diff --git a/user-guide/01-getting-started/00-gettingstarted.mdx b/user-guide/01-getting-started/00-gettingstarted.mdx index 20b064e27..78e60080d 100644 --- a/user-guide/01-getting-started/00-gettingstarted.mdx +++ b/user-guide/01-getting-started/00-gettingstarted.mdx @@ -11,7 +11,7 @@ import Card from '@site/src/components/Card';

Pioreactor 20ml assembly

- +
diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/01-introduction.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/01-introduction.md deleted file mode 100644 index 13451bc96..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/01-introduction.md +++ /dev/null @@ -1,64 +0,0 @@ ---- -title: Before you begin assembly -slug: /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 20ml v1.0 kit. This kit was sold between 2023 to May 2024. All kits sold after that were v1.1. You can also check by checking you have v1.0 if your plastic pieces have indented text, and not white text. - - - - - - - - -- 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/rpi-hat-assembly). - - diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/02-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/02-rpi-hat-assembly.md deleted file mode 100644 index dd3e3c4be..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/02-rpi-hat-assembly.md +++ /dev/null @@ -1,107 +0,0 @@ ---- -title: Assembling the Raspberry Pi and the HAT -slug: /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) -* 12mm hex standoffs (4x) -* 12mm hex standoffs-with-6mm-screws (4x) -* 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 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 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 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 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 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/pioreactor_20ml_v1.0/03-wetware-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/03-wetware-assembly.md deleted file mode 100644 index f5d2d6ab5..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/03-wetware-assembly.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -title: Wetware assembly -slug: /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'; - - - - -You will need: -* Vial holder -* Heating PCB -* Thermal pad (contains blue cover on one side and clear plastic on the other) -* Flat flex cable -* 4mm screws (2x) - - - ------ - - - -1. Remove the _clear_ plastic from one side of the thermal pad. -2. Place the side on the flat (aluminum) part of the heating PCB. Apply downwards pressure to secure it. -3. Remove the blue protective plastic on top of the thermal pad. -4. Flip the PCB over. On the white-&-beige cable connector, pull the beige-colored tabs outward to open it. -5. Insert the flex cable blue side down, copper side up, into the cable connector. -6. Then push the beige tabs back in to secure the flex cable. - - - ------ - - - -1. Identify the slot on the vial holder where the flex cable will go through. -2. Insert the flex cable in the vial holder, and through the slot, with the blue side of the cable facing upwards. -3. Pull the cable through until the heating PCB is flat with the bottom of the vial holder. -4. Secure the PCB from the bottom using the two 4mm screws. -5. **Important**: the screw heads should be flush against the bottom of the vial holder, that is, no gap. You may need to unscrew and screw in again, or use pliers. -6. Continue to the [next page](/user-guide/putting-it-together). - - - \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/04-faceplate-all-together.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/04-faceplate-all-together.md deleted file mode 100644 index 7f2294d55..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/04-faceplate-all-together.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -title: Attaching the wetware to the HAT asssembly -slug: /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'; - - - -* Fan -* Top faceplate (will have 4 x 30mm screws in it) - -:::info -These 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. 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 bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten. -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. -4. Use the screwdriver to check that the fan can spin freely without rubbing against the screws above. **Important: If there is contact or _near_-contact, slightly unscrew the 30mm screws underneath to provide more clearance**. - - - ------ - - - -1. Place the vial holder assembly onto the Raspberry Pi/HAT. - * The GPIO pins align with the side notch of the faceplate. -2. Using the 6mm screws, attach the top and bottom pieces in each corner. - - - - - - - -1. Open the flat flex cable connector on the HAT by pulling the tabs outward, like done previously. -2. Insert the flex cable copper-side up. -3. Push the tabs inward to secure the flex cable. -4. Insert the stirring power connector into PWM **channel 1** (unlabelled). -3. Continue to the [next page](/user-guide/optics-assembly). - - - ------ \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/05-optics-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/05-optics-assembly.md deleted file mode 100644 index aaadeb2f5..