Biological Networks — Construction, Topology & Community Detection (Hands-on)

Learn how to construct, analyze, and interpret biological networks from omics and literature sources. You will build graphs (PPI, gene–gene co-expression, metabolite–reaction, microbe–microbe) and apply robust topology analysis, centrality measures, and community detection to uncover modules and pathway-level insights. Deliverables include a reproducible notebook and a polished Cytoscape session.

Biological Networks: Construction, Topology & Community Detection

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Session Index

Session 1 — Data Sources & Network Construction Session 2 — Topology, Centralities & Robustness Session 3 — Community Detection & Module Biology Session 4 — Mini Capstone: Network Analysis Report

Session 1

Fee: Rs 8800

Data Sources & Network Construction

Network types & use-cases

PPI / gene co-expression regulatory / metabolite–reaction microbiome co-occurrence

Data ingestion & curation

edge lists / SIF / GraphML identifier mapping thresholds & filtering

Toolchain

Cytoscape igraph / NetworkX NDEx Gephi

Session 2

Fee: Rs 11800

Topology, Centralities & Robustness

Global & local structure

degree/strength distributions clustering, path lengths assortativity & motifs

Centrality portfolio

degree / betweenness / closeness eigenvector / PageRank k-core / articulation

Null models & robustness

configuration model percolation/attack simulations statistical testing

Session 3

Fee: Rs 14800

Community Detection & Module Biology

Algorithms & selection

Louvain / Leiden Infomap / Walktrap label propagation

Validation & interpretation

modularity Q / conductance stability / consensus clustering NMI/AMI vs. references

Biology of modules

GO/KEGG enrichment driver nodes & targets visual encodings in Cytoscape

Session 4

Fee: Rs 18800

Mini Capstone: Network Analysis Report

From raw table to insights: build, analyze & visualize a network

Theory + Practical

Reproducible outputs & packaging

notebook + Cytoscape .cys GraphML/SIF exports module annotations

Deliverables

PDF/HTML report .graphml / .sif / .cys requirements.txt/environment.yml

PDF

Biological Networks Training | Construction, Topology, Centrality & Community Detection

Biological Networks — Construction, Topology & Community Detection (Hands-on)