Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add a-attia/scicomp-research-skills --skill research-paper-writinggit clone --depth 1 https://github.com/a-attia/scicomp-research-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/a-attia/scicomp-research-skills/research-paper-writing)<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/research-paper-writing"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/research-paper-writing/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/research-paper-writing"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/research-paper-writing.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00068 | $0.01917 |
| Opus 5 | $0.00034 | $0.00958 |
| Sonnet 5 | $0.00014 | $0.00383 |
| Haiku 4.5 | $0.00007 | $0.00192 |
Grade A, and why
research-paper-writing scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 184 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Research Paper Writing
Overview
Use this skill to rewrite a research paper into a reviewer-friendly, high-clarity draft. Prioritize first-impression quality (figures/tables/layout), logical flow, and evidence-backed claims.
Core Workflow
- Clarify the paper story before sentence-level edits.
- Use section-specific guidance in
references/. - Rewrite paragraph-by-paragraph with one message per paragraph.
- Run reverse outlining after writing each section.
- Check every major claim in Abstract/Introduction against experimental evidence.
- Run final-paper adversarial review with
references/paper-review.md.
Global Principles
- Keep one paragraph for one message only.
- State the paragraph message in the first sentence.
- Make nouns self-contained; define new terms before reusing them.
- Maintain sentence-to-sentence flow (cause, contrast, consequence, or refinement).
- Iterate with adversarial self-review: read as a skeptical reviewer.
- Treat visual quality as core content, not decoration.
- Use a clean teaser and pipeline figure.
- Use readable, minimal-ink tables.
- Keep formatting consistent and tidy.
Paragraph Clarity Check (Important)
Use this quick test whenever the user asks whether a paragraph "flows" or is clear.
- Read as an external reader:
- Does this paragraph have one explicit message?
- Does the first sentence state what this paragraph will do?
- Are all key nouns/terms readable without hidden context?
- Does each sentence connect to the previous one with a clear relation (cause, contrast, consequence, refinement, example)?
- Run reverse outlining for the current section:
- Write down thesis/main claim.
- Write down each paragraph topic sentence.
- Write down the evidence/explanation points under each paragraph.
- Check mapping: topic sentence -> thesis, and evidence -> topic sentence.
- Revise or remove any paragraph that cannot be mapped cleanly.
- If flow is still weak, add temporary section headers and explicit transition phrases during revision, then remove unnecessary headers before finalizing.
What ships with it
37 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- references/abstract.md 3.5 KB
- references/conclusion.md 1.2 KB
- references/does-my-writing-flow-source.md 4.9 KB
- references/examples/abstract-examples.md 875 B
- references/examples/abstract/template-a.md 950 B
- references/examples/abstract/template-b.md 3.2 KB
- references/examples/abstract/template-c.md 1.7 KB
- references/examples/index.md 2.3 KB
- references/examples/introduction-examples.md 1.5 KB
- references/examples/introduction/novel-task-challenge-decomposition.md 1.5 KB
- references/examples/introduction/pipeline-not-recommended-abstract-only.md 2.9 KB
- references/examples/introduction/pipeline-version-1-one-contribution-multi-advantages.md 2.0 KB
- references/examples/introduction/pipeline-version-2-two-contributions.md 2.0 KB
- references/examples/introduction/pipeline-version-3-new-module-on-existing-pipeline.md 1.5 KB
- references/examples/introduction/pipeline-version-4-observation-driven.md 1.4 KB
- references/examples/introduction/technical-challenge-version-1-existing-task.md 2.6 KB
- references/examples/introduction/technical-challenge-version-2-existing-task-insight-backed-by-traditional.md 3.8 KB
- references/examples/introduction/technical-challenge-version-3-novel-task.md 1.6 KB
- references/examples/introduction/version-1-task-then-application.md 727 B
- references/examples/introduction/version-2-application-first.md 405 B
- references/examples/introduction/version-3-general-to-specific-setting.md 847 B
- references/examples/introduction/version-4-open-with-challenge.md 1.7 KB
- references/examples/method-examples.md 1.0 KB
- references/examples/method/example-of-the-three-elements.md 7.3 KB
- references/examples/method/method-writing-common-issues-note.md 355 B
- references/examples/method/module-design-instant-ngp.md 4.5 KB
- references/examples/method/module-motivation-patterns.md 410 B
- references/examples/method/module-triad-neural-body.md 763 B
- references/examples/method/neural-body-annotated-figure-text.md 2.8 KB
- references/examples/method/overview-template.md 2.0 KB
- references/examples/method/pre-writing-questions.md 479 B
- references/examples/method/section-skeleton.md 110 B
- references/experiments.md 4.4 KB
- references/introduction.md 15 KB
- references/method.md 6.1 KB
- references/paper-review.md 5.3 KB
- references/related-work.md 1.3 KB
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 184 lines · 68 tokens per session scan A 998961bc8602
research-paper-writing is a skill published in the GitHub repository a-attia/scicomp-research-skills (11 stars, last pushed 8d ago), licensed MIT. It adds 68 tokens to every session and 1,917 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
matlab
Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
exploratory-data-analysis
Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
mapping-to-snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…