
Genome Assembly and Annotation
EMBL-EBI is a global centre for biological data, developing and maintaining open data resources and open-source software that support life science research worldwide. Our services are used daily by researchers across academia, healthcare, and industry, and span genomics, transcriptomics, metagenomics, molecular interactions, chemistry, and functional annotation. EMBL-EBI develops and maintains a wide range of long-standing, high-impact resources, including Ensembl for genome data, the European Nucleotide Archive (ENA) for sequence data, MGnify for metagenomics analysis, and BioStudies for structured biological datasets. Together, these resources support data submission, analysis, integration, and reuse at global scale. Given the rapid growth and increasing complexity of biological data, EMBL-EBI operates a fast-evolving software ecosystem and continuously explores new approaches to data processing, storage, distribution, and visualisation. Our codebases are open source, our data are freely available, and we actively engage with the open-source community to ensure our infrastructure remains robust, scalable, and accessible. Through Google Summer of Code, EMBL-EBI offers contributors the opportunity to work on real-world scientific software, gaining experience in open-source development while contributing to tools and resources used by the global life science community.
GSoC Participation History
Technologies
Topics
Past Projects
Expose a Subset of ENA REST Services as MCP
The goal of this project is to provide a Model Context Protocol (MCP) server that is suitable for production and exposes expected REST endpoints from...
Building a Perturbation-Aware LLM for Multimodal In Silico Perturbation Modelling
Perturbation biology datasets across CRISPR screens, MAVE, and scPerturb-seq remain siloed in incompatible formats, making cross-modal reasoning...
Browser-Native Genomic Feature Search using SQLite WASM and JBrowse
This project implements a browser-native genomic feature search system for efficiently querying large GFF3 annotation datasets without requiring...
Annotation Metrics Reporting and Analysis Modules for the Ensembl Assembly/Annotation Tracking App
The Ensembl Assembly/Annotation tracking application stores rich quality metrics for thousands of genome annotations but currently lacks tooling to...
Expand genome metadata in Ensembl with AI tools
The Ensembl Plants and Metazoa platforms face a significant metadata gap where critical biological context, such as ploidy, strain, and sex, is...
Sequence similarity networks for the visualisation and exploration of MGnify Proteins
My proposal is to develop a scalable computational pipeline to construct, annotate, and visualise Sequence Similarity Networks (SSNs) for a...
Ask VEPai. Trained chatbot interface for Ensembl VEP web
Ensembl VEP's web interface offers dozens of configuration options for variant annotation, overwhelming new users and generating recurring helpdesk...
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