diff --git a/developer-guide/03-Background jobs/03-avoiding-od.md b/developer-guide/03-Background jobs/03-avoiding-od.md index 7086b7c0a..fa376ce88 100644 --- a/developer-guide/03-Background jobs/03-avoiding-od.md +++ b/developer-guide/03-Background jobs/03-avoiding-od.md @@ -78,6 +78,6 @@ enable_dodging_od=1 The diagram of timing, actions, and OD reading, looks like the following: -![](/img/developer-guide/background_job_dodging_timing.png) +![](/img/developer-guide/03-background-jobs/03-avoiding-od/background_job_dodging_timing.png) And you're done! \ No newline at end of file diff --git a/developer-guide/07-Plugins/02-adding-plugins-to-ui.md b/developer-guide/07-Plugins/02-adding-plugins-to-ui.md index 3825036df..111e718aa 100644 --- a/developer-guide/07-Plugins/02-adding-plugins-to-ui.md +++ b/developer-guide/07-Plugins/02-adding-plugins-to-ui.md @@ -17,7 +17,7 @@ You should have already added your plugin's Python code to your Pioreactor by so ### Adding a custom background job to the list of activities -![](/img/developer-guide/activities.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/activities.png) The list of activities, among other things, is sourced from either of two directories: @@ -52,11 +52,11 @@ published_settings: Saving it to either directory above, and refreshing the page: -![](/img/developer-guide/activities_with_example.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/activities_with_example.png) -![](/img/developer-guide/settings_with_example.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/settings_with_example.png) -![](/img/developer-guide/card_with_example.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/card_with_example.png) ### Adding a custom Python script to the list of activities @@ -84,7 +84,7 @@ See more information on the structure of your script [here](/developer-guide/int Suppose we wish to add our new automation, either installed from a package or via the `plugins` folder, to the drop-down list of automations users can choose from: -![](/img/developer-guide/dropdown_automations.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/dropdown_automations.png) This list is sourced from yaml files located on the leader's Raspberry Pi, in either of two directories: - `/var/www/pioreactorui/contrib/automations/`, is the source of the our built-in automations @@ -119,9 +119,9 @@ fields: If this file was saved to the folder `/home/pioreactor/.pioreactor/plugins/ui/contrib/automations/dosing`, we would see the following in the web interface (after refreshing): -![](/img/developer-guide/dropdown_automations_with_example.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/dropdown_automations_with_example.png) -![](/img/developer-guide/automations_example.png) +![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/automations_example.png) More examples of automation [yaml files here](https://github.com/Pioreactor/pioreactorui/tree/master/contrib/automations). diff --git a/developer-guide/07-Plugins/03-plugin-as-python-package.md b/developer-guide/07-Plugins/03-plugin-as-python-package.md index aa974e243..3febca337 100644 --- a/developer-guide/07-Plugins/03-plugin-as-python-package.md +++ b/developer-guide/07-Plugins/03-plugin-as-python-package.md @@ -151,7 +151,7 @@ function decorated with `@run.command` at the bottom of the file. See example [h This configuration file will contain additional configs that we want to add to our list of existing Configurations on the Pioreactor web interface. This file will be merged with the existing `config.ini` when the plugin is installed. -![](/img/developer-guide/python-package-new-config.png) +![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-new-config.png) :::tip A convention we've tried to follow is to use the section name convention of `[.config]` or `[.config]` in the configuration files. For example, our relay job has `[relay.config]` in its `additional_config.ini` and settings under it. @@ -399,13 +399,13 @@ There are two ways to do this: 1. Create an issue to have us edit the plugins.json file for you. 2. Fork from our repository to edit the plugins.json file, then create a pull