Glossary¶
This appendix defines terms related to Opentrons Flex. It omits industry-standard terms like "labware" unless the term has a special meaning in relation to Flex. For example, the definition for pipette describes the narrower meaning that the term has when using Flex, as opposed to any pipette you might find elsewhere in a lab.
The glossary is formatted to help you navigate within it and to other places in this manual. Words in italics indicate terms that are also defined in the glossary. Extremely common terms like "deck", "module", "pipette", and "protocol" aren't italicized, to improve readability. Links within definitions take you to the most relevant section that includes additional discussion of the term. And you can always use your PDF reader to search for every occurrence of a term to find even more information.
Above deck¶
Space that is on or above the level of the robot's deck area.
Aluminum block¶
See thermal block.
Ambient lighting¶
LEDs that illuminate the interior of Flex, which you can toggle on and off from the touchscreen or the Opentrons App.
Auxiliary ports¶
Ports on the back of the Flex labeled AUX-1 and AUX-2. The port connection type is an IEC M12 metric screw connector. See the Connections section in the System Description chapter.
A1 expansion slot¶
The area of the deck behind slot A1. When its cover is removed, the A1 expansion slot provides enough space to install the Thermocycler Module. See the Deck and working area section of the System Description chapter.
Below deck¶
The empty area below the robot's deck slots. This space provides clearance for module caddies that sit below the deck and allows for below-deck cable routing.
Caddy¶
See module caddy.
Calibration pin¶
A metal pin you attach to the gripper's jaws during gripper calibration. See the Gripper calibration section in the System Description chapter.
Calibration probe¶
A metal collar you attach to the nozzle of a pipette during pipette calibration, module calibration, and Labware Position Check. See the Pipette calibration section in the System Description chapter and the Module calibration section in the Modules chapter. See also the Labware Position Check section of the Software and Operation chapter.
Calibration square¶
The central part of a removable deck slot or module calibration adapter. The square is made of steel to reduce the chance of surface damage during calibration.
Camera¶
A built-in camera that provides an above-deck view inside the Flex enclosure.
Carrying handle¶
One of four aluminum handles that screw into the bottom corners of the robot. The handles help make Flex easier to lift. Lifting the robot requires two people. Using the handles is the best way to pick up Flex and move it.
Carrying handle cap¶
A flat metal cover that goes over the attachment point for a carrying handle. The caps close the handle openings in the frame and give the robot a clean appearance. See the [Physical components section][physical-components] in the System Description chapter.
Dashboard¶
The main screen for the robot, accessible by tapping the robot's name in the top left corner of the touchscreen. The dashboard gives you quick access to recently run protocols. See the Touchscreen operation section in the Software and Operation chapter.
Deck¶
The machined aluminum surface on which automated science protocols are executed. It includes the working area, staging area, and A1 expansion slot. See the Deck and working area section in the System Description chapter.
Deck border¶
The fixed portion of the deck around the four edges of the robot (outside of the area where deck slot
panels fit). It contains the removable accessory covers.
Deck fixture¶
Hardware items that replace standard deck slots. They let you customize the deck layout and
add functionality to your Flex. Deck fixtures include the staging area slots, trash bin, and waste chute.
Deck slot¶
A detachable panel on the deck area. Remove deck slots to install modules and for access to the space below the deck.
Ejector¶
The mechanism that automatically pushes tips off the nozzle of a pipette. See the Pipettes section in the System Description chapter.
Emergency Stop Pendant¶
An external accessory that you press to stop the robot immediately. Also referred to as the E-stop. See the Emergency Stop Pendant section in the System Description chapter.
Expansion slot¶
See A1 expansion slot.
Extension mount¶
The attachment point on the gantry for the Flex Gripper. See the [Movement system section][movement-system] in the System Description chapter.
Finishing cap¶
See carrying handle cap.
Firmware¶
The low-level software that controls the Flex robot and all of its peripheral systems. The Flex robot will automatically update the firmware on connected instruments and modules to stay in sync with the robot software version.
