Paper Writing & Submission

bio-alignment-io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, a…

doc-coauthoring

Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical s…

FlowIO

FlowIO is a lightweight Python library for reading and writing Flow Cytometry Standard (FCS) files. Parse FCS metadata, extract event data,…

paper-polish-workflow

Systematic top-down workflow for polishing academic papers. Structure to logic to expression with user confirmation at each step.

ppw:abstract

Generate or optimize academic paper abstracts using the 5-sentence Farquhar formula. Supports generate-from-scratch and restructure-existing…

ppw:caption

Generate or optimize figure/table captions for academic papers. Geography-aware: study area, CRS notation, data source. Writes output to.tex…

ppw:cover-letter

Generate submission-ready cover letters from paper content and target journal requirements. Includes contribution statement, data availabili…

ppw:de-ai

Detect and rewrite AI-generated patterns in English academic text. Two-phase workflow: scan with risk tagging, then batch rewrite. Triggers…

ppw:experiment

Analyze experiment results and generate discussion paragraphs for academic papers. Two-phase workflow: identify measurable findings (Phase 1…

ppw:logic

Verify logical consistency across paper sections. Traces argument chains and identifies gaps, unsupported claims, terminology inconsistencie…

ppw:polish

Polish English academic text through quick-fix or guided multi-pass workflow. Adapts to journal style with in-place editing and change track…

ppw:reviewer-simulation

Simulate peer review of academic papers with structured feedback. Produces bilingual review report with scoring and actionable suggestions.…

ppw:team

Orchestrate parallel paper processing. Split paper into sections and run any eligible Skill (polish, translation, de-ai) across sections via…

ppw:translation

Translate Chinese academic text into polished English for journal submission. Produces LaTeX output with bilingual comparison. 将中文学术草稿翻译为投稿级…

ppw:visualization

Recommend appropriate chart types for experimental data with rationale and tool hints. Geography-aware: choropleth, spatial scatter, kernel…

pysam

Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant f…

scientific-manuscript

Scientific manuscript writing and revision with journal-specific formatting.

scientific-problem-selection

This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or st…

slurm-job-script-generator

Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when…