proofread and fixes up through Labware Concepts

Author: ecormany

docs/flex/docs/installation/first-run.md

@@ -24,7 +24,9 @@ Follow the prompts on the touchscreen to get your robot connected so it can chec
 <figcaption>Network connection options. You need to have internet connectivity to set up Flex.</figcaption>
 </figure>
 
-**Wi-Fi:** Use the touchscreen to connect to Wi-Fi networks that are secured with WPA2 Personal authentication (most networks that only require a password to join fall under this category).
+### Wi-Fi
+
+Use the touchscreen to connect to Wi-Fi networks that are secured with WPA2 Personal authentication (most networks that only require a password to join fall under this category).
 
 !!! note 
     Flex does not support captive portals (networks that don't have a password but load a webpage to authenticate users after connecting).
@@ -56,11 +58,15 @@ Select your network from the dropdown menu or choose "Join other network..." and
 
 Each of these methods requires a username and password, and depending on your exact network configuration may require certificate files or other options. Consult your facility's IT documentation or contact your IT manager for details of your network setup.
 
-**Ethernet:** Connect your robot to a network switch or hub with an Ethernet cable. You can also connect directly to the Ethernet port on your computer, starting in robot system version 7.1.0.
+### Ethernet
+
+Connect your robot to a network switch or hub with an Ethernet cable. You can also connect directly to the Ethernet port on your computer, starting in robot system version 7.1.0.
+
+### USB 
 
-**USB:** Connect the provided USB A-to-B cable to the robot's USB-B port and an open port on your computer. Use a USB B-to-C cable or a USB A-to-C adapter if your computer does not have a USB-A port.
+Connect the provided USB A-to-B cable to the robot's USB-B port and an open port on your computer. Use a USB B-to-C cable or a USB A-to-C adapter if your computer does not have a USB-A port.
 
-To proceed with setup, the connected computer must have the Opentrons App installed *and running*. For details on installing the Opentrons App, see the [App Installation section][app-installation] of the Software and Operation chapter.
+To proceed with setup, the connected computer must have the Opentrons App installed *and running*. For details on installing the Opentrons App, see the [App Installation section][app-installation].
 
 ## Install software updates
 
@@ -76,8 +82,8 @@ Connect the included Emergency Stop Pendant (E-stop) to an auxiliary port (AUX-1
 <figcaption>Before and after connecting the Emergency Stop Pendant.</figcaption>
 </figure>
 
-Attaching and enabling the E-stop is *mandatory* for attaching instruments and running protocols on Flex. For more information on using the E-stop during robot operation, see the of the System Description chapter.
+Attaching and enabling the E-stop is *mandatory* for attaching instruments and running protocols on Flex. For more information on using the E-stop during robot operation, see the [When to Use the E-stop section][when-to-use-the-e-stop].
 
 ## Give your robot a name
 
-Naming your robot lets you easily identify it in your lab environment. If you have multiple Opentrons robots on your network, make sure to give them unique names. Once you've confirmed your robot's name, you'll be taken to your Opentrons Flex Dashboard. Likely the next step you'll want to take is attaching instruments, which is covered in the next section.
+Naming your robot lets you easily identify it in your lab environment. If you have multiple Opentrons robots on your network, make sure to give them unique names. Once you've confirmed your robot's name, you'll be taken to your Opentrons Flex Dashboard. Likely the next step you'll want to take is [attaching instruments][instrument-installation-and-calibration].

docs/flex/docs/installation/requirements.md

@@ -19,9 +19,15 @@ Space is a valuable commodity in almost every lab. Your Flex is going to need so
 !!! warning
     *Do not* position the sides or back of the Flex flush against a wall.
 
