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Understand the SAM format header, alignment records, FLAGs, MAPQ, CIGAR, and coordinate conventions — the foundation for all downstream BAM analysis.

Process BAM files with samtools — sort, index, merge, flagstat, mark duplicates, fixmate, depth, filter, and stream — the standard CLI toolkit for 2026.

Master the Seq, MutableSeq, and SeqRecord objects — slicing, immutability, ambiguity codes, alphabets, and the 2026 Biopython alphabet deprecation reality.

Compute GC content, molecular weight, melting temperature, isoelectric point, and instability index for DNA, RNA, and protein sequences.

Slice, subset, and extract regions from sequences and SeqRecords — including feature extraction, fuzzy ends, and the location algebra behind GenBank features.

Splice-aware RNA-seq alignment with STAR — the gold-standard aligner for novel junction discovery, with 2-pass mapping and genome-generation strategies for 2026.

Transcribe DNA to RNA (and back), translate coding sequences to protein using NCBI codon tables, and pick the right genetic code for mitochondria, plastids, or non-standard...

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM...

Supports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and...

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3...

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation...

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation,...

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or...

Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry,...

Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization...

Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK. Supports source-scoped search,...

Conducts systematic, scoping, and narrative literature reviews using PubMed, arXiv, bioRxiv, Semantic Scholar, and other appropriate sources. Use for research synthesis,...

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...

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an...

Guides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio). Applies to cell-free, E. coli, and Pichia...