request. -![](/img/developer-guide/python-package-pull-or-issue.png) +![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-pull-or-issue.png) In both cases, we will evaluate your plugin to ensure code quality and all requirements are met. Once your plugin is accepted, it will appear on the Plugins tab on the Pioreactor web interface. Users in the community can now easily click _Install_ to download your plugin onto their Pioreactors! -![](/img/developer-guide/python-package-plugins.png) +![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-plugins.png) ### Troubleshooting diff --git a/developer-guide/10-Hardware/05-pinout.md b/developer-guide/10-Hardware/05-pinout.md index 8a79bb9ea..d518e56d5 100644 --- a/developer-guide/10-Hardware/05-pinout.md +++ b/developer-guide/10-Hardware/05-pinout.md @@ -5,4 +5,4 @@ hide_table_of_contents: true --- -![](/img/developer-guide/pinout.png) \ No newline at end of file +![](/img/developer-guide/10-hardware/05-pinout/pinout.png) \ No newline at end of file diff --git a/developer-guide/20-User interface/04-adding-charts.md b/developer-guide/20-User interface/04-adding-charts.md index a9f4a825b..a1860ea9e 100644 --- a/developer-guide/20-User interface/04-adding-charts.md +++ b/developer-guide/20-User interface/04-adding-charts.md @@ -6,7 +6,7 @@ hide_table_of_contents: true You can add custom charts to the UI. Below is an example of adding a chart that displays historical and real-time CO2 sensor data. -![custom chart of CO2 reading](/img/developer-guide/custom_chart.png) +![custom chart of CO2 reading](/img/developer-guide/20-user-interface/04-adding-charts/custom_chart.png) ### Step 1 Create a yaml file with the following fields, and place it in `/home/pioreactor/.pioreactor/plugins/ui/contrib/charts/`. (Plugins can put the yaml file under `ui/contrib/charts` in there project folder - it will be added upon installation.) @@ -41,7 +41,7 @@ co2_readings=1 ... ``` -![](/img/developer-guide/adding_chart_to_config.png) +![](/img/developer-guide/20-user-interface/04-adding-charts/adding_chart_to_config.png) ### Troubleshooting diff --git a/developer-guide/99-architecture.md b/developer-guide/99-architecture.md index 34c08ecc1..9973deda9 100644 --- a/developer-guide/99-architecture.md +++ b/developer-guide/99-architecture.md @@ -4,4 +4,4 @@ slug: /architecture hide_table_of_contents: true --- -![The Pioreactor system architecture](/img/developer-guide/arch.png) +![The Pioreactor system architecture](/img/developer-guide/99-architecture/arch.png) diff --git a/experiments/02-Secondary level education/01-control-testing.md b/experiments/02-Secondary level education/01-control-testing.md index fff4d8bd2..0803a0ef8 100644 --- a/experiments/02-Secondary level education/01-control-testing.md +++ b/experiments/02-Secondary level education/01-control-testing.md @@ -17,7 +17,7 @@ Conduct a simple control test to evaluate results between Pioreactors, using the ## Requirements - + * At least two available Pioreactors * Dry baker's yeast @@ -41,7 +41,7 @@ With all factors the same, you should see similar normalized OD and growth rate Here are graphs we generated though our A/A test: -![](/img/experiments/aa-test-results.png) +![](/img/experiments/02-secondary-level-education/01-control-testing/aa-test-results.png) These kinds of tests make it easy to identify any unusual activity occurring in a specific Pioreactor (i.e, if it is missing an LED, temperature malfunctions, etc). In our case, though, both ran almost identically! Thus, we conclude that reliable comparisons can be drawn between these Pioreactors. @@ -56,4 +56,4 @@ These kinds of tests make it easy to identify any unusual activity occurring in 6. Select _Manage all Pioreactors_, and start _Stirring_ activity, _Temperature automation_ activity (set to an optimal temperature; ex. 30°C) and _OD reading_ activity. 7. Confirm that everything looks normal (ex: receiving optical density signal). 8. Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. -9. Watch growth progress on the _Overview_ page. \ No newline at end of file +9. Watch growth progress on the _Overview_ page. diff --git a/experiments/02-Secondary level education/caffeine-inhibition.md b/experiments/02-Secondary level education/caffeine-inhibition.md index 0de58c139..c9b8ebfeb 100644 --- a/experiments/02-Secondary level education/caffeine-inhibition.md +++ b/experiments/02-Secondary level education/caffeine-inhibition.md @@ -17,7 +17,7 @@ Use caffeine-containing liquids to inhibit the growth of your culture. ## Requirements - + * At least two available Pioreactors * Dry baker's yeast @@ -40,7 +40,7 @@ We used two Pioreactors and two vials containing 15 mL of YPD media. We added 1 The growth rate chart clearly demonstrates an inhibition of growth occurring in the sample containing tea: -![](/img/experiments/tea2-exp-results.png) +![](/img/experiments/02-secondary-level-education/caffeine-inhibition/tea2-exp-results.png) ## Recommendations @@ -60,4 +60,3 @@ We recommend trying different amounts of tea, coffee, or other caffeine containi 8. Confirm that everything looks normal (ex: receiving optical density signal). 9. Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. 10. Watch growth progress on the _Overview_ page. - diff --git a/experiments/02-Secondary level education/low-vs-high-conc-media.md b/experiments/02-Secondary level education/low-vs-high-conc-media.md index b1968d150..a21c6f993 100644 --- a/experiments/02-Secondary level education/low-vs-high-conc-media.md +++ b/experiments/02-Secondary level education/low-vs-high-conc-media.md @@ -17,7 +17,7 @@ Conduct a simple comparison of yeast growth between a low percent and high perce ## Requirements - + * At least two available Pioreactors * Dry baker's yeast @@ -58,7 +58,7 @@ We inoculated both with 100 uL of a yeast slurry using a micropipette. If this i As expected, growth diminished earlier for the culture inoculated in 1% YPD: -![](/img/experiments/ypd-conc-exp.png) +![](/img/experiments/02-secondary-level-education/low-vs-high-conc-media/ypd-conc-exp.png) ## Recommendations @@ -80,4 +80,3 @@ Consider lower or higher bounds for your media compositions. How much sooner wil 9. Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. 10. Optional: you can change the names of the Pioreactor in the UI to display the percent of media. 11. Students can watch growth progress on the _Overview_ page. - diff --git a/experiments/02-Secondary level education/salt-stress-on-yeast.md b/experiments/02-Secondary level education/salt-stress-on-yeast.md index 08dc5c6c1..9ea6e0d6c 100644 --- a/experiments/02-Secondary level education/salt-stress-on-yeast.md +++ b/experiments/02-Secondary level education/salt-stress-on-yeast.md @@ -20,7 +20,7 @@ Use your Pioreactor to model how cells are affected by high salt (hypertonic) so ## Requirements - + * At least two available Pioreactors * Dry baker's yeast @@ -61,7 +61,7 @@ To each vial, 0g, 0.225g, 0.45g, 0.675g and 0.9g of table salt were added, respe After approximately 26 hours, the following growth rates were recorded: -![](/img/experiments/salt_growth_rate.png) +![](/img/experiments/02-secondary-level-education/salt-stress-on-yeast/salt_growth_rate.png) We can summarize our results in the following table to highlight our data: @@ -104,4 +104,3 @@ The flexibility of the Pioreactor means you can do much more with this simple co 11. Confirm that everything looks normal on the _Overview_ page (ex: receiving optical density signal). 12. Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. 13. Watch the growth progress on the _Overview_ page! - diff --git a/experiments/02-Secondary level education/yeast-growth-by-temperature.md b/experiments/02-Secondary level education/yeast-growth-by-temperature.md index feff9f51f..5ffc6b610 100644 --- a/experiments/02-Secondary level education/yeast-growth-by-temperature.md +++ b/experiments/02-Secondary level education/yeast-growth-by-temperature.md @@ -20,7 +20,7 @@ Demonstrate the effect of temperature on yeast growth. ## Requirements - + * At least two available Pioreactors * Dry baker's yeast @@ -44,9 +44,9 @@ The following experiment was performed using four Pioreactors. Four vials contai Over the course of 12 hours, the following graphs were recorded: -![](/img/experiments/temperature_temp.png) +![](/img/experiments/02-secondary-level-education/yeast-growth-by-temperature/temperature_temp.png) -![](/img/experiments/temperature_growth_rate.png) +![](/img/experiments/02-secondary-level-education/yeast-growth-by-temperature/temperature_growth_rate.png) Though