more docs and fix build?

CamDavidsonPilon · CamDavidsonPilon · commit b1450ce84e7f · 2025-04-07T11:22:24.000-04:00
diff --git a/docusaurus.config.js b/docusaurus.config.js
@@ -1,11 +1,14 @@
 // @ts-check
 // Note: type annotations allow type checking and IDEs autocompletion
 
-const math = require('remark-math');
-const katex = require('rehype-katex');
+//const math = require('remark-math');
+//const katex = require('rehype-katex');
 
-const lightCodeTheme = require('prism-react-renderer/themes/github');
-const darkCodeTheme = require('prism-react-renderer/themes/dracula');
+import math from 'remark-math';
+import katex from 'rehype-katex';
+
+import lightCodeTheme from 'prism-react-renderer/themes/github';
+import darkCodeTheme from 'prism-react-renderer/themes/dracula';
 
 /** @type {import('@docusaurus/types').Config} */
 const config = {
diff --git a/user-guide/02-Experiment basics/02-prepare-vial-for-cultures.md b/user-guide/02-Experiment basics/02-prepare-vial-for-cultures.md
@@ -7,19 +7,27 @@ slug: /prepare-vial-for-cultures
 
 #### Cleaning the vial
 
-It's recommend to clean your vial before every use. The vial and cap can be cleaned with soapy water. A useful accessory for cleaning is a small bottle brush / test tube brush. Rinse the vial to remove any soap residue.
+It's recommend to clean your vial and vial cap before every use. The vial and cap can be cleaned with water and detergent. Rinse vial and cap to remove any soap residue.
+
+:::tip
+Two useful accessories for cleaning:
+
+1. small bottle brush / test tube brush.
+2. ~10ml syringe with luer lock attachment to pump soapy water in and out of the vial cap connectors.
+
+:::
 
 #### Choosing a volume for your culture
 
-We suggest using between **8ml to 16ml** volume of liquid in the vial.
+We suggest using between **8ml to 16ml** volume of liquid in the 20ml vials, and **10ml to 30ml** for 40ml vials.
 
 :::tip
 Some things to consider when selecting a volume: a lower volume will provide more aeration per mL since the liquid-air interface is fixed. A lower volume will also be more responsive to changes in temperature, and be able to achieve a higher maximum temperature. But too low and the vortex caused by stirring may start interfering with the Pioreactor's optical system (a lower RPM can fix this though).
 :::
 
-#### Position of tubes in cap
+#### Position of tubes/needles in cap
 
-Keep _at least_ 1 cap tube out of the liquid and well away from potential bubbles / foam that may occur. This will prevent gas pressure from building up. Something also to keep in mind: more tubes out of the liquid means more gas transfer with the ambient atmosphere.
+Keep _at least_ 1 cap tube/needle out of the liquid and well away from potential bubbles / foam that may occur. This will prevent gas pressure from building up. Something also to keep in mind: more tubes/needles out of the liquid means more gas transfer with the ambient atmosphere.
 
 If using pumps with your Pioreactor, see the note [below](/user-guide/prepare-vial-for-cultures#using-pumps-influx-and-efflux).
 
@@ -41,10 +49,6 @@ The glassware vial, stir bar and vial cap that come with your Pioreactor are all
 Don't have an autoclave? A kitchen pressure cooker works just as well. Still don't have that? You can use a stove top or hotplate: heat on a medium-low heat until boiling, and let boil for a few minutes. However, an autoclave or a pressure cooker is a more effective sterilizer.
 :::
 
-:::tip
-"Flick" away any trapped liquid in the cap's tubes.
-:::
-
 
 #### Using sterile filtration
 
@@ -53,17 +57,17 @@ Filtered media can be directly added to a sterilized glass vial, or via the (ste
 
 ### 4. Inoculation
 
-Ideally in a sterile environment, the vial's lid can be removed and the inoculant can be added. Alternatively, for additional sterility, a needle can be sent down a tube, without removing the cap at all.
+Ideally in a sterile environment, the vial's lid can be removed and the inoculant can be added. Alternatively, for additional sterility, a needle can be sent down a tube/needle, without removing the cap at all.
 