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/05-optics-assembly.md +++ /dev/null @@ -1,73 +0,0 @@ ---- -title: Connect the optics system -slug: /optics-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'; - - - - -1. You will need both PD cables (dark bulbs) and IR cable (clear bulb). -2. Insert the connector of either PD cable into **PD channel 1** (labelled on the faceplate). -3. Place the connector of the other PD cable into **PD channel 2**. -4. Insert the connector of the IR cable into **channel A** (labelled on the faceplate). - - - ------ - - - -1. Insert the bulb of the PD cable in **channel 2** into the pocket labeled **90°**. -2. _Slowly_ bend the bulb's leads 90 degrees, as seen. Secure with a LED pocket cap. - -:::caution -Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's ill-advised to bend them again. -::: - - -3. Insert the bulb of the IR cable in **channel A** into the pocket labeled **IR**. -4. Bend the leads 90 degrees and secure with a LED pocket cap. -5. Insert the bulb of the PD cable in **channel 1** into the pocket labeled **REF**. Orient the bulb's leads such that when bent 90 degrees, it does not interfere with the IR LED bulb next to it. -6. Bend the leads 90 degrees and secure with a LED pocket cap. - -:::tip -Inspect each LED and PD to confirm that neither of the leads are touching. -::: - - - ------ - - - -1. Push all remaining LED pocket caps onto each pocket. - - - - - - -This window covering is optional. You can add it to further reduce the light in the bioreactor, or you may leave it off to inspect the culture. - -1. You will need 4x 6mm screws, and the window cover. -2. Attach the window cover to the side of the vial holder using the screws. -3. Insert the glass vial into the Pioreactor. The vial should feel snug, but not very tight. If it feels too tight, try loosening the four 6mm screws slightly. - - - - - - - -1. Your Pioreactor assembly is complete! 🚀 -2. Leave the Pioreactor powered off, for now. -3. If you also have pumps, we'll assemble those later. -3. Next: begin installing the [software](/user-guide/software-set-up). - - diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/_category_.yaml b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/_category_.yaml deleted file mode 100644 index 8f2e1014c..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0/_category_.yaml +++ /dev/null @@ -1,3 +0,0 @@ -collapsed: true -collapsible: true -label: "Pioreactor 20ml v1.0" diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/01-version-upgrade.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/01-version-upgrade.md deleted file mode 100644 index efad1795c..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/01-version-upgrade.md +++ /dev/null @@ -1,67 +0,0 @@ ---- -title: Before you begin -slug: /hardware-setup-upgrade-version -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'; - - - - -You will need: -1. The parts provided in your upgrade kit: -* Top vial holder -* Bottom vial holder -* #024 O-ring -* #121 O-ring -* Top faceplate -* Flat headed 5mm screws (2x) -* 4mm screws (2x) -* 10mm screw (1x) -2. Your original Pioreactor v1.0, to be upgraded. -3. A Philip's head screwdriver. - - - -------- - - - -- 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/pioreactor-disassembly). - - \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/02-pioreactor-disassembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/02-pioreactor-disassembly.md deleted file mode 100644 index f6dd0dbaa..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/02-pioreactor-disassembly.md +++ /dev/null @@ -1,62 +0,0 @@ ---- -title: Disassembling the old Pioreactor -slug: /pioreactor-disassembly -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. Remove any vial placed in the vial holder. -2. Carefuly remove the LED caps. Set these aside. -3. Remove LED and PDs from their sockets. - -:::caution -If the LEDs/PDs are stuck in the socket, **do not pull!** Gently twist the bulb until it loosens from the socket to safely remove it. -::: - -4. Unplug the LED ans PDs from the HAT. Set aside the LED and PDs for later. -5. Unplug the fan and the heater flat-flex cable from the HAT. - - - -------- - - - -1. Remove the four 6mm screws from the top faceplate. Set screws aside. The top assembly of your Pioreactor should now be separate from the HAT and Raspberry Pi. -2. Partially unscrew the 30mm screws from the bottom of the faceplate, separating it from the vial holder. -3. Remove the fan from the fanplate. If required, use the screwdriver to **carefully** lever the fan out, applying force alternatively from all four sides. Set the fan aside for later. - - - -------- - - - -1. Unscrew the two 4mm screws from the bottom of the vial holder. Set these screws aside for later. -2. Remove the heater PCB and wire from the vial holder. Set aside for later. - - - -------- - - - -The following items from the disassembled v1.0 Pioreactor should be set aside to be used for the upgrade: -* LED (1x) and PDs (2x) -* Vial caps (6x or more) -* 6mm screws (4x) -* 4mm screws (2x) -* Fan PCB -* Heater PCB - -Proceed to the next page to continue. - - \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/03-build-vial-holder.