This is the development home of the workflow management system Snakemake. For general information, see

Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

Pyzotero: a Python client for the Zotero API

Jupyter notebook integration with Spyder

Generate API documentation with quarto

A cool place to store your Hi-C

ModuleFormer is a MoE-based architecture that includes two different types of experts: stick-breaking attention heads and feedforward experts. We released a collection of ModuleFormer-based Languag…

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

a snakemake pipeline to process ChIP-seq files from GEO or in-house

[IJCAI 2024] FactCHD: Benchmarking Fact-Conflicting Hallucination Detection

A fast and efficient tool for converting chromatin interaction data between genome assemblies

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Sims 4 Scripting Boilerplate Project

A legacy repository. Was replaced by distiller, cooler, and cooltools.

Relates to the article by Lioy, Cournac et al., Cell, 2018 (Functional partitioning of a bacterial chromosome through the interplay of nucleoid- associated proteins and the condensin MukBEF)