alterlab-domain-specific

Plugin alterlab-domain-specific from marketplace alterlab-academic-skills in AlterLab-IEU/AlterLab-Academic-Skills. Commands read from the repo's manifest — 6 days ago.

Skills (18)

• alterlab-adaptyv

  Prepares and validates Adaptyv Bio Foundry protein-testing submissions with no account — optimizes and pre-screens sequences locally (NetSolP/SoluProt heuristics, SolubleMPNN, ESM), assembles the experiment payload, and validates it offline against the Foundry's own type/method/sequence rules so it

• alterlab-aeon

  Runs time series machine learning with the aeon library — classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search via scikit-learn compatible APIs. Use when working with temporal data, sequential patterns, or time-indexed observations (univariate o

• alterlab-astropy

  Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, and world coordinate systems (WCS). Use when tasks involve coordinate transformations, unit conversions, FITS file manipulat

• alterlab-cirq

  Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware low-level circuit design, and noise characterization. Use when targeting Google Quantum AI processors or their Quantum Virtual Machine models (Willow, Sycamore-class Rainbow/Weber), I

• alterlab-digital-humanities

  Applies computational methods to humanities research — text mining and NLP (LDA/BERTopic topic modeling, sentiment, named entity recognition with spaCy/NLTK), corpus linguistics (concordance, collocation, keyness), digital archives (Dublin Core, TEI XML), GIS for history, network analysis, stylometr

• alterlab-fluidsim

  Runs computational fluid dynamics simulations with the FluidSim Python framework using pseudospectral FFT methods, with HPC support and output analysis. Use when simulating Navier-Stokes equations (2D/3D), shallow water equations, or stratified flows, or when analyzing turbulence, vortex dynamics, o

• alterlab-geniml

  Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomizat

• alterlab-geomaster

  Covers geospatial science across remote sensing, GIS, spatial analysis, and machine learning for earth observation — satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), raster and DEM operations, spectral indices (NDVI/EVI/NDWI), spatial statistics, point cloud processing, n

• alterlab-geopandas

  Reads, writes, and analyzes geospatial vector data with the GeoPandas Python library (shapefiles, GeoJSON, GeoPackage), with PostGIS support and integration with matplotlib, folium, and cartopy. Use for spatial analysis and geometric operations — buffer analysis, spatial joins and overlays between d

• alterlab-gtars

  Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/co

• alterlab-hypogenic

  Runs LLM-driven hypothesis generation and testing on labelled datasets with the HypoGeniC method — Claude generates, scores, and refines hypotheses in the conversation (keyless), or drives the HypoGeniC package with an LLM key. Combines literature insights with data-driven testing. Use when systemat

• alterlab-modal

  Write, validate, and locally test Python jobs for Modal — serverless containers, on-demand GPUs, and autoscaling — then deploy them to Modal's cloud. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that need GPU acceleration or dynamic

• alterlab-pennylane

  Trains and differentiates quantum circuits with PennyLane, a hardware-agnostic quantum machine-learning framework with automatic differentiation and PyTorch/JAX integration. Use when training quantum circuits via gradients (parameter-shift, backprop, adjoint), building hybrid quantum-classical model

• alterlab-pymatgen

  Analyzes and manipulates materials with the pymatgen toolkit — crystal structures and molecules, phase diagrams and thermodynamic stability, electronic structure (band structures, DOS), surfaces and interfaces, and Materials Project data access. Use when working with crystal structures in materials

• alterlab-qiskit

  Builds, transpiles, and runs quantum circuits with Qiskit, IBM's quantum computing framework, including Qiskit Runtime primitives (Sampler/Estimator), circuit transpilation, and error mitigation on IBM Quantum hardware. Use when targeting IBM Quantum backends, transpiling circuits, running Runtime s

• alterlab-qutip

  Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence, dissipation, quantum optics, cavity QED, or

• alterlab-remote-compute

  Dispatch long-running GPU/CPU jobs to remote compute with a provider-agnostic submit → poll → harvest pattern across SLURM/HPC (sbatch, squeue, sacct) and managed APIs (Modal, RunPod, GCP Batch / Vertex AI). Use when submitting a batch job to a cluster, polling job status, retrieving result artifact

• alterlab-social-science-methods

  Guides advanced social science research methods — discourse analysis (Fairclough CDA, Gee), conversation analysis, quantitative content analysis, Qualitative Comparative Analysis (QCA), process tracing, archival research, participatory/community-based research (PAR, CBPR), Delphi and Q methodology,

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