Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / L — from…
Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs.
End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations.
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…
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statis — 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 metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mappi — 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…
End-to-end time-course analysis from expression matrix to temporal patterns and enrichment. Covers temporal DE, Mfuzz soft clustering, optional rhythm detection, GAM trajectory…
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…
Use when after constructing a SummarizedExperiment object from raw metabolomics data via buildExperiment, or after batch correction and ratio computation steps, inspect rowData,…
Use when after successfully reading and validating a tab-delimited metabolomics file (containing mandatory columns: aliquot, compound, area, type, injection_time, batch) using…
Generate a structured biographical research template for a named person — listing the key facts to verify, the categories of information to gather, and the questions to ask during…
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…
Use when a task needs the judgment of a Biologist — designing a study and identifying its true experimental unit before data collection starts, running a power analysis to size a…
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…
Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, protein-ligand/DNA/RNA complexes, SMILES or CCD ligands,…
Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets.
Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead optimization, SAFE notation, QED or…
Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint. Use a local checkpoint or optionally download a pinned Hugging Face model bundle using HF_TOKEN if…
Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
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 a task needs the judgment of a Biostatistician — designing a clinical trial's sample size and analysis plan, choosing a survival-analysis or censoring-aware method,…
Biostatistics methods for clinical trials, epidemiology, and life sciences research. Reference when designing clinical trials, performing survival analysis, evaluating diagnostic…
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…
Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to…
Use when you have one or more small-molecule chemical structures (as SMILES, MOL, or SDF) and need to systematically explore their fate across mammalian biotransformation, human…
Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated…