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SynBioHub Usability User Study With Local Install

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cjmyers edited this page Jun 26, 2026 · 1 revision

SynBioHub Installation

Prerequisites

Open a command prompt/terminal. Opening the terminal depends on your operating system: on Windows, press

Win + R
and search wt or cmd

on macOS, press

Cmd + Space

and search for "Terminal"

and on Linux, press

Ctrl + Alt + T

Check whether Docker is installed. Type the following into the terminal.

docker --version

If not, download Docker Desktop:

After downloading Docker Desktop, open the application.

Check whether Git is installed:

git -v

If Git is not installed, download it from:

https://git-scm.com/downloads

Check whether node is installed:

node -v

If node is not installed, download it from:

https://nodejs.org/en/download

Create Workshop Directory

In a Terminal / Command Prompt, navigate to your working folder and create a new folder for this user study:

cd "your folder name"
mkdir SynBioHubWorkshop
cd SynBioHubWorkshop

Clone and Start SynBioHub

You should now be in the SynBioHubWorkshop folder. Run the following commands:

git clone -b snapshot https://github.com/synbiohub/synbiohub2-docker

docker compose -f ./synbiohub2-docker/docker-compose.yml up

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You should see the SynBioHub Docker process running inside Docker Desktop.

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Initial Setup

Open a browser and go to:

http://localhost:3333

You should see the setup page.

Part 1 — Instance Information

Enter:

Instance Name

SynBioHub Workshop

Other settings such as color can be customized optionally.

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Part 2 — Technical Details

  1. Click Show Advanced Options
  2. Click ok to Enable advanced options
  3. Change URI Prefix to:
https://synbiohub.org

This enables data uploads.

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Part 3 — Admin Account

Fill in all required fields to create the initial administrator account.

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Click:

Create My SynBioHub

Upload Data

  1. Download the zip file.
  2. Unzip the file inside your workshop folder
  3. Open a new terminal.
  4. Execute the commands below:
cd "your folder name"
cd SynBioHubWorkshop/igem_parts
node upload.js

You may get an error that says "cannot find module 'request'". Run:

npm install request

If you have other errors, please install those packages as well. If you continue to experience errors, please let someone know.

You should see output showing files being read and uploaded into SynBioHub.

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Verify Upload

After upload completes:

  1. Go to the SynBioHub home page at http://localhost:3333.
  2. Click Search Designs

You should now see the uploaded data.

Task 0: Study Instructions

Thank you for your interest in participating in this study. Please follow the steps below:

Step 1: Get your Participant ID from an administrator.

If you are doing this user study asynchronously, please email me (daniel.fang@colorado.edu) to receive your participant ID.

Step 2: Complete the Screening Form

Begin by completing the screening questionnaire to determine your eligibility for the study. Use ctrl+click on the link to open in a new tab. Screening Form

Step 3: Review and Sign the Consent Form

If you meet the eligibility requirements, the researcher will provide you with a paper copy of the informed consent form. Please read the form carefully and sign it if you agree to participate.

Step 4: Complete the Starter Questions

After signing the consent form, complete the starter questions. Use ctrl+click on the link to open in a new tab. Starter Questions

Step 5: Begin the Study

Once you have completed the starter questions, you may proceed to the study tasks.

Thank you for your participation.

Introduction for Participants for the Study (Read Before Starting)

You will be asked to complete a series of tasks using the SynBioHub system. These tasks are designed to reflect common activities such as searching for biological parts, submitting data, and managing collections.

You will complete tasks in both SynBioHub1 and SynBioHub2. You will be told before you start which order to use the systems. If your participant ID is odd, you will start with SynBioHub1. If your participant ID is even, please start with SynBioHub2.

The goal of this study is to understand user experiences with the system and to evaluate how well it supports common tasks.

After each task, you will be asked to fill out a table related to your experience.

Please read each task carefully and complete them in the order presented. Try to complete each task independently. If you encounter difficulties, please attempt to resolve them on your own before requesting assistance.

Each task includes a space where you can note anything that you found difficult or confusing. Please also record any assistance you received while completing the task.

Task 1: Account Setup

Create a new account, access the system, and update your profile. Complete the tasks below for both SynBioHub1 and SynBioHub2 in the order you were assigned.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Locate the option to register a new account in the top right of the screen.
  3. Fill out all required boxes with relevant information. If this is your second time completing this task, create a user separate from the first account. Also, please make this user separate from the admin account created earlier.
  4. To make things simpler, you can create a "sbh1" user for SynBioHub1 and a "sbh2" user for SynBioHub2.
  5. Complete the registration process.
  6. Log out of the system.
  7. Log back in using your credentials you used to create the account.
  8. Navigate to your profile page in the top right.
  9. Update your affiliation.
  10. Save your changes.
  11. Repeat the above steps for the other version of SynBioHub. You will need to register a second, different account for the second SynBioHub.
  12. Complete the survey table and accompanying questions for Task 1. Use ctrl+click on the link to open in a new tab. Task 1: Account Setup

