Raw Commands

The lower-level protocol surface used by biosimulant raw <command>. 80 commands total: 0 headless-supported, 80 desktop-only (not yet exposed through the CLI).

For task-driven usage, prefer the wrapper commands on CLI Commands. Use raw commands when you need exact desktop parity, when scripting against a command not yet wrapped, or when you want the machine-readable contract.

biosimulant commands list --json   # this catalog as JSON
biosimulant raw <name> --input '{}' --json

Tags: (long-running) commands stream progress and benefit from --json-stream. (mutating) commands change persisted state. (desktop public, not yet headless-supported) commands are visible in Desktop but not yet exposed through biosimulant raw.

Agent

agent_apply_proposal (mutating, desktop public, not yet headless-supported) — Apply a previously reviewed local lab proposal to the in-memory agent context.
agent_attach_model_creator_session (mutating, desktop public, not yet headless-supported) — Attach an existing native model-creator session to the active lab-agent session.
agent_cancel_session (mutating, desktop public, not yet headless-supported) — Cancel an active remote lab-agent session.
agent_connect_session_stream (long-running, desktop public, not yet headless-supported) — Connect to the event stream for a remote lab-agent session.
agent_create_session (mutating, desktop public, not yet headless-supported) — Create a remote lab-agent session for a local lab.
agent_delete_session (mutating, desktop public, not yet headless-supported) — Delete a remote lab-agent session.
agent_disconnect_session_stream (mutating, desktop public, not yet headless-supported) — Disconnect the active event stream for a remote lab-agent session and clear session-local bridge state.
agent_get_model_creator_session (desktop public, not yet headless-supported) — Fetch one persisted native model-creator session.
agent_get_session (desktop public, not yet headless-supported) — Fetch a remote lab-agent session.
agent_list_model_creator_reference_roots (desktop public, not yet headless-supported) — List read-only reference roots available to the native model creator.
agent_list_model_creator_sessions (desktop public, not yet headless-supported) — List persisted native model-creator sessions for a lab.
agent_list_sessions (desktop public, not yet headless-supported) — List remote lab-agent sessions for a local lab.
agent_read_model_creator_reference_file (desktop public, not yet headless-supported) — Read one bounded file from a native model-creator reference root.
agent_run_model_creator_command (long-running, mutating, desktop public, not yet headless-supported) — Run one approval-gated native model-creator command.
agent_run_model_creator_validation (long-running, mutating, desktop public, not yet headless-supported) — Run the native model-creator validation suite.
agent_search_model_creator_reference (desktop public, not yet headless-supported) — Search read-only reference roots for the native model creator.
agent_send_turn (mutating, desktop public, not yet headless-supported) — Send a prompt turn to a remote lab-agent session.
agent_set_model_creator_draft_node (mutating, desktop public, not yet headless-supported) — Update the draft node linked to a native model-creator session.
agent_start_model_creator (mutating, desktop public, not yet headless-supported) — Create a new native model-creator session for a lab-owned model scaffold.
agent_submit_tool_result (mutating, desktop public, not yet headless-supported) — Submit a local tool result back to a remote lab-agent session.
agent_sync_lab_context (mutating, desktop public, not yet headless-supported) — Sync local lab context into the in-memory agent context cache.
agent_update_model_creator_brief (mutating, desktop public, not yet headless-supported) — Update the structured brief for a native model-creator session.

App

get_dashboard_stats (desktop public, not yet headless-supported) — Fetch dashboard counts for local models, labs, and runs.
open_in_explorer (desktop public, not yet headless-supported) — Open a local path in the operating system file explorer.
open_in_terminal (desktop public, not yet headless-supported) — Open a local path in the operating system terminal.
open_in_vscode (desktop public, not yet headless-supported) — Open a local path in Visual Studio Code.

Auth

auth_logout (mutating, desktop public, not yet headless-supported) — Sign out of the Biosimulant Hub and clear stored credentials.
auth_receive_tokens (mutating, desktop public, not yet headless-supported) — Persist Hub login tokens delivered by desktop auth.
auth_status (desktop public, not yet headless-supported) — Inspect current Hub authentication status.

Chat

chat_get_thread (desktop public, not yet headless-supported) — Fetch the Hub chat thread for a model or lab.
chat_send_message (long-running, mutating, desktop public, not yet headless-supported) — Send a chat message to the Hub assistant for a model or lab.

Diagnostics

change_log_directory (mutating, desktop public, not yet headless-supported) — Move the desktop file logger into a new directory.
get_log_path (desktop public, not yet headless-supported) — Return the current desktop application log path.
record_diagnostics_event (mutating, desktop public, not yet headless-supported) — Record a local diagnostics event and attempt upload.
reset_log_directory (mutating, desktop public, not yet headless-supported) — Reset the file logger to the default data-dir log location.
write_log (mutating, desktop public, not yet headless-supported) — Append an application log line to the file logger.

