ClusterFinder

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Description

clusterfinder website  

ClusterFinder - metabolomic peak characterization and processing. The distinctive peak patterns are used in the interpretation of the resulting composite spectra because it is possible to discriminate the origin of every peak in the composite; 12C-derived molecules, 13C-derived molecules, artifacts and derivatives of exogenously applied compounds. The software package ClusterFinder™, achieves a data reduction of complex raw data, to concise, high value information:

Step 1: Characterize all peaks according to source (artifact, experimental (12C), control (13C), or standard)

Step 2: Remove all artifacts

Step 3: Align and pair all remaining peaks across all scans

Step 4: Normalize and identify all pairs

Step 5: Determine the relative 12C/13C ratios of analytes in each sample.

Step 6: Determine the statistical variance of the sample ratios.

Required Modules

Serial

  • clusterfinder

System Variables

  • HPC_CLUSTERFINDER_DIR - installation directory

Additional Information

Please note that the clusterfinder environment module is mainly used for deploying a new ClusterFinder (CF) release or for changing the 'clusterfinder' and 'clusterfinder-$version' symlinks. Once a CF release has been deployed it is not necessary to load that particular environment module to run 'clusterfinder' or 'clusterfinder-version' (E.g.: 'clusterfinder-718') for runing CF on the secim-svcs node, but it's needed for SLURM gui sessions.

To run the latest CF with Xpra within a SLURM gui session:

  • Load the gui module
module load gui
  • Start a gui session with the 'launch_clusterfinder_gui' command.
launch_clusterfinder_gui

If no arguments are provided default resources will be requested. See output of 'launch_clusterfinder_gui -h' command for the full help message.

To make a different resource request e..g 8gb of memory and 48 hour time limit add the respective arguments:

launch_clusterfinder_gui -m 8 -t 48
  • Run the client command that you see in the output of launch_clusterfinder_gui in a terminal on the client computer. See Xpra Windows Installation for details if you run Windows.

E.g. for user 'jdoe' with a session on i42a-s11.rc.ufl.edu on X11 port 1415 the listed client command to be pasted into MobaXTerm will be

xpra attach ssh:jdoe@i42a-s11.rc.ufl.edu:1415

The CF window should open up on your local machine.

Click on the MobaXTerm and use the Ctrl+c key combination to detach the connection, so you could reconnect later, say to monitor a run.

Usage Policy

ClusterFinder is licensed software. Please contact IROA Technologies with licensing questions. Licensed users need to be added to the 'clusterfinder' group for software deployment. Please open a support request to be added after a verification.