Tootfinder

Column Generation for Periodic Timetabling
Stephanie Riedm\"uller, Niels Lindner
https://arxiv.org/abs/2510.12466 https://arxiv.org/pdf/2510.12466

Column Generation for Periodic Timetabling
Periodic timetabling for public transportation networks is typically modelled as a Periodic Event Scheduling Problem (PESP). Solving instances of the benchmark library PESPlib to optimality continues to pose a challenge. As a further approach towards this goal, we remodel the problem by a time discretization of the underlying graph and consider arc-based as well as path-based integer programming formulations. For the path-based case, we use cycles on the graph expansion of the operational lines…

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks
David Kou\v{r}il, Trevor Manz, Tereza Clarence, Nils Gehlenborg
https://arxiv.org/abs/2509.13290 …

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. Availability…