smarts.bio: AI for biology

Ask the smarts.bio bioinformatics agent a question. It can search biological databases, run tools, and reason over results, returning a focused, concise answer optimized to come back quickly. Use this for most open-ended bioinformatics questions. For heavy, long-running work (multi-step pipelines, large analyses), use smarts_run_pipeline + smarts_run_status instead, which run asynchronously.

smarts_query

Get a link the user opens in their browser to upload files from their own computer into a workspace — for real files you cannot see, and for anything too large to pass inline. Show the returned URL to the user and ask them to open it; then poll smarts_upload_status to see what arrived. The link lasts 30 minutes and only works for the user who is signed in to smarts.bio. For content you already have in this conversation, use smarts_upload_file instead — it needs no browser trip.

smarts_request_upload

Get the status of a pipeline run by id.

smarts_run_status

Check an upload link created with smarts_request_upload: whether the user has uploaded yet, and the files that have arrived so far (with their keys, ready to use as tool or pipeline inputs). Call this after the user says they have uploaded.

smarts_upload_status

Get a pipeline's declared inputs (names, types, which are required, defaults) and its steps. Call this before smarts_run_pipeline so the input names you pass are exact — never guess them. Give pipeline_id for a built-in pipeline, or spec_file + workspace_id for a saved one.

smarts_get_pipeline

List available bioinformatics tools (BLAST, GATK, NCBI lookups, …), optionally filtered by category.

smarts_list_tools

List runnable pipelines: the built-in catalog (QC, alignment, RNA-seq, variant calling, …) and, when workspace_id is given, pipelines the user has saved in that workspace. Built-ins are run by pipeline_id; saved ones by spec_file. Call smarts_get_pipeline next to see what inputs a pipeline needs.

smarts_list_pipelines

List files and folders in a workspace directory.

smarts_list_files

List the workspaces the authenticated user can access.

smarts_list_workspaces

Get a shareable browser viewer URL for a workspace file. Works with many bioinformatics formats — sequence, alignment, variant, structure, molecule, and tabular data (FASTA, BAM, VCF, PDB, CSV, … are just examples). Try it for any file the user wants to view.

smarts_open_file