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

Browse collection Open repository

Current Collection

2 workflow manuscripts published

Methods practical scientific workflows examined in depth

Transparent each article explains the AI layer without hiding the original method

Editorial Frame

Each manuscript is written as a publication-style argument: it explains the scientific task, identifies the real points of operational friction, and shows how a transparent local AI interface can improve access and reuse without replacing the underlying method.

Collection

Structured Intelligence Manuscript Series

2 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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