Skip to content
Scriptorium
Search
Ctrl
K
Cancel
GitHub
Select theme
Dark
Light
Auto
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
GitHub
Select theme
Dark
Light
Auto
Conventions
The conventions subsection of the knowledge layer. Browse the individual documents from the sidebar.