Task 2: Discovery

Explore collections and search for a biological part.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Make sure you're the "sbh1" user if using SynBioHub1 or you're the "sbh2" user if using SynBioHub2. You can do this by clicking the user account button in the top right and seeing which account is logged in.
  3. Navigate to the home page. Click on browse design collections.
  4. Open the collection, iGEM Parts Registry, and view its contents.
  5. Change the filter to "Show All Objects".
  6. Type in “popS Receiver” into the search bar to filter the list of members of the collection.
  7. Return to the home page.
  8. Click search designs.
  9. Use the search feature to search for a biological part. In the search bar, type “LacI”.
  10. Apply at least one filter to the search results. Let’s apply a part role filter, so:promoter. You should see 6 results. On SynBioHub1, this is done through advanced search while SynBioHub2 allows you to filter items in the sidebar.
  11. Review the results list.
  12. Repeat the above steps for the other version of SynBioHub.
  13. Complete the survey table and accompanying questions for Task 2. Use ctrl+click on the link to open in a new tab. Task 2: Discovery

Task 3: Visualize Content

Explore and interpret visualization features for a biological part or design.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Make sure you're the "sbh1" user if using SynBioHub1 or you're the "sbh2" user if using SynBioHub2.
  3. Navigate to the Home page.
  4. Return to the search page. In the search bar, search for the biological part/design “BBa_F2620”
  5. Open the part/design page with BBa_F2620 as the ID.
  6. Examine the metadata of the part.
  7. Examine the displayed structure, components, or relationships.
  8. Minimize and reopen some of the tables. On SynBioHub2, you can move the tables around as well.
  9. Click on the sequence object. Afterwards, return to the previous page.
  10. Return to the main part page and scroll to the component Sequence Visualization. Compare this to the sequence on the previous page.
  11. Click on the luxR part inside the Sequence Visualization. Afterwards, return to the previous page.
  12. Check out the components table. Take note that the five parts in this table make up the entire BBa_F2620 Pops Receiver part. Click on the “BBa_R0040” part and take note of its visualization.
  13. Once you have completed the above steps, repeat the steps for the other version of SynBioHub
  14. Complete the survey table and accompanying questions for Task 3. Use ctrl+click on the link to open in a new tab. Task 3: Visualize Content

Task 4: Submission

Create a new collection and submit a biological part.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Make sure you're the "sbh1" user if using SynBioHub1 or you're the "sbh2" user if using SynBioHub2.
  3. Return to the home page.
  4. Navigate to the submit panel.
  5. Enter all required information for a new collection. Each time you do this, you need to create a unique new collection.
  6. Upload the provided part/design file for your current version of SynBioHub. Provided File: GeneticToggleSwitchDemo
  7. Submit the part to the collection.
  8. Click on the submission you submitted to make sure it was properly submitted.
  9. Repeat the above steps for the other versions of SynBioHub.
  10. Complete the survey table and accompanying questions for Task 4. Use ctrl+click on the link to open in a new tab. Task 4: Submission

Task 5: Curation

Locate your submitted part and update its information.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Make sure you're the "sbh1" user if using SynBioHub1 or you're the "sbh2" user if using SynBioHub2.
  3. Navigate to the home page.
  4. Go to your submissions section. Click on the collection you created in the previous task
  5. Set the collection to show all objects.
  6. Filter the members of the collection to show Module1.
  7. Open the Module1 part.
  8. Change the name of the part to "Genetic Toggle Switch".
  9. Change the description of the part to "This is the module for the genetic toggle switch".
  10. Make sure to save your changes.
  11. Return to the previous page, which should be the collection page.
  12. Edit the mutable field “references”. Enter the PubMedID "31423466".
  13. Save your changes.
  14. Repeat the above steps for the other version of SynBioHub.
  15. Complete the survey table and accompanying questions for Task 5. Use ctrl+click on the link to open in a new tab. Task 5: Curation

Task 6: Share Content

Download, share, and make your collection publicly accessible.

  1. Navigate to a local version of SynBioHub1: http://localhost:7777 or SynBioHub2: http://localhost:3333, as assigned.
  2. Make sure you're the "sbh1" user if using SynBioHub1 or you're the "sbh2" user if using SynBioHub2.
  3. Locate and open the collection you submitted in Task 4 and opened in Task 5.
  4. Locate the download options and download the collection in SBOL format.
  5. Locate the sharing options and generate or copy a shareable link.
  6. Add the second user you created as an owner of the collection.
  7. Navigate back to the collection containing your part.
  8. Locate the option to make the collection public.
  9. Publish the collection as a new public collection.
  10. Once you have completed the above steps, please repeat them for the other version of SynBioHub.
  11. Complete the survey table and accompanying questions for Task 6. Use ctrl+click on the link to open in a new tab. Task 6: Share Content

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