A-Cell Documents

A-Cell Documents

A-Cell Free Edition ; Introduction to A-Cell ; A-Cell Operation Manual ; A-Cell Leaflet

Learn Pathway Simulation in 10 Pages

Learn 4D Cell Simulation in 10 Pages

Learn Utilization of Cell Simulation in 10 Pages

Pathway Simulation by A-Cell: ERK Signal Transduction


A-Cell is cell simulation software. A-Cell model is constructed by the same way as you draw biochemical reactions on a paper. This enables wet experimental researchers to use A-Cell for simulating signal transduction of proteins under investigation and candidate druggable targets. In addition to pathways, models of equations, stimulation, and membrane potentials including action potentials (by Hodgkin-Huxley equation) are constructed by A-Cell.

You can watch movies on YouTube for constructing and simulating an A-Cell model of Michaelis-Menten type enzymatic reaction as an example of pathway simulation, and Simulated FRAP as an example of 4D cell simulation.

In addition, A-Cell offers a pronounced advantage of running 4D spatial-temporal simulations by constructing 3D shape and embedding reactions to local regions in the 3D shape model.

4D spatio-temporal simulation is essential, because it enables us to reach a conclusion that is not reached by simple pathway simulation. One example is shown here. The first step of cancer invasion is the development of small protrusions called invadopodia at the surface of cancer cells. On invadopodia, MT1-MMP, which is a membrane protein that degrade extracellular matrix (ECM), is highly expressed. In the simple pathway simulation, ECM was degraded as in experiments. In the 4D spatio-temporal simulation, however, ECM was not degraded. These results were curious, because a more realistic 4D model gave us a simulation result contradictory to the experimental observation. This implied that there existed unknown essential mechanism for ECM degradation. After an extensive search, we predicted that repetitive insertion of MT1-MMP was required for the ECM degradation, and in addition, the insertion interval should be shorter than 70 sec. These predictions by 4D simulation have been confirmed by wet experiments (Hoshino,D., et al., PLoS Comp.Biol., 2012, e1002479; Watanabe, A., et al., PLoS Comp.Biol., 2013, e1003086). We could not reach these unexpected results without 4D simulation. Thus, 4D simulation gives us essential mechanisms that are not revealed by pathway simulation without spatial modeling.

A-Cell has many distinctive features in addition to 4D simulation. All functions of A-Cell are described in “Introduction to A-Cell”. There are four editions of A-Cell. This will help in selecting an edition. Free edition of A-Cell is downloadable at the green banner on the top page. You can enjoy easy-to-use A-Cell environment.

Downloads A-Cell models in manuals

A-Cell models used in “Introduction to A-Cell” are downloadable here.

A-Cell models used in “A-Cell Operation manual” are downloadable here.

(When downloading models, a security warning may appear.)