- Web report
- Open Access
Monte Carlo cell simulations
- Chaitanya Athale
© BioMed Central Ltd 2001
- Received: 11 November 2001
- Published: 21 December 2001
The general Monte Carlo simulator of cellular microphysiology (MCell) on this site is a program that allows three-dimensional dynamic simulations of subcellular architecture and physiology
- Monte Carlo Simulation
- Cell Analysis
- Visualization Tool
- Cellular Physiology
- National Resource
A MCell mirror site is available.
The general Monte Carlo simulator of cellular microphysiology (MCell) on this site is a program that allows three-dimensional dynamic simulations of subcellular architecture and physiology. In addition to an introduction to the modeling of cellular physiology, details of probability and random-event-based methods and complex geometry generation are discussed. The MCell program can be downloaded after registration (free to academic users). The site provides a good introduction to researchers interested in using Monte Carlo Simulations (a random number based simulation method, with the physical process simulated directly by sampling a probability distribution function) to answer questions in cellular physiology and structure, as well as having much to offer for users of the MCell tool. There are links to other simulation tools such as NEURON and GENESIS and visualization tool sites such as Open Visualization Data Explorer and POV-Ray. The minimal nature of the site and the clear introduction to the simulation of microphysiology are its most striking features.
There is no mention of when the site was last updated, but the new downloading facility for the program was added in October 2001.
Monte Carlo simulation methods are not widely represented in cell-simulation websites, so the good overview of modeling in cell biology and the relevance of the Monte Carlo approach is welcome.
A lack of clear links on every page makes navigation difficult.
A hyperlink to each of the beta-test laboratories to see concrete results from applications of MCell would be desirable.
The National Partnership for Advanced Computational Infrastructure (NPACI) is an affiliate that supports efforts to parallelize (modify the program to do many calculations on different processors at the same time to speedup the program) the MCell tool. Related tools for modeling microphysiology are Virtual Cell at the National Resource for Cell Analysis and Modeling, StochSim for stochastic kinetics, Nanosimulation of the cytoskeleton for simulation of the cytoskeleton, and bio-medical data visualization tools such as Amira.