Research Tools
CATO integrates 200+ research tools spanning biomedical databases, genomics, pharmacology, molecular computation, and more. All tools are accessed through natural language in CATO Chat — simply describe what you need and CATO selects the appropriate tool automatically.
Most tools are available on all plans. Features marked with a tier badge require that plan or above.
Data Analysis & Visualization
Upload datasets and perform statistical analysis, machine learning, and visualization through natural language.
- •Upload and analyze 15+ file formats (CSV, Excel, Parquet, SAS, Stata, HDF5, FCS, and more)
- •Statistical tests: t-tests, ANOVA, chi-square, Mann-Whitney, regression, logistic regression, mixed models
- •Survival analysis: Kaplan-Meier curves, Cox proportional hazards, log-rank tests
- •Machine learning: classification, clustering, dimensionality reduction, feature importance (scikit-learn, XGBoost, LightGBM)
- •Bayesian modeling: PyMC, ArviZ, Bambi
- •Causal inference: propensity score matching, inverse probability weighting (DoWhy, MatchIt)
- •30+ publication-ready visualizations: forest plots, volcano plots, heatmaps, survival curves, violin plots, network graphs, and more
- •Python and R code execution in secure sandboxed environments
- •Export results as CSV, Excel, DOCX reports, or PowerPoint presentations
No-Code Figure Editor
Base+Visually customize any AI-generated chart without writing code.
- •Select, move, and resize chart elements (bars, labels, legends, annotations)
- •Edit text inline: titles, axis labels, tick marks, annotations
- •Change fill colors, stroke, and opacity with a colorblind-friendly palette
- •Add significance brackets for p-value annotations
- •Group and ungroup elements, reorder layers
- •Undo/redo with 50-step history and versioned snapshots
- •Export as high-resolution PNG (300 DPI) or SVG
- •Edited figures automatically used in follow-up reports and analyses
Biomedical Database Access
Query 37+ biomedical databases directly from chat.
- •Protein databases: UniProt, PDB, AlphaFold
- •Genomic databases: Ensembl, GnomAD, ClinVar, dbSNP
- •Drug and compound databases: ChEMBL, DrugBank, PubChem
- •Expression databases: GEO, ArrayExpress
- •Pathway databases: KEGG, Reactome, WikiPathways
- •Disease databases: OMIM, DisGeNET, OrphaNet
- •Clinical trial registries and regulatory databases
Genomics & Transcriptomics
Analyze sequencing data, gene expression, and epigenomic profiles.
- •Single-cell RNA-seq analysis and cell type annotation (scanpy, Seurat)
- •Single-cell epigenomics: scATAC-seq, scBS-seq analysis (EpiScanpy)
- •Differential gene expression (DESeq2, edgeR, limma, PyDESeq2)
- •ChIP-seq QC, visualization, and BAM processing (deepTools, pysam)
- •Gene set enrichment and pathway analysis (clusterProfiler, GSEApy)
- •Transcription factor and pathway activity inference (decoupler)
- •Variant annotation and interpretation (cyvcf2)
- •Microbiome analysis (phyloseq, DADA2)
- •Epigenomics: methylation analysis, ChIP-seq peak calling (methylKit, DiffBind)
Pharmacology & Drug Discovery
Screen compounds, predict properties, and model pharmacokinetics.
- •Molecular docking and binding affinity prediction
- •ADMET property prediction (absorption, distribution, metabolism, excretion, toxicity)
- •Drug interaction screening and safety profiling
- •Pharmacokinetic modeling and simulation
- •Drug-likeness screening (Lipinski rule-of-five, Veber rules)
- •Structure-activity relationship analysis
Molecular Biology & Sequence Analysis
Align sequences, design primers, and analyze molecular structures.
- •BLAST sequence alignment (blastn, blastp, blastx, tblastn)
- •Multiple sequence alignment and phylogenetic analysis
- •CRISPR guide RNA design and off-target prediction
- •Primer design and restriction site mapping
- •Codon optimization for expression systems
- •Protein structure prediction and analysis
Healthcare & Clinical Coding
Look up medical codes, provider information, and drug names.
