proofread through Protocols chapter all sections

Author: ecormany

docs/flex/docs/labware/definitions.md

@@ -22,7 +22,7 @@ You can use the Custom Labware Creator if your labware meets the following crite
 - Wells and tubes are uniform and identical.
 - All rows are evenly spaced (the space between rows is equal).
 - All columns are evenly spaced (the space between columns is equal).
-- Fits perfectly in one deck slot.
+- The labware fits perfectly in one deck slot.
 
 | Layout {style="width: 200px;"} | Description |
 | ------ | ----------- |
@@ -35,10 +35,10 @@ For other labware, consider the Custom Labware Service, outlined below. Or you c
 
 Get in touch with us if the labware you'd like to use isn't available in the library, if you can't create your own definitions, or because a custom item includes different shapes, sizes, or other irregularities described below. 
 
-- Wells and tube shapes vary.
+- Well or tube shapes vary.
 - Rows are not evenly spaced.
 - Columns are not evenly spaced.
-- Smaller than one deck slot (requires adapter) or spans multiple deck slots.
+- The labware is smaller than one deck slot (requires adapter) or spans multiple deck slots.
 
 | Layout {style="width: 200px;"} | Description |
 | ------ | ----------- |
@@ -59,7 +59,7 @@ A schema is a framework for organizing data. It sets the rules about what inform
 | `schemaVersion`     | Number    | Schema version used by a labware. The current version is `2`. |
 | `version`           | Integer   | An incrementing integer that identifies the labware version. Minimum version is `1`. |
 | `namespace`         | String    | See `safeString` in the JSON definitions section below. |
-| `metadata`          | Object    | Properties used for search and display. Accepts only:<ul><li>`displayName` (String): An easy-to-remember labware name.</li><li>`displayCategory`: Labels used in the UI to categorize labware. See `displayCategory` in the JSON definitions section below.</li><li>`displayVolumeUnits` (String): Labels used in the UI to indicate volume. Must be either µL, mL, or L.</li></ul> |
+| `metadata`          | Object    | Properties used for search and display. Accepts only:<ul><li>`displayName` (String): An easy-to-remember labware name.</li><li>`displayCategory`: Labels used in the UI to categorize labware. See `displayCategory` in the JSON definitions section below.</li><li>`displayVolumeUnits` (String): Labels used in the UI to indicate volume. Must be either `µL`, `mL`, or `L`.</li></ul> |
 | `brand`             | Object    | Information about the labware manufacturer or those products the labware is compatible with. |
 | `parameters`        | Object    | Internal parameters that describe labware characteristics. Accepts only:<ul><li>`format` (String): Determines labware compatibility with multichannel pipettes. Must be one of `96Standard`, `384Standard`, `trough`, `irregular`, or `trash`.</li><li>`quirks` (Array): Strings describing labware behavior. See the [Opentrons 96 Deep Well Adapter](https://github.com/Opentrons/opentrons/blob/03cd0336c6051c05fa66088fabec426c7b751a85/shared-data/labware/definitions/2/opentrons_96_deep_well_adapter_nest_wellplate_2ml_deep/1.json#L1108) definition.</li><li>`isTiprack` (Boolean): Indicates if labware is a tip rack (`true`) or not (`false`).</li><li>`tipLength` (Number): Required if labware is a tip rack. Specifies tip length (in mm), from top to bottom, as indicated in technical drawings or as measured with calipers.</li><li>`tipoverlap` (Number): Required if labware is a tip rack. Specifies how far tips on a tip rack are expected to overlap with the pipette's nozzle. Defined as tip length minus the distance between the bottom of the pipette and the bottom of the tip. The robot's calibration process may fine-tune this estimate.</li><li>`loadName`: Name used to reference a labware definition (e.g., `opentrons_flex_96_tiprack_50_ul`).</li><li>`isMagneticModuleCompatible` (Boolean): Indicates if labware is compatible with the Magnetic Module.</li><li>`magneticModuleEngageHeight`: How far the Magnetic Module will move its magnets when used with this labware. See `positiveNumber` in the JSON definitions section below.</li></ul> |
 | `ordering`          | Array     | An array that tracks how wells should be ordered on a piece of labware. See the [Opentrons 96 PCR Adapter](https://github.com/Opentrons/opentrons/blob/8569e32d2d918abb1f232f48a7b28385021215fd/shared-data/labware/definitions/2/opentrons_96_pcr_adapter/1.json#L2) example. |
@@ -80,6 +80,6 @@ A schema is a framework for organizing data. It sets the rules about what inform
 | :-------------- | :-------- | :------------------------------------------- |
 | `positiveNumber` | Number    | Minimum: 0.                      |
 | `brandData`     | Object    | Information about branded items. Accepts only:<br><ul><li>`brand` (String): Brand/manufacturer's name.</li><li>`brandId` (Array): OEM part numbers or IDs.</li><li>`links` (Array): Manufacturer URLs. Array items are strings.</li></ul> |
-| `displayCategory` | String    | Must be one of:<br><ul><li>`tipRack`</li><li>`tubeRack`</li><li>`reservoir`</li><li>`trash`</li><li>`wellPlate`</li><li>`aluminumBlock`</li><li>`adapter`</li><li>`other`</li></ul> |
+| `displayCategory` | String    | Must be one of:<br><ul><li>`tipRack`</li><li>`tubeRack`</li><li>`reservoir`</li><li>`trash`</li><li>`wellPlate`</li><li>`aluminumBlock`</li><li>`adapter`</li><li>`other`</li><li>`lid`</li></ul> |
 | `safeString`    | String    | A string safe to use for load names and namespaces. Lowercase letters, numerals, periods, and underscores only. |
 | `coordinates`   | Object    | Coordinates that specify a distance or position along the x-, y-, and z-axes. Accepts only:<br><ul><li>`x` (number)</li><li>`y` (number)</li><li>`z` (number)</li></ul> |