-![Opentrons Flex with arrows labeling width, height, and depth](../images/flex-dimensions.png "Opentrons Flex base dimensions") Opentrons Flex base dimensions.
-
-![Top view of Opentrons Flex, showing minimum side and back clearance.](../images/flex-clearance.png "Flex minimum clearance") Top view of Opentrons Flex, showing minimum side and back clearance.
+<figure markdown>
+![Opentrons Flex with arrows labeling width, height, and depth](../images/flex-dimensions.png "Opentrons Flex base dimensions")
+<figcaption>Opentrons Flex base dimensions.</figcaption>
+</figure>
+
+<figure markdown>
+![Top view of Opentrons Flex, showing minimum side and back clearance.](../images/flex-clearance.png "Flex minimum clearance")
+<figcaption>Top view of Opentrons Flex, showing minimum side and back clearance.</figcaption>
+</figure>
 
 ## Power consumption
 

docs/flex/docs/introduction.md

@@ -6,7 +6,7 @@ title: "Opentrons Flex: Introduction"
 
 Opentrons Flex is a liquid-handling robot designed for high throughput and complex workflows. The Flex robot is the base of a modular system that includes pipettes, a labware gripper, deck fixtures, on-deck modules, and labware — all of which you can swap out yourself. Flex is designed with a touchscreen so you can work with it directly at the lab bench, or you can control it from across your lab with the Opentrons App or our open-source APIs.
 
-Flex workstations come with all of the equipment — robot, hardware, and labware — that you need to get started automating common lab tasks. For other applications, Opentrons Flex runs on fully open-source software and firmware, and is reagent- and labware-agnostic, giving you control over how you design and run your protocols.
+Flex workstations come with all of the equipment — robot, hardware, and labware — that you need to get started automating common lab tasks. For other applications, Opentrons Flex runs on fully open-source software and firmware, and does not require proprietary reagents and labware, giving you control over how you design and run your protocols.
 
 ## What's new in Flex
 
@@ -15,7 +15,7 @@ Opentrons Flex is part of the Opentrons liquid handler series of robots. Users o
 | Feature | Description |
 | --- | --- |
 | **Pipette throughput** | Flex pipettes have 1, 8, or 96 channels. The 96-channel pipette operates on 12 times as many wells at once as the largest OT-2 pipette.                                                                                                                               |
-| **Pipette and tip capacities** | Flex pipettes have larger volume ranges (1–50 µL, 5–1000 µL) and can all work with any volume of Opentrons Flex tips. This is an improvement over OT-2 pipettes, which have smaller ranges and must use tips with a matching volume range.                         |
+| **Pipette and tip capacities** | Flex pipettes have larger volume ranges (1–50 µL, 5–1000 µL). The 5–1000 µL Flex pipettes can work with any volume of Opentrons Flex tips. This is an improvement over OT-2 pipettes, which have smaller ranges and must use tips with a matching volume range.                         |
 | **Gripper** | The Opentrons Flex Gripper picks up and moves labware around the deck automatically, without user intervention. The gripper enables more complex workflows within a single protocol run.                                                                             |
 | **Automated calibration** | Positional calibration of Flex pipettes and the gripper is fully automated. Press one button, and the instrument will move to precision-machined points on the deck to determine its exact position, saving that data for use in your protocols.                      |
 | **Touchscreen** | Flex has its own touchscreen interface that lets you control it directly, in addition to using the Opentrons App. Use the touchscreen to start protocol runs, check job status, and change settings right on the robot.                                                 |

docs/flex/docs/labware/concepts.md

@@ -26,7 +26,7 @@ Let's take a moment to unpack the concept of custom labware.
 
 As an example, the Opentrons Labware Library includes 96-well plates (200 µL) from Corning and Bio-Rad, but other manufacturers make these well plates too. And, thanks to commonly accepted industry standards, the differences among these ubiquitous lab items are minor. However, an ordinary 200 μL, 96-well plate from Stellar Scientific, Oxford Lab, or Krackeler Scientific (or any other supplier for that matter) is "custom labware" for the Flex because it isn't pre-defined in our Labware Library. Additionally, minor differences in labware dimensions can have a drastic impact on the success of your protocol run. For this reason, it's important to have an accurate labware definition for each labware you want to use in your protocol. 
 
