Recipe landscape

This cookbook pairs concrete life-science problems with recommended assemblies of the components catalogued elsewhere on this site. Each recipe is the answer to “I have this problem — what’s the simplest viable assembly that has evidence behind it?” The recipes are deliberately biased toward the lowest rung of the simplicity ladder that actually solves the problem.

Coverage by problem class

Literature triage

  • Triage a stack of new preprints in your field — One skill or MCP · Reported · Fully open · Laptop. Use the bio-research plugin in Claude Code to pull last-week bioRxiv and PubMed hits, rank by relevance, and produce a one-paragraph readout per paper.

Hypothesis generation

  • Enumerate analogs around a lead compound for SAR expansion — One skill or MCP · Proposed · Fully open · Laptop. Use the Datamol skill in Claude Code to enumerate standardized, drug-like analogs around a lead SMILES — tautomers, stereoisomers, and fragment-substituted variants — as a ranked SAR-expansion table.

  • Find selective genetic dependencies for a cancer context with DepMap — One skill or MCP · Reported · Fully open · Laptop. Use the DepMap skill to mine genome-wide CRISPR screens for genes selectively essential in a cancer lineage or genotype, corrected for copy-number bias.

  • Generate falsification-tested drug-repurposing hypotheses across corpora — Autonomous system · Proposed · Fully open · Laptop. Use the Hypothesis Crucible plugin to mine typed knowledge fragments from literature, Open Targets/ChEMBL/ClinicalTrials, and raw experimental data (GEO), bridge them Swanson-style into candidate drug-disease connections, then aggressively reject the non-novel, ungrounded, contradicted, and implausible — surfacing only survivors with a fragment-cited mechanism and a falsifiable experiment.

  • Predict a protein–protein complex to map the binding interface — One skill or MCP · Reported · Subscription required · Laptop. Use the Boltz plugin to co-fold two proteins into a complex and read off the candidate binding interface — sampling widely and ranking by consensus rather than trusting the top-1 confidence.

Experimental design

  • Annotate and verify an engineered plasmid construct — One skill or MCP · Reported · Fully open · Laptop. Use the pLannotate skill to auto-annotate an engineered plasmid — promoters, resistance markers, origins, tags — and verify a construct’s sequence before you clone or order it.

  • Design CRISPR sgRNAs for a gene knockout — One skill or MCP · Reported · Fully open · Laptop. Use the sgRNA Design skill to pick CRISPR-Cas9 knockout guides for a gene — preferring validated/CRISPick guides, falling back to Rule Set 2 + CFD de novo rules.

  • Design a Bayesian trial that borrows external control data — One skill or MCP · Proposed · Fully open · Laptop. Use the Bayesian Trials skill and RBesT to turn historical controls into a MAP prior with a declared effective sample size, then simulate what it costs under prior-data conflict.

  • Design a group-sequential trial with interim looks — One skill or MCP · Proposed · Fully open · Laptop. Use the Adaptive Designs skill and rpact to fix boundaries, simulate operating characteristics, and pre-specify any sample-size re-estimation rule before enrolment.

  • Design amino-acid sequences for a fixed protein backbone — Multi-tool harness · Reported · Fully open · Workstation with GPU. Design sequences for a target backbone with ProteinMPNN, then refold each candidate with ESMFold and keep only those whose self-consistency RMSD recovers the backbone.

  • Plan a synthetic route for a target molecule — One skill or MCP · Reported · Subscription required · Laptop. Drive the CovaSyn MCP retrosynthesis suite from Claude Code to propose buyable-starting-material routes to a target SMILES and capture them as a reproducible route table.

  • Predict an antibody–antigen complex to map an epitope — One skill or MCP · Reported · Subscription required · Laptop. Use the Boltz plugin to predict an antibody/nanobody–antigen complex and read off a candidate epitope — with explicit handling of the field’s low success rate and unreliable confidence ranking.

  • Prepare the correct protonation state of a ligand before docking — One skill or MCP · Proposed · Fully open · Laptop. Use the Rowan skill in Claude Code to predict macro-pKa and the dominant protonation state of ligands at physiological pH before docking or MD, as a reproducible prepared-ligand table.

