Use when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels,…
Use when targeting PLOS Biology (PLOS Biol) or deciding whether a general biology manuscript fits this open-access venue.
Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control.
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF…
Playbook for implementing/porting a new biomolecular model (protein folding, structure prediction, protein language model, diffusion structure head, MSA encoder, etc.) onto…
Run a deterministic physical-validity DRC over molecular docking poses with karyon. Use for pose validity, PoseBusters-style geometric checks,…
Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to…
Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
PCR、qPCR、测序引物和探针设计 skill。用于设计或验证 primer pair、TaqMan probe、molecular beacon、amplicon、Tm GC 二聚体发夹、SNP/repeat 避让和特异性检查交接。
Direct research projects by gathering team feedback and delegating implementation tasks. Writes publication-quality scientific text and coordinates bioinformaticians, software…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the n — from…
Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation — from…
Profile a medical-imaging dataset before any modelling decision is made — the acquisition grid, voxel spacing and orientation spread, the intensity domain, which label values are…
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq.
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
Patterns for protein structure prediction using AlphaFold2/ColabFold, structural analysis, model quality assessment, and integration with experimental data.
protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing.
Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
Performs pseudo-bulk differential gene expression analysis using DESeq2 or edgeR. Aggregates single-cell counts to sample-level pseudo-bulk data, then identifies differentially…
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
Plan, configure, validate, and document portable public-bioinformatics data acquisition. Use for GEO/GSE/GDS, SRA/ENA, TCGA/GDC, GTEx, DepMap, public expression matrices, raw…
Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text.
Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies.
Generate ~5 actionable research topic recommendations by querying PubMed E-utilities; use when a user provides a research direction/constraints and needs evidence-backed topic…
Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or…
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelin — from…
Use when running molecular quantum chemistry calculations in Python. Computes single-point energies, optimized geometries, vibrational frequencies, and population analysis using…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET…
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
Use when after feature clustering has been applied to co-eluting LC-MS features and mass-to-charge ratio matching to KEGG has produced an annotated table with adduct assignments.
Rapid topic mastery for video/content prep. Takes a topic → generates 5 research questions → parallel PubMed + web search → outputs McKinsey-style brief in 5 minutes.
Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find…
Use when when annotating .msp mass spectrometry files with chemical structure metadata and you need fast, offline molecular transformations (SMILES↔InChI, canonical SMILES…
Computes all numeric RDKit molecular descriptors from SMILES strings, filtering out NaN, constant, and infinite values to produce a clean feature matrix.
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Benchmark LLM reference recommendation capabilities by verifying every cited paper against Crossref, PubMed, arXiv, and DBLP.
Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess…
调控注释数据库 skill。用于 ENCODE、ReMap、Cistrome、JASPAR、RegulomeDB、Roadmap Epigenomics、UCSC/Genome Browser tracks、TF motif、peak set 和 enhancer/promoter 注释查询交接。
Audit a rehabilitation or physical therapy platform end-to-end -- evaluate recovery metrics tracking (ROM, strength, balance, gait), patient-reported outcomes (DASH, LEFS, NDI,…
Run arbitrary scripts on KBase compute nodes via the CDM Task Service (CTS). Use when the user needs to move compute off their notebook or local machine — e.g., running…
Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDT — from…
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular…
Use when after identifying precursor peptides from genome assemblies via BGC mining, when you need to enumerate the chemical space of PTM variants (lantibiotic, lassopeptide,…
Deterministic deep research via RivalSearchMCP. 9 tools: 5-engine web search (DuckDuckGo/Bing/Yahoo/Mojeek/Wikipedia), 9-platform social search (Reddit/HN/StackOverflow/D — from…
Deterministic deep research via RivalSearchMCP. 9 tools: 5-engine web search (DuckDuckGo/Bing/Yahoo/Mojeek/Wikipedia), 9-platform social search (Reddit/HN/StackOverflow/D — from…
Use when before constructing a DESeqDataSet from count data or tximport output, when you have raw RNA-seq samples that need to be annotated with experimental conditions, treatment…
Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin…
Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline.
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.
Use bioSkills to give an agent domain-specific bioinformatics procedures, tool choices, and guardrails for omics analysis workflows.