AI-Orchestrated Spatial Transcriptomics Bioinformatics Pipeline
AI-driven orchestration • Workflow coordination • Context management • Result interpretation
FASTQ files, spatial barcodes, quality control
Spatial regions, histology integration
Reference genome mapping, BAM generation
UMI counting, expression matrix
Cell typing, pathways, clinical integration
Genomic Reference Data
FGbio toolkit • FASTQ validation • UMI extraction • Reference genomes
TCGA Cancer Genomics
GDC Portal • Expression data • Mutation profiles • Clinical annotations
Core Processing
STAR alignment • QC filtering • Spatial mapping • UMI counting
Histology Integration
H&E images • Image registration • Feature extraction • Visualization
ML Foundation Models
DNABERT-2 • Geneformer • scGPT • Sequence embeddings
Cell Segmentation
Deep learning models • Nuclear detection • Cell phenotyping
Mock EHR System
Synthetic patient data • Clinical metadata • FHIR-compliant
Single-responsibility servers with clear interfaces. Easy to extend, test, and maintain.
4-layer security model. HIPAA-like patterns for clinical data. Input validation throughout.
Containerized deployment. Horizontal scaling. Monitoring and observability built-in.
Claude coordinates workflow execution, interprets results, and provides biological insights.
FGbio, TCGA, Hugging Face integration with industry-standard tools.
50M reads in <30 min. GPU acceleration. Distributed processing with Nextflow.