The Virtual Cell

LoewLM, Schaff JC.The Virtual Cell a software environment for computational cell biology. Trends Biotechnol 2001 19 401-6. 

National Resource for Cell Analysis and Modeling (NRCAM), home of the Virtual Cell, http //www.nrcam.uchc.edu/ (accessed October 2, 2005)... 

Slepchenko BM, Schaff JC, Macara I, Loew LM. Quantitative cell biology with the Virtual Cell. Trends Cell Biol 2003 13 570-6. 

B. M. Slepchenko, J. C. Schaff, I. Macara, and L. M. Loew, Quantitative cell biology with the virtual cell. TRENDS Cell Biol. 13(11), 570 577 (2003). 

J.C. Schaff, B.M. Slepchenko, Y.S. Choi, J. Wagner, D. Resasco, L.M. Loew, Analysis of nonlinear dynamics on arbitrary geometries with the virtual cell, Chaos 2001, 11, 115-131. 

A Mathematical component based on the Virtual Cell Math Description Language (VCMDL) that allows for access of mathematical formulae behind the biological model. 

So far we have created a physiological model and a geometrical model. Now we link them to form a complete application in the Virtual Cell. Go to the Applications panel on the right side of the physiological model, right click on LEGI (Fig. 4a), select Create Deterministic Application, and enter the name (e.g., Needle ) of this new application. Double... 

Back in the Application window, select this simulation and click Run. The simulation request will be sent to the Virtual Cell server to compute, and Running status will indicate completed when the simulation is successful (Fig. 6b). 

The complete Virtual Cell implementation of the complementary LEGI model (12) is freely available in the Virtual Cell. To access this model, go to the menu options in the main model window. Click File -> Open Biomodel. Under Shared Models, choose LiuYang and open the LEGI model. 

In the Virtual Cell, the default units are pM for volumetric concentrations and molecules/pm for membrane-bound species. The spatial dimension is in pm. 

Quantitative Cell Biology with the Virtual Cell. 

The main advantage of virtual cells is that they facilitate modeling of a complex network system, in a system of multistage lines, where each stage (see Fig. 30.6) is a virtual cell Mj, its entry and exit buffers are By and Btj+i, and Qy is the supply flow of parts, from buffer By to the virtual cell Mj [16, 17, 19-21]. 

If the radius of particle plus the virtual cell is d, then the IPS defined in Figure 6 can be expressed as ... 

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