Reproduce results from: Burkardt & Trenchea (2020)
A Snakemake workflow that reproduces the numerical experiments of Burkardt and Trenchea (2020) comparing explicit and fixed-point implicit midpoint ODE solvers. Both solvers are implemented from scratch in NumPy following the pseudocode in the paper and applied to two test systems: the humps ODE (a stiff scalar problem) and a predator-prey Lotka-Volterra system.
Output: Trajectory plots and phase-plane diagrams for each solver–problem combination, ensuring exact reproducibility of all six output figures.
Main steps
run_midpoint_explicit — runs the explicit midpoint solver on both ODEs, producing a summary text file and two PNG plots.
run_midpoint_fixed — runs the implicit fixed-point solver on both ODEs, producing an equivalent set of three outputs. Both rules are independent and can run in parallel.
No data
What is a RO-Crate?
A RO-Crate is a standardized research object package that bundles a workflow together with rich machine-readable metadata. Each RO-Crate contains:
- the workflow definition file (e.g. using Snakemake)
- a ro-crate-metadata.json file describing the workflow's purpose, inputs, outputs, and provenance
- references to tool dependencies, software versions, and execution environments
- persistent identifiers linking to related resources such as publications, datasets, or other workflow registries
This ensures that the workflow can be reliably shared, cited, validated, and re-executed in a reproducible manner. RO-Crates follow the RO-Crate specification and are natively supported by various platforms.
More information can be found here.
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