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EpiBuilder

What is EpiBuilder?

EpiBuilder is a scientific software for assembling, searching, and classifying linear B-cell epitopes, for research using approaches with partial or complete proteomes.

The software is designed as a multi-container application using Docker to execute a reproductible immunoinformatics workflow.

Who should use EpiBuilder?

The platform is designed for researchers and professionals working at the intersection of immunology, proteomics, and bioinformatics. It is ideal for anyone who needs to perform in silico analysis of epitopes to accelerate their research and particularly suited for proteome-wide epitope discovery.

Key application areas include:

• Infectious Diseases: identify target epitopes in pathogens, accelerating the development of vaccines and diagnostic tests;
• Oncology: identify epitopes in tumor proteins, enabling the selection of precise targets for the development of immunotherapies and cancer vaccines;
• Neuroscience: predict epitopes in nervous system proteins, facilitating the search for autoantibody biomarkers for the diagnosis of neurodegenerative diseases.

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Requirements

• Docker must be installed on your computer.
  • No need to install programming languages, databases, or libraries separately.
  • Suitable for use on personal machines, lab computers, or servers.
• Linux environment recommended

Step 1: Download the Docker Image (Only Once)

EpiBuilder is distributed as Docker images. If you are an end user, run this command only once to download the EpiBuilder image:

docker pull bioinfoufsc/epibuilder:latest

For development setup and guidelines, see README.dev.md

Step 2: Create and Start the EpiBuilder Container (Only Once)

Run the command below only once to create the container. This will also start it.

(CPU)

  docker run -it --name epibuilder \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v epibuilder-data:/tmp/epibuilder \
  -e EPIBUILDER_VOLUME=epibuilder-data \
  -e DOCKER_API_VERSION=1.44 \
  -p 80:80 \
  -p 8080:8080 \
  -p 5435:5432 \
  -p 5005:5005 \
  bioinfoufsc/epibuilder:latest

Tip 1: The --name epibuilder option ensures the container is reusable.

Step 3: Access the Web Interface

After starting the container, open your browser and go to:

http://localhost

You should see the EpiBuilder web interface.

Step 4: Reusing the Container (Next Times)

You do not need to run docker run again.

To start the container via Terminal or command-line interface (CLI):

docker start epibuilder

To stop the container via Terminal or command-line interface (CLI):

docker stop epibuilder

Login Credentials

Use the following to log in for the first time:

• Username: admin
• Password: admin

Note: The admin account can create other users.

Contributing

Contributions are welcome.

• Bug fixes, improvements, and new features must be submitted via Pull Request (PR)
• Please ensure your changes are tested before submission
• Follow the existing project structure and conventions

For development setup and guidelines, see README.dev.md

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Citation

If you use EpiBuilder in your research, please cite:

Moreira RS, Filho VB, Calomeno NA, Wagner G, Miletti LC. EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes. Bioinformatics and Biology Insights, 2022. https://doi.org/10.1177/11779322221095221