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Roadmap
How-to guides
How-to guides
Install
First run
Convert your manuscript to markdown
Reference
Reference
CLI commands
Skills
MANUSCRIPT_STATE.yaml schema
Concepts
Concepts
DESIGN
knowledge
Knowledge layer
prior-art
Prior art
Agentic AI for scientific writing and discovery
AI writing failure modes
Established AI writing tools for academic prose
The manubot lineage: manuscript-as-software
AI-assisted peer review platforms and tools
Reference managers and citation philosophy
scientific-writing
Scientific writing
Corpus-based stylometry: what's defensible for author-voice extraction
Discipline conventions beyond biomedicine
ESL writers and the Swales / Hyland tradition
Hayes-Flower writing model and cognitive load in scientific prose
Literature-search strategies: from boolean queries to citation chasing
narrative-frameworks
Plain language and lay summaries in scientific writing
Quantitative quality measures: what they can and cannot tell us
reader-expectation-approach
Reporting guidelines (EQUATOR Network)
significance-positioning
style-guides
Visualization and figure design in scientific manuscripts
peer-review
Peer review
AI Peer Review: What's Validated, What's Speculative
Common Critiques: A Taxonomy from the Literature
CRediT, ICMJE, and the authorship landscape
Critique Quality: What Makes Review Feedback Actually Useful
Editorial decision-making and desk rejection
Predatory publishing: detection, taxonomy, and the moving landscape
Preprint landscape: servers, post-publication review, and the moving boundary
Reviewer Archetypes: What the Evidence Shows
Venue selection: how researchers choose where to submit
citations
Citations
Citation accuracy: evidence base
Citation overreach: spin, amplification, and primary-vs-review cascades
CSL and bibliographic standards
Hallucination in LLM-generated citations
editing
Editing
Copyediting vs developmental editing: the editing taxonomy
Revision research: what evidence says about effective revision
Semantic preservation: how to think about "preserving meaning" measurably
grants
Grants
Grant writing evidence: what's actually known about what wins
NIH significance patterns: what funded grants look like
Reviewer archetypes for grant review
critique-techniques
Critique techniques
Argument mapping: diagramming structure to expose gaps
Citation–claim alignment: verifying that a cited source supports its claim
Forensic methodology: the science-of-science sleuthing toolkit
Internal consistency: detecting contradictions and drift within a single manuscript
Logical-fallacy detection in scientific writing
Research-gap detection: methodology and LLM-specific failure modes
Statistical inconsistency: forensic detection of reporting errors
reproducibility
Reproducibility
The reproducibility crisis as the framing context for scriptorium
author-roles
Author Roles
Author Career Stage and Role: Behavioral Evidence
EAL Scholarly Writing: Behavioral Evidence
conventions
Conventions
Declared-work scope: where scriptorium does and does not operate
Guidance level: how much framing each skill adds around its work
Start here — the mental model
Declared-work scope
Guidance level
Workflow stage
Case study — bariatric-surgery discussion paragraph
CLI vs MCP server
Trace schema
Glossary
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Citations
The citations subsection of the knowledge layer. Browse the individual documents from the sidebar.
