Scientific Tooling / Structured Intelligence / Manuscripts

Scientific Writing

Publication-ready entry points for the Structured Intelligence manuscript series.

These manuscripts explain why each scientific workflow matters, where the practical barriers lie, and how a transparent local AI layer can make those methods easier to use, inspect, and reuse without obscuring the original work.

Methods in context Operational barriers explained Transparent AI mediation
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Collection

Structured Intelligence Manuscript Series

3 web editions Methods and positioning Independent AI interface layer

Article 01

NCBI / Literature

NCBI E-utilities in the AI Era

A manuscript on turning E-utilities into reusable literature retrieval, review extraction, and research update workflows.

PubMed workflows AI-mediated retrieval
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Article 02

CDD / Annotation

RPS-BLAST in the AI Era

A manuscript on wrapping standalone RPS-BLAST and `rpsbproc` into a reusable AI-mediated domain-annotation workflow.

Standalone CDD Explainable execution
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Article 03

NGS / Orchestration

NGS Analysis Expert

A manuscript on orchestrating end-to-end genomic data workflows — from public database search and data download through variant calling, RNA-seq, single-cell analysis, and metagenomics — with a skill-based AI agent and 35 composable skills.

NGS pipelines AI orchestration
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