  • Prioritize tumor neoantigens for a personalized cancer vaccine — One skill or MCP · Validated · Institutional access · Workstation with GPU. Use the Neoantigen Prediction skill to turn a patient’s somatic variants, HLA type, and tumor RNA into a filtered, tiered neoantigen shortlist for vaccine design.

  • Scan a protein for candidate CD4 T-cell (helper) epitopes — One skill or MCP · Validated · Fully open · Laptop. Use the MHC Class II Prediction skill to rank a protein’s peptides for HLA-DR/DQ/DP binding, nominating CD4 T-helper epitope candidates for vaccine design.

  • Scan a protein for candidate CD8 T-cell epitopes — One skill or MCP · Validated · Fully open · Laptop. Use the MHC Binding Prediction skill to rank a protein’s peptides for MHC class I binding and presentation, nominating CD8 T-cell epitope and neoantigen candidates.

  • Scan a therapeutic antibody for glycosylation sites — One skill or MCP · Proposed · Fully open · Laptop. Use the Glycoengineering skill to scan an antibody sequence for N-glycosylation sequons and O-glycosylation hotspots before committing to a cell-line or developability campaign.

  • Set up a protein molecular dynamics simulation in GROMACS from a PDB ID — One skill or MCP · Proposed · Fully open · Workstation with GPU. Drive the GROMACS Copilot component of molecule-mcp to take a PDB ID through topology, solvation, ion neutralisation, minimisation, NVT/NPT equilibration, and a short production MD, with RMSD/RMSF/Rg analysis on the resulting trajectory.

Data analysis

  • Analyze a Perturb-seq CRISPR screen for perturbation effects — One skill or MCP · Proposed · Fully open · Workstation with GPU. Use the Perturb-seq Analysis skill to assign guides, remove escapers, test with a calibrated method, and rank perturbations by E-distance.

  • Analyze a single-cell TCR repertoire alongside gene expression — One skill or MCP · Reported · Fully open · Laptop. Use the scirpy Analysis skill to QC paired single-cell TCR chains, define clonotypes, quantify clonal expansion, and overlay clonality on the transcriptomic UMAP.

  • Analyze an existing MD trajectory for stability, flexibility, and contacts — One skill or MCP · Proposed · Fully open · Workstation with GPU. Drive the MDAnalysis skill (MDTraj as backup) to take a finished GROMACS/AMBER/NAMD trajectory through RMSD/RMSF/Rg, contact maps, H-bonds, and PCA without writing the analysis script by hand.

  • Analyze the SAR of a measured compound series — One skill or MCP · Reported · Fully open · Laptop. Drive the SAR Analysis skill over a CSV of assayed analogs to decompose the common scaffold, tabulate R-group vs potency, and surface activity cliffs for the next lead-optimization round.

  • Annotate TCR antigen specificity by clustering and database lookup — One skill or MCP · Validated · Fully open · Laptop. Use the TCR-Epitope Binding skill to group CDR3 sequences into shared-specificity clusters and match them against VDJdb, IEDB, and McPAS-TCR.

  • Annotate a single bacterial genome assembly — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the Bakta Claude skill to annotate one bacterial or archaeal assembly — CDS, rRNA/tRNA, CRISPR arrays — into NCBI-compatible GFF3/GenBank with a feature summary.

  • Annotate cell types in a single-cell dataset — One skill or MCP · Reported · Fully open · Laptop. Use the SciAgent CellTypist skill to put reference-backed cell-type labels on a QC’d AnnData, escalating to the popV consensus skill when you need ensemble uncertainty.

  • Assemble a tissue reference atlas from the CELLxGENE Census — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the cellxgene-census Claude skill to slice a tissue- or disease-specific AnnData from the CZ CELLxGENE Census, optionally fetching the precomputed scVI embedding for reference mapping or downstream integration.

  • Benchmark an ADMET property with PyTDC — One skill or MCP · Reported · Fully open · Laptop. Drive the PyTDC Claude skill to load a Therapeutics Data Commons ADMET dataset with its leaderboard split, train or score a baseline model, and emit the standard TDC metrics so a new method can be compared head-to-head against the leaderboard.

