Projects
From bioinformatics to ecological AI systems
cat project_philosophy.txt
My work spans from open-source bioinformatics tools for the scientific community to cutting-edge AI systems that integrate ecological intelligence. Each project embodies my commitment to resilient, accessible technology that operates within planetary boundaries while enhancing human capabilities.
Current AI Edge Computing Projects
BioDOG (Biological Database-Oriented Generation)
A framework that bridges protein language models with biological ontologies, enabling enhanced analysis of complex biological systems through context-aware AI.
- Interfaces between protein language models and established biological ontologies
- Creates structured representations of complex biological knowledge
- Enables cross-modal reasoning between text and biological data
- Designed for resource-efficient deployment in research environments
Mahakala
A lightweight, edge-deployable AI system designed for resource-constrained environments with ecological awareness built into its architecture.
- Optimized for deployment on low-power devices and intermittent connectivity
- Implements novel resource-aware computing algorithms
- Features built-in privacy protections and local-first operation
- Adapts computational load based on available renewable energy
Localized LLM Deployment Framework
Creating accessible infrastructure for community-oriented AI technology that respects privacy and operates independently of centralized cloud systems.
- Reproducible deployment system using declarative NixOS configurations
- Community-first design prioritizing accessibility and transparency
- Integration with local knowledge bases and context repositories
- Optimized for consumer hardware with minimal resource requirements
EcoAgent
An autonomous agent framework designed to monitor and assist with ecological restoration projects, combining edge sensing with AI-driven analysis and decision support.
- Distributed sensor network integration for environmental monitoring
- AI-driven analysis of ecosystem health and recovery patterns
- Decision support for restoration interventions and adaptive management
- Low-impact deployment designed for minimal ecological disturbance
Scientific Bioinformatics Projects
MarFERReT (Marine Functional Reference Eukaryotic Transcriptomes)
An open-source, version-controlled reference library of marine microbial eukaryote proteins, addressing the underrepresentation of marine organisms in existing genetic databases.
- Comprehensive collection with tens of millions of validated reference proteins
- Preserved taxonomic granularity from strain to species level
- Flexible framework for building custom reference libraries
- Rigorous cross-validation to identify quality and contamination issues
North Pacific Eukaryotic Gene Catalog
A comprehensive catalog of metatranscriptome assemblies and annotations for marine microbial eukaryotes in the North Pacific Ocean, providing essential reference data for oceanographic research.
- Contains over 200 million environmental gene sequences with functional annotations
- Region-specific focus on the North Pacific ecosystem
- Facilitates collaborative research in marine microbial ecology
- Illuminates patterns of gene expression across time and space
Diel Transcriptional Cascades
Investigation of the daily (diel) rhythms of gene expression in open-ocean eukaryotic plankton communities, revealing synchronized biological processes driven by light cycles.
- Mapped temporal organization of gene expression in marine microbial communities
- Identified key regulatory elements controlling diel oscillations
- Demonstrated niche differentiation through temporal specialization
- Connected gene expression to metabolic activity in the ocean
grep "continuity" project_trajectory.txt
The trajectory from bioinformatics to AI Edge Computing reflects a natural evolution—from analyzing complex biological systems to designing technological systems that embody biological principles of resilience, efficiency, and ecological harmony.