Results for “biological-pathway”

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

Applies physical principles to model biological systems, including protein folding, membrane transport, molecular forces, and neural signaling.

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.

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.

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

Validates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).

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.

Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.

Analyzes raw genomic data (FASTQ/VCF) to generate non-medical wellness, longevity, and pharmacogenomic optimization protocols while keeping DNA processing local and private.

Loads and processes whole-slide pathology images, builds spatial graphs, trains deep learning models, and analyzes multiplexed immunofluorescence data across 160+ slide formats.

Design and evolve engineering team structures for fast flow of change using the Team Topologies framework, including Conway's law, four team types, three interaction modes, and cognitive load management.

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.

Explains cellular structures, membrane transport, energetics, signaling, and division, connecting molecular events to organismal function.

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).

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

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

Use when a researcher asks where to start, which project skill fits the current stage of a study, or in what order literature scoping, source access, vault upkeep, drafting, citation verification, disclosure, and review response should run.

Translates raw genomic data into personalized health, longevity, and pharmacogenomic protocols for AI agents.

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.

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

Writes or updates pathway pages for Alan Hirsch's platform, following a 12-section architecture that grounds frameworks in Scripture and story, offers practices, and invites course-based formation.

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Migrate React class component lifecycle methods (componentWillMount, componentWillReceiveProps, componentWillUpdate) to React 18.3.1 compliant patterns with decision trees and before/after code examples.

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.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

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.

当在个人发展的某个领域（心智、身体、精神、职业）达到“失调阶段”（即对现状感到厌倦、停滞或不满，但尚未麻木）时，用于主动进入一个能加速学习和成长的“心流”或“痴迷”状态（即“渠道”）

Teleological physiology analysis framework for understanding biological systems through multi-constraint optimization. Use when analyzing physiological mechanisms, explaining apparent biological "inefficiencies", preparing for medical examinations (CICM/ANZCA Primary), understanding why biological systems are designed the way they are, or when seeking deeper mechanistic understanding beyond descriptive knowledge. Triggers on questions like "why is X designed this way", "what purpose does Y serve", "how is Z optimized", analysis of physiological trade-offs, or exploration of evolutionary/design constraints.

Generate pragmatic CI/CD pipelines from detected project stack signals, with fast baseline generation, repeatable checks, and environment-aware deployment stages.

Design product-led growth loops, activation paths, and expansion mechanics for a software product. Use when the team needs onboarding-to-value planning, sharing or collaboration loops, retention hooks, or realistic post-launch growth motions tied to product usage.

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.

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