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SynBioSuite Tutorial Test

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Gonzalo Vidal edited this page Jun 13, 2026 · 2 revisions

SynBioSuite Tutorial: Test

This tutorial completes the handoff from Build to Test.

You will:

  1. Finish the Build stage by creating a Strain.
  2. Create Sample Designs that describes reusable sample compositions.
  3. Create a Study that describe the relationship between assays and samples linked to measurement data.

All by downloading, filling, and uploading the required Excel templates.

By the end of this page, you should have:

  • One Strain workbook imported into SynBioSuite and uploaded to SynBioHub.
  • One Sample Design workbook imported into SynBioSuite and uploaded to SynBioHub.
  • One Study workbook imported into SynBioSuite and uploaded to SynBioHub.
  • One Study file on SynBioSuite created from those files.

Important

Strain creation is listed under Build in SynBioSuite. It appears in this Test tutorial because it is the final Build artifact needed before you can describe samples and create a study.

Contents

  1. Before you begin
  2. Finish Build: create the strain record
  3. Create the sample design
  4. Create the study metadata
  5. Create and upload the study
  6. Final checklist

0. Before you begin

You should already have completed the earlier tutorial stages:

  • Resources: parts, chassis, media, chemicals, and other reusable resources have been imported.
  • Design: the sc2 design has been created. (Optional)
  • Build: the sc2 plasmids have been created, annotated, saved, and uploaded.

You will also need:

  • Chrome or another Chromium-based browser.
  • Access to the same local SynBioSuite working folder used in the earlier tutorial pages.
  • SynBioHub credentials.
  • The blank Excel templates for:

Tip

Use the same SynBioHub instance and collection style that you used in the Resources and Build tutorials so you have access to the linked components.

1. Finish Build: create the strain digital representation

A strain describes the biological organism that will be tested. In this tutorial, the strain should connect the chassis (host strain) to the built plasmids from the Build stage.

  1. Open SynBioSuite in Chrome.
  2. Open the same local working folder used in the previous tutorial pages.
  3. In the left sidebar, select Build.
  4. Find the section called Strains.
  5. Click Download Template.
  6. Fill out the Strains template and rename (sugested name MD5_Strains).
  7. Click Import Strains.
  8. Select the Strains template that you filled.
  9. Follow the pop up to select a SynBioHub repository, provide your credentials, and create or select a collection.
  10. Confirm and check your data on the selected collection URL displayed on the card.

Note

The filename helps you find the workbook on your computer. The IDs inside the workbook are what SynBioSuite uses to connect objects.

Important

Do not continue to Sample Design until the strain record is visible in SynBioHub.

2. Start Test: create sample designs digital representations

A sample design describes the composition of samples and re-used across replicates. It should answer:

  • Which strain is being tested?
  • Which media is being used?
  • Which supplements were added and in which concentration?
  1. In SynBioSuite, select Test from the left sidebar.
  2. Find the section called Sample Design.
  3. Click Download Template.
  4. Fill out the Sample Design template and rename (sugested name MD5_SampleDesign).
  5. Click Import Sample Designs.
  6. Select the Sample Design template that you filled.
  7. Follow the pop up to select a SynBioHub repository, provide your credentials, and create or select a collection.
  8. Confirm and check your data on the selected collection URL displayed on the card.

Important

Do not continue to Study until the sample design record is visible in SynBioHub.

3. Test: upload study metadata information

Study metadata describes the experiment as a whole. It tells another researcher what the study is, who performed it, which assays were performed, what samples were measured to obtain experimental data and how the study should be interpreted.

  1. In SynBioSuite, select Test.
  2. Find the section called Study Metadata.
  3. Click Download Template.
  4. Fill out the Study template and rename (sugested name MD5_Study_metadata).
  5. Click Import Metadata.
  6. Select the Study Metadata template that you filled.

Note

This workflow uploaded the template to the SynBioSuite file system. The collection will be selected later on.

4. Finish Test: create study digital representation

A Study object connects the study metadata, and optionally experimental results or plate reader outputs, into one uploadable record.

In this tutorial, the Study Metadata workbook is required. Results and plate reader output can be added later if they are not available yet.

  1. In SynBioSuite, select Test.
  2. Find the section called Studies.
  3. Create a new Study (sugested name MD5_Study).
  4. Link study metadata and experimental data using drag and drop.
  5. Follow the pop up to select a SynBioHub repository, provide your credentials, and create or select a collection.
  6. Confirm and check your data on the selected collection URL displayed on the card.

Important

Study Metadata is required. Experimental Results and Plate Reader Output are optional at this point unless the tutorial instructor has provided them.

6. Final checklist

Before leaving the Test stage, confirm the following.

Build handoff

  • A Strain workbook was created.
  • The Strain workbook was imported under Build > Strains.
  • The Strain ID is stable and readable.
  • The Strain record refers to the correct chassis or host.
  • The Strain record refers to the correct built plasmids or build components.

Sample design

  • A Sample Design workbook was created.
  • The Sample Design workbook was imported under Test > Sample Designs.
  • The Sample Design refers to the correct Strain ID.
  • Each condition has a clear Condition ID.
  • Each sample has a unique Sample ID.
  • Replicates are labeled clearly.
  • Plate wells or sample locations are included if the experiment uses them.

Study metadata

  • A Study Metadata workbook was created.
  • The Study Metadata workbook was imported under Test > Metadata or Test > Study Metadata.
  • The Study has a stable Study ID.
  • The Study Metadata refers to the correct Sample Design ID.
  • The Study Metadata refers to the correct Strain ID.
  • Contact, date, protocol, and measurement information are included where known.

Study creation and upload

  • A Study object was created under Test > Studies.
  • Study Metadata was added to the Study.
  • Experimental Results were added if available.
  • Plate Reader Output was added if available.
  • The Study was uploaded to the correct SynBioHub instance or prepared for upload.
  • The uploaded collection name and description are understandable.

Troubleshooting

SynBioSuite cannot find my file

Check that the file is saved in the local working folder that SynBioSuite opened through Chrome.

The upload fails

Check that:

  • You are logged into SynBioHub.
  • You selected the correct SynBioHub instance.
  • The workbook is saved.
  • The workbook is still .xlsx or .xlsm.
  • Required fields are not blank.
  • IDs match exactly across Strain, Sample Design, and Study Metadata.

My strain does not appear in the Sample Design step

Check that the Strain workbook was imported under Build > Strains before starting the Sample Design.

My Sample Design does not appear in the Study step

Check that the Sample Design workbook was imported under Test > Sample Designs before creating Study Metadata or the Study.

I do not have results yet

You can create the Study with Study Metadata first. Add Experimental Results and Plate Reader Output later when they are available.

Suggested files created in this tutorial

File Purpose
MD5_Strains.xlsm Strain workbook
MD5_SampleDesign.xlsm Sample Design workbook
MD5_Study_metadata.xlsm Study Metadata workbook
MD5_Study Study object

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