Research · Skill set · 16 skills
Scientific Python
Correct, current usage of scientific Python libraries: single-cell atlases, cheminformatics, molecular dynamics, graph learning, quantum circuits, large arrays and GPU speed-ups.
Open in PhởSkills in this set
- CZ CELLxGENE Census
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene…
- Cirq - Quantum Computing with Python
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for…
- Datamol Cheminformatics Skill
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors…
- Histolab
Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile extraction, H&E stain normalization…
- LaminDB
Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections…
- Molecular Dynamics
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production…
- Molfeat — Small-molecule featurization
Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors…
- GPU Optimization for Python with NVIDIA
GPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, pandas…
- PennyLane
Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum algorithms, quantum machine…
- polars-bio
Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and…
- TileDB-VCF
Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results…
- PyTorch Geometric (PyG)
Supports PyTorch Geometric (PyG) graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and…
- TorchDrug
Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein…
- Transformers
Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks. Applies when…
- Vaex
Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion. Use for larger-than-RAM HDF5…
- Zarr Python
Stores and queries chunked N-D scientific arrays with Zarr-Python 3, including codecs, sharding, S3/GCS storage, and NumPy/Dask/Xarray integration. Use for array layout, bounded…
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Frequently asked questions
What is in the Scientific Python skill set?
16 skills: CZ CELLxGENE Census, Cirq - Quantum Computing with Python, Datamol Cheminformatics Skill, Histolab, LaminDB, Molecular Dynamics, and 10 more.
Is the Scientific Python skill set free?
Yes. It is published by K-Dense under the MIT licence and works with a free Phở account.
How do I add Scientific Python to Phở?
Press Open in Phở and add the set once. From then on Phở picks the right skill from it whenever a request matches.
Copied unchanged from K-Dense-AI/claude-scientific-skills at commit a25cf9e and credited to K-Dense, who is not affiliated with Phở. The full instructions and licence text ship with the skill inside Phở.