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SkillsMP a collecté 240 skills depuis AlterLab-IEU/AlterLab-Academic-Skills. Ouvrez un skill pour examiner sa source et ses détails.
AlterLab-IEU/AlterLab-Academic-SkillsAffichage de 40 skills collectés sur 240.
Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets…
Langue du texte source : anglais
Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating…
Langue du texte source : anglais
Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra,…
Langue du texte source : anglais
Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound…
Langue du texte source : anglais
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free…
Langue du texte source : anglais
Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric…
Langue du texte source : anglais
Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a…
Langue du texte source : anglais
Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding…
Langue du texte source : anglais
Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms,…
Langue du texte source : anglais
Writes comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, pathology, lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries) — with templates, regulatory…
Langue du texte source : anglais
Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS…
Langue du texte source : anglais
Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or…
Langue du texte source : anglais
Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images,…
Langue du texte source : anglais
Generates concise (3-4 page), focused medical treatment plans in LaTeX/PDF format across all clinical specialties — general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management —…
Langue du texte source : anglais
Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of…
Langue du texte source : anglais
Composes existing AlterLab skills into multi-agent agentic workflows using current Claude Code subagent and Claude Agent SDK orchestration patterns: parallel subagent fan-out, sequential pipelines, judge panels, adversarial verification, and loop-until-clean…
Langue du texte source : anglais
Scales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file…
Langue du texte source : anglais
Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or…
Langue du texte source : anglais
Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering),…
Langue du texte source : anglais
Fast in-memory DataFrame analytics with Polars — lazy evaluation, parallel execution, and an Apache Arrow backend for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory, for 1-100GB datasets, ETL pipelines, or a faster pandas…
Langue du texte source : anglais
Bayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variational inference, LOO/WAIC model comparison, and posterior predictive checks. Use when fitting Bayesian or hierarchical models, estimating posteriors…
Langue du texte source : anglais
Multi-objective optimization with pymoo — NSGA-II, NSGA-III, MOEA/D, Pareto-front computation, constraint handling, and standard benchmarks (ZDT, DTLZ). Use when solving multi-objective or constrained optimization problems, computing Pareto-optimal…
Langue du texte source : anglais
Scalable deep-learning training with PyTorch Lightning — organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, build data pipelines and callbacks, log to W&B or TensorBoard, and run distributed training (DDP, FSDP, DeepSpeed). Use…
Langue du texte source : anglais
Classical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practice reference documentation. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality…
Langue du texte source : anglais
Survival analysis and time-to-event modeling in Python with scikit-survival. Use when working with censored survival data, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating predictions with concordance index…
Langue du texte source : anglais
Model interpretability and explainability with SHAP (SHapley Additive exPlanations) — feature importance and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use when explaining ML model predictions, computing feature importance, debugging models,…
Langue du texte source : anglais
Process-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-based events. Use when simulating systems where entities contend for shared resources over time, such as manufacturing systems, service operations,…
Langue du texte source : anglais
Guided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-formatted reporting. Use when choosing the appropriate statistical test for data, verifying test assumptions, computing power/sample size, or producing…
Langue du texte source : anglais
Statistical modeling in Python with statsmodels — OLS, GLM, mixed models, and ARIMA with detailed diagnostics, residuals, and inference. Use when fitting specific model classes for econometrics, time series, or rigorous inference with coefficient tables and…
Langue du texte source : anglais
Symbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas. Use when exact symbolic…
Langue du texte source : anglais
Zero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts and prediction intervals from CSV/DataFrame/array inputs, with a preflight system checker for RAM/GPU. Use to forecast any univariate series (sales,…
Langue du texte source : anglais
Graph Neural Networks with PyTorch Geometric (PyG) — node and graph classification, link prediction, GCN, GAT, and GraphSAGE layers, heterogeneous graphs, and molecular property prediction. Use when building or training GNNs for geometric deep learning on…
Langue du texte source : anglais
Pre-trained transformer models with Hugging Face Transformers for NLP, computer vision, audio, and multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech…
Langue du texte source : anglais
Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessing (e.g., HDBSCAN), and supervised or parametric UMAP. Use when projecting high-dimensional data to low dimensions for visualization,…
Langue du texte source : anglais
Out-of-core tabular analytics with Vaex for billion-row datasets that exceed RAM — lazy evaluation, fast aggregations, big-data visualization, and ML on a single machine. Use when working with large CSV/HDF5/Arrow/Parquet files, computing fast statistics on…
Langue du texte source : anglais
Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Dask/Xarray compatibility. Use when storing or reading large N-D scientific arrays, streaming chunked data to/from cloud object stores, or…
Langue du texte source : anglais
Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance,…
Langue du texte source : anglais
Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of…
Langue du texte source : anglais
Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or…
Langue du texte source : anglais
Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data.…
Langue du texte source : anglais