An agentic scriptorium for scholarly writing — coordinated AI capabilities for manuscripts, grants, and reviews.
Skill Claude CodeCodex
Improve a manuscript section's logical and argumentative coherence while preserving every citation, statistic, and declared terminology choice. Produces a structural diagnosis, a proposed outline, the revised text with a diff against the source, and a preservation report. Invoke ONLY when the user explicitly asks for…
Skill Claude CodeCodex
Audit the manuscript's Author Contributions section against ICMJE's four authorship criteria and CRediT's 14 contributor roles. Flag what's missing per author, suggest how to map who-did-what to canonical CRediT roles, and (when targetvenue is set) compare against journal-specific variants. Operates on the declared…
Skill Claude CodeCodex
Audit existing citations in a manuscript for claim-support alignment, primary-vs-review mismatch, causal overreach, and unsupported assertions. Reports findings as structured markdown. Does NOT add or invent citations.
Skill Claude CodeCodex
Propose page-limit-driven length reductions on a manuscript section while preserving every citation, every declared statistic, every core claim, and every declared terminology choice. Emits a structured markdown report with per-edit diffs, a preservation report, and a list of edits NOT proposed because compression…
Skill Claude CodeCodex
Author-side pre-submission audit that flags triggers likely to result in desk rejection before peer review — scope/audience mismatch, format and length issues, missing or weak required sections, weak significance framing, and presentation problems editors triage on. Outputs a structured markdown report with a…
Skill Claude CodeCodex
Explain scriptorium itself, a named skill, or a named MANUSCRIPTSTATE field. With no argument, gives a whole-system overview (what scriptorium is, what each skill does, how the shared state ties them together). With an argument, drills into that skill or field — what it does, what it consumes, what it produces, and…
Skill Claude CodeCodex
Audit text-only alignment between figure captions and the body-text sentences that reference them. For every figure, classify the caption ↔ body-text-reference pair as aligned / partially aligned / misaligned / cannot determine, and flag pattern-level issues (orphan figure, phantom figure, panel mismatch, axis/units…
Skill Claude CodeCodex
Identify gaps in existing draft prose — claims under-supported, premises missing, related work not engaged with, counterarguments not addressed, internal-consistency mismatches — and suggest directions for filling them. Output is a structured taxonomy of gap findings, each anchored to a specific manuscript passage…
Skill Claude CodeCodex
Conversationally bootstrap MANUSCRIPTSTATE.yaml for a new or existing manuscript directory. Infers what it can from the filesystem (title, sections, bibliography paths) and asks the author about the subjective fields (coreclaims, knownweaknesses, terminology, audience). Validates against the JSON Schema before…
Skill Claude CodeCodex
Flag sentences that are statistical outliers in the manuscript along three narrow dimensions — length, syntactic complexity, and nominalization density — for human review. Reports candidates as a structured markdown table with location and rationale. Does NOT produce a quality score, a grade, or a pass/fail. Does NOT…
Skill Claude CodeCodex
Run an EQUATOR Network reporting-guideline checklist (CONSORT, STROBE, PRISMA, ARRIVE, STARD, TRIPOD/TRIPOD+AI, CARE, COREQ, CHEERS, plus AI extensions) against a manuscript and classify every checklist item as present / partial / missing / not-applicable. For each item, anchors the classification in a quoted passage…
Skill Claude CodeCodex
Read the manuscript's methods section (and abstract/title for context) and infer which EQUATOR Network reporting guideline applies — CONSORT for RCTs, STROBE for observational, PRISMA for systematic reviews, ARRIVE for animal research, TRIPOD/TRIPOD+AI for prediction models, STARD for diagnostic accuracy, CARE for…
Skill Claude CodeCodex
Author-side simulation of peer review across four attentional lenses (methodological skeptic, domain expert, translational/clinical, statistical). Surfaces likely major and minor critiques, fatal concerns, enthusiasm drivers, and concrete revision suggestions. Output is structured markdown. NOT for editorial-side use…
Skill Claude CodeCodex
Detect terminology drift across a manuscript and enforce the preferred / forbidden / synonyms lists declared in MANUSCRIPTSTATE.yaml. Reports inconsistencies with exact occurrence locations and suggests normalizations. Does NOT modify the manuscript without explicit author consent.
Skill Claude CodeCodex
Conversational onboarding for new users. Three or four turns. Greets, asks what the user is working on (manuscript, grant, review, or exploring), walks through the relevant subset of scriptorium, shows an example MANUSCRIPTSTATE.yaml, and ends with a concrete next move (usually scriptorium:init). Does no work on the…
Skill Claude CodeCodex
Assess venue fit for a manuscript and return a tiered set of candidate venues (likely fit / stretch / probably premature) with per-venue rationale, fit caveats per axis (scope, audience, methodological, novelty, significance, open-access/cost), and explicit predatory-venue refusal. Handles three author states …