systems-pharmacology

PySB add-on providing domain-specific macros and models for empirical and mechanistic PK/PD modeling.

Datasets and source code for reproducing the paper 'Integrating multiple evidence sources to predict adverse drug reactions based on systems pharmacology model'.

Software tool for the compilation of Heta-based QSP modeling platform

Open Source QSP model describing SARS-CoV-2 virus and host cell life cycles, immune response and therapeutic treatments

SynProtX is a deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance the prediction of synergistic effects in anti-cancer drug combinations.

Open-source framework for reproducible mechanistic virtual clinical trials, combining population PBPK simulation, trial design, physiological perturbation, PK analysis, immutable provenance, and researcher-ready reporting.

Parsing and transformation of units of measurements

Code for transformation of Matlab/Simbiology model to JSON format

A from-source reproduction of the Shah & Betts platform antibody PBPK model, applied to denosumab bone-tissue exposure, validated against the published bone ABC benchmark

A statistical framework for detecting significant drug combination synergies in cancer. By leveraging tissue-specific reference null distributions across multiple synergy metrics, we compute empirical p-values to standardize synergy detection, uncover novel interactions, and enable rigorous evaluation of drug combinations.

DRIFT (Drug-target Response Integrated Flux Trajectory) is a multi-scale stochastic framework designed to bridge the gap between molecular binding events and systemic metabolic phenotypes.

Utilities for working with SLV and DAT files.

Several lectures on Cancer Systems Pharmacology for IGP Bioregulation II

Accessory R functions to support DBSolveOptimum

Physiologically based pharmacokinetic-pharmacodynamic (PBPK/PD) model of oral melatonin with circadian oscillator coupling, virtual population simulation, and interactive Shiny app for personalized dosing.

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AI VIVO (AIVIVO LTD) is a Cambridge, England based drug-discovery company that combines systems pharmacology with artificial intelligence to accelerate the identification and de-risking of therapeutic candidates.