Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence…
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matche — from…
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector bindi — from…
Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative…
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation.
Computes metabolic-engineering strain designs on genome-scale models with StrainDesign (OptKnock, RobustKnock, minimal cut sets, OptCouple) and cameo (heuristic knockout and FSEOF…
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA pe — from…
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA pe — from…
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes,…
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution — from…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision…
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs.
End-to-end genome annotation pipeline from assembled contigs to functional annotation, covering repeat masking, gene prediction, and functional assignment for both prokaryotic and…
Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it.
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait — from…
Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining — from…
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA a — from…
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with l — from…
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiment — from…
Use when you have a filtered FT-ICR MS peak list (m/z values and assigned molecular formulas per sample) and wish to reconstruct biochemical transformation networks ab initio to…
Use when a task needs the judgment of a Biochemist — determining enzyme kinetics (Km/Vmax, inhibition mechanism) from rate data, choosing a structural-biology method (X-ray…
Bioinformatics literature analysis workflow extraction and customized plan design. Triggered only when the user explicitly refers to a specific paper: the user requests extracting…
Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural…
Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard database lookups.
Specialist AI agent persona for computational biology and bioinformatics research. Expert in protein structure analysis, molecular docking, kinase biology, drug-target…
Use when a task needs the judgment of a Bioinformatics Scientist — designing a differential-expression or GWAS analysis with correct multiple-testing correction, calling and…
Advanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq.
Use when a task needs the judgment of a bioinformatics technician — running or QC-gating a next-generation sequencing pipeline, triaging a failed or borderline sequencing run,…
Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all…
Use when before executing a complex bioinformatics pipeline (such as Hi-C data processing) that depends on multiple third-party tools with explicit version constraints.
Patterns for building, maintaining, and scaling bioinformatics workflows. Covers Nextflow, Snakemake, WDL/Cromwell, container orchestration, and best practices for reproducible…
Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks.
Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks.
Use when evaluating biological relevance, methodological appropriateness, or scientific validity of bioinformatics approaches, or when choosing between analysis methods/software…
Comprehensive biology expert from molecular biology to ecology, covering cell biology, genetics, evolution, and physiology
OneScience 生信 datapipe 和 adapter skill。用于 biology/protenix/simplefold/openfold/evo2 数据读取、FASTA/MSA/PDB/mmCIF/JSON/SMILES 到模型 batch 的桥接、adapter…
Use when a task needs the judgment of a Biology Professor at a research university — writing or defending an NIH/NSF grant budget, deciding authorship order on a paper, navigating…
Design biomarker-driven enrichment strategies for clinical trials, predicting responder populations and quantifying the impact of enrichment on statistical power, probability of…
24 biomedical research skills. Trigger: medical research, clinical trials, genomics, bioinformatics. Design: domain databases, wet-lab/dry-lab methods, and ethical compliance…
Use when a task needs the judgment of a biomedical/bioengineering engineer — running a design control phase (inputs, outputs, verification, validation) for a medical device,…
AI-powered biomedical manuscript generation with docx output. Activates when user provides Chinese draft/outline and requests full English research paper.
Use when after biomolecular class labels have been assigned to features in a TWIM-MS dataset and you have raw ion mobility arrival time measurements.
Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or…
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees.
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API — from…
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API — from…
Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI.
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO.
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories.
Use when you have assembled microbial genomes (nucleotide FASTA files) and want to identify biosynthetic potential and group related BGCs for downstream linking with metabolomic…