  • Build a clonal lineage tree from CRISPR scar recorders — One skill or MCP · Proposed · Fully open · Workstation with GPU. Use the Lineage Tracing skill to turn recorder reads into a character matrix, reconstruct trees with several solvers, and check topology robustness before interpreting.

  • Build a phylogenetic tree from a set of sequences — One skill or MCP · Proposed · Fully open · Laptop. Use the phylogenetics Claude skill to take a FASTA of homologous sequences through MAFFT alignment, IQ-TREE 2 maximum-likelihood inference with bootstrap support, and an annotated tree figure.

  • Build a protein interaction network and rank hub genes — One skill or MCP · Reported · Fully open · Laptop. Feed a gene list to the STRING skill to build a PPI network, then rank hub proteins by degree/centrality and detect modules — the canonical “which of these genes matter most” step.

  • Build a resting-state functional-connectivity matrix from preprocessed fMRI — One skill or MCP · Reported · Fully open · Laptop. Use the Nilearn skill in Claude Code to turn fMRIPrep-preprocessed BOLD into an atlas ROI-to-ROI functional-connectivity matrix with confound regression, as a re-runnable script.

  • Call peaks and find enriched motifs from ChIP-seq or ATAC-seq — Multi-tool harness · Proposed · Fully open · Laptop. Chain the MACS3 peak-calling skill into the HOMER motif skill to turn aligned ChIP-seq/ATAC-seq BAMs into a called-peak set with nearest-gene annotation and enriched TF motifs.

  • Characterize a protein–protein interface from a structure you already have — One skill or MCP · Proposed · Fully open · Laptop. Use the Interface Analysis skill to get contact residues and buried surface area from a solved or predicted complex — and to decide whether the interface is real or crystal packing.

  • Compare bulk TCR/BCR repertoires across samples from raw immunosequencing reads — Multi-tool harness · Proposed · Institutional access · Workstation with GPU. Assemble clonotypes with MiXCR, normalize samples to a common depth with VDJtools, then compare diversity, clonality and overlap as a committed pipeline.

  • Compute 16S microbiome alpha/beta diversity from a BIOM table — One skill or MCP · Proposed · Fully open · Laptop. Use the scikit-bio Claude skill to take a BIOM feature table and sample metadata through Shannon/Simpson/Faith’s PD, UniFrac, PCoA, and PERMANOVA in one chat.

  • Compute DTI scalar maps (FA/MD/AD/RD) from diffusion MRI — One skill or MCP · Reported · Fully open · Laptop. Use the DIPY skill in Claude Code to fit a diffusion tensor to a DWI volume and emit FA/MD/AD/RD maps plus ROI statistics, as a re-runnable script.

  • Compute HRV from an ECG recording — One skill or MCP · Proposed · Fully open · Laptop. Use the NeuroKit2 Claude Skill to clean an ECG trace, detect R-peaks, and return time-domain, frequency-domain, and non-linear HRV indices from a single conversation.

  • Compute a bacterial pan-genome from a set of genome assemblies — Multi-tool harness · Proposed · Fully open · Workstation with GPU. Annotate a panel of bacterial assemblies with Bakta, then cluster genes into core/accessory partitions with Roary to get a pan-genome and presence/absence matrix.

  • Decide whether a suspicious cluster is a doublet artifact — One skill or MCP · Proposed · Fully open · Laptop. Use the bioSkills Doublet Detection skill plus two orthogonal checks to rule on whether an intermediate single-cell cluster is real or two cells in one droplet.

  • Define a phenotype cohort in an OMOP CDM database — Multi-tool harness · Proposed · Institutional access · Laptop. Build a frozen OMOP concept set with OMOPHub, then count and characterise the cohort in your CDM with pyomop, emitting a portable attrition table.

  • Detect and rank druggable pockets on a protein structure — One skill or MCP · Proposed · Fully open · Laptop. Enumerate surface cavities on an apo structure with fpocket, rank them for ligandability with P2Rank, and emit a docking box — one Claude Skill.

  • Detect somatic copy-number variants from tumor sequencing — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the CNVkit Claude Skill to call somatic gene amplifications and deletions from tumor WES/targeted-panel BAMs and export segmented, plotted copy-number profiles.

  • Dock a ligand library into a target structure with DiffDock — One skill or MCP · Proposed · Fully open · Workstation with GPU. Drive DiffDock from Claude Code to generate per-ligand binding poses against a PDB or AlphaFold target, filter by confidence, and emit a ranked pose set ready for MM/PBSA rescoring or visualization.

  • Extract event-related potentials from EEG epochs — One skill or MCP · Reported · Fully open · Laptop. Use the MNE-Python EEG skill in Claude Code to filter, ICA-clean, epoch around event markers, and average a raw continuous EEG file into per-condition evoked responses.

  • Extract neuronal traces from a calcium imaging movie — One skill or MCP · Proposed · Fully open · Workstation with GPU. Use the Calcium Imaging Analysis Guide skill to pick motion correction, ROI extraction, neuropil correction and dF/F for two-photon or miniscope data, captured as a re-runnable script.

  • Extract spectral features from resting-state EEG — One skill or MCP · Proposed · Fully open · Laptop. Use the EEG Processing skill in Claude Code plus specparam/FOOOF to turn eyes-closed resting recordings into per-channel band power and aperiodic exponents.

  • Extract structured variables from free-text clinical notes — Claude Code alone · Validated · Fully open · Laptop. Use Claude Code alone to extract predefined variables from de-identified clinical notes into a reviewable, provenance-tracked registry table.

  • Filter a virtual screening hit list with drug-likeness rules and structural alerts — One skill or MCP · Reported · Fully open · Laptop. Use the MedChem skill in Claude Code to cascade Lipinski / Veber / PAINS / BRENK filters over a SMILES hit list and emit a triaged CSV with per-rule flags and a final keep/drop column.

  • Find differentially abundant proteins in a label-free proteomics experiment — One skill or MCP · Proposed · Fully open · Laptop. Use the MaxQuant skill to take LFQ raw files to a filtered protein table and a differential-abundance list whose imputation sensitivity is reported, not hidden.

  • Find differentially regulated phosphosites, not just changed proteins — One skill or MCP · Proposed · Fully open · Laptop. Use the MaxQuant skill on a paired phospho-enriched and unenriched run to get site-level regulation calls that are not just protein-abundance changes in disguise.

  • Find which taxa differ between microbiome groups — One skill or MCP · Proposed · Fully open · Laptop. Use the bioSkills Differential Abundance skill to test an amplicon feature table with several compositionally-aware methods and report their consensus, not one tool’s hit list.

  • Fit a dose-response curve and report a defensible IC50 — One skill or MCP · Proposed · Fully open · Laptop. Drive the ToolUniverse Dose-Response skill to fit 4PL curves to plate-assay data, gate them on fit quality, and emit IC50 with AUC and per-replicate spread.

  • Fit a drift-diffusion model to choice and reaction-time data — One skill or MCP · Proposed · Fully open · Laptop. Use the Drift-Diffusion Model skill in Claude Code with PyDDM to decompose two-choice accuracy and RT into drift rate, boundary, bias and non-decision time.

  • Fit a survival model to censored clinical outcomes — One skill or MCP · Proposed · Fully open · Laptop. Use the scikit-survival Claude Skill to fit Cox and Random Survival Forest models to censored time-to-event data and report concordance with proper validation.

  • Handle missing endpoint data in a confirmatory trial — One skill or MCP · Proposed · Fully open · Laptop. Use the Missing Data Sensitivity skill to fix an estimand, run MMRM as primary, and build a reference-based and tipping-point sensitivity package.

  • Identify a bacterial isolate from its 16S rRNA sequence — One skill or MCP · Reported · Fully open · Laptop. Use the BLAST MCP server to search a Sanger 16S rRNA read against a pinned reference database and assign genus/species by the standard identity thresholds.

