All organizations · GSoC 2026 · Science and medicine, Data

Genome Assembly and Annotation

Unleashing the potential of big data in biology

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 …

  • python
  • mysql
  • docker
  • pytorch
  • nextflow
  • machine learning
  • genomics
  • big data
  • cloud
  • hpc

Project ideas

16 ideas on its 2026 ideas page; of the 16 that state a difficulty: 2 easy, 12 medium, 2 hard. Sizes: 13 medium, 3 large. 24 mentors named.

  1. Expose a Subset of ENA REST Services as MCP medium medium
  2. Creating a knowledge graph from a subset of ENA and BioSamples data large hard
  3. Annotation metrics reporting & analysis modules for the Ensembl Assembly/Annotation tracking app medium easy
  4. Development of a refinement tool to identify selenoproteins in Ensembl genesets medium medium
  5. Expanding a pipeline for small non-coding RNA (sncRNA) identification in Ensembl Genomes medium medium
  6. Expand genome metadata in Ensembl with AI tools medium medium
  7. BUSCO-Missing Investigator (BMI): a reproducible pipeline to explain “missing/fragmented BUSCOs” medium medium
  8. Ask VEPai. Trained chatbot interface for Ensembl VEP web medium medium
  9. nf-core/vep: Extending and standardising Ensembl VEP workflow for nf-core medium medium
  10. Building a perturbation-aware LLM for mMultimodal in-silico perturbation modelling large hard
  11. Designing an open access Ensembl GraphQL Workshop medium medium
  12. Standardised evaluation for microbiome dataset classifiers medium medium
  13. Sequence similarity networks for the visualisation and exploration of MGnify Proteins large easy
  14. A genomic feature database in the browser medium medium
  15. Design and API-aware UI generation using MCP servers and Figma APIs medium medium
  16. Expose BioSamples submission and search capabilities as MCP tools for AI-assisted metadata interacti medium medium

Read the ideas page. Ideas are for scope reference; never copy one into a proposal.

History

In GSoC since 2021, 4 years. Projects per year: '21: 3, '22: 6, '23: 5, '26: 7.

On GitHub

85 repositories pushed to in the last year. Main languages: Python (41), Perl (17), TypeScript (5), Ruby (4), Dockerfile (2), HTML (2).

Links and channels

go deeper in your terminal
git-into-gsoc org "Genome Assembly and Annotation" --shortlist
git-into-gsoc repos "Genome Assembly and Annotation"
git-into-gsoc issues --org "Genome Assembly and Annotation"
or ask your assistant:
"Which Genome Assembly and Annotation repositories merge
newcomers' pull requests, and which beginner
issues are still free?"

Those commands read live data: which repositories merge outside pull requests, and which beginner issues nobody has claimed. Install in two minutes.