Development Of An Agent-Based Toolkit For Modeling Complex Biological Systems


Alex was one of the primary software developers of Swarm, a pioneering open-source agent-based modeling (ABM) toolkit developed at the Santa Fe Institute for the sciences of complexity. Swarm has been used extensively to conceive and prototype complex systems models ranging from development genetics, ecological fish dynamics, bacterial colonies to economic models of supply chains and stockmarkets.

In the biological space this has included collaborations with domain-specific scientists to prototype and build models using Swarm and other ABM tools. Specific projects have ranged across multiple biological disciplines including:

  • Pharmacology: consulting and coding of a model of individual variability in drug response systems

  • Ecology: consulting on an agent-based model to explore scaling relationships between canopy size and tree size in forests

  • Computational neuroscience: complete coding of a spatial agent-based model to model the evolution of neural networks to test hypotheses about how hierarchical neuronal structures emerge.

  • Theoretical biology: coding a spatial version of AlChemy (ALgorithmic CHEMistry), an abstraction of chemistry to understand the emergence and evolution of the self-organization of cellular membranes.

  • Systems biology: models of transcription factor network evolution that incorporate biological realistic details drawn from experimental data, yet are computationally tractable.

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