paulflang

cell_cycle_model

cell_cycle_petab

cell_cycle_time_course

PEtab_nlme_extension

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

paulflang/cell_cycle_petab

paulflang/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.

paulflang/SbmlInterface.jl

Interface between the Systems Biology Markup Language and Julia

paulflang/cell_cycle_model

paulflang/cell_cycle_time_course

paulflang/PEtab_nlme_extension

paulflang/2020-software-engineering-ci

paulflang/2020-software-engineering-day1

Day 1 course content for the SABS-R3 module: Software Engineering, 2020

paulflang/2020-software-engineering-day2

Day 2 course content for the SABS-R3 module: Software Engineering, 2020

paulflang/2020-software-engineering-day3

Day 3 course content for the SABS-R3 module: Software Engineering, 2020

paulflang/2020-software-engineering-day4

Day 4 course content for the SABS-R3 module: Software Engineering, 2020

paulflang/2020-software-engineering-day6

testing and continuous integration

paulflang/AMICI

Advanced Multilanguage Interface to CVODES and IDAS

paulflang/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

paulflang/CirculatorySystemModels.jl

paulflang/ColPrac

Contributor's Guide on Collaborative Practices for Community Packages

paulflang/MathML.jl

Julia MathML parser

paulflang/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

paulflang/OxThesis_template

LaTeX template for an Oxford University thesis

paulflang/PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

paulflang/PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

paulflang/pyPESTO

python Parameter EStimation TOolbox

paulflang/SBML.jl

Julia interface to the Systems Biology Markup Language (SBML) library

paulflang/SBMLBioModelsRepository.jl

paulflang/sbmlgist

paulflang/sbmltoodepy

A tool for creating Python implementations of SBML models.

paulflang/SciMLBenchmarks.jl

Scientific machine learning (SciML) benchmarks, AI for science, and (differential) equation solvers. Covers Julia, Python (PyTorch, Jax), MATLAB, R

paulflang/SciMLDocs

paulflang/sysbio-glossary

A glossary of computational systems biology concepts I encountered during my doctoral research.

paulflang/TestCI