Drafts

clear_lab_draft (mutating, desktop public, not yet headless-supported) — Delete a saved local draft for a lab.
get_lab_draft (desktop public, not yet headless-supported) — Fetch a saved local draft for a lab.
save_lab_draft (mutating, desktop public, not yet headless-supported) — Save a draft manifest and layout for a local lab.

Jobs

cancel_job (mutating, desktop public, not yet headless-supported) — Cancel a tracked background job.
get_job (desktop public, not yet headless-supported) — Fetch a tracked background job.
list_jobs (desktop public, not yet headless-supported) — List tracked background jobs.

Labs

change_lab_directory (mutating, desktop public, not yet headless-supported) — Move a local lab into a different directory or link it to an existing folder.
create_lab (mutating, desktop public, not yet headless-supported) — Create a new local lab.
create_owned_model_in_lab (mutating, desktop public, not yet headless-supported) — Create a new owned model inside a local lab workspace.
delete_lab (mutating, desktop public, not yet headless-supported) — Delete a local lab and its persisted files.
export_lab_project (desktop public, not yet headless-supported) — Export a lab source tree or local lab id into a .bsilab package.
get_lab (desktop public, not yet headless-supported) — Fetch a local lab by ID.
hydrate_lab_package_references (long-running, mutating, desktop public, not yet headless-supported) — Resolve and cache package-backed model and sub-lab dependencies for a local lab.
import_lab_directory (mutating, desktop public, not yet headless-supported) — Import a local lab directory or manifest.
import_lab_into_lab_from_path (mutating, desktop public, not yet headless-supported) — Import a sub-lab from disk directly into a local lab workspace.
import_model_into_lab_from_path (mutating, desktop public, not yet headless-supported) — Import a model from disk directly into a local lab workspace.
inspect_owned_dependency (desktop public, not yet headless-supported) — Inspect a vendored dependency inside a local lab.
link_lab_directory (mutating, desktop public, not yet headless-supported) — Link an existing local lab directory into the desktop library without copying it.
list_labs (mutating, desktop public, not yet headless-supported) — List local labs.
list_owned_models_index (desktop public, not yet headless-supported) — List owned model snapshots indexed from local lab workspaces.
rename_lab (mutating, desktop public, not yet headless-supported) — Rename a local lab.
save_lab (mutating, desktop public, not yet headless-supported) — Persist the manifest and optional layout for a local lab.
vendor_lab_into_lab (long-running, mutating, desktop public, not yet headless-supported) — Vendor a child lab into a local lab as an owned copy.
vendor_model_into_lab (long-running, mutating, desktop public, not yet headless-supported) — Vendor a model into a local lab as an owned copy.
vendor_owned_model_into_lab (mutating, desktop public, not yet headless-supported) — Vendor an owned model from another local lab into the current lab.

Runs

cancel_run (mutating, desktop public, not yet headless-supported) — Cancel an active local run.
create_run (mutating, desktop public, not yet headless-supported) — Create a pending local run record.
get_run (desktop public, not yet headless-supported) — Fetch a local run by ID.
get_run_results (desktop public, not yet headless-supported) — Fetch stored results for a local run.
list_run_logs (long-running, desktop public, not yet headless-supported) — List persisted log lines for a local run.
list_runs (desktop public, not yet headless-supported) — List local runs.
open_run_report (mutating, desktop public, not yet headless-supported) — Generate a local browser report for a stored run and optionally open it.
start_local_run (long-running, mutating, desktop public, not yet headless-supported) — Execute a pending local run.
sync_remote_run (mutating, desktop public, not yet headless-supported) — Update a mirrored remote run in the local run store.

Runtime

detect_python (desktop public, not yet headless-supported) — Inspect the current managed and unmanaged Python state.
runtime_get_bootstrap_status (desktop public, not yet headless-supported) — Fetch managed runtime bootstrap status.
runtime_retry_bootstrap (long-running, mutating, desktop public, not yet headless-supported) — Retry managed runtime bootstrap.
runtime_start_bootstrap (long-running, mutating, desktop public, not yet headless-supported) — Start managed runtime bootstrap.
setup_executor_venv (long-running, mutating, desktop public, not yet headless-supported) — Prepare the managed executor environment.

Settings

change_data_directory (mutating, desktop public, not yet headless-supported) — Move desktop data into a new data directory.
get_data_directory (desktop public, not yet headless-supported) — Return the effective desktop data directory.
get_settings (desktop public, not yet headless-supported) — Fetch persisted desktop settings.
reset_app_data (mutating, desktop public, not yet headless-supported) — Delete all desktop models, labs, runs, and settings.
update_settings (mutating, desktop public, not yet headless-supported) — Update persisted desktop settings.

CLI Commands — task-grouped wrapper commands.
CLI Overview — install, auth, scripting.

Commands Overview