Publications

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

Nianping Liu, Xuanzhi Chen, Miao Cui, Xiaoying Liao, Xiaoke Song, Sairam Pantham, Weize Xu, Xiaojie Qiu

Preprint · 2026 · Stanford University

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.