Microbiologists

Scikit Bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

K-Dense-AI18.8k

Sequence Alignment

A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.

Mouse Colony Planner

Calculate breeding timelines and cage requirements for transgenic mouse colonies

实验室工具

Arrive Guideline Architect

Generate ARRIVE 2.0 compliant animal research protocols with structured experimental design, sample size calculations, and reporting checklists. Ensures transparency, reproducibility, and ethical compliance in in vivo studies.

计算化学

Serial Dilution Calculator

Generate qPCR/ELISA dilution protocols with precise pipetting steps

foryourhealth111-pixel1.6k

Structural Variant Analysis Workflow

Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inversions, translocations), assesses pathogenicity using ACMG-adapted criteria, evaluates gene disruption and dosage sensitivity, and provides clinical interpretation with evidence grading. Use when analyzing CNVs, large deletions/duplications, chromosomal rearrangements, or any structural variants requiring clinical interpretation.

FreedomIntelligence2.1k

科学计算

Flowio

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

天文与物理

Omero Integration

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

foryourhealth111-pixel1.6k

foryourhealth111-pixel1.6k

Neuropixels Data Analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

学术

Research Lookup

Look up current research information using the Parallel Chat API (primary) or Perplexity sonar-pro-search (academic paper searches). Automatically routes queries to the best backend. Use for finding papers, gathering research data, and verifying scientific information.

K-Dense-AI1.6k

Tooluniverse Metagenomics Analysis

Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keyword, retrieve taxonomic profiles and functional annotations, classify genomes with GTDB taxonomy, and find related publications. Use for human gut microbiome, soil/ocean metagenomics, and environmental microbiology research.

mims-harvard1.3k

Stem Cell & Organoid Research

Research stem cells, iPSCs, organoids, and cell differentiation using ToolUniverse tools. Covers pluripotency marker identification, differentiation pathway analysis, organoid model characterization, cell type annotation, and disease modeling. Integrates CellxGene/HCA for single-cell atlas data, CellMarker for cell type markers, GEO for stem cell datasets, and pathway tools for differentiation signaling. Use when asked about stem cells, iPSCs, organoids, cell reprogramming, pluripotency, differentiation protocols, or 3D culture models.

mims-harvard1.3k

Microbiome Research

Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keyword, retrieve taxonomic profiles and functional annotations, classify genomes with GTDB taxonomy, and find related publications. Use for human gut microbiome, soil/ocean metagenomics, and environmental microbiology research.

mims-harvard1.3k

科学计算

Metabolomics Research

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.

效率与集成

Protocols.io Integration

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

计算化学

Biomni

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

学术

Biomedical Search

Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.

数据工程

Opentargets Database

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

调试

Metabolomics Workbench Database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

Claw Metagenomics

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

ClawBio724

Kraken2 Taxonomic Classifier

Kraken2 taxonomic classification skill for rapid metagenomic read assignment

a5c-ai575

Cytotoxicity Assay Analyzer

Nanotoxicology skill for in vitro cytotoxicity assessment and cell viability analysis

a5c-ai575

Qiime2 Microbiome Analyzer

QIIME2 microbiome analysis skill for 16S rRNA profiling and diversity analysis

a5c-ai575

Bio Metagenomics Functional Profiling

Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.

Bio Metagenomics Strain Tracking

Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.

Bio Imaging Mass Cytometry Phenotyping

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

Bio Fragment Analysis

Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.

Bio Metagenomics Abundance

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.

Bio Hi C Analysis Hic Data Io

Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.