Skill UI

COBRApy is a Python library for constraint-based reconstruction and analysis of genome-scale metabolic models, letting you load SBML/JSON/YAML models, perform FBA/FVA/sampling, and study gene or reaction knockouts for systems biology and metabolic engineering.

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

Query the STRING REST API to retrieve protein-protein interaction networks, map identifiers, visualize evidence-weighted edges, and run GO/KEGG/Pfam enrichment for systems biology analysis.

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

COBRApy is a comprehensive Python library for Constraint-Based Reconstruction and Analysis (COBRA) of metabolic models. It enables users to simulate complex cellular metabolism, performing crucial analyses such as Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), and virtual gene/reaction knockouts. It is an essential tool for systems biology research and metabolic engineering design.

LaminDB is an open-source, lineage-native lakehouse designed for managing complex biological datasets and computational workflows. It makes diverse scientific data (like scRNA-seq, AnnData) queryable, traceable, and compliant with FAIR principles. Core capabilities include robust data lineage tracking, schema validation, ontology-backed annotation (Bionty), and unified querying across multiple cloud/local storage systems. It is essential for bioinformatics research and building reproducible data infrastructure.