git:20260628.9edbf07 to git:20260721.2758b4c
3 added, 3 removed. Audit A to A.
# Ocean Genomics Research
Comprehensive research repository documenting deep-ocean genomics, eDNA metabarcoding, AI-driven protein structure prediction, and the computational biology toolchain for marine biodiversity discovery.
## Purpose
This repository serves as:
1. **Scientific documentation** of ocean genomics methods, tools, and discoveries
2. **Reference architecture** for building agentic bioinformatics workflows
3. **Skill source** for the `ocean-genomics` agent skill
4. **Knowledge base** bridged into the Obsidian vault for cross-session reasoning
## Structure
```
ocean-genomics/
├── docs/
│ ├── architecture/ # System design, pipeline diagrams
│ │ ├── sequencing-pipeline.md
│ │ ├── edna-metabarcoding.md
│ │ ├── protein-structure-prediction.md
│ │ └── ai-genomics-convergence.md
│ ├── references/ # Scientific references, database catalogs
│ │ ├── tools-inventory.md
│ │ ├── marine-databases.md
│ │ ├── foundation-models.md
│ │ └── mcp-servers.md
│ └── conversations/ # Session logs (auto-generated)
├── scripts/ # Bridge scripts, analysis utilities
├── assets/ # Diagrams, figures
└── CLAUDE.md # This file
```
## Key Topics
- **Molecular Biology Fundamentals**: DNA → RNA → Protein → Structure → Function
- **Sequencing Technologies**: Illumina short reads, Oxford Nanopore long reads, MinION portable
- **eDNA Metabarcoding**: Water sampling → filtration → CO1 amplification → species ID
- **Metagenomics**: Shotgun sequencing of environmental samples for functional + taxonomic profiling
- - **Protein Structure Prediction**: AlphaFold 3, ESMFold, OpenFold-3, ColabFold, Boltz-2
- - **Foundation Models**: Evo 2 (DNA), ESM-2 (protein), ProGen3 (protein generation)
- - **Marine Databases**: OBIS, BOLD, DOO, Tara Oceans, ESM Metagenomic Atlas
+ - **Protein Structure Prediction**: ESMFold2, AlphaFold 3, OpenFold-3, ColabFold, Boltz-2
+ - **Foundation Models**: Evo 2 (DNA), ESMC (protein, current gen), ESM-2 (legacy), ProGen3 (protein generation)
+ - **Marine Databases**: OBIS, BOLD, DOO, Tara Oceans, ESM Metagenomic Atlas (Meta), ESM Atlas (Biohub)
- **Pipeline Orchestration**: Nextflow + nf-core, Snakemake, QIIME2
- **MCP Integration**: gget-MCP, bio-mcp, BioinfoMCP
## Conventions
- Scientific accuracy is paramount — cite sources for all claims
- Use SI units and standard bioinformatics notation
- File formats: FASTQ, FASTA, SAM/BAM, VCF, BED/GFF
- Gene names in italics (*CO1*, *16S*), protein names in Roman (AlphaFold, ESM-2)