Modelling & Simulation

PhosKinTime

Python package for analyzing proteomics data, including time-course modelling and visualization.

PhosCrosstalk

Systems-level phospho-network ODE modelling framework integrating PTM crosstalk, kinase-substrate networks, and phosphosite time-series with multi-objective evolutionary optimisation.

Pharmacokinetic Modeling

Built an SBML-based ODE model of Tirzepatide to study how the drug is absorbed, distributed, and processed in the body.

Hsp90 smFRET Analysis Pipeline

Single-molecule FRET kinetic modelling with multistart optimisation, bootstrapping, and sensitivity analysis.

PhosphoVelocity

Bayesian phosphosite velocity modelling pipeline for LC-MS/MS time-course phosphoproteomics, reconstructing latent trajectories and phosphorylation velocity to infer kinase activity dynamics.

Allen Cahn tumour growth model

High-performance JAX-based simulator for the non-isothermal Allen Cahn tumour growth model, coupling tumour cells, temperature, and nutrient dynamics with spectral or finite difference solvers.

Cancer robustness-load trade-off (RLTO) model

A practical Python framework inspired by the robustness-load trade-off (RLTO) model described in Choi et al. (Science Advances, 2026), but reframed for cancer systems biology.

CNA-ResistDynamics

Dynamical modelling of chemotherapy resistance from liquidCNA measurements.

Pipelines & Workflows

SARS-CoV-2 lineage reconstruction

Nextflow-powered pipeline for SARS-CoV-2 genome reconstruction.

Genome Read Mapping and Annotation

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

Codon Analyzer

Nextflow DSL2 pipeline for DNA multi-FASTA analysis with per-record fanout into Perl processing modules.

CETSAxNADPH

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

Algorithms & Infrastructure

Sequence Aligner

A high-performance tool for global and local sequence alignment using Needleman-Wunsch, Smith-Waterman, and LCS algorithms, accelerated with MPI, OpenMP, and SIMD for DNA and protein sequences.

SequenceMSAligner

A high-performance tool for Multiple Sequence Alignment using AVX2 + affine gap combination.

PyNetPhorest

Modern Python re-implementation of NetPhorest for kinase-substrate scoring and phosphorylation crosstalk analysis.

PyNetworKIN

A modernised Python 3 port of the original NetworKIN 3.0 tool (Linding, Jensen, Horn & Kim, 2005–2013), extended to support STRING v12 protein interaction data

bio-sea-pearl

Hybrid Python + Perl bioinformatics toolkit for sequence alignment, Markov modeling, sequence analysis, and FM-index-based search, unified under a single Python CLI and API.

ode2sbml

Python package for converting Python-defined ODE systems into SBML Level 3 Version 2 models and PEtab bundles for parameter estimation.

Visualization

Fast DP Plotter

Rust-accelerated dot plot renderer for bioinformatics data, available as a Python library, CLI, and desktop GUI.

Applied Bioinformatics & ML

Liver Prediction

ML-based classification of liver cancer tissues with transcriptomic & epigenomic analysis.

Prostate Cancer Biomarker Discovery

Identifying potent biomarkers for prostate cancer through pathway mining and gene-expression meta-analysis.