docs/flex/docs/labware/types.md

@@ -6,7 +6,7 @@ This section covers the different types of labware included in the Opentrons Lab
 
 ## Reservoirs 
 
-Opentrons Flex works by default with single-well and multi-well reservoirs. [Reservoirs on the Opentrons Labware Library](https://labware.opentrons.com/?category=reservoir) are automation-ready right out of the box.
+Opentrons Flex works by default with single-well and multi-well reservoirs. [Reservoirs on the Opentrons Labware Library](https://labware.opentrons.com/#/?category=reservoir) are automation-ready right out of the box.
 
 <figure class="side-by-side" markdown>
 ![Single-well reservoir labware.](../images/labware-1-well-reservoir.png "Single-well reservoir")
@@ -21,7 +21,7 @@ Try creating a custom labware definition with the [Opentrons Labware Creator](ht
 
 ## Well plates 
 
-The Opentrons Flex works by default with well plates in a variety of well configurations. This category includes standard depth and deep well plates, with various well bottom shapes. [Well plates on the Opentrons Labware Library](https://labware.opentrons.com/?category=wellPlate) are automation-ready right out of the box. 
+The Opentrons Flex works by default with well plates in a variety of well configurations. This category includes standard depth and deep well plates, with various well bottom shapes. [Well plates on the Opentrons Labware Library](https://labware.opentrons.com/#/?category=wellPlate) are automation-ready right out of the box. 
 
 <figure class="side-by-side" markdown>
 ![24-well plate labware.](../images/labware-24-well-plate.png "24-well plate")
@@ -49,7 +49,7 @@ Try using the Opentrons Labware Creator to make a custom labware definition if a
 
 ## Lids
 
-Opentrons Flex works by default with lids that fit on top of certain other labware to protect their contents. Labware Library contains lids that fit on well plates, as well as lids that are packaged with and fit on top of Opentrons Flex tip racks.
+Opentrons Flex works by default with lids that fit on top of certain other labware to protect their contents. [Labware Library contains lids](https://labware.opentrons.com/#/?category=lid) that fit on well plates, as well as lids that are packaged with and fit on top of Opentrons Flex tip racks.
 
 For a full example of a well plate lid, reference the [Opentrons Tough PCR Auto-Sealing Lid definition](https://github.com/Opentrons/opentrons/blob/edge/shared-data/labware/definitions/2/opentrons_tough_pcr_auto_sealing_lid/1.json) on GitHub. Importantly, the definition lists the other types of labware that the lid fits on.
 
@@ -76,7 +76,7 @@ When ordering or reordering, tips and racks come in two different packaged confi
 
 ### Tip-pipette compatibility 
 
-Flex pipette tips work with all single- and multi-channel Opentrons Flex 50 µL and 1000 µL pipettes. Flex pipette tips are designed for the Opentrons Flex pipettes. Flex tips are not backwards compatible with Opentrons OT-2 pipettes, nor can you use OT-2 tips on Flex pipettes. 
+Flex pipette tips are designed for the Opentrons Flex pipettes. Flex tips are not backwards compatible with Opentrons OT-2 pipettes, nor can you use OT-2 tips on Flex pipettes. 
 
