openscience

Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.

ADMET property prediction for drug candidates. Full pharmacokinetic panel (Caco-2, PPB, clearance, CYP), toxicity (hERG, AMES, DILI), drug-likeness (Lipinski, QED), using RDKit descriptors and TDC models.

Interpretable ADMET analysis with mechanistic reasoning. Maps liabilities to structural causes and biological pathways. Based on CoTox (Park 2025) and DrugR (Liu 2026).

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.

PyTorch library for audio generation including text-to-music (MusicGen) and text-to-sound (AudioGen). Use when you need to generate music from text descriptions, create sound effects, or perform melody-conditioned music generation.

Autonomous AI agent platform for building and deploying continuous agents. Use when creating visual workflow agents, deploying persistent autonomous agents, or building complex multi-step AI automation systems.

Training patterns for autoregressive neural PDE solvers (FNO, DeepONet, CNO). Covers rollout training, noise injection for stability, multi-component loss functions (H1, frequency-sensitive, boundary-aware), per-channel normalization for coupled multi-variable systems, and the PDEBench nRMSE metric. Use when training any neural operator that predicts time-dependent PDE solutions.

Activation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference than GPTQ with better accuracy preservation, or for instruction-tuned and multimodal models. MLSys 2024 Best Paper Award winner.

Expert guidance for fine-tuning LLMs with Axolotl - YAML configs, 100+ models, LoRA/QLoRA, DPO/KTO/ORPO/GRPO, multimodal support

Bayesian parameter estimation with MCMC (emcee) and probabilistic programming (PyMC). Posterior distributions, corner plots, model evidence, convergence diagnostics. Use when you need full posterior distributions, not just point estimates.

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Hybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand complexes.

Microscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

Vision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-the-art zero-shot performance.

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

Use this when you are working on file operations like reading, writing, scanning, or deleting files. It summarizes the preferred file APIs and patterns used in this repo. It also notes when to use filesystem helpers for directories.

Computational cancer genomics workflows. Somatic mutation detection and annotation, structural variation characterization, copy number analysis, tumor purity/ploidy estimation, NMF metagene extraction, and DNA damage response network analysis. For cancer mutation databases use cosmic-database; for variant clinical significance use clinvar-database.

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.