local-bio-toolkit

# Local Bio Toolkit Use the bundled `local-bio-tools` MCP. This layer is deliberately small and capability-based: PyMOL renders structures; SnapGene opens sequence/vector files; Cytoscape opens network files; Fiji opens microscopy images. ## Selection rule | Need | Tool | Allowed action | |---|---|---| | Produce a molecular-structure image | PyMOL | headless render with a fixed visual preset | | Inspect an existing construct or sequence record | SnapGene | open a compatible local file after an explicit user request | | Inspect an existing biological network | Cytoscape | open a compatible local file after an explicit user request | | Inspect an existing microscopy image | Fiji/ImageJ | open a compatible local file after an explicit user request | Run `local_bio_tool_status` before acting. If a tool is absent, report the missing capability and the supported environment-variable override; do not install, download, or substitute software without direction. ## Safety boundary - Accept only an existing user-selected file and a format on the allowlist. - Do not execute arbitrary PyMOL code, macros, plugins, shell fragments, or application arguments. - Do not launch a graphical desktop application unless the user explicitly asked to open it. - Do not modify the source file. Save PyMOL output only to the requested PNG path. - Processing stays local; no file is transmitted to a website or public API. ## Conversation delivery For PyMOL output, visually inspect the generated PNG and show it directly in the conversation. Explain representation, coloring, background, and structural evidence limits. A rendered model does not establish binding, function, or experimental structure quality.