 Flex pipettes only accept tips with capacities less than or equal to the pipette capacity. 
 
@@ -110,7 +110,7 @@ The tip rack adapter is compatible with the Opentrons Flex Gripper. You can use
 ![NEST tubes in two sizes.](../images/labware-tubes.jpg "NEST tubes")
 </figure>
 
-The [Opentrons 4-in-1 Tube Rack system](https://opentrons.com/products/4-in-1-tube-rack-set) works with the Opentrons Flex by default. [Tube rack combinations on the Opentrons Labware Library](https://labware.opentrons.com/?category=tubeRack) are automation-ready right out of the box. 
+The [Opentrons 4-in-1 Tube Rack system](https://opentrons.com/products/4-in-1-tube-rack-set) works with the Opentrons Flex by default. [Tube rack combinations on the Opentrons Labware Library](https://labware.opentrons.com/#/?category=tubeRack) are automation-ready right out of the box. 
 
 The Opentrons 4-in-1 tube rack supports a wide variety of tube sizes, singly or in different size (volume) combinations. These include a: 
 
@@ -127,15 +127,15 @@ Try creating a custom labware definition using the [Opentrons Labware Creator](h
 
 ## Aluminum blocks 
 
-Aluminum blocks ship with the Temperature Module GEN2 and can be purchased separately as a [three-piece set](https://opentrons.com/products/aluminum-block-1-5-2-0ml-tubes). The set includes a flat bottom plate, a 24-well block, and a 96-well block. 
+[Aluminum blocks on the Labware Library](https://labware.opentrons.com/#/?category=aluminumBlock) work with the Temperature Module GEN2 or directly on the deck. A flat bottom plate, a 24-well block, and a 96-well block are available for purchase from Opentrons.
 
-The Opentrons Flex uses aluminum blocks to hold sample tubes and well plates on the Temperature Module or directly on the deck. When used with the Temperature Module, the aluminum blocks can keep your sample tubes, PCR strips, or plates at a constant temperature between 4 °C and 95 °C. 
+The Opentrons Flex uses aluminum blocks to hold sample tubes or well plates. When used with the Temperature Module, the aluminum blocks can keep your sample tubes, PCR strips, or plates at a constant temperature between 4 °C and 95 °C. 
 
 ### Flat bottom plate 
 
 ![The flat bottom plate with the Opentrons Flex logo.](../images/temperature-module-block-flat.png "Flex flat bottom plate")
 
-The flat bottom plate for Flex ships with the Temperature Module's caddy and is compatible with various ANSI/SLAS standard well plates. This flat plate differs from the plate that ships with the Temperature Module itself or the separate three-piece set. It features a wider working surface and chamfered corner clips. These features help improve the performance of the Opentrons Flex Gripper when moving labware onto or off of the plate. 
+The flat bottom plate for Flex ships with the Temperature Module's caddy and is compatible with various ANSI/SLAS standard well plates. This flat plate differs from the plate that ships with the Temperature Module itself. It features a wider working surface and chamfered corner clips. These features help improve the performance of the Opentrons Flex Gripper when moving labware onto or off of the plate. 
 
 !!! note
     You can tell which flat bottom plate you have because the one for Flex has the words "Opentrons Flex" on its top surface. The one for OT-2 does not. 

docs/flex/docs/protocols/designer.md

@@ -39,11 +39,11 @@ Protocol Designer:
 | Protocol setup | Specify your robot, pipettes, modules, and other hardware (like the Flex Gripper). |
 | Protocol overview | View protocol details like instruments, liquids, and the protocol starting deck at a glance. |
 | Edit protocol | Edit the starting deck, define liquids, and create protocol steps. |
-| Export protocol | Save and import your protocol into the Opentrons App to run on the Flex. |
+| Export protocol | Save your protocol file, which is ready to import into the Opentrons App and run on the Flex. |
 
 ## Part 1: Create a protocol
 
-When you launch Protocol Designer, click to **Create a protocol**. Start by selecting pipettes and, if needed, a Flex Gripper to use with the Flex. You can also customize modules and fixtures, like the waste chute, trash bin, and staging areas, to optimize deck space. Only modules and fixtures compatible with Flex are available. 
+When you launch Protocol Designer, click to **Create a protocol**. Start by selecting pipettes and, if needed, a Flex Gripper. You can also customize modules and fixtures, like the waste chute, trash bin, and staging areas, to optimize deck space. Only modules and fixtures compatible with Flex are available. 
 