- •NPI registry lookup for healthcare providers
- •ICD-10 diagnosis and procedure code search
- •HCPCS Level II code lookup for medical supplies and services
- •RxNorm drug name normalization and mapping
- •Clinical trial protocol analysis
Literature Intelligence
Search, extract evidence, and generate reviews from scientific literature.
- •Search PubMed and BioRxiv from chat with automatic citations
- •Fetch paper abstracts and full-text (open access via PMC)
- •Batch paper retrieval for efficient multi-paper analysis
- •AI-powered evidence extraction with PICO framework
- •Systematic review generation with inline citations
- •Citation export in BibTeX, RIS, and CSV formats
7-Source Parallel Literature Search
Pay-as-you-go+Search across PubMed, BioRxiv, arXiv, OpenAlex, Semantic Scholar, ClinicalTrials.gov, and Patents simultaneously with AI query optimization and relevance reranking.
- •AI-optimized query planning across all 7 sources
- •Automatic deduplication and relevance scoring
- •Semantic reranking via Semantic Scholar embeddings
- •Study type filtering (RCT, meta-analysis, review, cohort, case-control)
- •Citation network analysis with PageRank
- •Watch queries with automatic refresh for ongoing monitoring
Molecular Computation
Base+Predict structures, compute properties, and visualize molecules.
- •RNA and DNA secondary structure prediction with minimum free energy calculation (ViennaRNA)
- •Molecular property computation from SMILES (LogP, TPSA, molecular weight, H-bond donors/acceptors)
- •Drug-likeness screening with Lipinski rule-of-five analysis
- •Interactive 3D molecular visualization (PDB, SDF, MOL2, CIF, XYZ formats)
- •Bioinformatics CLI tools: BLAST+, Samtools (sort, index, flagstat), Bedtools (intersect, merge, coverage)
- •Reproducibility export as Jupyter notebooks with full environment specs
Polymer & Nanoparticle Design
Base+Access polymer science resources, design guides, and reference data.
- •Search 170+ polymer design resources and reference data
- •DLVO theory and colloidal stability analysis
- •PEG brush theory and surface modification guides
- •DPD self-assembly simulation resources
- •Polyplex and lipid nanoparticle formulation references
- •RAFT monomer libraries and nucleic acid property tables
Additional Research Domains
Specialized tools across immunology, cancer biology, microbiology, and more.
- •Immunology: flow cytometry gating, immunophenotyping, antibody characterization
- •Cancer biology: tumor mutation analysis, somatic variant calling, DNA damage response
- •Microbiology: bacterial growth modeling, biofilm quantification, genome annotation
- •Cell biology: migration tracking, morphology analysis, cell cycle quantification
- •Biochemistry: enzyme kinetics, CD spectroscopy, thermodynamic calculations
- •Systems biology: metabolic modeling, flux balance analysis, gene regulatory networks
- •Bioengineering: codon optimization, metabolic engineering, Golden Gate assembly design
- •Bioimaging: cell segmentation, microscopy analysis, colocalization metrics
- •Causal inference: treatment effects, propensity scoring, uplift modeling (DoWhy, CausalML, CausalLib)
- •Time series: auto-ARIMA forecasting, seasonal decomposition (statsmodels, pmdarima)
- •Proteomics pipelines: MaxQuant output analysis, QC, and normalization (MSPypeline)
Molecular Dynamics Simulation
Enterprise+Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis.
- •Run MD simulations with AMBER14 and CHARMM36 forcefields
- •Implicit, explicit, and vacuum solvent models
- •Trajectory analysis: RMSD, RMSF, radius of gyration, hydrogen bonds, contacts
- •Background job submission for long-running computations
- •Automated energy minimization and equilibration
How to use: Open any project, go to the Chat tab, and describe your research task in plain English. CATO automatically identifies which tools to use based on your request. You can also ask "What tools can help me with [topic]?" to discover relevant capabilities.