bioRxivBioinformaticsPreprint
Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems
Nianping Liu, Xuanzhi Chen, Miao CuiiD, Xiaoying Liao, Xiaoke Song, Sairam Pantham, Weize XuiD, Xiaojie QiuiD
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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