Register fermentation data (for PPP and IFP)

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This guide is tailored to the Pre-Pilot Plant and the Integrated Fermentation Platform teams at Biosustain.

🎯 This guide will show you how to use the Benchling template “Registering Fermentation Data in Benchling” to keep track of fermentation experiments and the samples they generate.

📝 Create a new Notebook Entry using a Template

The first step is to create a new Notebook Entry using the Fermentation Template.

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If your team has created its own version of the Template, select that instead while creating the Notebook Entry.

Follow this video to learn how to do it:

Summary of the steps:

  1. Navigate to the Benchling folder where you want to register fermentation data for your experiment.

  2. Create an Entry from Template and select the template Registering Fermentation Data in Benchling in the folder Fermentation Reports (LIMS).

Once you have created the Entry, you can start filling in the relevant tables.

🔍 Steps 1 to 3 - Experiment, Media and Strains

After creating the Notebook Entry, you are ready to start planning your experiment by creating the following entities:

  • Step 1 - Register Experiment

  • Step 2 - Register Media

  • Step 3 - Register Strains

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  1. The tables included in these steps may be omitted if you have already registered the entities beforehand.

  2. Entities created through these tables will be found in the same folder where the Notebook Entry is located. You can move them manually into the correct folder through the expanded view.

Follow this video for an example of how to fill the first three steps:

🧪 Steps 4 and 5 - Fermentation Cultures and Timepoint samples

These steps cover logging details for each stage of the fermentation train (e.g., reactor settings, final OD, culture volume) and recording metadata for samples retrieved from the main fermentation (e.g., OD, time, cells/ml, sample type).

  • Step 4 - Register Fermentation Cultures and Results (Pre-optional, pre-final, main cultures)

  • Step 5 - Register Timepoint Samples

Follow this video for an example of how to fill the tables in steps 4 and 5:

🔬 Steps 6 to 8 - Creating Samples for Analysis

The last steps cover creating samples for analysis, assigning them a storage location, and submitting the Workflow to Analytics or the Pre-Pilot Plant.

  • Step 6 - Register Analytical Submission Samples

  • Step 7 - Move Analytical Submission Samples in a storage location

  • Step 8 - Submit Workflow to Analytics

The videos below show how to achieve this.

☑️ Create and store Analytical Submission Samples

☑️ Create a Workflow

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Analytics/PPP must have Write access to the project where the samples are located.



If you have any question, don’t hesitate to contact us at lims_support@biosustain.dtu.dk.