Scientific Agent Skills for Codex

Skills (177)

• 13c-metabolic-flux — 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 diagnostics. Use for 13C-MFA, carbon tracing, mass…
• adaptyv — Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies to Adaptyv Foundry, its target catalog, binding screening and…
• aeon — This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed…
• alphagenome — Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing…
• analytical-method-validation — Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE…
• anndata — 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 models use scvi-tools; for population-scale queries use…
• arbor — Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization. Uses persistent hypotheses, isolated experiments, evidence propagation and…
• arboreto — 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 Dask execution, sparse expression inputs, and network…
• astropy — 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 or debugging astronomical data analysis code with Astropy.
• autoskill — Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts or composition recipes for review. Requires a reachable Screenpipe HTTP API, normally on localhost:3030…
• benchling-integration — 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 the v2 API.
• bgpt-paper-search — 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 literature reviews, evidence synthesis, and finding…
• bids — 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 capture, EMG, MR spectroscopy, behavioral), querying BIDS…
• biopython — Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis…
• bioservices — Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and integrated biological data workflows with…
• bulk-rnaseq — Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2…
• cantera — Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition…
• cellprofiler — Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence…
• 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 expression slices, Census summary counts, source H5AD URIs/downloads, embeddings…
• cirq — Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use…
• citation-management — Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find…
• clinical-decision-support — Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Supports aggregate or synthetic research documentation and traceability, excluding patient care…
• clinical-reports — 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 aggregate inputs and verified source-fact manifests; every…
• cobrapy — 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 systems biology and metabolic engineering.
• consciousness-council — Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, separates evidence from assumptions and values, and synthesizes a conditional recommendation. Use when the user…
• dask
• database-lookup
• datalad
• datamol
• deepchem
• deepspot-m
• deeptools
• depmap
• dhdna-profiler
• diffdock
• dnanexus-integration
• esm
• etetoolkit
• exa-search
• experimental-design
• exploratory-data-analysis
• fictiv
• flowio
• flowkit
• fluidsim
• folklore-variant-evidence
• generate-image
• geniml
• genomic-coordinates
• genomic-intelligence
• geomaster
• geopandas
• get-available-resources
• gget
• ginkgo-cloud-lab
• glycoengineering
• gtars
• histolab
• hugging-science
• hypogenic
• hypothesis-generation
• imaging-data-commons
• infographics
• iso-standards-readiness
• lab-hardware-cad
• labarchive-integration
• lamindb
• latchbio-integration
• latex-posters
• liteparse
• literature-review
• mageck
• marine-carbonate-chemistry
• markdown-mermaid-writing
• market-research-reports
• markitdown
• matchms
• matlab
• matplotlib
• medchem
• modal
• molecular-dynamics
• molfeat
• ncats-arax
• networkx
• neurokit2
• neuropixels-analysis
• nextflow
• nmrglue
• nwb-conversion
• omero-integration
• onekgpd
• ontology-term-resolution
• open-notebook
• openpiv
• opentrons-integration
• optimize-for-gpu
• pacsomatic
• paper-lookup
• paperclip
• paperzilla
• parallel-web
• pathml
• pathogen-variant-surveillance
• pathway-enrichment
• peer-review
• pennylane
• phylogenetics
• pi-agent
• pkpd-modeling
• polars-bio
• polars
• pptx-posters
• primekg
• primer-design
• protocolsio-integration
• pufferlib
• pybamm
• pycalphad
• pydeseq2
• pydicom
• pyhealth
• pylabrobot
• pymatgen
• pymc
• pymoo
• pyopenms
• pysam
• pytdc
• pytorch-lightning
• pyzotero
• qiime2-amplicon
• qiskit
• qutip
• rdkit
• relion
• relsa-severity-assessment
• research-grants
• research-lookup
• rowan
• scanpy
• scholar-evaluation
• scientific-brainstorming
• scientific-critical-thinking
• scientific-schematics
• scientific-slides
• scientific-visualization
• scientific-writing
• scikit-bio
• scikit-learn
• scikit-survival
• scvelo
• scvi-tools
• seaborn
• shap
• simpy
• stable-baselines3
• statistical-analysis
• statistical-power
• statsmodels
• sympy
• tamarind
• tellurium
• tiledbvcf
• timesfm-forecasting
• torch-geometric
• torchdrug
• transformers
• treatment-plans
• umap-learn
• uncertainty-and-units
• usfiscaldata
• vaex
• venue-templates
• waypoint-bio
• what-if-oracle
• zarr-python