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/03-build-vial-holder.md deleted file mode 100644 index 451e6c6fb..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/03-build-vial-holder.md +++ /dev/null @@ -1,58 +0,0 @@ ---- -title: Building the vial holder -slug: /building-vial-holder -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'; - - - -:::info -The vial holder of the v1.1 now comes in two halves; a top vial holder and a bottom vial holder. Both have grooves to insert O-rings for a more secure hold on your vials and increased protection against leaks. The thinner O-ring (#024) fits into the top piece. The thicker O-ring (#121) lines the bottom piece. The O-rings are pre-lubricated with a silicone-based lube. -::: - -1. 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, making sure to not twist the O-ring. -2. Run your finger inside the now-occupied groove, pushing the O-ring into place to ensure a snug fit. -3. 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. -4. Push the O-ring into place to ensure a snug fit. - - - -------- - - - -1. Place the window cover over the window. It should fit snuggly. -2. Attach it using four 4mm screws (2 provided in the upgrade kit, and 2 previously used in the old v1.0). - - - -------- - - - -1. Remove the thermal pad from the heater PCB. -2. Place it aside so that the sticky side is upward. Take care to not dirty the thermal pad. -3. Insert the flex cable below the O-ring and into the groove. Pull it through. -4. 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. -5. **While maintaining pressure**, flip the piece over and insert the two M2.5-CS 5mm screws into the holes. -6. **While maintaining pressure**, take turns screwing each in until both are flush, and the heater PCB is securely attached to the bottom vial holder. -7. Stick the thermal pad back onto the heater PCB, sticky side down. - - - -------- - - - -1. Screw the top and bottom vial holder sections together. -2. Set this aside and proceed to the next page. - - \ No newline at end of file diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/04-pioreactor-reassembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/04-pioreactor-reassembly.md deleted file mode 100644 index 9a7a7ac72..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/04-pioreactor-reassembly.md +++ /dev/null @@ -1,91 +0,0 @@ ---- -title: Reassembling the Pioreactor -slug: /pioreactor-reassembly -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'; - -import Tabs from '@theme/Tabs'; -import TabItem from '@theme/TabItem'; - - - -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 ends of the M3 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 and inspect 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 now comes with a button extension to provide easier access when 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 force and torque with the other hand until the screw is secure in the hole. Once established, a screwdriver can finish the job. Tightening until you feel resistance. - - - -------- - - - -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 compressing the button below prematurely. You should feel a "click" when you depress the button extension. -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). - - - ------ - - - -1. Insert the connector of the IR cable into channel A (labelled on the faceplate). -2. Insert the connector of either PD cable into PD channel 1 (labelled on the faceplate). -3. Place the connector of the other PD cable into PD channel 2. -4. Insert the bulb of the IR cable into the pocket labeled IR. -5. Insert the bulb of the PD cable in channel 1 into the pocket labeled REF. -6. Insert the bulb of the PD cable in channel 2 into the pocket labeled 90°. - -:::caution -Avoid over-stressing the LED/PD leads, or applying too much force too quickly. -::: - -7. Secure all bulbs with LED caps. -8. Push all remaining LED caps onto each pocket. - - - ------- - - - -Your new v1.1 Pioreactor is now assembled! Let's configure the software, too. - -1. Plug in your Pioreactor. -2. In the Pioreactor's specific config.ini (not the shared one), add the following configuration: - ``` - [pioreactor] - model=pioreactor_20ml - version=1.1 - ``` -3. Optional: we recommend rebooting the Pioreactor. -4. Optional: perform a [self-test](/user-guide/running-self-test) to confirm everything works as expected. - - diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/_category_.yaml b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/_category_.yaml deleted file mode 100644 index 4f314dd6f..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.0_to_v1.1/_category_.yaml +++ /dev/null @@ -1,3 +0,0 @@ -collapsed: true -collapsible: true -label: "Pioreactor 20ml v1.0 → v1.1" diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/01-v11-introduction.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/01-v11-introduction.md deleted file mode 100644 index ac5493da0..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/01-v11-introduction.md +++ /dev/null @@ -1,65 +0,0 @@ ---- -title: Before you begin assembly -slug: /20ml-v11-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 20ml v1.1 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/rpi-hat-assembly). - - diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/02-v11-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/02-v11-rpi-hat-assembly.md deleted file mode 100644 index 910842140..