ARCADE

Agent-based Representation of Cells And Dynamic Environments (ARCADE) is a biological modeling framework for simulating complex, hetergeneous agents within dynamic environments. Available on Github here.

CARCADE

CAR T-cell Agent-based Representation of Cells And Dynamic Environments (CARCADE) is a biological modeling framework for simulating CAR T-cell therapies complex, hetergeneous solid tumors within dynamic environments. It was built by extending the ARCADE framework. Available on Github here.

DUETT

Detection of Unknown Events with Tunable Thresholds (DUETT) provides a systematic and automated method to detect RNA folding events in SHAPE-Seq datasets. Available on Github here.

PubMed modeling search strings

Python code that generates the search strings used in the Current Opinion in Biotechnology Multi-class and multi-scale models of complex biological phenomena review. Click here to download.

SWING

Sliding Window Inference for Network Generation (SWING) is a network inference framework that identifies associations between genes using time-series gene expression data. SWING is based on multivariate Granger causality and sliding window regression and is currently implemented in Python. Available on Github here.

Network inference performance complexity

Data browser for Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants. Click here to view.