  • Identify an unknown compound from an MS/MS spectrum — One skill or MCP · Proposed · Fully open · Laptop. Use the matchms skill in Claude Code to clean an unknown MS/MS spectrum and rank candidate identities by spectral similarity against a reference library.

  • Infer a gene-regulatory network from single-cell RNA-seq — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the Arboreto Claude skill to run GRNBoost2 on a QC’d single-cell AnnData and recover a ranked TF–target edge list — the first step of a SCENIC regulon pipeline.

  • Infer cell-cell communication from single-cell RNA-seq — One skill or MCP · Proposed · Fully open · Laptop. Use the LIANA-MCP server to run multiple ligand-receptor methods on an annotated AnnData object, aggregate their ranks, and plot the consensus communication network.

  • Infer transcription-factor and pathway activities from expression — One skill or MCP · Proposed · Fully open · Laptop. Drive the decoupler-MCP server to score per-cell or per-sample transcription-factor (CollecTRI) and pathway (PROGENy) activities from an expression matrix, then read off the regulators that move between conditions.

  • Integrate multi-omics layers into interpretable factors with MOFA+ — One skill or MCP · Proposed · Fully open · Laptop. Use the MOFA+ Claude skill to jointly decompose several omics layers on the same samples into a handful of latent factors, then read off which factors capture biology and which layers drive them.

  • Integrate multiple single-cell RNA-seq datasets across batches — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the scvi-tools skill in Claude Code to fit scVI (or scANVI when labels are available) on a concatenated AnnData of multiple batches, returning a batch-corrected latent space and integrated UMAP.

  • Localize a fiber/probe implant tip in an Allen CCF subregion from 2D histology — Multi-tool harness · Proposed · Fully open · Laptop. Batch-register coronal histology with DeepSlice, detect each fiber tip, and read its Allen CCF subregion plus a hit/miss-vs-target verdict — a scripted QUINT replacement.

  • Measure cortical thickness and subcortical volumes across a cohort — One skill or MCP · Proposed · Fully open · HPC or cloud cluster. Drive FreeSurfer recon-all over a T1w cohort with one pinned version, Euler-number QC, and a morphometry table that carries its quality covariate.

  • Parse FCS flow-cytometry files for downstream immunophenotyping — One skill or MCP · Proposed · Fully open · Laptop. Use the FlowIO Claude skill to parse FCS 2.0/3.0/3.1 files into tidy DataFrames with channel categorisation and batch metadata extraction, ready for downstream immunophenotyping or QC.

  • Predict ADMET properties for a compound series with an ML predictor — One skill or MCP · Reported · Fully open · Laptop. Drive the ADMETlab MCP server to batch-predict ~119 ML ADMET endpoints (with uncertainty) for a SMILES series, then commit a triaged CSV, pinned client env, and a provenance record.

  • Predict RNA secondary structure and target-site accessibility — One skill or MCP · Proposed · Fully open · Laptop. Use the ViennaRNA skill to fold an RNA, get its MFE structure, base-pair probabilities, and the accessibility of a candidate target site — for siRNA/sgRNA/ASO design or riboswitch analysis.

  • Predict gene-knockout phenotypes with flux balance analysis — One skill or MCP · Proposed · Fully open · Laptop. Use the COBRApy Claude Skill to load a genome-scale metabolic model and screen single/double gene deletions for growth phenotypes and essential genes.

  • Predict hospital readmission from EHR data — One skill or MCP · Proposed · Institutional access · Workstation with GPU. Use the PyHealth Claude Skill to build a 30-day readmission predictor on MIMIC/OMOP EHR data with a reproducible dataset → task → model → metrics pipeline.

  • Profile ChIP-seq or ATAC-seq signal around genomic features — One skill or MCP · Proposed · Fully open · Laptop. Use the deepTools Claude Skill to turn aligned ChIP-seq/ATAC-seq BAMs into normalized bigWig tracks and TSS/peak-centered profile and heatmap figures.

  • Profile shotgun metagenome taxa with Kraken2 and Bracken — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the Kraken2 skill to classify shotgun metagenomic reads to taxa and re-estimate abundances with Bracken, with database and confidence-threshold choices recorded.

