Team:BCCS-Bristol/Modeling-Software

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BSim

Pre-Compiled Versions

[http://2008sw.igem.org/bccs_bristol/bin/BSim.jar BSim.jar] (Compiled on Mac OS X 10.5.5 (Intel) using Java 1.5.0_16) - If problems are experienced using this JAR file this may be related to the version of Java that you are using. In this case we recommend compiling the program from the source code available on this page.

Source Code

[http://2008sw.igem.org/bccs_bristol/src/BSim_Source.zip BSim Source Code] (zip file)

User Guide

BSim User Guide

Acknowledgements

We would like to acknowledge the use of several export libraries provided by the following people.

  • Werner Randelshofer ([http://www.randelshofer.ch http://www.randelshofer.ch]) - QuickTimeExportStream class which allows for movies to be written to a file.
  • David J. Eisenberg (david@catcode.com) - PNGEncoder.java class that allows for a graphic context to be written to a file.

GRN Matlab Scripts

Sender

[http://2008sw.igem.org/bccs_bristol/src/GRN/sender.m Sender GRN] - Models the concentrations of mRNA and proteins for the sender part of the GRN.

[http://2008sw.igem.org/bccs_bristol/src/GRN/varyCpxR.m Vary CpxR concentration] - Shows levels of AHL outputted by sender when CpMax is varied.

Transport

[http://2008sw.igem.org/bccs_bristol/src/GRN/transport.m Transport] - Analyses how the concentration of a given chemical varies over time due to a diffusion process.

Reciever

[http://2008sw.igem.org/bccs_bristol/src/GRN/reciever.m Reciever GRN] - Models the concentrations of mRNA and proteins for the reciever part of the GRN.

[http://2008sw.igem.org/bccs_bristol/src/GRN/compareRecieverInput.m Vary AHL concentration] - Shows levels of mCherry outputted by reciever when levels of AHL are varied.


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