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