Program scope

RapidCell is designed for large-scale simulations of chemotaxis performed by bacterium E. coli. Single-cell simulation is ok, too.

No fancy graphic, but detailed output about each bacterium at any moment. Works under all operating systems.

The high-throughput data can be analysed in Matlab or similar software.

Key features

Simulation of cells swimming in 2D with realistic run and tumble times, and with effect of rotational diffusion.

Simultaneous running of up to 1,000,000 cells on your desktop (no need for parallel/super computer).

Model correctly reproduces the high sensitivity of the chemotactic pathway (FRET experiments).

Multiple flagellar motors are simulated explicitly (!), and their number affect run and tumble times.

Gradient of attractant can be chosen from 8 pre-defined shapes, or defined by user.

Composition of receptor cluster (Tar and Tsr receptors) can be defined by user.

Protein levels (CheA, CheR, CheB, CheY) can be altered to simulate mutants.

Runs on any operational system (tested on Windows XP, Suse Linux, Mac OS X).

Source code is simple and open.

FAQ

Q: Does it simulate cell swimming in 3D?

A: No, RapidCell simulates swimming of cells in 2D space, which is sufficient for most research applications. For a full 3D simulation, you may try a full-scale simulator AgentCell, which inspired the development of RapidCell.

Q: How is the chemotaxis pathway simulated?

A: It is simulated in a hybrid way, that is neither purely by differential equations nor stochastically, but using a hybrid of both. 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). This enables high performance of the program and desired accuracy. See (Vladimirov et al., 2008) for full model description.

Q: Is it accurate?

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. 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. It is as realistic as I could make it based on available experimental data.

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Downloads

Download RapidCell with GUI (all OS)

Program in platform-independent Java class-files, along with sources. GUI is written in Java Swing using Eclipse SDK, and it was tested under Windows XP, MacOS X and Linux Suse 10.2.

Here you can download previous version (1.3)

Screenshots

How to run RapidCell

Unpack RapidCell into your home folder. If you are Windows user, double click on RapidCellwin.exe. In other operating systems, open the terminal window.
Make sure Java is installed in your system (check Java here).

Using the terminal window, go to the RapidCell directory cd YOUR_HOME_FOLDER/RapidCell;
Run the precompiled binaries (*.class files):
java -cp ./bin Run Set the desired parameters and click Run button. After RapidCell is complete, the output is written into 2 txt-files (tab-delimited):

individuals.out 

(variables of individual cells over time)

averages.out 

(variables over time, averaged over the population)

Analysis of output in Matlab, Python, or R

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Compilation from sources

The program is already compiled and runs as is. If you changed the sources, you need to compile them again. Here are short instructions. Make sure that  javac command works in your current directory. If not, check that you have the Java SE Development Kit 6 (JDK 6), or download the latest version from http://java.sun.com/javase/6/download.jsp (download the JDK, not the JRE.)

If  javac command still does not work after JDK installation, set up the PATH variable to include your JDK binaries folder (jdk1.6.0_<version>/bin). See more information about setting PATH at Java Tutorial

Compile the program javac *.java Run the program java -cp . Run

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Copyright

You can freely use the RapidCell program and any of its parts for academic or educational purposes (non-commercial), using citation of the original paper (Vladimirov et al., 2008).

References

1. Vladimirov, N., Lebiedz, D., Sourjik, V. (2010) Predicted auxiliary navigation mechanism of peritrichous chemotactic bacteria. PLoS Comput Biol 6(3): e1000717.
2. Vladimirov, N., Sourjik, V. (2009) Chemotaxis: how bacteria use memory. (REVIEW). Biological Chemistry 2009 Nov; 390(11):1097-104. download PDF, 139 Kb
3. Vladimirov, N. (2009) Multiscale Modeling of Bacterial Chemotaxis. PhD Thesis. University of Heidelberg. download PDF, 9,257 Kb
4. Vladimirov N, Løvdok L, Lebiedz D, Sourjik V, (2008). Dependence of bacterial chemotaxis on gradient shape and adaptation rate. PLoS Comput Biol 4(12): e1000242. Free text in PubMed
   

Contact

Please, feel free to report bugs, give suggestions and provide any other feedback to the author, Nikita Vladimirov, PhD (nikita.vladimirov AT gmail.com). About the author

Any collaboration is highly welcome!

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