Software

Mechanistic framework for reconstructing phosphorylation dynamics from time-resolved molecular measurements and kinase–substrate networks using ODE models, constrained optimization and sensitivity analysis.

Methods ODE modelling · constrained optimization · sensitivity analysis

Bayesian phosphosite-velocity pipeline for reconstructing latent trajectories and kinase-activity dynamics from time-course LC–MS/MS phosphoproteomics.

Methods Bayesian inference · latent trajectories · phosphoproteomics

SBML-based ordinary differential equation model of tirzepatide absorption, distribution and elimination, developed as a reproducible pharmacokinetic modelling study.

Methods PBPK · ODEs · SBML · parameter estimation

Single-molecule FRET kinetic modelling workflow using multistart optimization, bootstrap analysis and sensitivity analysis.

Methods kinetic modelling · multistart optimization · bootstrapping

JAX-based simulation of a non-isothermal Allen–Cahn tumour-growth model coupling cell, temperature and nutrient dynamics with spectral or finite-difference solvers.

Methods PDEs · JAX · spectral methods · finite differences

Python framework adapting the robustness–load trade-off model described by Choi et al. to questions in cancer systems biology.

Methods quantitative modelling · parameter exploration

Dynamical modelling of chemotherapy-resistance trajectories from longitudinal liquidCNA measurements.

Methods dynamical systems · liquid biopsy · treatment response

CETSA-MS modelling toolkit for dose–response analysis, binder classification, Bayesian inference, curve typing and proteome-wide stability networks.

Methods CETSA-MS · Bayesian inference · dose–response modelling

Nextflow workflow for reproducible SARS-CoV-2 genome reconstruction and lineage analysis from Illumina reads.

Methods Nextflow · containers · genome reconstruction

Nextflow workflow for mapping sequencing reads to a reference genome and annotating matches with gene, TSS, CpG and repeat metadata.

Methods Nextflow · read mapping · genomic annotation

Nextflow DSL2 workflow for multi-FASTA sequence analysis with per-record fan-out to modular processing steps.

Methods Nextflow DSL2 · sequence analysis · Perl

Python package that converts Python-defined ODE systems into SBML Level 3 models and PEtab bundles for parameter estimation.

Methods SBML · PEtab · model interoperability

Parallel implementation of global and local alignment and longest-common-subsequence algorithms for nucleotide and protein sequences.

Methods C++ · MPI · OpenMP · SIMD

Multiple-sequence alignment implementation combining AVX2 acceleration with affine-gap scoring.

Methods C++ · AVX2 · sequence alignment

Python reimplementation of NetPhorest for kinase–substrate scoring and phosphorylation-crosstalk analysis.

Methods kinase prediction · network biology · Python

Python 3 port of NetworKIN 3.0, with support for contemporary STRING protein-interaction data.

Methods kinase prediction · protein networks · Python

Hybrid Python and Perl toolkit for sequence alignment, Markov modelling, sequence analysis and FM-index search through a unified CLI and API.

Methods sequence algorithms · FM-index · Python · Perl

Rust-accelerated dot-plot renderer for bioinformatics data, provided as a Python library, command-line tool and desktop interface.

Methods Rust · Python · scientific visualization