Paul Lang's repositories
SBML2Julia
A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.
SbmlInterface.jl
Interface between the Systems Biology Markup Language and Julia
2020-software-engineering-day1
Day 1 course content for the SABS-R3 module: Software Engineering, 2020
2020-software-engineering-day2
Day 2 course content for the SABS-R3 module: Software Engineering, 2020
2020-software-engineering-day3
Day 3 course content for the SABS-R3 module: Software Engineering, 2020
2020-software-engineering-day4
Day 4 course content for the SABS-R3 module: Software Engineering, 2020
2020-software-engineering-day6
testing and continuous integration
Benchmark-Models-PEtab
A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
ColPrac
Contributor's Guide on Collaborative Practices for Community Packages
ModelingToolkit.jl
An acausal modeling framework for automatically parallelized scientific machine learning (SciML) in Julia. A computer algebra system for integrated symbolics for physics-informed machine learning and automated transformations of differential equations
OxThesis_template
LaTeX template for an Oxford University thesis
sbmltoodepy
A tool for creating Python implementations of SBML models.
SciMLBenchmarks.jl
Scientific machine learning (SciML) benchmarks, AI for science, and (differential) equation solvers. Covers Julia, Python (PyTorch, Jax), MATLAB, R
sysbio-glossary
A glossary of computational systems biology concepts I encountered during my doctoral research.