-Also, while custom labware could be an esoteric, one-off piece of kit, most of the time it's just the tips, plates, tubes, and racks used every day in labs all over the world. Again, the only difference between Opentrons labware and custom labware is that the custom labware is not predefined in the software that powers the robot. The Flex can, and does, work with other basic labware items or something unique, but you need to record that item's characteristics in a labware definition JSON file and import that data into the Opentrons App. See the [Labware Definitions section][labware-definitions] below for more information. 
+Also, while custom labware could be an esoteric, one-off piece of kit, most of the time it's just the tips, plates, tubes, and racks used every day in labs all over the world. Again, the only difference between Opentrons labware and custom labware is that the custom labware is not predefined in the software that powers the robot. The Flex can, and does, work with other basic labware items or something unique, but you need to record that item's characteristics in a labware definition JSON file and import that data into the Opentrons App. See the [Labware Definitions section][labware-definitions] for more information. 
 
 To sum up, labware includes:
 

docs/flex/docs/labware/index.md

@@ -9,6 +9,6 @@ This chapter covers how Opentrons Flex works with labware, both in software and
 - [Labware concepts](./concepts.md) describes how Opentrons software encodes and uses information about physical labware items in your lab.
 - [Labware types](./types.md) gives examples of the categories of labware that you'll find in the Opentrons Labware Library. 
 - Certain types of labware are [compatible with the Opentrons Flex Gripper](./gripper.md) for automated movement around the deck. (All labware can be moved manually.) 
-- Custom [labware definitions](./definitions) let you take labware you've modified or manufactured for your scientific application and get them working with Flex. This section describes all the features available for first-party and custom labware defined by our JSON labware schema.
+- [Labware definitions](./definitions) are the files Flex uses to understand the dimensions and characteristics of labware. This section describes all the features available for Opentrons-verified and custom labware defined by our JSON labware schema.
 
 You can purchase labware from the [Opentrons shop](https://opentrons.com/products/categories/tips-&-labware) or the original equipment manufacturers. And, Opentrons is always working to verify new labware definitions. See the [Labware Library](https://labware.opentrons.com/) for the latest listings. 

docs/flex/docs/modules/absorbance-plate-reader.md

@@ -22,7 +22,7 @@ The plate reader uses 96 separate detection units for rapid sample analysis. The
 
 ### Gripper compatibility
 
-The Opentrons Flex Gripper is required when using the plate reader. The Gripper is needed to move labware and the plate reader's lid, onto and off the module.
+The Opentrons Flex Gripper is required when using the plate reader. The gripper is needed to move labware and the plate reader's lid, onto and off the module.
 
 ### Deck placement
 

docs/flex/docs/modules/hepa-uv.md

@@ -12,7 +12,7 @@ title: "Opentrons Flex: HEPA/UV Module"
 The top-mounted Opentrons Flex HEPA/UV Module is a clean air and ultraviolet (UV-C) disinfectant accessory for the Flex liquid handling robot. It contains a mesh pre-filter, a HEPA filter, and two UV lights. During operation, the HEPA system creates a positive pressure environment inside the Flex enclosure, which helps protect samples from contamination. When running the UV lights and air filtration for a full, 15-minute cycle, the HEPA/UV module can achieve ISO-5 clean bench standards within the Flex enclosure.
 
 !!!warning
-    The HEPA/UV Module is not a biosafety cabinet. Do not use it with pathogens or to filter particles smaller than 0.3 micrometers (μM).
+    The HEPA/UV Module is not a biosafety cabinet. Do not use it with pathogens or to filter particles smaller than 0.3 micrometers (μm).
 
 ## HEPA/UV Module features
 

docs/flex/docs/modules/index.md

@@ -11,7 +11,7 @@ This chapter summarizes the functions and physical specifications of modules tha
 !!! tip
     - For complete instructions on module installation and use, refer to the quickstart guide that shipped with your unit or find its manual in the [Modules category](/modules/) of the Opentrons Documentation website.
 