 How much inoculant should you add? That depends on the concentration of your inoculant. From our experience, we create a dense culture/stock culture by adding some amount of culture to sterile media or water, and then inoculate our vials from this stock. 
 
 For example, we add 0.5 grams of dried Baker's yeast to 15 mL of YPD broth, then store it in a fridge for further use. 
 
 We recommend measuring with a micropipette. If you are using a dropper, hold it vertically for more accurate, consistent drops.
 
-### 5. Adjusting tube lengths (Optional)
+### 5. Adjusting tube/needle lengths (Optional)
 
-Keep the bottoms of the tubes in the cap from being submerged in your media to avoid creating a pressured environment. Adjust each luer lock end until the other end of the tube is above liquid level.
+Keep the bottoms of the tubes/needles in the cap from being submerged in your media to avoid creating a pressured environment. Adjust each luer lock end until the other end of the tube/needle is above liquid level.
 
 ### 6. Handling the glass
 
@@ -84,13 +88,14 @@ Next, you can [start your experiment](/user-guide/set-up-an-experiment) in the b
 ### Extra
 #### Using pumps: influx and efflux.
 
-When using the Pioreactor with pumps, you'll be using the four luer lock tubes as influx and efflux. The tubes, which are identical lengths, can be moved up and down, and we suggest using this as a way to "label" tubes, and to control the maximum volume in the vial. This can be done before sterilization. Here's how:
+When using the Pioreactor with pumps, you'll be using the four luer lock tubes/needle as influx and efflux. The tubes/needles, which are identical lengths, can be moved up and down, and we suggest using this as a way to "label" tubes, and to control the maximum volume in the vial. This can be done before sterilization. Here's how:
+
+Two tubes/needles can be pulled such they are aligned high, near the tapered "shoulder" of the vial, and out of the vial's liquid. These two tubes/needles will be the liquid influx. For some operations, like a chemostat, you'll only be using one of these, but some operations require more than one influx.
 
-One tube can be pulled high up, so that about a millimeter is showing on the underside of the cap. This will be our air influx and efflux (recall that when liquid is added or removed, air needs to be removed or added respectively to not create a pressure difference).
+The third tube is the liquid efflux tube. It will be positioned such that it controls the final amount of volume in the vial. Fill your vial to the desired final volume using water. Pull the tube down such that its end just touches the top of the liquid when the cap is fully screwed on. It may take some minor adjustments to achieve this.
 
-Two tubes can be pulled such they are aligned with the bottom rim of the cap. These two tubes will be the liquid influx tubes. For some operations, like a chemostat, you'll only be using one of these tubes, but some operations require more than one influx.
+The fourth tube is the air exchange tube. This tube should be positioned such that it is above the liquid level, and not touching the liquid. This will allow for gas exchange with the ambient atmosphere.
 
-The final tube is the liquid efflux tube. It will be positioned such that it controls the final amount of volume in the vial. Fill your vial to the desired final volume using water. Pull the final tube down such that its end just touches the top of the water when the cap is fully screwed on. It may take some minor adjustments to achieve this.
 
 :::info
 How does this maintain a constant volume throughout operation? When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but **then the efflux pump runs again for an additional few seconds**.  The efflux pump is run for an additional few seconds to eliminate any volume differences or deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step guarantees that that volume of liquid never exceeds the end of the efflux tube.
diff --git a/user-guide/02-Experiment basics/10-manual-led-dosing.md b/user-guide/02-Experiment basics/10-manual-led-dosing.md
@@ -22,7 +22,7 @@ Cycling is good for cleaning pumps, priming tubes with media, or filling your vi
 Under the _Dosing_ tab, you can also run specific pumps (media, waste, and alt-media) for a specific duration, volumes (if calibrated), or continuously. The latter will run until the *Stop* button is pressed.
 
