[Technical skill catalog](../skills.md) · [Workflow examples](../examples.md)

# Scientific skill guides

Explore **177 skills** through guides written for scientists. Each guide explains
what the skill helps you do, what information it needs, what it produces, and how
to interpret the results. You will also find an example research request, a workflow
image, and links to setup and technical instructions.

Browse by area:

- [Scientific databases and data access](#scientific-databases--data-access)
- [Scientific integrations](#scientific-integrations)
- [Scientific packages](#scientific-packages)
- [Scientific thinking and analysis](#scientific-thinking--analysis)

## Scientific Databases & Data Access

- [Database Lookup](database-lookup.md)
- [DepMap](depmap.md)
- [Folklore Variant Evidence](folklore-variant-evidence.md)
- [Imaging Data Commons](imaging-data-commons.md)
- [PrimeKG](primekg.md)
- [NCATS ARAX](ncats-arax.md)
- [U.S. Treasury Fiscal Data](usfiscaldata.md)
- [Ontology Term Resolution](ontology-term-resolution.md)
- [Pathogen Variant Surveillance](pathogen-variant-surveillance.md)
- [Hugging Science](hugging-science.md)

## Scientific Integrations

### Laboratory Information Management Systems (LIMS) & R&D Platforms

- [Benchling Integration](benchling-integration.md)

### Cloud Platforms for Genomics & Biomedical Data

- [DNAnexus Integration](dnanexus-integration.md)

### Laboratory Automation

- [Opentrons Integration](opentrons-integration.md)
- [Ginkgo Cloud Lab](ginkgo-cloud-lab.md)

### Electronic Lab Notebooks (ELN)

- [LabArchives Integration](labarchive-integration.md)
- [Open Notebook](open-notebook.md)

### Workflow Platforms & Cloud Execution

- [LatchBio Integration](latchbio-integration.md)
- [Nextflow](nextflow.md)
- [pacsomatic](pacsomatic.md)

### Microscopy & Bio-image Data

- [OMERO Integration](omero-integration.md)

### Protocol Management & Sharing

- [Protocols.io Integration](protocolsio-integration.md)

## Scientific Packages

### Bioinformatics & Genomics

- [Primer Design](primer-design.md)
- [MAGeCK](mageck.md)
- [QIIME 2 Amplicon](qiime2-amplicon.md)
- [AlphaGenome](alphagenome.md)
- [AnnData](anndata.md)
- [Arboreto](arboreto.md)
- [Biopython](biopython.md)
- [BioServices](bioservices.md)
- [Bulk RNA-seq](bulk-rnaseq.md)
- [Cellxgene Census](cellxgene-census.md)
- [deepTools](deeptools.md)
- [FlowIO](flowio.md)
- [FlowKit](flowkit.md)
- [gget](gget.md)
- [Genomic Coordinates](genomic-coordinates.md)
- [Genomic Intelligence](genomic-intelligence.md)
- [geniml](geniml.md)
- [Gtars](gtars.md)
- [OneKGPd](onekgpd.md)
- [Waypoint Bio](waypoint-bio.md)
- [Polars-Bio](polars-bio.md)
- [pysam](pysam.md)
- [PyDESeq2](pydeseq2.md)
- [Pathway Enrichment](pathway-enrichment.md)
- [Scanpy](scanpy.md)
- [scVelo](scvelo.md)
- [scvi-tools](scvi-tools.md)
- [scikit-bio](scikit-bio.md)
- [TileDB-VCF](tiledbvcf.md)
- [Zarr](zarr-python.md)

### Data Management & Infrastructure

- [DataLad](datalad.md)
- [LaminDB](lamindb.md)
- [Modal](modal.md)
- [Optimize for GPU](optimize-for-gpu.md)

### Cheminformatics & Drug Discovery

- [nmrglue](nmrglue.md)
- [Datamol](datamol.md)
- [DeepChem](deepchem.md)
- [DiffDock](diffdock.md)
- [MedChem](medchem.md)
- [Molfeat](molfeat.md)
- [PyTDC](pytdc.md)
- [RDKit](rdkit.md)
- [Rowan](rowan.md)
- [TorchDrug](torchdrug.md)

### Pharmacology & Pharmacometrics

- [PK/PD Modelling](pkpd-modeling.md)

### Preclinical Research & Animal Welfare

- [RELSA Severity Assessment](relsa-severity-assessment.md)

### Proteomics & Mass Spectrometry

- [matchms](matchms.md)
- [pyOpenMS](pyopenms.md)

### Microscopy, Medical Imaging & Digital Pathology

- [CellProfiler](cellprofiler.md)
- [DeepSpot-M](deepspot-m.md)
- [histolab](histolab.md)
- [PathML](pathml.md)
- [pydicom](pydicom.md)

### Healthcare AI & Clinical Machine Learning

- [PyHealth](pyhealth.md)

### Clinical Documentation & Decision Support

- [Clinical Decision Support](clinical-decision-support.md)
- [Clinical Reports](clinical-reports.md)
- [Treatment Plans](treatment-plans.md)

### Neuroscience & Electrophysiology

- [NWB Conversion](nwb-conversion.md)
- [BIDS](bids.md)
- [NeuroKit2](neurokit2.md)
- [Neuropixels-Analysis](neuropixels-analysis.md)

