title: Cell++--simulating biochemical pathways.
abstract: BACKGROUND
  With the generation of a wealth of information, detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context.
  
  
  RESULTS
  Focusing on three case studies, we highlight the potential impact of spatial organization in the evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic efficiency, simulations also demonstrated features consistent with the phenomenon of metabolic channeling.
  
  
  BACKGROUND
  Cell++ is licensed under the GNU general public license (GPL) and has been successfully implemented under Linux and IRIX operating systems. Source code together with a simple tutorial is available at http://www.compsysbio.org/CellSim/.
authors.affiliation: Hospital for Sick Children, 555 University Avenue Toronto, ON, M5G 1X8, Canada.
authors.forename: Chris
authors.initials: C
authors.lastname: Sanford
authors.forename: Matthew L K
authors.initials: ML
authors.lastname: Yip
authors.forename: Carl
authors.initials: C
authors.lastname: White
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
mesh_terms: D001671:Biochemistry / Q000379:methods*; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome