Skill rating

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scan

Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uploading CAD parts, configuring process, material, finish, threads, tolerances and ins

Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or

Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile

Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignment, and produces schema validat

Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task benchmark

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks,

Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine learning for Earth observation. Use when processing sate

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Das

Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-ga

Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces. Use for

Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions. Use for raw 1D NMR processing, ppm-axis verifi

Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity. Supports cancer-selec

Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect s

Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measu

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment

Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene phase portraits, builds velocity graphs, estimates r

Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion captu

Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former Forge workflows

Evaluates scientific claims and evidence quality. Applies to experimental design validity, biases and confounders, statistical interpretation, evidence grading frameworks (GRADE, Cochrane Risk of Bias

Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel

Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates non-executing mutation plans. The bundled client makes bounded official-host GET requests on

Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, separates evidence from assumptions and values, and synthesi

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes traj

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, scikit-learn, NetworkX, scikit-i

Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, mat

Compiles current scholarly evidence for a scientific manuscript or research brief when the user explicitly asks to gather literature, references, background evidence, competing findings, or a manuscri

Formats and structurally validates local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed professionals. Use for source traceability

Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions. Explores favorable, reference, adverse, wild-card, contrarian, and se

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree s

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for gen

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, allele statistics, QC, a

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, and tile dataset prep

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clus

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows

Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles pop

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and

Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, infer

Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue dock

Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone is plannin

Calculates sample sizes and statistical power for study planning. Applies when someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable eff

Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwork, concept art, visual assets, logos,

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 l

Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis,

Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. Use for early-st

Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload.

Formulates evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis

Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, p