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Scientific computing and academic tools.

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academic

397

paragraph-curator

Structured paragraph curation for C5: **select -> evaluate -> subset -> fuse**, so drafts converge instead of only expanding. **Trigger**: paragraph curator, curation, select evaluate fuse, paragraph selection, 选段, 评价, 融合, 收敛, 去冗余. **Use when**: you are in C5, `sections/*.md` exist, and the writing loop drifts toward 'longer by accumulation' (repetition, redundant paragraphs, weak synthesis). **Skip if**: evidence packs are thin / `evidence-selfloop` is BLOCKED; or you are pre-C2 (NO PROSE). **Network**: none. **Guardrail**: do not invent facts; do not add/remove citation keys; do not move citations across subsections; keep section-level claims consistent with `output/ARGUMENT_SKELETON.md# Consistency Contract`.

WILLOSCAR

research

academic

397

appendix-table-writer

Curate reader-facing survey tables for the Appendix (clean layout + high information density), using only in-scope evidence and existing citation keys. **Trigger**: appendix tables, publishable tables, survey tables, reader tables, 附录表格, 可发表表格, 综述表格. **Use when**: you have C4 artifacts (evidence packs + anchor sheet + citations) and want tables that look like a real survey (not internal logs). **Skip if**: `outline/tables_appendix.md` already exists and is refined (>=2 tables; citation-backed; no placeholders; not index-y). **Network**: none. **Guardrail**: no invented facts; no pipeline jargon; no paragraph cells; use only keys present in `citations/ref.bib`.

WILLOSCAR

research

academic

397

thesis-citation-enhance-review

为中文毕业论文补强并核验引用：找出必须有引文支撑的句子，扩展候选文献，检查引用与论断是否匹配，并回写参考文献与正文引用。 **Trigger**: 引用补强, citation enhance, 文献补充, 引用核验, 毕业论文参考文献检查. **Use when**: 正文已有一定稳定度，需要系统补足背景、定义、对照工作和关键结论的引用支撑，并检查是否存在误引或漏引。 **Skip if**: 还没有稳定正文，或当前仅在做早期结构重构。 **Network**: optional. **Guardrail**: 不为了堆引用而堆引用；引用必须与论断匹配；先补对，再补多。

WILLOSCAR

research

academic

397

thesis-style-polisher

对中文毕业论文做最终润色与去 AI 味：重点处理章首导言、章末小结、贡献描述、总结与展望中的模板腔、宣传腔与 AI 口癖。 **Trigger**: 论文润色, thesis style polish, 去 AI 味, 中文论文风格统一, 章首导言润色, 总结展望润色. **Use when**: 结构、证据、数据和编译已经基本稳定，需要做最后一轮中文学位论文风格收口。 **Skip if**: 正文结构还在大改，或关键引用 / 数字 / 图表还没稳定。 **Network**: none. **Guardrail**: 不用润色掩盖结构问题；不引入新事实；先去模板腔，再做措辞提升。

WILLOSCAR

research

academic

397

thesis-chapter-reconstructor

围绕毕业论文主线重构章节：把原论文式叙事改成学位论文式叙事，重写章节目标、内容比重、前后承接与论证方式。 **Trigger**: 章节重构, chapter reconstructor, 毕业论文主线重构, paper 变 thesis, 章节改写. **Use when**: 你已经知道每份材料在毕业论文中的角色，但当前章节仍然像原论文翻译、拼接或卖点展示。 **Skip if**: 当前只是做局部句子润色，或章节角色尚未确定。 **Network**: none. **Guardrail**: 不是翻译论文；不是简单删减；必须围绕毕业论文主线重写章节目标与承接关系。

WILLOSCAR

research

academic

395

paper-2-web

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

jimmc414

research

academic

395

paper-2-web

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

jimmc414

research

scientific-computing

395

tooluniverse

Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

jimmc414

research

academic

395

scholar-evaluation

Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill should be used when assessing research papers, evaluating literature reviews, scoring research methodologies, analyzing scientific writing quality, or applying structured evaluation criteria to academic work. Provides comprehensive assessment across multiple dimensions including problem formulation, literature review, methodology, data collection, analysis, results interpretation, and scholarly writing quality.

jimmc414

research

academic

395

peer-review

Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

jimmc414

research

academic

395

scientific-critical-thinking

Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.

jimmc414

research

academic

395

literature-review

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

jimmc414

research

academic

395

literature-review

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

jimmc414

research

academic

395

scientific-writing

Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.

jimmc414

research

astronomy-physics

393

sc-best-practices-skills-index

Skills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.

aristoteleo

research

bioinformatics

393

openst-skills-index

Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.

aristoteleo

research

bioinformatics

393

omics-analysis-skills-index

Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.

aristoteleo

research

bioinformatics

393

database-access-skills-index

Skills for querying and downloading data from genomic, transcriptomic, and single-cell databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, and large-scale single-cell data.

aristoteleo

research

computational-chemistry

392

ship-safe-red-team

Run a multi-agent red team scan — 16 specialized security agents scan for 80+ attack classes including injection, auth bypass, SSRF, supply chain, Supabase RLS, MCP security, agentic AI, RAG poisoning, PII compliance, and more. Use when the user wants a deep security analysis beyond just secrets.

asamassekou10

research

academic

391

web-research

Structured approach to conducting thorough web research with source citation

cloudshipai

research

computational-chemistry

389

common-dast-tooling

Standardize usage of Dynamic Application Security Testing (DAST) tools (ZAP, Nuclei, Nikto) and custom AI-driven curl probes for adversarial system testing. Use when advising on or running dynamic security scans on local/staging environments. (triggers: DAST, dynamic scan, zap, nuclei, nikto, curl probe, pentest, dynamic analysis)

HoangNguyen0403

research

computational-chemistry

389

common-dast-tooling

Standardize usage of Dynamic Application Security Testing (DAST) tools (ZAP, Nuclei, Nikto) and custom AI-driven curl probes for adversarial system testing. Use when advising on or running dynamic security scans on local/staging environments. (triggers: DAST, dynamic scan, zap, nuclei, nikto, curl probe, pentest, dynamic analysis)

HoangNguyen0403

research

lab-tools

389

ios-performance

Profile and optimize iOS apps with Instruments, memory management, and rendering techniques. Use when profiling iOS apps with Instruments or optimizing memory and rendering. (triggers: **/*.swift, Instruments, Allocations, Leaks, dequeueReusableCell)

HoangNguyen0403

research

computational-chemistry

388

atomic-red-team-testing

Execute and validate adversary emulation tests using Atomic Red Team. Covers standard atomics, custom atomics (T9999.XXX), deployment workflows, and detection validation.

MHaggis

research

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