Fixture¶
See deck fixture.
Frame¶
The outer metal structure of the robot.
Front door¶
The hinged clear panel on the front of the robot.
Gantry¶
The robot's positioning system that moves attached instruments horizontally (on the x- and y-axis). See the [Movement system section][movement-system] in the System Description chapter.
Gripper¶
The Opentrons Flex Gripper, an instrument that picks up labware and moves it around the deck automatically.
Home gantry¶
The act of moving the gantry to a defined position at the back right of the working area.
Instrument¶
Any component that attaches to the gantry and manipulates liquids or labware on the deck. Examples include the 1- , 8- , and 96-channel pipettes, and the gripper.
Instrument mount¶
Attachment point for an instrument. Examples include the pipette mounts and the extension mount for the gripper. See the [Movement system section][movement-system] in the System Description chapter.
Jaws¶
The moving pincers of the gripper. See the Gripper specifications section in the System Description chapter.
JSON protocol¶
A standardized scientific procedure written as a JavaScript object notation file. The Opentrons Protocol Designer outputs JSON protocols.
JSON schema¶
A set of requirements for the structure and contents of a JavaScript object notation file. For example, all of the Opentrons labware definitions are formatted according to a particular JSON schema, while JSON protocols follow another schema.
Labware clips¶
The plastic pieces at the corners of deck slots. Labware clips hold labware in place.
Labware Creator¶
The Opentrons Labware Creator is a no-code, web-based tool that uses a graphical interface to help you create a labware definition file to import into the Opentrons App. After importing it, your custom labware is available to the Flex robot and the Python Protocol API.
Labware Library¶
The Opentrons Labware Library lists the durable and consumable items you can use with the Flex by default, without customization. It includes things like well plates, reservoirs, tips, tip racks, and tubes.
Labware offset¶
Positional data that is created and stored by running Labware Position Check. Flex takes these offsets into account when moving to a particular type of labware in a particular deck slot.
Labware Position Check¶
A guided process to visually check and adjust pipette movement relative to a piece of labware, with a resolution of 0.1 mm. See the Labware Position Check section in the Software and Operation chapter.
Lift handles¶
See carrying handles.
Lights¶
See ambient lighting or status light.
Maintenance position¶
A specific gantry position at the front left side of the working area. The gantry moves to this position to facilitate adding or removing instruments.
Module¶
A peripheral that occupies a deck slot. Most modules are controlled by the robot via a USB connection. The Heater-Shaker, Temperature Module, and Thermocycler are all powered modules. The Magnetic Block is an unpowered module. See the Modules chapter.
Module caddy¶
A container that holds a module. It is used to attach modules to the deck area and help with module removal. Caddies place your labware closer to the deck surface and allow for below-deck cable routing.
Module calibration adapter¶
An adapter that sits on top of a module and is used to automatically calibrate module position.
Mounting plate¶
See 96-channel mounting plate.
Nozzle¶
The working end of a pipette. Flex pipettes pick up disposable tips by pressing the nozzles down into them. See the Pipettes section in the System Description chapter.
Opentrons App¶
Software used to control a Flex (or other Opentrons robots) from a laptop or desktop computer. The Opentrons App is available for Mac, Windows, and Linux. See the Opentrons App section in the Software and Operation chapter.
Paddle¶
Part of the gripper that grasps and holds labware. Paddles are replaceable wear items. See the Gripper specifications section in the System Description chapter.
Pinned protocol¶
Protocols you have saved for easy access at the top of the All Protocols tab on the touchscreen. See the Protocol management section in the Software and Operation chapter.
Pipette¶
Opentrons Flex Pipettes are configurable devices used to move liquids throughout the working area during the execution of protocols. There are several Flex pipettes, which can handle volumes from 1 µL to 1000 µL in 1, 8, or 96 channels. See the Pipettes section in the System Description chapter.
Pipette mount¶
The attachment point on the gantry for a pipette. See the [Movement system section][movement-system] in the System Description chapter.
Profile¶
See Thermocycler profile.
