ReferencesCLICommands

CLI Commands

Every command the canonical biosimulant CLI exposes, grouped by domain. This page is generated from biosimulant --help; for the lower-level protocol catalog used by biosimulant raw <command>, see Raw Commands.

Global flags available on every command:

  • --json — machine-readable output
  • --json-stream — newline-delimited JSON for long-running operations
  • --no-open — suppress browser launches
  • --data-dir <DATA_DIR> — override the desktop data directory
  • --profile <PROFILE> — select a non-default profile

Utilities

Top-level commands for setup, inspection, and the raw protocol bridge.

biosimulant doctor

biosimulant doctor

biosimulant which

biosimulant which

biosimulant install-cli

biosimulant install-cli

biosimulant uninstall-cli

biosimulant uninstall-cli

biosimulant commands list

biosimulant commands list

biosimulant raw

biosimulant raw [--input <INPUT>] <COMMAND>

Arguments

  • &lt;COMMAND&gt;

Options

  • --input &lt;INPUT&gt;

auth

Sign in to the Hub, inspect token state, and sign out. Tokens are stored in the OS keychain when available; see the CLI Overview for the full auth model.

biosimulant auth login

biosimulant auth login [--access-token <ACCESS_TOKEN>] [--refresh-token <REFRESH_TOKEN>] [--email <EMAIL>]

Options

  • --access-token &lt;ACCESS_TOKEN&gt; — [env: BIOSIMULANT_ACCESS_TOKEN=]
  • --refresh-token &lt;REFRESH_TOKEN&gt; — [env: BIOSIMULANT_REFRESH_TOKEN=]
  • --email &lt;EMAIL&gt;

biosimulant auth status

biosimulant auth status

biosimulant auth logout

biosimulant auth logout

labs

Manage local lab source trees, lab-scoped models, public registry discovery, .bsilab packaging, release manifests, and publishing.

biosimulant labs init

biosimulant labs init [--name <NAME>] [--description <DESCRIPTION>] [--force] [PATH]

Arguments

  • [PATH]

Options

  • --name &lt;NAME&gt;
  • --description &lt;DESCRIPTION&gt;
  • --force

biosimulant labs list

biosimulant labs list [--search <SEARCH>]

Options

  • --search &lt;SEARCH&gt;

biosimulant labs search

biosimulant labs search [--tags <TAGS>] [--page <PAGE>] [--page-size <PAGE_SIZE>] [QUERY]

Arguments

  • [QUERY]

Options

  • --tags &lt;TAGS&gt;
  • --page &lt;PAGE&gt;
  • --page-size &lt;PAGE_SIZE&gt;

biosimulant labs info

biosimulant labs info <REFERENCE>

Arguments

  • &lt;REFERENCE&gt;

biosimulant labs versions

biosimulant labs versions [--page <PAGE>] [--page-size <PAGE_SIZE>] <REFERENCE>

Arguments

  • &lt;REFERENCE&gt;

Options

  • --page &lt;PAGE&gt;
  • --page-size &lt;PAGE_SIZE&gt;

biosimulant labs get

biosimulant labs get <ID>

Arguments

  • &lt;ID&gt;

biosimulant labs create

biosimulant labs create [--description <DESCRIPTION>] <TITLE>

Arguments

  • &lt;TITLE&gt;

Options

  • --description &lt;DESCRIPTION&gt;

biosimulant labs import

biosimulant labs import <PATH>

Arguments

  • &lt;PATH&gt;

biosimulant labs pull

biosimulant labs pull [--target <TARGET>] [--force] [--no-deps] <REFERENCE>

Arguments

  • &lt;REFERENCE&gt;

Options

  • --target &lt;TARGET&gt;
  • --force
  • --no-deps

biosimulant labs save

biosimulant labs save [--manifest-file <MANIFEST_FILE>] [--wiring-layout-file <WIRING_LAYOUT_FILE>] <ID>

Arguments

  • &lt;ID&gt;

