openscience

Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.

Provides guidance for LLM post-training with RL using slime, a Megatron+SGLang framework. Use when training GLM models, implementing custom data generation workflows, or needing tight Megatron-LM integration for RL scaling.

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

Pareto-aware molecular design balancing multiple ADMET properties simultaneously. Based on MultiMol (Yu 2025) and MOLLM (Ran 2025).

MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.

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.

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.

Serverless inference, fine-tuning, embeddings, image generation, and batch processing on 200+ open-source models via an OpenAI-compatible API. Use when you need fast, cost-effective access to open-source LLMs without managing infrastructure.

Provides guidance for fine-tuning LLMs using the Tinker cloud training API from Thinking Machines Lab. Use when running supervised fine-tuning, reinforcement learning (GRPO/PPO), or LoRA training on cloud GPUs via Tinker's managed infrastructure instead of local compute.

Calculates training costs for Tinker fine-tuning jobs. Use when estimating costs for Tinker LLM training, counting tokens in datasets, or comparing Tinker model training prices. Tokenizes datasets using the correct model tokenizer and provides accurate cost estimates.

On-demand GPU clusters and training jobs with git-style interface. Use when you need multi-node GPU clusters (B200, H200, H100), persistent NFS storage, or batch training jobs with the TensorPool CLI.

Multi-cloud orchestration for ML workloads with automatic cost optimization. Use when you need to run training or batch jobs across multiple clouds, leverage spot instances with auto-recovery, or optimize GPU costs across providers.

Run governed Modal sandbox jobs through OpenScience's compute_job JobBroker. Use for one-off CPU/GPU commands, explicit file uploads and captures, dependency provisioning, resource selection, approval, dispatch, and results. This skill does not install or invoke the Modal Python SDK or CLI.

GPU-accelerated scientific research on Modal — simulations, numerical methods, Monte Carlo, molecular dynamics, large-scale data processing. NOT for ML training or inference (use gpu-training or modal skills instead).

Disconnect-safe patterns for long-running ML training on Modal serverless GPU. Covers the deploy+spawn pattern (survives laptop shutdown/SSH disconnect), checkpoint-resume for preemption recovery, PyTorch/CUDA version pinning, volume reload/commit discipline, and batch parameter sweeps. Use for any training job >30 min where losing progress is expensive. Complements the broader `modal-serverless-gpu` skill.

Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.