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/02-v11-rpi-hat-assembly.md +++ /dev/null @@ -1,107 +0,0 @@ ---- -title: Assembling the Raspberry Pi and the HAT -slug: /20ml-v11-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) -* 12mm hex standoffs (4x) -* 12mm hex standoffs-with-6mm-screws (4x) -* 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 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 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 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 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 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/pioreactor_20ml_v1.1/03-v11-wetware-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/03-v11-wetware-assembly.md deleted file mode 100644 index 7b1694a42..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/03-v11-wetware-assembly.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -title: Wetware assembly -slug: /20ml-v11-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 of the v1.1 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) fits into the top piece. The thicker O-ring (#121) lines the bottom piece. The O-rings are lubricated with a silicone-based lube. -::: - -1. 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. -2. Run your finger inside the vial holder, pushing the O-ring into place to ensure a snug fit. -3. 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. -4. Push the O-ring into place to ensure a snug fit. - - - -------- - - - -1. Place the window cover over the window. It should fit snuggly. -2. Attach it using four 4mm screws (2 provided in the upgrade kit, and 2 previously used in the old v1.0). - - - -------- - - - - -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. Flip the holder and insert the two flat M2.5-CS 5mm screws into the holes. -4. **While maintaining pressure**, take turns screwing each in until both are secure, and the heater pcb is securely attached to the bottom vial holder. - - - ------ - - - -1. Remove the _clear_ plastic from one side of the thermal pad. -2. Place on the flat (aluminum) part of the heating PCB. Apply downwards pressure to secure it. -3. Remove the blue protective plastic on top of the thermal pad. - - - - ------ - - - -1. Screw the top and bottom vial holder sections together. -2. Set this aside and proceed to the next page. - - diff --git a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/04-v11-faceplate-all-together.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/04-v11-faceplate-all-together.md deleted file mode 100644 index 85faa586b..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/04-v11-faceplate-all-together.md +++ /dev/null @@ -1,67 +0,0 @@ ---- -title: Attaching the wetware to the HAT asssembly -slug: /20ml-v11-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'; - - - -* Fan -* Top faceplate (will have 4 x 30mm screws in it) -* One 5mm screw - -:::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 silver 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 and inspect 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 now comes with a button extension to provide easier access when 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 a lot of force. - - - -------- - - - -1. Place the vial holder assembly onto the Raspberry Pi/HAT. The GPIO pins align with the side notch of the faceplate. -2. Using the 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. -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/pioreactor_20ml_v1.1/05-v11-optics-assembly.md b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/05-v11-optics-assembly.md deleted file mode 100644 index ffd26dc04..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/05-v11-optics-assembly.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: Connect the optics system -slug: /20m-v11-optics-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'; - - - - -1. You will need both PD cables (dark bulbs) and IR cable (clear bulb). -2. Insert the connector of the IR cable into **channel A** (labelled on the faceplate). -3. Insert the connector of either PD cable into **PD channel 1** (labelled on the faceplate). -4. Place the connector of the other PD cable into **PD channel 2**. - - - ------ - - - - -1. Insert the bulb of the IR cable into the pocket labeled IR. -2. Insert the bulb of the PD cable in channel 1 into the pocket labeled REF. -3. Insert the bulb of the PD cable in channel 2 into the pocket labeled 90°. - -:::caution -Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's ill-advised to bend them again. -::: - -7. Secure all bulbs with LED caps. -8. Push all remaining LED caps onto each pocket. - - - -------- - - - -Your new v1.1 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/pioreactor_20ml_v1.1/_category_.yaml b/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/_category_.yaml deleted file mode 100644 index 5c65d38f3..000000000 --- a/user-guide/01-getting-started/01-assembly_guides/pioreactor_20ml_v1.1/_category_.yaml +++ /dev/null @@ -1,3 +0,0 @@ -collapsed: true -collapsible: true -label: "Pioreactor 20ml v1.1"