Protocol¶
An automated task or procedure you program to run on Opentrons robots, including Opentrons Flex. You can also search for, download, and use ready-made protocols from the Opentrons Protocol Library.
Protocol Designer¶
A web-based, no-code tool for developing JSON protocols that run on Opentrons robots, including Opentrons Flex. See the Protocol Designer section in the Protocol Development chapter and https://designer.opentrons.com.
Protocol Library¶
A public, searchable library that hosts protocols authored by Opentrons or by members of the Opentrons community. See the Protocol Library section in the Protocol Development chapter and https://library.opentrons.com.
Protocol run¶
A particular instance of Flex performing the actions specified in a protocol file. Only a single protocol run can be active at any given time. Flex stores historical data on the time and outcome of the 20 most recent protocol runs.
Python protocol¶
A protocol script written using the Opentrons Python Protocol API. See the Writing and running scripts section in the Protocol Development chapter.
Python Protocol API¶
A Python package that exposes a wide range of liquid handling features on Opentrons robots. See the Python Protocol API section in the Protocol Development chapter and the online Opentrons Python Protocol API documentation.
Removable deck slot¶
See deck slot.
Run¶
See protocol run.
Side covers¶
Detachable panels on the side of the robot, used for module exhaust and external cable routing. See the Connections section in the System Description chapter.
Side windows¶
Fixed clear panels on the right and left sides of the robot.
Staging area¶
The right-hand side of the deck (column 4), which is only accessible by the gripper. This area requires special staging area slots for use. See the Staging area section in the System Description chapter.
Staging area slot¶
Staging area slots are ANSI/SLAS compatible deck pieces that replace the standard slots in column 3 (A3 to D3) and extend a new slot into the staging area. You can install a single slot or a maximum of four slots to create a new column (A4 to D4) along the right side of the deck. See the Staging area section in the System Description chapter.
Status light¶
A strip of color LEDs along the top front of the robot. This light provides at-a-glance information about the robot. Different colors and patterns of illumination can communicate various success, failure, or idle states. See the Touchscreen and LED displays section in the System Description chapter.
Thermal adapter¶
Aluminum blocks that attach to the Heater-Shaker and hold labware. See the Thermal adapters section in the Modules chapter.
Thermal block¶
Aluminum blocks that attach to the Temperature Module and hold labware to facilitate heating, cooling, and maintaining temperature. See the Thermal blocks section in the Modules chapter.
Thermocycler profile¶
A sequence of temperature changes used by the Thermocycler to perform heat-sensitive reactions. See the Thermocycler profiles section in the Modules chapter.
Tip rack adapter¶
An aluminum bracket used by the 96-channel pipette to attach a full rack of pipette tips. See the Pipettes section in the System Description chapter.
Touchscreen¶
The interactive LCD screen mounted to the front of the robot. See the Touchscreen and LED displays section in the System Description chapter.
Trash bin¶
A removable trash container. By default, it occupies slot A3 on the deck.
USB ports¶
Connections for Flex accessories, modules, and computers. See the USB and auxiliary connections section in the System Description chapter.
User Kit¶
A box that contains tools, fasteners, and spare parts. Every Flex robot ships with a User Kit.
Waste chute¶
A deck fixture that transfers liquids, tips, tip racks, and well plates from the Flex enclosure to a trash receptacle placed below its external opening.
Working area¶
The physical space above the deck that is accessible for pipetting. See the Deck and working area section in the System Description chapter.
Workstation¶
Opentrons Flex workstations include the Flex robot, instruments, modules, accessories, and labware needed to automate a particular application. See the Flex workstations section in the Introduction.
Z-axis carriage¶
The gantry component that includes the pipette mounts and the extension mount for the gripper. It moves these instruments along the z-axis (up and down) to locate them precisely during protocol execution. See the [Movement system section][movement-system] in the System Description chapter.
96-channel mounting plate¶
A metal frame that mounts to the z-axis carriage. It holds the 96-channel pipette to the gantry.