Posts

Representing Multi-Scale Systems using Directed Acyclic Graphs

August 07, 2025

Implementation of a data-oriented data structure: a directed acyclic graph. The data structure can be used to build large systems of many hierarchically related components while keeping cache-friendly memory allocations.
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Data-Oriented Design in Biology

February 25, 2025

Data oriented programming principles are good practise in software development. Here I set out to describe how such principles could aid in building better models, with a particular focus on my own field - biophysics.
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essay

Simulation Based Inference on the Lorenz System

May 25, 2024

Short introduction and walkthrough on how to use simulation based inference with an example using the Lorenz system.
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A Python tool for Streamlining Parameter Search in Computational Biology

September 03, 2023

Orca provides tools for sequentially running generative models to obtain a well organized dataset of parameters and their associated observables from model simulations.
inference
Python
SnakeMake