Results for “biobank-schema”

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Provides reference documentation and code patterns for using Biopython to handle biological sequences, file formats, database access, alignments, structures, and phylogenetics.

Design an application database schema from product flows and backend responsibilities. Use when the team needs core entities, relationships, lifecycle fields, indexes, audit needs, tenancy boundaries, and migration-minded schema planning for an MVP or production system.

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

Analyzes biochemical processes, including enzyme kinetics, metabolic pathways, and biomolecule characterization, with practical techniques and examples.

Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.

Generate typed SDK bindings (Pydantic v2 models, TypeScript types) from the Bloodbank JSON Schema tree at `bloodbank/schemas/bloodbank/v1/**` (Draft 2020-12). Uses `datamodel-code-generator` and `json-schema-to-typescript` — NOT the deprecated hand-rolled Holyfields generators. Use when generating event-contract bindings for a Bloodbank consumer, importing typed CloudEvents envelopes into another project, or scaffolding a `bloodbank-contracts` SDK package. Trigger keywords — "bloodbank SDK", "bloodbank contracts", "Pydantic from bloodbank schemas", "TypeScript types for bloodbank events", "bloodbank.v1.* types", "event contract bindings", "datamodel-code-generator", "json-schema-to-typescript", "regenerate SDK", "CloudEvents bindings". Do NOT use for schema authoring (edit `bloodbank/schemas/` directly per `docs/event-naming.md` §12), runtime envelope validation (use `BLOODBANK_HOOK_VALIDATE=1`), schema-tree consistency (`mise run smoketest:schemas`), or generic JSON Schema codegen unrelated to Bloodbank.

Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Use when converting GenBank format files to table format as part of the Entrez Direct toolkit from bioconda.

Expert en biotechnologies avancées (bioinformatics, genomics, CRISPR, drug discovery, DZ research)

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

A股智能分析与智能选股工具。维护动态股票池(最多30支),按高科技×中小市值×好业绩原则筛选,推送买卖信号。含独立技术面择时分(-10~+10)用于判断买卖时机。A股投资、股市分析、量化选股。

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Supabase-first database schema design for Nick's app stack. Generate production-ready Postgres schemas, Supabase SQL migrations, RLS policies, TypeScript types, seed data, role-aware access patterns, and schema checklists from plain English requirements. Use when starting any new project database, designing or reviewing schemas, adding tables, planning migrations, or turning product requirements into Supabase-ready data models. Bias toward product-led schema design, MVP discipline, core-workflow-first modeling, and avoiding premature table/role sprawl.

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Volume-based PUMP token reward system with day-indexed epochs, pro-rata distribution, accumulator tracking, and cross-program claiming on Solana.

Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.

Manages a MariaDB database schema across its lifecycle using the MariaDB Schema Management plugin via the mariadb-shell MCP server, covering project creation, versioned development, releases, and deployment.

Provides a framework for proactive health monitoring and optimization, treating the human body as an asset to be maintained through telemetry, diagnostics, and interventions.

Performs constraint-based metabolic modeling with COBRApy: FBA, FVA, gene knockouts, flux sampling, and SBML model handling for systems biology and metabolic engineering.

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

Advises against testosterone therapy in men with biochemical recurrence after prostate cancer treatment due to very limited data and potential risk of progression. Consider when a patient has a rising PSA after definitive therapy and the clinician evaluates testosterone for hypogonadism, questioning whether TTh is safe in BCR.

Design prospective clinical studies by selecting and classifying endpoints, estimating sample size and power for two-arm designs, and scoring study plans for feasibility with phase-gate decisions.

Score and rank options contracts for any ticker using a multi-factor model covering liquidity, IV attractiveness, Greeks balance, and risk/reward. Returns scored option chains with the best contracts highlighted.

Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

MAMBA v2.0 — Range-bound high water + regime protection. A trading strategy config override based on the VIPER skill with three protective gates: BTC regime filter, per-asset cooldown after losses, and hard leverage cap at 10x.

Access and analyze drug information from the DrugBank database — drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. Use when working with pharmaceutical data, drug discovery research, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task needing detailed drug and drug-target records from DrugBank. Part of the AlterLab Academic Skills suite.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.