Scientific Paper

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](./scripts/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](./references/error-catalog.md) to identify issues by category.
3. Load [methodology checklist](./references/methodology-checklist.md) and run the appropriate checklist for the paper's study type.
4. Load [threats-to-validity](./references/threats-to-validity.md) to audit the validity section.
5. Load [paper-structure](./references/paper-structure.md) 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)

1. 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](./references/venues.md) for venue-specific criteria and expectations.
3. Load [error-catalog.md](./references/error-catalog.md) and [threats-to-validity.md](./references/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]

1. 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](./references/methodology-checklist.md) for that type.
4. Run each checklist item and flag gaps.
5. Load [error-catalog.md](./references/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](./references/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](./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](./references/paper-structure.md) for the appropriate template.
3. Use [assets/paper-template.tex](./assets/paper-template.tex) as the LaTeX starting point.
4. Load [latex-conventions.md](./references/latex-conventions.md) for repo-specific setup.
5. Load [venues.md](./references/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](./references/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](./scripts/validate-bib.py):

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

1. 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)

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

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: woliveiras
• Source: woliveiras/geremmyas
• License: MIT

Install and usage instructions live in the source repository linked above.