### Protein Engineering & Design

- [RELION](relion.md)
- [Adaptyv](adaptyv.md)
- [ESM (Evolutionary Scale Modeling)](esm.md)
- [Glycoengineering](glycoengineering.md)
- [Molecular Dynamics](molecular-dynamics.md)
- [Tamarind](tamarind.md)

### Systems Biology & Kinetic Modeling

- [13C Metabolic Flux](13c-metabolic-flux.md)
- [Tellurium](tellurium.md)

### Machine Learning & Deep Learning

- [aeon](aeon.md)
- [Cirq](cirq.md)
- [PufferLib](pufferlib.md)
- [PyMC](pymc.md)
- [PyMOO](pymoo.md)
- [PyTorch Lightning](pytorch-lightning.md)
- [PennyLane](pennylane.md)
- [Qiskit](qiskit.md)
- [QuTiP](qutip.md)
- [scikit-learn](scikit-learn.md)
- [scikit-survival](scikit-survival.md)
- [SHAP](shap.md)
- [Stable Baselines3](stable-baselines3.md)
- [statsmodels](statsmodels.md)
- [TimesFM Forecasting](timesfm-forecasting.md)
- [Torch Geometric](torch-geometric.md)
- [Transformers](transformers.md)
- [UMAP-learn](umap-learn.md)

### Chemical Oceanography

- [Marine Carbonate Chemistry](marine-carbonate-chemistry.md)

### Materials Science & Chemistry

- [pycalphad](pycalphad.md)
- [Astropy](astropy.md)
- [COBRApy](cobrapy.md)
- [Pymatgen](pymatgen.md)

### Engineering & Simulation

- [Cantera](cantera.md)
- [PyBaMM](pybamm.md)
- [Lab Hardware CAD](lab-hardware-cad.md)
- [Fictiv](fictiv.md)
- [MATLAB/Octave](matlab.md)
- [FluidSim](fluidsim.md)
- [OpenPIV](openpiv.md)
- [SimPy](simpy.md)
- [SymPy](sympy.md)

### Data Analysis & Visualization

- [Dask](dask.md)
- [GeoMaster](geomaster.md)
- [GeoPandas](geopandas.md)
- [Matplotlib](matplotlib.md)
- [NetworkX](networkx.md)
- [Polars](polars.md)
- [Seaborn](seaborn.md)
- [Uncertainty & Units](uncertainty-and-units.md)
- [Vaex](vaex.md)

### Phylogenetics & Evolutionary Biology

- [ETE Toolkit](etetoolkit.md)
- [Phylogenetics](phylogenetics.md)

### Agent Frameworks

- [Pi Agent](pi-agent.md)

### Autonomous Research & Optimization Frameworks

- [Arbor](arbor.md)

### Scientific Communication & Publishing

- [BGPT Paper Search](bgpt-paper-search.md)
- [pyzotero](pyzotero.md)
- [Citation Management](citation-management.md)
- [Generate Image](generate-image.md)
- [Infographics](infographics.md)
- [LaTeX Posters](latex-posters.md)
- [Market Research Reports](market-research-reports.md)
- [PPTX Posters](pptx-posters.md)
- [Scientific Schematics](scientific-schematics.md)
- [Scientific Slides](scientific-slides.md)
- [Venue Templates](venue-templates.md)

### Document Processing & Conversion

- [MarkItDown](markitdown.md)
- [LiteParse](liteparse.md)
- [Markdown & Mermaid Writing](markdown-mermaid-writing.md)

### Laboratory Automation & Equipment Control

- [PyLabRobot](pylabrobot.md)

### Tool Discovery & Computational Resources

- [Autoskill](autoskill.md)
- [Get Available Resources](get-available-resources.md)

### Research Methodology & Proposal Writing

- [Paperclip](paperclip.md)
- [Paperzilla](paperzilla.md)
- [Paper Lookup](paper-lookup.md)
- [Research Grants](research-grants.md)
- [Research Lookup](research-lookup.md)
- [Scholar Evaluation](scholar-evaluation.md)

### Regulatory & Standards Evidence Preparation

- [ISO Standards Readiness](iso-standards-readiness.md)
- [Analytical Method Validation](analytical-method-validation.md)

## Scientific Thinking & Analysis


### Analysis & Methodology

- [Experimental Design](experimental-design.md)
- [Exploratory Data Analysis](exploratory-data-analysis.md)
- [Hypothesis Generation](hypothesis-generation.md)
- [HypoGeniC](hypogenic.md)
- [Literature Review](literature-review.md)
- [Peer Review](peer-review.md)
- [Scientific Brainstorming](scientific-brainstorming.md)
- [Scientific Critical Thinking](scientific-critical-thinking.md)
- [Scientific Visualization](scientific-visualization.md)
- [Scientific Writing](scientific-writing.md)
- [Statistical Analysis](statistical-analysis.md)
- [Statistical Power](statistical-power.md)

### Decision & Scenario Analysis

- [Consciousness Council](consciousness-council.md)
- [DHDNA Profiler](dhdna-profiler.md)
- [What-If Oracle](what-if-oracle.md)

### Web Search & Information Retrieval

- [Exa Search](exa-search.md)
- [Parallel Web](parallel-web.md)