Skill UI

Integrate Benchling's Python SDK and REST v2 API to automate life-science lab data: registry entities (DNA, RNA, proteins), inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.

Comprehensive Python toolkit for molecular biology: sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access. Ideal for batch processing, custom bioinformatics pipelines, and BLAST automation.

Unified Python interface to 40+ bioinformatics web services for cross-database queries, identifier mapping, sequence analysis, and pathway discovery in a single workflow.

Google Quantum AI's open-source Python framework for designing, simulating, and running quantum circuits. Build NISQ circuits, model noise, run parameter sweeps, optimize circuits, and execute on Google, IonQ, AQT, Pasqal, or Azure Quantum backends.

COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of genome-scale metabolic models. It supports FBA, FVA, gene knockouts, flux sampling, and SBML I/O for systems biology and metabolic engineering.

Pythonic RDKit wrapper for molecular cheminformatics: parse and standardize SMILES, compute descriptors and fingerprints, cluster compounds, generate 3D conformers, and run parallel drug-discovery workflows.

A Python library for molecular machine learning, offering diverse featurizers, MoleculeNet benchmarks, graph neural networks, and pretrained models for property and ADMET prediction.

DeepTools is a comprehensive Python command-line toolkit for processing and analyzing high-throughput sequencing data. It supports quality control, normalization, sample comparison, and generating publication-quality visualizations for ChIP-seq, RNA-seq, and ATAC-seq experiments. Key features include converting BAM to bigWig, assessing sequencing depth, creating heatmaps around genomic features, and performing correlation analysis. Ideal for bioinformatics workflows requiring robust genomic data processing and visualization.

Use the esm Python SDK with ESM3 and ESMC for protein sequence generation, embeddings, function conditioning, structure prediction, inverse folding, and Forge/Biohub inference workflows.

Read, inspect, and write Flow Cytometry Standard (FCS) 2.0/3.0/3.1 files with FlowIO 1.4.0 in Python. Extract event data as NumPy arrays, inspect HEADER/TEXT/channel metadata, handle multi-dataset files, and export FCS 3.1 without compensation or gating.

Geniml validates genomic interval workflows, BED files, and model compatibility for ML/statistical analysis. Plan Region2Vec/scEmbed runs, inspect tokenizers, and assess consensus universes locally without network requests. Requires Python 3.10+ and uv for reproducible bioinformatics ML pipelines.

Guidance and local audit tooling for Python workflows using GeoPandas GeoSeries, GeoDataFrame, spatial operations, and vector data I/O, covering reproducible environments, CRS and antimeridian rules, correctness gates, and privacy safeguards.