  • Quantify a western blot from a scanned image — One skill or MCP · Reported · Fully open · Laptop. Use the Western Blot Quantification skill to detect bands, normalize target to a loading control, aggregate replicates, and emit a committed densitometry table.

  • Quantify bulk RNA-seq FASTQ into a gene-level counts matrix — Multi-tool harness · Proposed · Fully open · Laptop. Chain the fastp and Salmon skills, then aggregate with tximport, to turn raw bulk RNA-seq FASTQ into the gene-level counts matrix a DE analysis needs.

  • Rank a compound library against a target by predicted binding affinity — One skill or MCP · Reported · Subscription required · Laptop. Use the Boltz plugin’s hosted small-molecule screen to rank a SMILES library against a target by predicted binding affinity — no local GPU — and treat the score as a binder/non-binder enrichment filter, not a quantitative ranker.

  • Rank the conformers and tautomers of a small molecule with semi-empirical QM — One skill or MCP · Proposed · Fully open · Laptop. Drive the ChemGraph MCP server to optimize and free-energy-rank enumerated tautomers and conformers at GFN2-xTB, emitting a populations table instead of one guessed structure.

  • Reconstruct B-cell clonal lineages from AIRR-seq — One skill or MCP · Reported · Fully open · Laptop. Use the Immcantation BCR Analysis skill to cluster AIRR-seq reads into clonal families, quantify somatic hypermutation and selection, and infer germline-rooted lineage trees.

  • Register longitudinal medical scans to a common frame — One skill or MCP · Reported · Fully open · Workstation with GPU. Drive SimpleITK from Claude Code to rigidly then deformably align a patient’s baseline and follow-up CT/MRI, propagate contours, and emit a reproducible transform + warped volume.

  • Run a GWAS on case-control genotype data — One skill or MCP · Proposed · Fully open · Workstation with GPU. Drive PLINK2 from QC through PCA-adjusted logistic-regression association on a case-control cohort, returning Manhattan-ready summary stats.

  • Run bulk RNA-seq differential expression from a counts matrix — One skill or MCP · Reported · Fully open · Laptop. Use the PyDESeq2 Claude Skill to fit a negative-binomial GLM from a counts matrix and sample-condition table, returning ranked log2 fold-change and BH-adjusted p-values.

  • Run first-pass QC on a single-cell RNA-seq dataset — One skill or MCP · Reported · Fully open · Laptop. Use Anthropic’s single-cell-rna-qc skill to MAD-filter a 10x .h5 or AnnData .h5ad file and emit standard QC figures before downstream Scanpy or scvi-tools work.

  • Run functional enrichment on a gene list — One skill or MCP · Reported · Fully open · Laptop. Use the gget Claude skill to run a gene list through Enrichr against GO, KEGG, Reactome, and disease libraries, then ask Claude to summarise the enriched terms back to the biology with explicit citations.

  • Score a drug-combination screen for synergy — One skill or MCP · Proposed · Fully open · Laptop. Drive the ToolUniverse Drug Synergy skill to pick the right reference model (Bliss / HSA / Loewe / ZIP / Chou-Talalay) for your combination data and classify a two-drug pairing as synergistic, additive, or antagonistic.

  • Score point mutations for functional impact with a protein language model — One skill or MCP · Proposed · Fully open · Workstation with GPU. Use the ESM skill to compute zero-shot masked-marginal log-likelihood-ratio scores for a list of point mutations, ranking them by predicted functional effect without any labelled data.

  • Screen a bacterial genome for resistance and virulence genes — One skill or MCP · Reported · Fully open · Laptop. Use the BLAST MCP server to search a bacterial assembly’s proteins against CARD and VFDB, emitting a curated resistance- and virulence-gene profile with a committed script and pinned databases.

  • Segment an organ or tumor in a medical image with nnU-Net — One skill or MCP · Reported · Fully open · Workstation with GPU. Drive nnU-Net’s self-configuring framework from Claude Code to train and run a voxel-accurate segmentation model for an organ or lesion in CT/MRI, with 5-fold cross-validated Dice.

