scientific-paper

name	scientific-paper
description	End-to-end workflow for creating, reviewing, and critiquing scientific papers with rigorous methodology. Use when: writing papers, reviewing papers, literature reviews. Do not use: for blog posts, technical documentation.

Scientific Paper Skill

Complete workflow for empirical SE research: paper creation, deep review, SLR, methodology critique, peer-review simulation, and LaTeX conventions.

Modes of Operation

Mode	Trigger phrases	What it does
create	"create paper", "new paper", "paper template", "criar artigo"	Scaffolds paper structure + LaTeX template
review	"review paper", "revisar paper", "find errors"	Full structured review: methodology, writing, validity
critique	"critique", "metodologia", "methodological errors", "erros metodológicos"	Deep methodology critique using error catalog
peer-review	"peer review", "referee report", "simulate reviewer", "parecerista"	Generates structured referee report (Summary / Strengths / Weaknesses / Questions / Recommendation)
slr	"systematic review", "SLR", "revisão sistemática", "literature review"	Guides SLR protocol from scratch
methodology-check	"check methodology", "rigor", "validity", "research design"	Runs methodology checklist for study type
data-presentation	"figures", "tables", "charts", "data viz", "plots", "benchmark results"	Reviews data presentation choices
bib-validate	"validate bibliography", "check citations", "missing citations", "bib"	Runs validate-bib.py to catch orphaned \cite{} and missing .bib entries

Step-by-Step Procedures

Mode: review - Full Paper Review

1. Ask for the paper file or content (paper.tex or text paste).
2. Load error catalog to identify issues by category.
3. Load methodology checklist and run the appropriate checklist for the paper's study type.
4. Load threats-to-validity to audit the validity section.
5. Load paper-structure to verify completeness of all sections.
6. Produce structured output:
   • Critical errors (must fix before submission)
   • Major concerns (likely desk-reject or major revision)
   • Minor issues (polish, clarity, consistency)
   • Positive observations (what is done well - important for balance)
7. For each issue: location (section/paragraph) → problem → recommended fix.

Mode: peer-review - Referee Report Simulation

1. Ask for paper content + target venue (EMSE, ICSE, FSE, MSR, arXiv, etc.).
2. Load venues.md for venue-specific criteria and expectations.
3. Load error-catalog.md and threats-to-validity.md.
4. Write a complete referee report in the style of the target venue:

SUMMARY
[2–3 sentences: what the paper does and its main claim]

STRENGTHS
1. ...
2. ...
3. ...

WEAKNESSES / MAJOR CONCERNS
1. ...
2. ...

MINOR COMMENTS
1. ...

SPECIFIC QUESTIONS FOR AUTHORS
1. ...

RECOMMENDATION
[ ] Accept  [ ] Minor Revision  [X] Major Revision  [ ] Reject

CONFIDENCE: [Reviewer expertise 1–5]

5. Provide a separate "author's perspective" note: what changes would move the paper from current recommendation to Accept.

Mode: critique - Methodology Critique

1. Identify the study type from the paper (case study / benchmarking / experiment / SLR / survey).
2. If the paper is a case study, use the scientific-case-study-research skill for case definition, units of analysis, protocol, triangulation, chain of evidence, ethics, and threats to validity.
3. Load methodology-checklist.md for that type.
4. Run each checklist item and flag gaps.
5. Load error-catalog.md and map identified issues to error categories.
6. Prioritize by severity: conclusion validity > internal validity > construct validity > external validity.

Mode: slr - Systematic Literature Review

1. Load systematic-review-protocol.md.
2. Walk through each phase: motivation → RQs → search string → databases → inclusion/exclusion → quality assessment → data extraction → synthesis.
3. Use assets/slr-protocol-template.md to scaffold the protocol document.
4. Validate search string completeness (synonyms, acronyms, Boolean operators).
5. Check that each RQ maps to a data extraction field and a synthesis method.

Mode: create - New Paper Scaffold

1. Determine study type and target venue.
2. Load paper-structure.md for the appropriate template.
3. Use assets/paper-template.tex as the LaTeX starting point.
4. Load latex-conventions.md for repo-specific setup.
5. Load venues.md for venue formatting requirements.
6. Scaffold folder: papers/YYYY-short-slug/ with paper.tex, title-page.tex, README.md.

Mode: data-presentation - Figures and Tables Review

1. Load data-presentation.md.
2. Audit each figure/table: chart type appropriateness, axis labels, units, error bars, statistical significance markers, color accessibility, caption completeness.
3. Flag misleading visualizations (e.g., truncated y-axis, missing baseline, no variance shown).

Mode: bib-validate - Bibliography Validation

1. Locate paper.tex and *.bib file in the workspace.
2. Run validate-bib.py:

   python scripts/validate-bib.py --tex paper.tex --bib references.bib
   

3. Report:
   • Orphaned \cite{}: keys used in .tex but missing from .bib
   • Unused entries: keys in .bib never cited in .tex
   • Malformed entries: missing required BibTeX fields (author, title, year)
4. Run after any round of work where new citations were added; skip if no new \cite{} keys were introduced.

Key Resources

Resource	Purpose
methodology-checklist.md	Rigor checklists by study type
error-catalog.md	Catalog of methodological and writing errors
paper-structure.md	Section templates by paper type
systematic-review-protocol.md	Full Kitchenham SLR protocol
threats-to-validity.md	Wohlin validity framework for SE research
latex-conventions.md	Repo LaTeX conventions and anonymization
venues.md	EMSE / ICSE / FSE / MSR / arXiv submission checklists
data-presentation.md	Figures, tables, and benchmark data visualization
paper-template.tex	Ready-to-use LaTeX template
slr-protocol-template.md	Fillable SLR protocol document
validate-bib.py	Bibliography validation script

Write like a human

Even in formal academic prose, keep out the AI writing tells reviewers now flag:

• No em dashes and no curly quotes; use straight quotes.
• Cut AI vocabulary: "delve", "leverage", "robust", "crucial", "pivotal", "testament", "underscore", "showcase", "intricate", "meticulous", "landscape" (as an abstract noun).
• Remove significance padding ("stands as a testament to", "plays a pivotal role"), trailing "-ing" analysis clauses ("...highlighting its significance"), and copula avoidance ("serves as" for "is").
• Do not use "novel" or "state-of-the-art" without a named comparator. Attribute claims to a citation, not to "experts" or "studies".
• Open sections with the finding or claim, not "In this paper" or "It is important to note". Do not close sections with "In summary"/"In conclusion" restatements.