Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g — from…
Formulate testable scientific hypotheses — null/alternative, variables, controls, falsifiability — with explicit variables and statistical plan.
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propo — from…
Build and operate the "Scientific Hypothesis Prioritization for legal and policy workflows" capability for legal and policy workflows.
Assess paper and journal impact using OpenAlex citation counts, optional Altmetric data, and curated journal impact-factor references.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data m — from…
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and — from…
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN — from…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening an — from…
Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Produces a structured, plain-language briefing on the state of scientific research for a given topic — summarising what is established, what is contested, and what remains unknown.
Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools.
Use when targeting 《科学管理研究》(Scientific Management Research — 内蒙古自治区软科学研究会主办的科学管理/科技政策双月刊) or deciding whether a Chinese S&T-management/policy manuscript fits this venue.
High-impact scientific manuscript preparation for journals like Nature, Blood, Cell. Use when writing abstracts, introductions, methods, results, discussions, or figure legends.
Scientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA/ARRIVE), writing principles…
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing.
The scientific method as an epistemological framework for producing reliable knowledge. Covers observation, question formation, hypothesis construction, experimental testing, data…
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assis — from…
Summarises a scientific paper in plain language — covering the research question, methodology, key findings, limitations, and implications — so a journalist can accurately report…
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validi — from…
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO.
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell anal — from…
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel…
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, finger — from…
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery — from…
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomi — from…
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 preprocessin — from…
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimized for LLM processing.
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data process — from…
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library fi — from…
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python.
Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows.
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational mate — from…
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and infer — from…
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization pro — from…
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA — from…
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, loggi — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for m — from…
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality re — from…
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figu — from…
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figu — from…
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, G — from…
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensio — from…