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  • Getting started
    • Prior Knowledge and Graphs
    • Constrained Optimization
    • Multi-commodity Network Flows
    • Acyclic Flows
  • Network methods
    • Shortest paths
    • Steiner Trees (STs)
    • Prize-Collecting Steiner Trees (PCSTs)
  • Metabolism
    • Flux Balance Analysis (FBA)
    • Sparse FBA
    • Multi-condition sparse FBA
    • Context-specific models (iMAT)
    • Multi-condition iMAT
  • Signaling
    • CARNIVAL
    • Multi-condition CARNIVAL
  • Interactomics
  • Interoperability
    • COBRApy: Constraint-based metabolic modeling in Python
    • LIANA+: An all-in-one cell-cell communication framework
    • Decoupler: Ensemble of methods to infer biological activities
    • Omnipath: intra- & intercellular signaling knowledge
    • NetworkX: Network Analysis in Python
    • CVXPY: Convex optimization, for everyone
    • PICOS: A Python interface to conic optimization solvers
  • User guide
  • Getting started

Getting started#

  • Prior Knowledge and Graphs
    • Manually creating a graph
    • Edge attributes
    • Importing graphs
    • Saving and reading
    • Hypergraphs
  • Constrained Optimization
    • The Knapsack Problem
    • A more complex knapsack
  • Multi-commodity Network Flows
  • Acyclic Flows
    • Largest DAG from a given source and sink vertex
    • Largest DAG from any source to any sink

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