EFM Calculation

Running EFMtool from DOS prompt (other OSs would be similar)

  • Download cna2efmtool.m for conversion of CNA models to native EFMtool models.
    Instructions for use are contained within the file.
  • Download and extract the .bat file, Dos Execution batch file and place in a directory with an extracted efmtool instance, put the 4 files from the converter in "..\efmtool\tmp", and execute the batch file.
  • You can edit the .bat file for your circumstances, to adjust the -Xmx option as described in "update Java.opts" below, or take advantage of EFMtool options not available in CNA. Refer to CreateFluxModeOpts.m for a description of EFMtool options.

As of CellNetAnalyzer version 2013.1 the material discussed below is no longer relevent, it remains so that those users who opt to continue use of version 2012.1 or lower may be aware and informed.

Maximizing CellNetAnalyzer (CNA) Performance in 64-bit environments

Mex Files
Some functions within CNA are accelerated through the use of precompiled code (mex files). The CNA authors currently only provide pre-compiled 32-bit mex files. Thus, these features are unavailable on 64-bit systems. The source code for the mex files is provided with CNA package and can be recompiled in MATLAB 64-bit. We compiled Windows versions of these files and for convenience provide them for download here. The CNA manual and the MATLAB documentation describe the process necessary to compile the source code.

EFMtool upgrade
The EFMtool version supplied with CNA is an old version (ver. 4.4.4). This is easily corrected by replacing it after you have installed CNA.

CalculateFluxModes Bug
A further complication is that the 4.4.4 version of EFMtool contains a bug in in CalculateFluxModes.m; however, the authors of CNA added their own code to this file to make it work with CNA. We have merged the CNA version with the latest version of this file to restore full EFMtool functionality to CNA.

Update Java.opts
Updated: Prior to 18 september 2013, this file wasn't downloading properly.
The java.opts file is used by CNA to define the Java settings for EFMtool. The provided file isn't optimal. Our java.opts file optimizes the Java VM for EFMtool.

  • Download the java.opts file
  • Edit the -Xmx parameter to match your computer's RAM by allowing 2 GB for the OS. For example if you have 48 GB of RAM, set this to -Xmx46g.
  • Put this file at "..\CellNetAnalyzer\code\ext\efmtool".

There have been issues with this file downloading correctly. With word wrap on, the file should appear as below: java.opts