Claude Skills by AlterLab-IEU

Part of the AlterLab Academic Skills suite for faculty and researchers. Academic paper writing skill with 12-agent pipeline. v2.4: LaTeX output formatting hardening — mandatory apa7 class, text justification fix, table column width formula, bilingual abstract centering, standardized font stack, PDF must compile from LaTeX. Supports IMRaD, literature review, theoretical, case study, policy brief, and conference paper structures. APA 7.0 (default), Chicago, MLA, IEEE, Vancouver citation formats...

Part of the AlterLab Academic Skills suite for faculty and researchers. Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates alterlab-deep-research, alterlab-paper-writer, and alterlab-paper-reviewer into a seamless 9-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates. Triggers on: academic pipeline, rese...

Part of the AlterLab Academic Skills suite for faculty and researchers. Comprehensive course and teaching design assistant. Supports backward design (Wiggins & McTighe), constructive alignment (Biggs), Bloom's taxonomy alignment, rubric generation, assessment design (formative/summative), syllabus drafting, lesson planning, inclusive pedagogy, and online/hybrid course architecture. Triggers on: course design, syllabus, learning outcomes, rubric, assessment design, lesson plan, backward design...

Part of the AlterLab Academic Skills suite for faculty and researchers. Comprehensive thesis and dissertation supervision assistant. Supports dissertation structure guidance (proposal through defense), chapter-by-chapter writing support (introduction, literature review, methodology, results, discussion), supervision strategies, committee management, defense preparation, timeline planning, feedback integration, formatting requirements (APA 7, Chicago, university styles), viva voce preparation,...

Part of the AlterLab Academic Skills suite. Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

Part of the AlterLab Academic Skills suite. 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,...

Part of the AlterLab Academic Skills suite. 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...

Part of the AlterLab Academic Skills suite. Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.

Part of the AlterLab Academic Skills suite. High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.

Part of the AlterLab Academic Skills suite. Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Part of the AlterLab Academic Skills suite. Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Part of the AlterLab Academic Skills suite. Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.

Part of the AlterLab Academic Skills suite. 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.

Part of the AlterLab Academic Skills suite. Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival...

Part of the AlterLab Academic Skills suite. 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, P...

Part of the AlterLab Academic Skills suite. 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.

Part of the AlterLab Academic Skills suite. Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.

Part of the AlterLab Academic Skills suite. 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.

Part of the AlterLab Academic Skills suite. Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.

Part of the AlterLab Academic Skills suite. Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill whe...

Part of the AlterLab Academic Skills suite. Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.

Part of the AlterLab Academic Skills suite. Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

Part of the AlterLab Academic Skills suite. This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.

Part of the AlterLab Academic Skills suite. UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

Part of the AlterLab Academic Skills suite. Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that ...

Part of the AlterLab Academic Skills suite. Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.

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. Part of the AlterLab Academic Skills suite.

Search and retrieve preprints from arXiv via the Atom API. Use this skill when searching for papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics by keywords, authors, arXiv IDs, date ranges, or categories. Part of the AlterLab Academic Skills suite.

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies. Part of the AlterLab Academic Skills suite.

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. Part of the AlterLab Academic Skills suite.

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. Part of the AlterLab Academic Skills suite.

Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling. Part of the AlterLab Academic Skills suite.

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry. Part of the AlterLab Academic Skills suite.

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching. Part of the AlterLab Academic Skills suite.

Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions. Part of the AlterLab Academic Skills suite.

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine. Part of the AlterLab Academic Skills suite.

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication. Part of the AlterLab Academic Skills suite.

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities. Part of the AlterLab Academic ...

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank. Part of the AlterLab ...

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats. Part of the AlterLab Academic Skills suite.

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research. Part of the AlterLab Academic Skills suite.

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite.

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis. Part of the AlterLab Academic Skills suite.

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis. Part of the AlterLab Academic Skills suite.

Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting non-coding variant effects. Part of the AlterLab Academic Skills suite.

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores. Part of the AlterLab Academic Skills suite.

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification. Part of the AlterLab Academic Skills suite.

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses. Part of the AlterLab Academic Skills suite.