subtle, non-linear patterns of growth rate are observed between the temperatures. Key data points are summarized in the following table: diff --git a/experiments/02-Secondary level education/yeast-in-ethanol.md b/experiments/02-Secondary level education/yeast-in-ethanol.md index 9632c050f..43a002102 100644 --- a/experiments/02-Secondary level education/yeast-in-ethanol.md +++ b/experiments/02-Secondary level education/yeast-in-ethanol.md @@ -113,7 +113,7 @@ This technique produces halving ethanol percentages of 0%, 1.5%, 3%, and 6% to b After approximately 18 hours, the following implied growth rates were recorded: -![](/img/experiments/ethanol_gr.png) +![](/img/experiments/02-secondary-level-education/yeast-in-ethanol/ethanol_gr.png) We can summarize our results in the following table: diff --git a/experiments/03-University level education/01-algae-day-night-cycle.md b/experiments/03-University level education/01-algae-day-night-cycle.md index 27cc37224..66088cd00 100644 --- a/experiments/03-University level education/01-algae-day-night-cycle.md +++ b/experiments/03-University level education/01-algae-day-night-cycle.md @@ -16,7 +16,7 @@ This experiment will show the growth curve of algae over a 20h:4h day/night cycl ## Requirements - + * At least one available Pioreactor * Algae @@ -41,7 +41,7 @@ Typical experiments use a 16h:8h day night cycle, but we've adjusted the time pe For this style of experiment, let's investigate our normalized OD results: -![](/img/experiments/nod_algae_intensity.png) +![](/img/experiments/03-university-level-education/01-algae-day-night-cycle/nod_algae_intensity.png) Adjusting just one factor (light intensity) where one is twice as high as the other yielded an approximate doubling of growth in the vial subjected to higher light intensity! @@ -76,4 +76,3 @@ Change the names of the Pioreactor in the UI to organize your vials. 12. Watch the growth progress on the Overview page. - diff --git a/experiments/04-Research and beyond/temp-cycle.md b/experiments/04-Research and beyond/temp-cycle.md index d1c33499f..f0d160db4 100644 --- a/experiments/04-Research and beyond/temp-cycle.md +++ b/experiments/04-Research and beyond/temp-cycle.md @@ -42,7 +42,7 @@ Check out our [blog post](https://pioreactor.com/blogs/pioreactor/using-custom-a Once we [exported our data](/user-guide/export-data), we charted our yeast growth rate against the temperature readings to generate the following graph: -![](/img/experiments/yeast_growth_vs_temp.png) +![](/img/experiments/04-research-and-beyond/temp-cycle/yeast_growth_vs_temp.png) ## Recommendations diff --git a/static/img/developer-guide/background_job_dodging_timing.png b/static/img/developer-guide/03-background-jobs/03-avoiding-od/background_job_dodging_timing.png similarity index 100% rename from static/img/developer-guide/background_job_dodging_timing.png rename to 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Software guides

- +
- diff --git a/user-guide/01-getting-started/02-software-set-up.mdx b/user-guide/01-getting-started/02-software-set-up.mdx index 90c1bfd8d..b17207981 100644 --- a/user-guide/01-getting-started/02-software-set-up.mdx +++ b/user-guide/01-getting-started/02-software-set-up.mdx @@ -31,47 +31,47 @@ We'll start with your blank microSD card. 1. Download the latest version of [Raspberry Pi Imager](https://www.raspberrypi.org/software/) for your operating system and install it. 3. Open the newly-installed Raspberry Pi Imager. 4. Immediately, click **"App Options"** - ![Click "App options"](/img/user-guide/app_options.png) + ![Click "App options"](/img/user-guide/01-getting-started/02-software-set-up/app_options.png) 4. Click **Edit** next to _Content Repository_. - ![Click "Edit" to choose repository](/img/user-guide/content_repo.png) + ![Click "Edit" to choose repository](/img/user-guide/01-getting-started/02-software-set-up/content_repo.png) 5. Choose **Use Custom URL**, and paste the value: `https://pioreactor.com/imager/os-list.json` - ![Add our repo URL](/img/user-guide/edit_repo.png) + ![Add our repo URL](/img/user-guide/01-getting-started/02-software-set-up/edit_repo.png) 6. Click **Apply & restart**. 7. Choose your RPi model. Select **Next**. - ![Choose your RPi model](/img/user-guide/choose_rpi.png) + ![Choose your RPi model](/img/user-guide/01-getting-started/02-software-set-up/choose_rpi.png) 8. Choose the operating system **Pioreactor**. Click **Next**. - ![Choose your Pioreactor](/img/user-guide/choose_pio_os.png) + ![Choose your Pioreactor](/img/user-guide/01-getting-started/02-software-set-up/choose_pio_os.png) 9. Choose the **latest** OS on the list (at the top). Click **Next**. - ![Choose latest](/img/user-guide/latest_os.png) + ![Choose latest](/img/user-guide/01-getting-started/02-software-set-up/latest_os.png) 10. Choose the **Leader + Worker**. Click **Next**. - ![Choose leader + worker](/img/user-guide/pio_lw_os.png) + ![Choose leader + worker](/img/user-guide/01-getting-started/02-software-set-up/pio_lw_os.png) 11. Insert your micro SD card if you haven't already. Select your Storage device (it may be a different icon than shown). - ![Choose storage](/img/user-guide/choose_storage.png) + ![Choose storage](/img/user-guide/01-getting-started/02-software-set-up/choose_storage.png) 12. Input a unique name for this Pioreactor. Some names that we use for our first Pioreactor: `pioreactor01`, or `leader`, or `pio01`. _Don't_ use `pioreactor` or `raspberrypi`. - ![Choose hostname](/img/user-guide/choose_hostname.png) + ![Choose hostname](/img/user-guide/01-getting-started/02-software-set-up/choose_hostname.png) Click **Next**. 13. Change localization preferences. Click **Next**. - ![Choose localization](/img/user-guide/choose_localization.png) + ![Choose localization](/img/user-guide/01-getting-started/02-software-set-up/choose_localization.png) 14. Check **Set username and password**. Enter the following: - **username**: `pioreactor`. - **password**: `raspberry`. - Note: You can change the password later. - ![Choose username](/img/user-guide/choose_username.png) + ![Choose username](/img/user-guide/01-getting-started/02-software-set-up/choose_username.png) Click **Next**. 15. Enter your network name into SSID network name, and WiFi password. Optional: leave blank if using ethernet. Click **Next**. :::tip If you are having difficulty connecting to a network, like at a university that may not easily incorporate Raspberry Pi's, [there's a built-in solution for creating a local access point](/user-guide/local-access-point)) and a [solution for internet-sharing from a PC via ethernet](/user-guide/internet-sharing). ::: - ![Choose wifi](/img/user-guide/choose_wifi.png) + ![Choose wifi](/img/user-guide/01-getting-started/02-software-set-up/choose_wifi.png) 16. Confirm that **Enable SSH** is active, and **Use password authentication**. Click **Next**. - ![Choose ssh](/img/user-guide/choose_ssh.png) + ![Choose ssh](/img/user-guide/01-getting-started/02-software-set-up/choose_ssh.png) 17. Click **Write** to begin writing your image to the micro SD card. - ![write image](/img/user-guide/write_image.png) -18. A prompt *may* appear asking for permission to write, accept it. Writing will take up to 5 minutes. Perfect time for a tea break. Screenshot of what your settings should look like + ![write image](/img/user-guide/01-getting-started/02-software-set-up/write_image.png) +18. A prompt *may* appear asking for permission to write, accept it. Writing will take up to 5 minutes. Perfect time for a tea break. Screenshot of what your settings should look like 10. Once writing is complete, remove the microSD card, and place it into the Raspberry Pi. **Your Raspberry Pi's power should be unplugged before inserting the microSD card**. The microSD slot is located on the PWM side of the Pioreactor. Example for a Raspberry Pi A model: - ![Insert the microSD card into a Raspberry Pi A model](/img/user-guide/place-micro-sd-card.JPG) + ![Insert the microSD card into a Raspberry Pi A model](/img/user-guide/01-getting-started/02-software-set-up/place-micro-sd-card.JPG) 11. Plug power into your Raspberry Pi. LEDs onboard the Raspberry Pi may start to light up momentarily. After **a few minutes**, your Pioreactor HAT will briefly blink a blue LED, telling us it is ready.