Pioreactor software setup

The plugins go onto the card while you flash it, so the unit boots ready. Text as in AEP-Plugin/README.md.

1. Two changes to make while following Pioreactor’s software set-up guide, which comes next:

   • At its step 3, in App Options, switch off Eject media when finished (1) before you set the Content Repository (2), so the card stays mounted after the write.

     

   • At its step 15, for your leaderThe Pioreactor that hosts the web interface and config.ini for a cluster. A single stand-alone unit is its own leader (Leader + Worker)., leave the Wi-Fi page blank if you can’t add devices to your lab’s Wi-Fi then reach them through it (typical at universities); the leader Pioreactor then makes its own network.

   • WorkerA Pioreactor that runs experiments under a leader. It has no web interface of its own and takes its config.ini from the leader.-only units: follow the same steps with a Worker image. Flash each worker with the step 15 Wi-Fi page set to network pioreactor, password raspberry, and at step 3 below do not drag the local_access_point file across. The plugin installs when you add the unit from the leader’s Inventory page. HotspotThe leader makes its own Wi-Fi network, pioreactor (password raspberry). Use it where you cannot add devices to the site Wi-Fi. cluster: boot the leader first.

   With those in mind, follow Pioreactor’s software set-up guide up to Write, and come back here while the card writes.

2. Download and unzip the AEP card bundle.

3. When the write finishes, drag the pioreactor folder from the bundle onto the bootfs drive. If you left the Wi-Fi page blank (for the leader Pioreactor to make its own network), also drag across the local_access_point file, after changing GB in it to your country code*. DO NOT drag it across for workers, or if you set your Pioreactors up to join a Wi-Fi network. If the card was ejected anyway, remove and reinsert it.

4. Eject the card. One change to the rest of Pioreactor’s guide: for a unit that makes its own Wi-Fi, join the network pioreactor (password raspberry) and open http://pioreactor.local. Then continue the guide from its step 18; the model dialog at its step 21 does not appear, because the bundle has set the model. electroPioreactor is under Activities on the unit’s Manage page, and the precision temperature pluginThe Pioreactor software plugin that runs the Precision Temperature Upgrade Kit's sensor. The AEP card bundle installs it; the MEP bundle has none. is installed.

   * If your country code is not GB, open local_access_point in TextEdit/Notepad and replace GB with the ISO two-letter code (CA, IE, DE, AU, NZ, GL, US, etc.; see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2) and save; the file should contain just those two letters. Do nothing if you live in the United Kingdom of Great Britain and Northern Ireland (GB).

If it is missing, put the card back in your computer: pioreactor/plugins/failed/ on bootfs holds the wheelA Python package file (.whl). The card bundle carries the plugins as wheels; one that fails to install lands in pioreactor/plugins/failed/ on bootfs, with a log. and a log of what went wrong.

Without the card bundle (older Pioreactor OS)

Pioreactor OS needs boot-partition plugin support for the card route. On an older release: flash and boot as Pioreactor’s guide says, run pio update (26.5.0 is the minimum), set the unit’s model to the XR variant in Inventory, add the XR photodiode channel values to config.ini from the end of the XR assembly guide, and install the plugins over SSHSecure Shell: a command line on the Pioreactor from your computer's terminal, for example ssh [email protected]. as in AEP-Plugin/README.md.

Notes

• On the recording the unit was named ed06: location (Edinburgh) plus unit number.
• Until the model is set to XR in Inventory, ODOptical density: how cloudy the culture is, read from scattered light. It tracks cell growth. readings are interpreted against the wrong channel map.

Parts

• 1×microSD cardpart
• 1×Precision Temperature Upgrade Kitearlier stepOnly with temperature kit

Tools

• 1×Computer with microSD card readertool

Check your work

1. Fallback route only (no card bundleA zip from the electroPioreactor releases page. Copied onto the card's bootfs drive, it installs the plugins and sets the model on first boot.): which Pioreactor software version is the unit running?

   • 26.5.0 or later
   • Older than 26.5.0
   • Older, and pio update fails offline
   Show the answer

   Answer: 26.5.0 or later

   • If you see Older than 26.5.0: Run pio update.
   • If you see Older, and pio update fails offline: Flash the latest image instead, or give the unit internet over a cable: see Internet over an ethernet cable in Check the plugin.

2. In Inventory, which model does this unit show?

   • Pioreactor 40 ml, standard v1.5
   • Pioreactor 40 ml, XR variant
   • Pioreactor 20 ml, v1.1
   Show the answer

   Answer: Pioreactor 40 ml, XR variant

   • If you see Pioreactor 40 ml, standard v1.5: Set it to the XR variant in Inventory. Until then, ODOptical density: how cloudy the culture is, read from scattered light. It tracks cell growth. readings are interpreted against the wrong channel map.
   • If you see Pioreactor 20 ml, v1.1: Set it to the 40 ml XR variant in Inventory. Until then, OD readings are interpreted against the wrong hardware.

3. Fallback route only (no card bundleA zip from the electroPioreactor releases page. Copied onto the card's bootfs drive, it installs the plugins and sets the model on first boot.): which XR photodiode channel values does config.ini hold?

   • Some of those listed at the end of the XR assembly guide
   • None: only the stock v1.5 photodiode values
   • All those listed at the end of the XR assembly guide
   Show the answer

   Answer: All those listed at the end of the XR assembly guide

   • If you see Some of those listed at the end of the XR assembly guide: Add the rest, as listed at the end of the XR assembly guide.
   • If you see None: only the stock v1.5 photodiode values: Add them as listed at the end of the XR assembly guide.

4. What does Plugins in the Pioreactor UI show for pioreactor-precision-temperature-pluginThe Pioreactor software plugin that runs the Precision Temperature Upgrade Kit's sensor. The AEP card bundle installs it; the MEP bundle has none.?

   Only with temperature kit

   • Listed as installed
   • Missing: the install needed internet
   • Missing: the card's failed log names it
   Show the answer

   Answer: Listed as installed

   • If you see Missing: the install needed internet: Give the unit internet over a cable (see Internet over an ethernet cable in Check the plugin), then install it.
   • If you see Missing: the card's failed log names it: Read the log in pioreactor/plugins/failed/ on the card's bootfs drive, then install it over SSHSecure Shell: a command line on the Pioreactor from your computer's terminal, for example ssh [email protected]. as in AEP-Plugin/README.md.

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