Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI

Multiscale Developments of the Cellular Potts Model

(2012) M. Scianna et al.   MULTISCALE MODELING & SIMULATION

Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion

(2012) Vivi Andasari et al.   PLoS One

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

Software that goes with the flow in systems biology

(2010) Michael Hucka et al.   BMC BIOLOGY

A hybrid approach to multi-scale modelling of cancer

(2010) J. M. Osborne et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration

(2010) S. Hoehme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems

(2009) T. Sutterlin et al.   BIOINFORMATICS

Chaste: A test-driven approach to software development for biological modelling

(2009) Joe Pitt-Francis et al.   COMPUTER PHYSICS COMMUNICATIONS

Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis

(2009) Tao Sun et al.   PLoS One

Angiogenesis and vascular remodelling in normal and cancerous tissues

(2008) Markus R. Owen et al.   JOURNAL OF MATHEMATICAL BIOLOGY

GemCell: A generic platform for modeling multi-cellular biological systems

(2007) Hila Amir-Kroll et al.   THEORETICAL COMPUTER SCIENCE