 Protocol Designer protocols can control multiple Flex modules of the same type, except for the Thermocycler. At any time, you can edit the protocol to change your hardware configuration. 
 
@@ -132,14 +132,14 @@ Protocol Designer can help you save time and stay organized when your protocol u
 
 To prevent errors, Protocol Designer displays hints, warnings, and error descriptions as you create and edit a protocol. Deleting a module or labware used in your protocol, running out of tips in a transfer step, or leaving a labware latch closed can all result in a Protocol Designer errors. 
 
-Click on any step that appears in red in the protocol timeline and follow the text instructions to fix errors. We recommend resolving all warnings and errors to avoid problems in your workflow. For more details, see the Protocol Designer [instruction manual](https://insights.opentrons.com/hubfs/Protocol%20Designer%20Instruction%20Manual.pdf "instruction manual").
+Click on any step that appears in red in the protocol timeline and follow the text instructions to fix errors. We recommend resolving all warnings and errors to avoid problems in your workflow.
 
 
 ## Part 3: Export a protocol
 
-When you're finished creating and editing your protocol, click **Done** in the upper right to return to the protocol overview. Click **Export protocol** to download your protocol file. 
+When you've finished creating and editing your protocol, click **Done** in the upper right to return to the protocol overview. Click **Export protocol** to download your protocol file. 
 
-To run your protocol, import it into the Opentrons App (see the Software and Operation chapter for details on installing and using the Opentrons App). Then, run your protocol from the app or send it to your Flex to run from the touchscreen. 
+To run your protocol, [import it into the Opentrons App][import-a-protocol]. Then, run your protocol from the app or send it to your Flex to run from the touchscreen. 
 
 ## Modify an existing protocol
 

docs/flex/docs/protocols/development-service.md

@@ -2,7 +2,7 @@
 title: "Opentrons Flex: Custom Protocol Service"
 ---
 
-# Custom Protocol Development service
+# Custom Protocol Development Service
 
 Opentrons provides a [Remote Custom Protocol Development service](https://opentrons.com/instrument-services) for applications not already included in the Protocol Library. Our comprehensive authoring and validation service has a turnaround time of two weeks. As part of the service, Opentrons field applications scientists will:
 

docs/flex/docs/protocols/library.md

@@ -42,4 +42,4 @@ Click on a protocol to go to its detail page, which provides even more informati
 
 - **Protocol steps:** A list of steps written by the protocol author, as well as a visual deck map and list of liquids specified in the protocol file.
 
-The details page also provides basic instructions for downloading and running the protocol. For more information on importing a protocol to the Opentrons App and setting up a run, see the [Transferring Protocols to Flex section][transferring-protocols-to-flex] in the Software and Operation chapter.
+The details page also provides basic instructions for downloading and running the protocol. For more information on importing a protocol to the Opentrons App and setting up a run, see the [Transferring Protocols to Flex section][transferring-protocols-to-flex].

docs/flex/docs/protocols/ot-2.md

@@ -2,7 +2,7 @@
 title: "Opentrons Flex: OT-2 Protocols"
 ---
 
-# OT-2 protocols
+# OT-2 Protocols
 
 There are hundreds of OT-2 protocols in the Protocol Library, and you may have created your own OT-2 protocols for your lab. Opentrons Flex can perform all the basic actions that the OT-2 can, but OT-2 protocols aren't directly compatible with Flex. However, with a little effort, you can adapt an OT-2 protocol so it will run on Flex. This lets you have parity across different Opentrons robots in your lab, or you can extend older protocols to take advantage of new features only offered on Flex.
 
@@ -27,7 +27,7 @@ Flex uses different types of pipettes and tip racks than OT-2, which have their
 For example, you could convert an OT-2 protocol that uses a P300 Single-Channel GEN2 pipette and 300 µL tips to a Flex protocol that uses a Flex 1-Channel 1000 µL pipette and 1000 µL tips:
 
 ```python
- Original OT-2 code
+# Original OT-2 code
 def run(protocol: protocol_api.ProtocolContext):
     tips = protocol.load_labware("opentrons_96_tiprack_300ul", 1)
     left_pipette = protocol.load_instrument(
@@ -36,7 +36,7 @@ def run(protocol: protocol_api.ProtocolContext):
 ```
 
 ```python
- Modified Flex code
+# Modified Flex code
 def run(protocol: protocol_api.ProtocolContext):
     tips = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "D1")
     left_pipette = protocol.load_instrument(