Pannotator integrated with Medpipe provides immunological and subcellular location features using a microservice

Two powerful tools have joined forces to revolutionize our understanding of proteins and their functions. Pannotator, a sophisticated program for annotating pan-genomes, has been seamlessly integrated with Medpipe. This advanced tool provides crucial immunological and subcellular location features. This groundbreaking integration was achieved through an innovative approach called microservices, marking a significant milestone in bioinformatics.

Microservices: The Backbone of Integration

Microservices represent a cutting-edge architectural style in software development. Applications are built as a collection of small, independent services. Each service excels in a specific function and communicates with others through well-defined APIs. This approach enhances the modularity, scalability, and maintainability of complex software systems, making it ideal for integrating diverse bioinformatics tools.

The Synergy of Pannotator and Medpipe

The integration of Pannotator and Medpipe through microservices has created a powerful, unified platform for genomic analysis. This synergy offers researchers a comprehensive toolset with numerous advantages:

1. Enhanced functionality: Users can now perform pan-genome annotations and obtain detailed immunological and subcellular location information in one streamlined process, significantly expanding the scope of their analyses. 
2. Improved efficiency: By eliminating the need to switch between multiple tools, researchers can save valuable time and resources, accelerating the pace of scientific discovery.
3. Seamless updates: The microservices architecture allows for independent updates of Pannotator and Medpipe without disrupting the entire system, ensuring that researchers always have access to the latest features and improvements.
4. Unparalleled scalability: Microservices' modular nature facilitates easy expansion of features and the addition of new tools, future-proofing the platform for evolving research needs.
5. Increased accessibility: The integration promotes collaboration and innovation by making these sophisticated tools more accessible to a wider range of researchers and developers.

"Microservices have revolutionized the way we approach bioinformatics tools, allowing for more flexible and scalable solutions. After the article's publication, for instance, in a couple of days, I installed and made available two other mirrors for our Medpipe microservice, accounting now for three dedicated servers in case of failure of one of the microservice demands. My limitation is the number of dedicated machines I have at the moment.", explains Dr. Anderson Santos, head of the Computational Biology and Bioinformatics Laboratory (Comp2Bio) at the Federal University of Uberlândia. "This integration of Pannotator with Medpipe exemplifies how we can leverage existing tools to enhance genomic analysis capabilities."

Key Components of the Integration

The integration utilizes a microservice called Med$\mu\sigma$, which executes Medpipe through a RESTful API. This architecture enhances modularity and scalability, allowing for seamless communication between the two tools. Specific API endpoints, such as /v1/medpipe/run, enable Pannotator to perform annotations efficiently, facilitating asynchronous execution and status retrieval.

Functional Enhancements and User-Friendly Features

With this integration, Pannotator now provides comprehensive data on proteins' subcellular location, immunological potential, Mature Epitope Density (MED), and classification in relation to Gene Ontology (GO). The microservice offers detailed documentation, example requests, and logs, making it accessible for researchers to utilize genomic data effectively.

Impact on Biological Research and Future Prospects

This integration has far-reaching implications for various areas of biological research:

-   Vaccine development: The integrated tool can significantly accelerate the identification of potential vaccine targets by providing comprehensive protein analysis.
-   Drug discovery: Researchers can gain deeper insights into protein functions and locations, facilitating the identification of novel drug targets.
-   Evolutionary studies: The ability to analyze pan-genomes across multiple species offers unprecedented opportunities to unravel evolutionary relationships and adaptations.
-   Broader applicability: The Medpipe microservice is not limited to Pannotator; it can be integrated with other genomic analysis tools, providing flexibility for diverse research applications.

According to Dr. Anderson Santos, a Professor at the Faculty of Computing, Federal University of Uberlândia, and coordinator of the Comp2Bio laboratory, "The use of vaccines to prevent common bacterial diseases in underdeveloped countries like Brazil is still promising for future generations, unlike expensive and difficult-to-produce antibiotics and anti-inflammatory products. I hope that tools like Medpipe microservice, which helps to produce vaccines, start to be used more broadly and that vaccines start to substitute the multibillion-dollar industry of antibiotics." Dr. Santos, who has extensive experience in genome assembly and annotation, also emphasizes the importance of interdisciplinary approaches in bioinformatics research.

As technology continues to advance, we can anticipate further integrations and innovations in biological research tools. The successful application of microservices in this field demonstrates how software engineering principles can be leveraged to accelerate scientific discovery and deepen our understanding of life at the molecular level.

By making these sophisticated tools more accessible and efficient, we are opening up new frontiers for researchers, students, and even citizen scientists to contribute to the exciting world of biological research, potentially leading to groundbreaking discoveries in genomics, proteomics, and beyond.

This paper was published in Biomedical Informatics.
Gonçalves R, Santos A. Pannotator integrated with Medpipe provides immunological and subcellular location features using a microservice. Biomed. Inform. 2024(1):0002.