-    - For details on integrating modules into your protocols, see the [Protocol Designer section](protocol-development.md#protocol-designer) of the Protocol Development chapter or the [Hardware Modules section](https://docs.opentrons.com/v2/new_modules.html) of our Python API documentation.
+    - For details on integrating modules into your protocols, see the [Protocol Designer section](../protocols/designer.md) of the Protocol Development chapter or the [Hardware Modules section](https://docs.opentrons.com/v2/new_modules.html) of our Python API documentation.
 
 
 ## Supported modules

docs/flex/docs/modules/thermocycler.md

@@ -19,7 +19,7 @@ The Thermocycler's block can heat and cool, and its lid can heat, with the follo
 
 - Thermal block temperature range: 4–99 °C
 
-- Thermal block maximum heating ramp rate: 4.25 °C/s from GEN2 ambient to 95 °C
+- Thermal block maximum heating ramp rate: 4.25 °C/s from ambient to 95 °C
 
 - Thermal block maximum cooling ramp rate: 2.0 °C/s from 95 °C to ambient
 
@@ -39,7 +39,7 @@ The Thermocycler works with two different plate seals to help protect your sampl
 
 | Lid Type | Description |
 |----|----|
-| Opentrons Tough PCR Auto-sealing Lid | These sterile, single-use PCR plate lids help prevent cross-contamination and evaporation during Thermocycler incubation periods. The lids are Gripper-compatible and can be stacked directly on the deck or placed in a special deck riser. |
+| Opentrons Tough PCR Auto-sealing Lid | These sterile, single-use PCR plate lids help prevent cross-contamination and evaporation during Thermocycler incubation periods. The lids are gripper-compatible and can be stacked directly on the deck or placed in a special deck riser. |
 | Rubber Automation Seal | These are adhesive-backed ethylene propylene diene monomer (EPDM) seals you manually apply to the Thermocycler lid. Rubber seals can be reused up to 20 times; however, unlike the Opentrons Tough Auto-sealing Lid, they are not sterile. The seals must be cleaned and sanitized before each use. |
 
 !!!warning

docs/flex/docs/preface.md

@@ -16,7 +16,7 @@ If you prefer a guided approach, this manual is structured so you can follow it
 
 - **Get started with Flex.** If you need to set up your Flex, follow the detailed [installation instructions](installation/index.md). Then familiarize yourself with the components of Flex in the [system description](system-description/index.md).
 
-- **Set up your deck.** Configuring the deck enables different scientific applications on Flex. [Modules](modules/index.md) are Opentrons peripherals that you can install into or on top of the deck to perform specific scientific tasks. Flex works with out of the box with a wide range of [labware](labware/index.md) for holding liquids.
+- **Set up your deck.** Configuring the deck enables different scientific applications on Flex. [Modules](modules/index.md) are Opentrons peripherals that you can install into or on top of the deck to perform specific scientific tasks. Flex works out of the box with a wide range of [labware](labware/index.md) for holding liquids.
 
 - **Run a protocol.** The core use of Flex is running standardized scientific procedures, known as [protocols](protocols/index.md). Opentrons offers several ways to get ready-made protocols or design them yourself. To run your protocol, use the [touchscreen](touchscreen/index.md) or the [Opentrons App](opentrons-app.md). Both the touchscreen and app let you perform other tasks and customize your robot's settings.
 
@@ -34,7 +34,7 @@ If you prefer a guided approach, this manual is structured so you can follow it
 
 ## Notes and warnings
 
-Throughout this manual, you'll find specially formatted note and warning blocks. Notes provide helpful information that may not be obvious in the ordinary course of using Flex. Pay special attention to warnings---they are only used in situations where you run the risk of personal injury, damage to equipment, loss or spoilage of samples or reagents, data loss, or other harm.
+Throughout this manual, you'll find specially formatted note and warning blocks. Notes provide helpful information that may not be obvious in the ordinary course of using Flex. Pay special attention to warnings: they are only used in situations where you run the risk of personal injury, damage to equipment, loss or spoilage of samples or reagents, data loss, or other harm.
 
 Notes and warnings look like this: