diff --git a/src/components/AssemblyInstructionBlock.js b/src/components/AssemblyInstructionBlock.js index e3013b7f0..ecf121844 100644 --- a/src/components/AssemblyInstructionBlock.js +++ b/src/components/AssemblyInstructionBlock.js @@ -26,7 +26,7 @@ export default function AssemblyInstructionBlock({children, title, images}) {

{title} #

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100644 index 000000000..c5834afa1 Binary files /dev/null and b/static/img/user-guide/hardware-assembly/40ml/window-pieces.png differ diff --git a/static/img/user-guide/hardware-assembly/pioreactor_40ml_v1.0_splash.jpeg b/static/img/user-guide/hardware-assembly/pioreactor_40ml_v1.0_splash.jpeg new file mode 100644 index 000000000..dc23d2726 Binary files /dev/null and b/static/img/user-guide/hardware-assembly/pioreactor_40ml_v1.0_splash.jpeg differ diff --git a/user-guide/01-getting-started/00-gettingstarted.mdx b/user-guide/01-getting-started/00-gettingstarted.mdx index 2ba63d66b..20b842a24 100644 --- a/user-guide/01-getting-started/00-gettingstarted.mdx +++ b/user-guide/01-getting-started/00-gettingstarted.mdx @@ -8,17 +8,23 @@ import Card from '@site/src/components/Card';

Choose from the guides below:

+

Pioreactor 40ml assembly

+ +
+ +
+

Pioreactor 20ml assembly

-
- +
+

Upgrade kits and accessories

-
- +
+ @@ -26,7 +32,7 @@ import Card from '@site/src/components/Card';

Software guides

-
+
diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/01-40ml-introduction.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/01-40ml-introduction.md new file mode 100644 index 000000000..15bb1807b --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/01-40ml-introduction.md @@ -0,0 +1,65 @@ +--- +title: Before you begin assembly +slug: /40ml-hardware-setup-intro +hide_table_of_contents: true +--- + +import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBlock'; +import Highlight from '@site/src/components/Highlight'; +import Admonition from '@theme/Admonition'; + +import * as colors from '@site/src/components/constants'; + + + + You can expect the assembly to take approximately 20-30 minutes. + + +------- + + + +You will need the following items to assemble your Pioreactor: + +1. Your own Raspberry Pi (RPi). Displayed are three examples. +2. A Philip's head screwdriver. +3. The Pioreactor 40ml kit. + + + +------- + + + +- Before starting a step, read all instructions and view all photos at the bottom of each step. +- Most of the labels are scaled 1:1 and can be used to identify parts. + +:::info +Missing a part? Email us at `hello@pioreactor.com`, we're happy to help. +::: + + + + +------- + + + +Here are some tips to prevent damage to the electronics: +- **Keep the electronics inside the ESD bag** right until you are asked to install them. +- **Always touch the sides of the board** while manipulating with it. Avoid touching the chips, capacitors, and other parts of the electronics. +- **Before you touch the electronics**, use any conductive (steel) structure nearby to neutralize any electro-static energy. +- **Be extra cautious in rooms with carpets**, which are a source of electrostatic energy. +- Clothes made of wool and certain synthetic fabrics can easily gather static electricity. It is safer to wear **cotton clothing**. + + + +------- + + + +- If you get stuck, missing a piece, or are unsure of something, **let us know**! +- You can reach out to us at `hello@pioreactor.com`! +- Continue to the [next assembly instructions](/user-guide/40ml-rpi-hat-assembly). + + diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/02-40ml-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/02-40ml-rpi-hat-assembly.md new file mode 100644 index 000000000..065dd54b0 --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/02-40ml-rpi-hat-assembly.md @@ -0,0 +1,107 @@ +--- +title: Assembling the Raspberry Pi and the HAT +slug: /40ml-rpi-hat-assembly +hide_table_of_contents: true +--- + +import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBlock'; +import Highlight from '@site/src/components/Highlight'; +import * as colors from '@site/src/components/constants'; + +import Tabs from '@theme/Tabs'; +import TabItem from '@theme/TabItem'; + + + + +1. You will need: +* A Raspberry Pi of your choosing. Displayed are three options - you just need one. +* Hex nuts (4x) +* M2.5 12mm hex standoffs (4x) +* M2.5 12mm hex standoffs-with-6mm-screws (4x) +* M2.5 10mm screws (4x) +* Bottom faceplate +* HAT PCB + + +2. Check the GPIO pins on the HAT PCB to confirm that they are straight and not touching another GPIO pin. + + + +----- + + + + + + + + +1. If using a half-size Raspberry Pi (aka a Zero model), switch to the tab above called "Raspberry Pi Zero" to see Zero specific instructions. + +:::tip +The 40 GPIO pins (standing for general-purpose input/output) form a distinct row on one side of the Raspberry Pi. Note the orientation of these pins to help you assemble correctly! +::: + +2. Orientation: the base will have a flat edge and an edge with an indent. The GPIO pins sit along the indent, seen on the left in the images. +3. Insert the M2.5 10mm screws into the holes. +4. Hand screw a hex nut onto each screw. +5. Place the Raspberry Pi on top, aligning the holes, with the GPIO pins on the left. Note: your Raspberry Pi may look different than the one displayed. + + + + +----- + + + +1. Hand screw on the M2.5 12mm hex standoffs-with-6mm-screw in each corner. +2. Place the HAT PCB on top. Push down *from the corners* to secure it in place. The HAT PCB's GPIO connector will line up with the RPi's GPIO pins and may require a slight force to compress down. You can also use the next Tip below to help apply force. + +3. Hand screw the M2.5 12mm hex standoffs in each corner, on top of the HAT. + +:::tip +By screwing down the standoffs, they'll help compress the HAT onto the RPi, too. +::: + +4. Put this aside and proceed to the next page. + + + +----- + + + + + +:::tip +The 40 GPIO pins (standing for general-purpose input/output) form a distinct row on one side of the Raspberry Pi. Note the orientation of these pins to help you assemble correctly! +::: + +1. Orientation: the base will have a flat edge and an edge with an indent. The GPIO pins sit along the indent, seen on the left in the images. +2. Insert the 10mm screws into the holes. +3. Hand screw the hexnuts on the screws along the flat edge of the bottom faceplate. Hexnuts are only needed on one side because of the size of the Raspberry Pi Zero. +4. Place the Raspberry Pi along the indented edge of the faceplate, with the GPIO pins on the left. +5. Hand screw on the M2.5 12mm hex standoffs-with-6mm-screw in each corner. + + + + +----- + + + +1. Place the HAT on top. Push down to secure it in place. The HAT PCB's GPIO connector will line up with the RPi's GPIO pins, and may require a slight force to compress down. You can also use the next Tip below to help apply force. + +2. Hand screw the M2.5 12mm hex standoffs in each corner, on top of the HAT. + +:::tip +By screwing down the standoffs, you can use these standoffs to help compress the HAT onto the RPi, too. +::: + +3. Put this aside and proceed to the next page. + + + + + diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/03-40ml-wetware-assembly.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/03-40ml-wetware-assembly.md new file mode 100644 index 000000000..f6b4612b2 --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/03-40ml-wetware-assembly.md @@ -0,0 +1,81 @@ +--- +title: Wetware assembly +slug: /40ml-wetware-assembly +hide_table_of_contents: true +--- + +import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBlock'; +import Highlight from '@site/src/components/Highlight'; +import * as colors from '@site/src/components/constants'; + +import Tabs from '@theme/Tabs'; +import TabItem from '@theme/TabItem'; + + + +:::note +The vial holder comes in two halves; a top vial holder and a bottom vial holder. Both have sections to insert O-rings for a more secure hold on your vials and increased protection against leaks. The thinner O-ring (#024) with an X-shaped cross section fits into the top piece. The thicker O-ring (#121) lines the bottom piece. +::: + +1. The O-rings are pre-lubricated with a silicone-based lubricant. If needed, remove any excess lubricant from the O-rings. +2. The top vial holder has a groove within the body where the thinner #024 O-ring sits. Carefully insert the O-ring using your fingers. Make sure to not twist the O-ring. +3. Run your finger inside the vial holder, pushing the O-ring into place to ensure a snug fit. +4. The bottom vial holder has a groove for the thicker #121 O-ring. The O-ring will sit between the base of the holder and the heater PCB. Carefully insert the O-ring using your fingers. Make sure to not twist the O-ring. +5. Push the O-ring into place to ensure a snug fit. + + + +------- + + + +1. Place the window cover over the window. It should fit snugly. +2. Attach it using four M2.5 4mm screws. + + + +------- + + + + +1. On the heater PCB, locate the white-&-beige cable connector, pull the beige-colored tabs outward to open it. +2. Insert the flex cable blue side down, copper side up, into the cable connector. +3. Then push the beige tabs back in to secure the flex cable. + + + + +------ + + + + + +1. Insert the other end of the flex cable below the O-ring and into the groove. Pull it through. +2. Apply pressure on the back of the heater PCB so that it lies flat on the O-ring. Maintain this pressure for the next steps. +3. **While maintaining pressure**, flip the holder and insert the two M2.5-CS 5mm screws into the holes - **don't tighten fully yet**. +4. **While maintaining pressure**, take turns screwing each in until both are reasonably tight, and the heater PCB is securely attached to the bottom vial holder. + + + +----- + + + +1. Remove the _clear_ plastic from one side of the thermal pad. This exposes a sticky side on the thermal pad. +2. Place on the flat (aluminum) part of the heating PCB. Lightly apply downwards pressure to secure it and remove any air bubbles trapped.. +3. Remove the blue protective plastic on top of the thermal pad. + + + + +----- + + + +1. Screw the top and bottom vial holder sections together so that the IR label is positioned above the flat-flex-cable. +2. Set this aside and proceed to the next page. + + diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/04-40ml-faceplate-all-together.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/04-40ml-faceplate-all-together.md new file mode 100644 index 000000000..be95b3824 --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/04-40ml-faceplate-all-together.md @@ -0,0 +1,155 @@ +--- +title: Attaching the wetware to the HAT asssembly +slug: /40ml-putting-it-together +hide_table_of_contents: true +--- + +import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBlock'; +import Highlight from '@site/src/components/Highlight'; +import * as colors from '@site/src/components/constants'; + +import Tabs from '@theme/Tabs'; +import TabItem from '@theme/TabItem'; + + + + + + +:::note +Newer versions of the top faceplate will come with risers (2x) to secure the fan to the faceplate. See _Version 2_ tab for assembly instructions. +::: + +1. For this version, you will need: + + * Fan + * Top faceplate (will have 4x 30mm screws in it) + * M2.5 10mm screw (1x) + + +:::info +The fan and top faceplate come assembled - leave them together. If they are not assembled, attach the fan onto the faceplate with the cable oriented toward the side labelled "PWM". +::: + + + + +----- + + + +1. Push the fan onto the top faceplate, orienting it such that the wire is pointing towards the button. +2. Place the vial holder on top of the four ends of the 30mm screws. The screw ends should fit into four holes on the bottom of the vial holder. The flat flex cable should follow the arrow on the faceplate. +3. Holding it together, finish screwing the M3 30mm screws on the bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten. + + :::caution + You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew partially and inspect the end of the screw for any plastic debris. + ::: + +4. The screw heads will be flush with the faceplate, and there should be no screw threads showing between the vial holder and the faceplate. + + + + +----- + + + +The top faceplate comes with a button extension to provide easier access to pushing the button. + +1. Flip over the assembly. +2. Insert the 10mm screw into the hole under the button extension. +3. Place one finger behind the extension and apply torque with the other hand until the screw is secure in the hole. This may require some force. Once established, you can use a screwdriver to finish screwing it in under you feel sufficient resistance. Don't over-tighten! + + + +----- + + + +1. Place the vial holder assembly onto the Raspberry Pi/HAT's corners. The GPIO pins align with the side notch of the faceplate. +2. Using the M2.5 6mm screws, attach the top and bottom pieces in each corner. +3. Check that the screw for the button extension is in the right position and not prematurely compressing the button under it (you should feel a "click" when pressing the button extension). Temove the top and screw in the M2.5 10mm screw more if you detect a problem. +4. Open the flat flex cable connector on the HAT by pulling the tabs outward, like done previously. Insert the flex cable copper-side up. +5. Push the tabs inward to secure the flex cable. +6. Insert the stirring power connector into PWM channel 1 (unlabelled). +7. Continue to the next page. + + + + + + + + + + +1. For this version, you will need: + + * Fan + * Top faceplate + * M2.5 10mm screw (1x) + * 30mm screws (4x) + * Risers (2x) + + + +----- + + + +1. Screw the 30mm screws about halfway into the bottom of the top faceplate. +2. Push the fan onto the top faceplate, orienting it such that the wire is pointing towards the button. +3. Align a riser onto the edge of the fan, such that the fan is sandwiched between it and the top faceplate. Place it along the same edge as the PWM labels. +4. Holding the stack firmly, screw the 30mm screws into the risers such that screws poke through the top of the riser by ~2-3 mm. Repeat for the second riser on the opposite side of the fan. + + + +----- + + + + +1. Place the vial holder on top of the four ends of the 30mm screws. The screw ends should fit into four holes on the bottom of the vial holder. The flat flex cable should follow the arrow on the faceplate. +2. Holding it together, finish screwing the M3 30mm screws on the bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten. + + :::caution + You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew partially and inspect the end of the screw for any plastic debris. + ::: + +3. The screw heads will be flush with the faceplate, and there should be no screw threads showing between the vial holder and the faceplate. + + + + +----- + + + +The top faceplate comes with a button extension to provide easier access to pushing the button. + +1. Flip over the assembly. +2. Insert the 10mm screw into the hole under the button extension. +3. Place one finger behind the extension and apply torque with the other hand until the screw is secure in the hole. This may require some force. Once established, you can use a screwdriver to finish screwing it in under you feel sufficient resistance. Don't over-tighten! + + + +----- + + + +1. Place the vial holder assembly onto the Raspberry Pi/HAT's corners. The GPIO pins align with the side notch of the faceplate. +2. Using the M2.5 6mm screws, attach the top and bottom pieces in each corner. +3. Check that the screw for the button extension is in the right position and not prematurely compressing the button under it (you should feel a "click" when pressing the button extension). Temove the top and screw in the M2.5 10mm screw more if you detect a problem. +4. Open the flat flex cable connector on the HAT by pulling the tabs outward, like done previously. Insert the flex cable copper-side up. +5. Push the tabs inward to secure the flex cable. +6. Insert the stirring power connector into PWM channel 1 (unlabelled). +7. Continue to the next page. + + + + + + \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/05-40ml-optics-assembly.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/05-40ml-optics-assembly.md new file mode 100644 index 000000000..f2356bdb2 --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/05-40ml-optics-assembly.md @@ -0,0 +1,76 @@ +--- +title: Connect the optics system +slug: /40ml-optics-assembly +hide_table_of_contents: true +pagination_next: null +--- + +import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBlock'; +import Highlight from '@site/src/components/Highlight'; + +import * as colors from '@site/src/components/constants'; + + + + +1. You will need both PD cables (dark bulbs) and IR cable (clear bulb). _Note that PD cables are now 3.5" long instead of 4"_. + +:::tip +Inspect each LED and PD to confirm that their leads are not touching each other. +::: + +2. Insert the connector of the IR cable into **channel A** (labelled on the faceplate). +3. Insert the bulb of the IR cable into the **pocket labeled IR**. +4. _Slowly_ bend the bulb's leads 90 degrees, as seen. + +:::caution +Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's ill-advised to bend them again. +::: + +5. Secure the bulb in place with an LED cap. + + + + +----- + + + + +1. Plug the connector of one PD cable into **channel 1**. +2. Insert the bulb of that cable into the **REF pocket**. +3. _Slowly_ bend the bulb's leads 90 degrees, as seen. + +:::caution +Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's ill-advised to bend them again. +::: + +4. Secure the bulb with an LED cap. + + + +------- + + + +1. Take a moment to orient the other PD cable such that it bends in the right direction for the black connector to insert into **channel 2**. See the image for more detail. +2. In this orientation, **_but without connecting the cable to the channel_**, insert the bulb into the pocket labeled 90°. +3. Bend the leads gently in the direction of the channel. +4. Secure the bulb with an LED cap. +5. Plug the connector into **channel 2**. +6. Push all remaining LED caps onto each pocket. + + + + +------------------- + + + + +Your new 40ml Pioreactor is now assembled! 🚀 + +Next: begin installing the [software](/user-guide/software-set-up). + + + \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/_category_.yaml b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/_category_.yaml new file mode 100644 index 000000000..c2b0b5812 --- /dev/null +++ b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml/_category_.yaml @@ -0,0 +1,3 @@ +collapsed: true +collapsible: true +label: "Pioreactor 40ml" diff --git a/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/01-v11-introduction.md b/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/01-v11-introduction.md index ac5493da0..bc64b829a 100644 --- a/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/01-v11-introduction.md +++ b/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/01-v11-introduction.md @@ -60,6 +60,6 @@ Here are some tips to prevent damage to the electronics: - If you get stuck, missing a piece, or are unsure of something, **let us know**! - You can reach out to us at `hello@pioreactor.com`! -- Continue to the [next assembly instructions](/user-guide/rpi-hat-assembly). +- Continue to the [next assembly instructions](user-guide/20ml-v11-rpi-hat-assembly). diff --git a/user-guide/30-Advanced/02-networking/10-networking.md b/user-guide/30-Advanced/02-networking/10-networking.md index eb12053b2..fe1a266dd 100644 --- a/user-guide/30-Advanced/02-networking/10-networking.md +++ b/user-guide/30-Advanced/02-networking/10-networking.md @@ -145,7 +145,7 @@ broker_address=192.168.0.3 ### I am using static IPv4s, how do I set this up? -You can put worker ipv4s in the shared config.ini file under `cluster_addresses` section. For example, for worker01: +You can put worker ipv4s in the shared config.ini file under `cluster.addresses` section. For example, for worker01: ```ini [cluster.addresses]