  • Segment and quantify cells in a microscopy image — One skill or MCP · Reported · Fully open · Laptop. Use the Cellpose skill to segment cells or nuclei in fluorescence/brightfield images and extract per-cell counts, areas, and intensities to a committed table.

  • Sort spikes from a Neuropixels recording end-to-end — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the K-Dense neuropixels-analysis skill in Claude Code to take a raw SpikeGLX or Open Ephys Neuropixels recording through preprocessing, drift correction, and Kilosort4 to curated single units.

  • Superpose two protein structures and quantify where they differ — One skill or MCP · Proposed · Fully open · Laptop. Superpose a predicted model onto an experimental structure (or apo onto holo) with the PyMOL skill, then report global RMSD, per-residue deviation, and a rendered overlay.

  • Test whether a proposed RNA structure is actually conserved — One skill or MCP · Proposed · Fully open · Laptop. Use the Covariation Analysis skill to test a proposed RNA secondary structure with R-scape, and to establish whether the alignment even has the power to reject it.

  • Test which immune populations differ between groups in a cytometry cohort — Multi-tool harness · Proposed · Fully open · Laptop. Chain three bioSkills cytometry skills to compensate, cluster, and test a spectral-flow or CyTOF cohort for differential abundance and state without pseudoreplication.

  • Tile and stain-normalize a whole-slide image for ML — One skill or MCP · Reported · Fully open · Workstation with GPU. Use the histolab skill to turn a gigapixel H&E slide into a tissue-masked, stain-normalized tile dataset with a committed, re-runnable script.

  • Track animal pose in behavioral video — One skill or MCP · Proposed · Fully open · Workstation with GPU. Use the DeepLabCut skill in Claude Code to go from behavioral video to a filtered, quality-controlled keypoint table with kinematics and provenance recorded.

  • Track single particles and measure their diffusion coefficient — One skill or MCP · Reported · Fully open · Laptop. Use the trackpy skill to locate and link particles across video-microscopy frames, then compute MSD and diffusion coefficients into a committed trajectory table.

  • Train a QSAR model from your own assay data and predict untested compounds — One skill or MCP · Proposed · Fully open · Laptop. Use the ChemLint MCP in Claude Code to clean an assay CSV, featurize, train and cross-validate a QSAR model with an applicability domain, then score an untested library.

  • Vet a PDB structure before you build on it — One skill or MCP · Proposed · Fully open · Laptop. Judge whether a deposited structure — or one specific loop or side chain in it — is reliable enough to dock against, measure, or build a mechanism on.

Knowledge synthesis

Manuscript prep

  • Draft a Phase 2/3 clinical-trial protocol from an indication brief — One skill or MCP · Reported · Fully open · Laptop. Use the Anthropic clinical-trial-protocol plugin to expand a short indication / endpoint brief into an FDA/NIH-compliant Phase 2/3 protocol draft, with regulatory pathway, competitive landscape, and sample-size calculation already wired in.

Workflow automation

  • Convert raw analytical instrument data to Allotrope ASM JSON — One skill or MCP · Reported · Fully open · Laptop. Drop a raw instrument file (cell counter, plate reader, HPLC, qPCR) onto Claude Code and get back valid Allotrope Simple Model JSON, a flattened CSV for LIMS, and a standalone Python parser script.

  • Organize a raw DICOM dataset into a BIDS layout — One skill or MCP · Proposed · Fully open · Laptop. Drive HeuDiConv or dcm2bids from Claude Code via the K-Dense BIDS skill to convert a raw DICOM dump into a validated BIDS dataset ready for BIDS-Apps and OpenNeuro submission.

How evidence is distributed

The cookbook mixes three evidence levels:

  • Validated — at least one peer-reviewed paper or independent benchmark reports the assembly working.
  • Reported — a preprint, blog post, or case study documents someone running the assembly.
  • Proposed — rational composition from the catalog; no documented attempt is yet known.

Use the front-matter on each recipe to filter by the bar you need.

Gaps

Problem classes with no recipes yet are listed above as _No recipes yet._. Subject areas that are under-covered are noted in the curator’s internal state file as Deferred candidates and surfaced here when they cluster into a pattern.