Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research ideas or exploring interdisciplinary connections.
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Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.
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AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the AiZynthFinder/AiZynthExpander Python API, one-step disconnections, custom stocks via smiles2stock, scorers, Retro*/breadth-first/DFPN search alternatives, and reading output.json.gz / trees.json. Use for synthesis route planning, synthesizability screening, and building-block/precursor search. For reaction barriers use neb-irc-activation-energy; for 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
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Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
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Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
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PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, activity), retrosynthesis, drug-target interaction (DTI), and pretraining on large molecular datasets. Provides GNN layers (GraphConv, GAT, MPNN), pretrained models, and benchmark datasets.
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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.
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Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling with offline fallbacks, cross-condition comparisons, and answer-first reporting. Consult when running enrichment with clusterProfiler or gseapy.
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Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.
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Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
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Query ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; fetch details by NCT ID; filter by status; paginate; export CSV. For clinical research, patient matching, and trial portfolio analysis.
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Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.
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Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.
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Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel NumPy), Bags, Futures, Schedulers. Scales laptop to HPC cluster. For single-machine speed use polars; for out-of-core without cluster use vaex.
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Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.
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Fast in-memory DataFrame with lazy evaluation, parallel execution, Arrow backend. Use for tabular data in RAM (1–100 GB) when pandas is too slow. Expression API: select, filter, group_by, joins, pivots, window. Lazy mode enables predicate/projection pushdown. Reads CSV, Parquet, JSON, Excel, DBs, cloud. Larger-than-RAM: Dask; GPU: cuDF.
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Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends. For IP landscape analysis, competitor monitoring, prior art search, and tech forecasting in life sciences and biotech.
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Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.
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Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
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Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.
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Science (AAAS) figure preparation: resolution (150-300+ DPI), formats (PDF/EPS/TIFF), RGB color, Myriad/Helvetica fonts, strict image manipulation policies including gamma adjustment disclosure.
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Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.
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Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats. Use when given a data file for initial exploration or to pick an analysis before a pipeline.
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LLM-driven hypothesis generation/testing on tabular data. Three methods: HypoGeniC (data-driven), HypoRefine (literature+data), Union. Iterative refinement, Redis caching, multi-hypothesis inference. Manual: hypothesis-generation; ideation: scientific-brainstorming.
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