8 projects
ode2sbml
Convert Python ODE systems to SBML (Level 3 Version 2) and PEtab bundles
acthermal-tumor
A non-isothermal Allen-Cahn tumor growth simulator using JAX and exponax
fastdpplot
None
cetsax
CETSA analysis and deep learning toolkit for binding curves, hit calling, and proteome-wide ligand-responsiveness prediction.
bio-sea-pearl
Sequence analysis and bioinformatics utilities in Python and Perl.
pynetworkin-bio
Kinase-substrate network prediction: PostgreSQL, Numba, pynetphorest, live data, false-negative recovery
pynetphorest
Modern, extensible Python toolkit for kinase–substrate and phosphorylation-crosstalk analysis. Rebuilds the NetPhorest/NetworKIN logic in pure Python, adds causal writer→reader predictions, ML models trained on PTMcode2, whole-proteome scoring, and Snakemake workflows. Designed for phosphoproteomics, systems biology, and large-scale signaling reconstruction.
phoskintime
PhosKinTime is a Python toolkit for ODE‑based modeling of phosphorylation kinetics and transcriptional time‑series, featuring parameter estimation, sensitivity analysis, steady‑state computation, and interactive visualization.