 :::caution
-Careful not to overflow your vial! The vial can hold 20ml, but stay well below this.
+Careful not to overflow your vial! The Pioreactor doesn't know how much liquid is currently in the vial. Stay well below the max volume of the vial for safety.
 :::
 
 ![UI showing how to add media.](/img/user-guide/add_media.png)
diff --git a/user-guide/03-Extending your Pioreactor/07-using-pumps.md b/user-guide/03-Extending your Pioreactor/07-using-pumps.md
@@ -78,14 +78,14 @@ Read the [calibration instructions](/user-guide/hardware-calibrations#pump-calib
 ## Using pumps in experiments
 
 :::caution
-We strongly recommended you don't run peristaltic pumps *continuously* for hours at a time. By continuously, we mean "always moving liquid". The inner tubing has a lifetime and may wear out during operation, causing a leak. **If you need to move liquid continuously for long periods of time, you need a different pump design**.
+We strongly recommended you don't run peristaltic pumps *continuously* for hours at a time. By continuously, we mean "the pump motor is always on". The inner tubing has a lifetime and may wear out during operation, causing a leak. **If you need to move liquid continuously for long periods of time, you need a different pump design**.
 :::
 
 
 
 ### Sterilizing the pumps before and after experiments
 
-To avoid contamination, pumps should be sterilized before and after use.
+To avoid contamination, pump tubing and connectors should be sterilized before and after use.
 
 #### Using heat
 
@@ -94,16 +94,17 @@ To avoid contamination, pumps should be sterilized before and after use.
 
 #### Using bleach and ethanol
 
+:::caution
+It's important to not keep harsh chemicals, like bleach, in the tubing and stainless steel needles for long. Cleaning should always end with flushing the tubes with water or something inert.
+:::
+
 1. Create a 10% bleach dilution, or high concentration alcohol, in a container. Place the sink and source tubes of each pump you're sterilizing in the beaker.
 2. On the UI, in the _Pioreactors_ tab, click _Manage_ and go to the _Dosing_ tab.
 3. _Run continuously_ to cycle the disinfectant solution through each pump that you're using.
 <img src="/img/user-guide/dosing_in_ui.png" width="735" style={{margin: "15px auto", display:"block"}}/>
-4. _Interrupt_ after sufficient cycling, at least 2 minutes.
-5. If finishing an experiment, repeat the above with water. If starting an experiment, you'll need to prime the pumps, see the next section.
-
-:::caution
-It's important to not keep harsh chemicals, like bleach, in the silicone tubing for long. Cleaning pumps should always end with flushing the tubes with water or something inert.
-:::
+4. _Stop_ after sufficient cycling, at least 2 minutes, but no more than 5 minutes.
+5. **Important**: If finishing an experiment, repeat the above with water to purge the harsh chemicals from the lines.
+6. If starting an experiment, you'll need to prime the pumps, see the next section.
 
 
 ### Preparing for experiments
diff --git a/user-guide/29-Automations/02-dosing-automations.md b/user-guide/29-Automations/02-dosing-automations.md
@@ -88,7 +88,7 @@ This automation moves a preset amount of `volume` every `duration` minutes using
 
 When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but **then the efflux pump runs again for an additional few seconds**. The efflux pump is run for an additional few seconds to eliminate any volume deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step helps guarantee that that volume of liquid never exceeds the end of the efflux tube. See `waste_removal_multiplier` parameter below.
 
-### Why does my influx pump only partially add what's required? What are subdoses?
+### Why does my influx pump only partially add the amount of liquid required? What are subdoses?
 
 To further avoid overflow, we limit how much liquid is added in a single pump cycle. If the amount of liquid to be added is greater than the `max_dose_volume`, then the liquid is divided into smaller doses (halved until those new doses are less than `max_subdose` parameter), with the waste-pump run in between to avoid overflow. These small doses are called _subdoses_. You can change the maximum subdose value with the parameter `max_subdose`, see below.
 
