Literature Review

Brainstorming

Enforces a design-first approach: explore context, ask clarifying questions one at a time, propose 2-3 approaches with trade-offs, write a d…

Brainstorming Research Ideas

Ten complementary frameworks for structured research ideation: Problem-First vs Solution-First, Abstraction Ladder, Tension Hunting, Cross-P…

bio-longread-alignment

Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use…

bio-machine-learning-atlas-mapping

Map query cells to reference atlases with scANVI or Symphony.

bio-methylation-bismark-alignment

Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation in…

bio-microbiome-taxonomy-assignment

Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and ex…

bio-phasing-imputation-reference-panels

Select and prepare reference panels (1KGP, HRC, TOPMed) for imputation.

bio-read-alignment-bwa-alignment

Align short reads to reference genome with BWA-MEM.

bio-read-qc-contamination-screening

Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacteria…

bio-reference-operations

Download, index, and manage reference genome FASTA files.

biomni-research-agent

BioMni research-focused agent with literature, database, and analysis integration.

BioPython

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipul…

bioRxiv

This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive…

deep-research

Execute autonomous multi-step deep research on any topic. Use when the user asks for comprehensive research, literature reviews, competitive…

deep-research-swarm

Multi-agent swarm for deep scientific research with parallel literature synthesis.

gene-database

NCBI Gene is a comprehensive database integrating gene information from diverse species. It provides nomenclature, reference sequences (RefS…

get-paper

Search Google Scholar via Chrome DevTools MCP, let the user select a paper, and retrieve its BibTeX entry. 通过 Chrome DevTools MCP 在 Google S…

leads-literature-mining

LEADS literature mining: automated extraction of biological findings from papers.

Literature Review

Conduct systematic, comprehensive literature reviews following rigorous academic methodology. Search multiple literature databases, synthesi…

opentargets-database

The Open Targets Platform is a comprehensive resource for systematic identification and prioritization of potential therapeutic drug targets…

parallel-web

This skill provides access to **Parallel Web Systems** APIs for web search, deep research, and content extraction. It is the **primary tool…

pdf

This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libra…

ppw:literature

Search academic literature via Semantic Scholar MCP, select papers interactively, and generate verified BibTeX entries. 文献检索与BibTeX生成，通过Sema…

ppw:repo-to-paper

Scan an experiment repo and generate a complete paper outline (H1/H2/H3) with user approval checkpoints at each level, then generate body te…

ppw:update

Sync local skills and references from the GitHub repo. Triggers on update skills, sync skills, 更新技能, 同步技能.

research-literature

Research literature management: search, organize, and synthesize scientific papers.

scikit-learn

This skill provides comprehensive guidance for machine learning tasks using scikit-learn, the industry-standard Python library for classical…

search-strategy

Design systematic search strategies for scientific literature and databases.

USPTO

USPTO provides specialized APIs for patent and trademark data. Search patents by keywords/inventors/assignees, retrieve examination history…