Install and run COMETS

You are being re-directed to the new COMETS homepage (http://runcomets.org)

These instructions are relevant only for COMETS versions 1.x.x. The instructions to install and run COMETS version 2.0.0 and up are here.

In order to run COMETS you must have Java installed on your system. Java can be downloaded and installed from here. Make sure that you have the Java bin directory in your PATH system variable.

Installing COMETS

Windows:

COMETS for Windows is distributed as an archived .zip file. To extract it double-click on it or right-click and choose Extract All… This will create a directory comets_win_X_Y_Z, where X_Y_Z is the version number.

The directory contains two batch files: comets_w32 and comets_w64 for 32 and 64 bit architecture correspondingly. COMETS is run by double-clicking on one of the batch files. Choose the batch file that corresponds to your architecture.

Linux:

COMETS for Linux is distributed as an archived comets_X.Y.Z.tar.gz file, where X.Y.Z is the version number. To extract it, run it in a terminal:

$tar -zxvf comets_X.Y.Z.tar.gz

where X.Y.Z are replaced with the version numbers.

This will create a directory comets_X.Y.Z. It contains INSTALL file. To install and run COMETS read the INSTALL file.

Running COMETS

Graphical User Interface (GUI)

The command line to run COMETS with a Graphical User Interface (GUI) is:

java -classpath $COMETS:$GLPK-JAVA
     -Djava.library.path=$LIBGLPK:$LIBGLPK_JAVA
     edu.bu.segrelab.comets.Comets
     -loader edu.bu.segrelab.comets.fba.FBACometsLoader

where:

$COMETS is the path to the comets.jar executable .jar file,
$GLPK-JAVA is the path to the glpk-java.jar file,
$LIBGLPK and $LIBGLPK_JAVA are the paths to the directories where
GLPK and GLPK-JAVA libraries are installed.

In Linux the GLPK and GLPK-JAVA libraries are typically installed in:

$LIBGLPK=/usr/local/lib
$LIBGLPK_JAVA=/usr/local/lib/jni

The glpk-java.jar file is typically in:

$GLPK-JAVA=/usr/local/share/java/glpk-java.jar

The typical command line in Linux is therefore:
java -classpath ./comets.jar:/usr/local/share/java/glpk-java.jar
     -Djava.library.path=/usr/local/lib:/usr/local/lib/jni
     edu.bu.segrelab.comets.Comets
     -loader edu.bu.segrelab.comets.fba.FBACometsLoader

In the Windows comets_X_Y_Z package the comets.jar file is in the comets_X_Y_Z/bin directory and

the libraries are in the comets_X_Y_Z/lib directory.

Script File Option

COMETS can be run without the GUI by including the option -script in the command line:

java -classpath $COMETS:$GLPK-JAVA
     -Djava.library.path=$LIBGLPK:$LIBGLPK_JAVA
     edu.bu.segrelab.comets.Comets
     -loader edu.bu.segrelab.comets.fba.FBACometsLoader
     -script $SCRIPT

where $SCRIPT is the path to a script file. If the script file is in the
current directory, this path is simply

$SCRIPT=./script_file

where “script_file” is the name of the file.

The format of the script file is:

load_comets_parameters  filename
load_package_parameters  filename
load_layout  filename
batch_list_file output_filename
batch_param_1  start  increment  last
batch_param_2  start  increment  last
...
batch_param_N  start  increment  last

load_comets_parameters: This line tells the script where to find the comets parameters file
load_package_parameters: This line tells the script where to find the package parameters file (may be different for all packages)
load_layout: Tells the script where to find the COMETS layout file (contains model file information, media layout, etc.)
batch_list_file: Tells the script where to store the list of parameters that were applied to each batch run.
batch_param_N: Tells the script to perform a batch run, varying the given numerical (or boolean) parameter. This is similar to Matlab format: ‘start’ is the first value, then it is modified by ‘increment’ for each batch, until it reaches the ‘last’ value (or goes past it). If there are multiple batch runs, these are all layered together. So, for each increment of the first parameter, it will completely run batches while varying all proceeding parameters. The log files of each batch run will be named according to the batch numbers given in batch_list_file, so it’s useful to include that line.

Parameters Files Option

When COMETS starts a set of default values for its parameters is loaded. These default values can be overwritten using the -params and -pkgparams command options. Either or both of the two options should be appended to the command line as:

-params parameters_file

-pkgparams package_parameters_file

The two parameters files contain the values of the general parameters, such as number of threads, names of output files etc. in the parameters_file and package specific, for example FBA specific, parameters in the package_parameters_file. Detailed description of the parameters and their default values is here.