Options

  • --manifest-file &lt;MANIFEST_FILE&gt;
  • --wiring-layout-file &lt;WIRING_LAYOUT_FILE&gt;

biosimulant labs rename

biosimulant labs rename <ID> <TITLE>

Arguments

  • &lt;ID&gt;
  • &lt;TITLE&gt;

biosimulant labs delete

biosimulant labs delete <ID>

Arguments

  • &lt;ID&gt;

biosimulant labs open

biosimulant labs open [--target <TARGET>] [--no-window] [PATH]

Arguments

  • [PATH]

Options

  • --target &lt;TARGET&gt;
  • --no-window

biosimulant labs package

biosimulant labs package [--out <OUT>] [--package <PACKAGE_NAME>] [--visibility <VISIBILITY>] [LAB]

Arguments

  • [LAB]

Options

  • --out &lt;OUT&gt;
  • --package &lt;PACKAGE_NAME&gt;
  • --visibility &lt;VISIBILITY&gt; — [default: private] [possible values: private, public]

biosimulant labs release validate

biosimulant labs release validate <MANIFEST>

Arguments

  • &lt;MANIFEST&gt;

biosimulant labs release build

biosimulant labs release build [--out <OUT>] <MANIFEST>

Arguments

  • &lt;MANIFEST&gt;

Options

  • --out &lt;OUT&gt; — [default: dist/biosimulant-packages]

biosimulant labs release publish

biosimulant labs release publish [--out <OUT>] [--dry-run] <MANIFEST>

Arguments

  • &lt;MANIFEST&gt;

Options

  • --out &lt;OUT&gt; — [default: dist/biosimulant-packages]
  • --dry-run

biosimulant labs release ci

biosimulant labs release ci [--out <OUT>] [--publish] <MANIFEST>

Arguments

  • &lt;MANIFEST&gt;

Options

  • --out &lt;OUT&gt; — [default: dist/biosimulant-packages]
  • --publish

biosimulant labs sync-status

biosimulant labs sync-status <LAB>

Arguments

  • &lt;LAB&gt;

biosimulant labs vendor-model

biosimulant labs vendor-model <LAB_ID> <MODEL_ID> <ALIAS>

Arguments

  • &lt;LAB_ID&gt;
  • &lt;MODEL_ID&gt;
  • &lt;ALIAS&gt;

biosimulant labs change-model

biosimulant labs change-model <LAB_ID> <ALIAS> <NEW_MODEL_ID>

Arguments

  • &lt;LAB_ID&gt;
  • &lt;ALIAS&gt;
  • &lt;NEW_MODEL_ID&gt;

biosimulant labs inspect-owned

biosimulant labs inspect-owned [--owner-base-path <OWNER_BASE_PATH>] [--expected-revision <EXPECTED_REVISION>] <OWNED_PATH>

Arguments

  • &lt;OWNED_PATH&gt;

Options

  • --owner-base-path &lt;OWNER_BASE_PATH&gt;
  • --expected-revision &lt;EXPECTED_REVISION&gt;

biosimulant labs add-model

biosimulant labs add-model [--as <ALIAS>] [LAB_OR_MODEL]

Arguments

  • [LAB_OR_MODEL] — …

Options

  • --as &lt;ALIAS&gt;

biosimulant labs validate

biosimulant labs validate [--strict] [LAB]

Arguments

  • [LAB]

Options

  • --strict

biosimulant labs run

biosimulant labs run [--target <TARGET>] [--force] [--no-deps] [--parameters-file <PARAMETERS_FILE>] [--simulation-config-file <SIMULATION_CONFIG_FILE>] [--results-file <RESULTS_FILE>] [--open] [--report-file <REPORT_FILE>] [LAB]

Arguments

  • [LAB]

Options

  • --target &lt;TARGET&gt;
  • --force
  • --no-deps
  • --parameters-file &lt;PARAMETERS_FILE&gt;
  • --simulation-config-file &lt;SIMULATION_CONFIG_FILE&gt;
  • --results-file &lt;RESULTS_FILE&gt;
  • --open
  • --report-file &lt;REPORT_FILE&gt;

biosimulant labs serve

biosimulant labs serve [--host <HOST>] [--port <PORT>] [LAB]

