Skill rating

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. Use when autho

Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, qu

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX e

Drafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistenc

Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance. Use for lit

Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use this skill for sc

Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, T

Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or agg

Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHI

Organizes research with the self-hosted Open Notebook alternative to NotebookLM. Supports source ingestion (PDFs, web pages, audio, video, and Office documents), cited document chat, text and vector s

Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing pri

Supports machine learning in Python with scikit-learn. Applies when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model e

Queries the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treas

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifi

Creates and customizes scientific plots with Matplotlib. Used for fine-grained control over plot elements, novel plot types, and scientific workflows. Export to PNG/PDF/SVG for publication. For quick

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` package, its task configs, hypothesis banks, or HypoB

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, an

Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and m

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query la

Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table

Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ benchmarks

Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexin

Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producin

Supports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast for

Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testi

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or t

Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks o

Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR, PET) and pathology AI datasets, metadata SQL, visual

Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Use whenever a user wants to comp

Provides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking peop

Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census sum

Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and re

Supports PyTorch Geometric (PyG) graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use w

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 working with AutoModel,

Fits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX. Supports coefficient inference, marginal effects, model comparison and time series foreca

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 I/O, format migration,

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 FASTQ data. Use for coor

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-b

Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity. Use when code impor

Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum algorithms, quantum machine learning, simulator valida

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and kno

Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection,

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3 or local API. Applies

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic

Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for syste

Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and containers-run. Use when cloning or fetching data

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3