UW Bio UW ChemE eScience AICS
Lab Affiliations: NU CSB NU NICO UW CMB

Published Code


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.


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.


Dynamic Inference Of NEtwork Structure Using Singular values (DIONESUS) is a scalable recursive algorithm based on partial least squares regression. On a millisecond time-scale, this algorithm reconstructs a large phosphoproteomic signaling network from microwestern array data. Coming soon!


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.

Data Browsers

Network inference performance complexity

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