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- MATLAB 2009 MACOS JDK MAC OS
- MATLAB 2009 MACOS JDK FULL
- MATLAB 2009 MACOS JDK SIMULATOR
- MATLAB 2009 MACOS JDK DOWNLOAD
(2009) Chemotaxis: how bacteria use memory. Navigation mechanism of peritrichous chemotactic bacteria.
MATLAB 2009 MACOS JDK DOWNLOAD
(JDK 6), or download the latest version fromĭoes not work after JDK installation, set up the PATH variable If not, check that you have the Java SE Development Kit 6 If you changed the sources, you need to compile them again. The program is already compiled and runs as is. (variables over time, averaged over the population)Īnalysis of output in Matlab, Python, or R (variables of individual cells over time) Set the desired parameters and click Run button.Īfter RapidCell is complete, the output is written into 2 txt-files Run the precompiled binaries (*.class files): Using the terminal window, go to the RapidCell directory Make sure Java is installed in your system In other operating systems, open the terminal window. If you are Windows user, double click on RapidCellwin.exe.
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GUI is written in Java Swing using Eclipse SDK, and it was tested under Windows XP, MacOS X and Linux Suse 10.2. Program in platform-independent Java class-files, along with sources. It is as realistic as I could make it based on available experimental data.ĭownloads Download RapidCell with GUI (all OS) Cellular parameters are taken from available literature: receptor cluster composition, number of flagellar motors per cell, cell swimming speed, rotational diffusion and the angle of cell tumbling. Yes, it accurately reproduces the main characteristics of cell response to attractant addition/removal: drop/rise of CheY-P, rate of receptor methylation and demethylation, clockwise and counter-clockwise switching times of flagellar motors, running and tumbling times of a swimming cell.
MATLAB 2009 MACOS JDK FULL
See (Vladimirov et al., 2008) for full model description. This enables high performance of the program and desired accuracy. Fast reactions are simulated by algebraic equations (ligand binding, phosphorylation of CheA and CheY), slow reactions by ordinary differential equations (receptor methylation/demethylation), and major stochastic events by stochastic methods (flagellar motor switching). Q: How is the chemotaxis pathway simulated?Ī: It is simulated in a hybrid way, that is neither purely by differential equations nor stochastically, but using a hybrid of both.
MATLAB 2009 MACOS JDK SIMULATOR
For a full 3D simulation, you may try a full-scale simulator AgentCell, which inspired the development of RapidCell.
MATLAB 2009 MACOS JDK MAC OS
Runs on any operational system (tested on Windows XP, Suse Linux, Mac OS X).Ī: No, RapidCell simulates swimming of cells in 2D space, which is sufficient for most research applications. Protein levels (CheA, CheR, CheB, CheY) can be altered to simulate mutants. Gradient of attractant can be chosen from 8 pre-defined shapes, or defined by user.Ĭomposition of receptor cluster (Tar and Tsr receptors) can be defined by user. Multiple flagellar motors are simulated explicitly (!), and their number affect run and tumble times. Model correctly reproduces the high sensitivity of the chemotactic pathway (FRET experiments). Simultaneous running of up to 1,000,000 cells on your desktop (no need for parallel/super computer). Simulation of cells swimming in 2D with realistic run and tumble times, and with effect of rotational diffusion.