},
  note = {CC BY-NC},
}
RIS
TY  - UNPB
TI  - Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems
AU  - N. Liu
AU  - X. Chen
AU  - M. Cui
AU  - X. Liao
AU  - X. Song
AU  - S. Pantham
AU  - W. Xu
AU  - X. Qiu
PY  - 2026
DA  - 2026/08/30
PB  - bioRxiv
DO  - 10.64898/2026.08.30.743167
UR  - https://www.biorxiv.org/content/10.64898/2026.08.30.743167v1
AB  - Scientific software is often locked in its source language, callable from others but not natively extensible or built upon. We present Bio-Babel (biobabel.stanford.edu), an autonomous framework that rebuilds software natively in target ecosystems and makes it agent-callable, shipping each package with an agent-readable contract of its usage. Reconstructing a hierarchical, interdependent R-to-Python single-cell stack, Bio-Babel reproduced the originals faithfully and revealed pancreatic differentiation dynamic defects under graded SWI/SNF loss.
ER  -