Arguments

  • [LAB]

Options

  • --host &lt;HOST&gt; — [default: 127.0.0.1]
  • --port &lt;PORT&gt; — [default: 8765]

biosimulant labs publish

biosimulant labs publish [--visibility <VISIBILITY>] [LAB]

Arguments

  • [LAB]

Options

  • --visibility &lt;VISIBILITY&gt; — [default: private] [possible values: private, public, preserve]

runs

Create, start, cancel, and inspect local and remote simulation runs. For lab-first workflows, prefer biosimulant labs run and biosimulant labs serve.

biosimulant runs list

biosimulant runs list [--lab-id <LAB_ID>] [--model-id <MODEL_ID>] [--status <STATUS>]

Options

  • --lab-id &lt;LAB_ID&gt;
  • --model-id &lt;MODEL_ID&gt;
  • --status &lt;STATUS&gt;

biosimulant runs get

biosimulant runs get <ID>

Arguments

  • &lt;ID&gt;

biosimulant runs create

biosimulant runs create [--lab-id <LAB_ID>] [--model-id <MODEL_ID>] [--parameters-file <PARAMETERS_FILE>] [--simulation-config-file <SIMULATION_CONFIG_FILE>]

Options

  • --lab-id &lt;LAB_ID&gt;
  • --model-id &lt;MODEL_ID&gt;
  • --parameters-file &lt;PARAMETERS_FILE&gt;
  • --simulation-config-file &lt;SIMULATION_CONFIG_FILE&gt;

biosimulant runs start

biosimulant runs start [--open] [--report-file <REPORT_FILE>] <ID>

Arguments

  • &lt;ID&gt;

Options

  • --open
  • --report-file &lt;REPORT_FILE&gt;

biosimulant runs open

biosimulant runs open [--report-file <REPORT_FILE>] <ID>

Arguments

  • &lt;ID&gt;

Options

  • --report-file &lt;REPORT_FILE&gt;

biosimulant runs cancel

biosimulant runs cancel <ID>

Arguments

  • &lt;ID&gt;

biosimulant runs results

biosimulant runs results <ID>

Arguments

  • &lt;ID&gt;

biosimulant runs logs

biosimulant runs logs [--since-seq <SINCE_SEQ>] <ID>

Arguments

  • &lt;ID&gt;

Options

  • --since-seq &lt;SINCE_SEQ&gt;

biosimulant runs upload

biosimulant runs upload <ID>

Arguments

  • &lt;ID&gt;

biosimulant runs remote catalog

biosimulant runs remote catalog

biosimulant runs remote create

biosimulant runs remote create <PAYLOAD_FILE>

Arguments

  • &lt;PAYLOAD_FILE&gt;

biosimulant runs remote get

biosimulant runs remote get <ID>

Arguments

  • &lt;ID&gt;

biosimulant runs remote results

biosimulant runs remote results <ID>

Arguments

  • &lt;ID&gt;

runtime

Inspect and prepare the managed Python runtime that executes simulations.

biosimulant runtime status

biosimulant runtime status

biosimulant runtime detect-python

biosimulant runtime detect-python

biosimulant runtime prepare

biosimulant runtime prepare

settings

Read and update persisted desktop settings, including the data directory and dashboard layout.

biosimulant settings get

biosimulant settings get

biosimulant settings update

biosimulant settings update [--settings-file <SETTINGS_FILE>]

Options

  • --settings-file &lt;SETTINGS_FILE&gt;

biosimulant settings data-dir

biosimulant settings data-dir

biosimulant settings dashboard

biosimulant settings dashboard

biosimulant settings logs-path

biosimulant settings logs-path

jobs

List and inspect tracked background jobs (long-running operations like Hub downloads or runtime bootstrap).

biosimulant jobs list

biosimulant jobs list

biosimulant jobs get

biosimulant jobs get <ID>

Arguments

  • &lt;ID&gt;

Related

OverviewRaw Commands