Multiscale Modelling Tool: Mathematical modelling of collective behaviour without the maths

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

(2018) J. Kyle Medley et al.   PLoS Computational Biology

Ten simple rules for documenting scientific software

(2018) Benjamin D. Lee   PLoS Computational Biology

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

(2016) Brian Drawert et al.   PLoS Computational Biology

A Design Pattern for Decentralised Decision Making

(2015) Andreagiovanni Reina et al.   PLoS One

Perspective: Stochastic algorithms for chemical kinetics

(2013) Daniel T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

A Mechanism for Value-Sensitive Decision-Making

(2013) Darren Pais et al.   PLoS One

StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes

(2013) Timo R. Maarleveld et al.   PLoS One

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

(2012) Philipp Thomas et al.   PLoS One

StochKit2: software for discrete stochastic simulation of biochemical systems with events

(2011) K. R. Sanft et al.   BIOINFORMATICS

Stop Signals Provide Cross Inhibition in Collective Decision-Making by Honeybee Swarms

(2011) T. D. Seeley et al.   SCIENCE

Efficient Formulations for Exact Stochastic Simulation of Chemical Systems

(2009) Sean Mauch et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Independence and interdependence in the nest-site choice by honeybee swarms: Agent-based models, analytical approaches and pattern formation

(2009) Tobias Galla   JOURNAL OF THEORETICAL BIOLOGY