Bio-Babel (biobabel.stanford.edu) is a framework for rebuilding scientific software ecosystem natively in another language and making it callable by agents, which contains four parts, namely Bio-Babel-toolkit,Bio-Babel-MCP, Bio-Babel-annotator, and Bio-Babel-Bench. Bio-Babel also ships a contract for each translated package to allow easy access by AI agents, such as Codex, Claude code, PantheonOS and others. Bio-Babel-Toolkit is the build side, driving coding agents to produce the translated packages, ensuring each member of the target ecosystem to ship a contract in its own source tree. Bio-Babel-annotator writes that contract, and Bio-Babel-MCP serves it to agents as a read-only surface. Sepcifically, the Bio-Babel-Toolkit workflow consists of 13 consecutive steps, grouped into preparation (steps 1-8), implementation (step 9) and validation (steps 10-13). The package of interest is first parsed to create a dependency graph between different functions where each node corresponds to a function while the directional edge indicates the dependencies between functions. Circularly connected components in the graph are firstly grouped into strongly connected components (SCC). At step 9 the export-dependency graph is merged through a greedy merging algorithm to form different dependency-ordered translation slices, e.g. S1, S2, etc, each translated through an diagnose-and-test loop, either in tandem (if slices are dependent) or in parallel (if slices are independent), that iterates until equivalence between the translated and original implementation is reached. From steps 10 to 13, the validation system reviews functions, renders visuals and runs tutorials to confirm the function and package translation accuracy. Bio-Babel has four layers to translate a hierarchical R-based ecosystem to Python ecosystem. The package registration and contract system allow convenient calling of the converted packages. Every converted package ships a_biobabel/ contract, where two entry-point groups (manifest, detectors) register into a registry serving the agent as a read-only MCP surface.