MicrobeMS: A Matlab Toolbox for Analysis of Microbial MALDI-TOF Mass Spectra.


What is MicrobeMS Downloading MicrobeMS How to install MicrobeMS License Conditions How to obtain a license

 
What is MicrobeMS?
Specification of computer configuration
Downloading MicrobeMS
How to install MicrobeMS pcode?
License Conditions
How to obtain a license?
What are the differences between 32-bit and 64-bit releases of MicrobeMS?
Relevant publications
Useful Links

What is MicrobeMS?
 
The software package available from MicrobeMS is a program designed specifically for the analysis of MALDI-TOF mass spectra from microbial samples. The MicrobeMS software was developed by Peter Lasch at the Robert-Koch-Institut (RKI) in Berlin/Germany and can be used to identify microbial strains and species based on their mass spectral patterns. The program is a Matlab-based comprehensive package that operates under Windows 2000/XP/Vista or Windows 7. Original MALDI-TOF mass spectra in the format defined by Bruker Daltonics can be imported, processed and converted to a Matlab data matrix format specific to the MicrobeMS program.
 
MicrobeMS was originally named after Peter Lasch's daughter Mara (M.A.R.A.-MS - software for Microbial ARchive Analysis), which was not a good idea at all (see this link!). Although the web pages have been already revised for the most part, the old name is still used in some instances (domain name, e-mail address, etc.)
 
The software permits standard mass spectral manipulations such as smoothing, baseline correction, normalization, peak detection, and other functions. Due to the fact that the software runs also in a complete Windows 64-bit environment the number of spectra in the data sets is limited only by the amount of available memory (RAM).
 
Specification of computer configuration
  1. Processor: 32-bit or 64-bit CPU from Intel or AMD (Matlab pcode), the stand-alone version requires a 64-bit CPU.
  2. Operating system: Microsoft Windows 2000/XP/Vista or 7/8/8.1 (32-bit or 64-bit version for Matlab pcode, 64-bit Windows for the stand-alone version of MicrobeMS)
  3. Matlab R2014a (The Mathworks) or newer (pcode version only)
  4. MATLAB Compiler Runtime (MCR), 64-bit version of MCR 8.3 (R2014a) (stand-alone version only)
  5. MicrobeMS will be installed either as a Matlab toolbox, or as a stand-alone software. Matlab pcode, or the installation archive for the stand-alone version can be both downloaded from this website.
  6. Memory: 2 GB (1024 MB) minimum. In order to use the full advantages of the 64-bit architecture, the amount of installed memory (RAM) should be larger than 4 GB (8-32 GB recommended).
Downloading MicrobeMS
 
microbems.v.080.setup.zip (MicrobeMS v.080 standalone (64-bit), Feb 2017)
 
microbems.v.078.setup.zip (MicrobeMS v.078 standalone (64-bit), Nov 2016)
 
pcode-microbems-v078.zip (MicrobeMS v.078, Matlab pcode, Oct 2016)
 
pcode-microbems-v073.zip (MicrobeMS v.073, Matlab pcode, Jun 2015 )
 
161027-ZENODO-Peaklist-(30-Peaks,fact-1,6).pkf MALDI-TOF MS data base required for identification, [Oct 2016],
   compatible with MicrobeMS version 0.78 and later, see also the publication A MALDI-TOF Mass Spectrometry Database
   for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch Institute (RKI)
at ZENODO
 
161027-ZENODO-Metadata.pdf documentation of the RKI MALDI-TOF MS data base
 
ecoli-filelist-oct16.muf (MALDI-TOF mass spectra from strains of Escherichia coli, not compatible with earlier versions of MicrobeMS < 0.78!)
 
ecoli-peaklist-oct16.pkf (peaklists of E. coli spectra, not compatible with earlier versions of MicrobeMS < 0.78!)
 
MALDI-Fields.xls MS Excel document required to define and write metadata
 
Escherichia.zip example data, original MALDI-TOF mass spectra (Escherichia coli, Bruker file format)
 

 
How to install MicrobeMS as a stand-alone application?
 
    Prerequisites:
     
  1. MicrobeMS is Matlab based, so please verify that the MATLAB Compiler Runtime (MCR) is installed (MCR R2014a [8.3] Windows, 64-bit version). If the MCR is not installed, download the Windows 64-bit version of the MCR for R2014a from the MathWorks web site by navigating to
     
    NOTE: Administrator rights are required for running the MCR installer.
     
    Installation of MicrobeMS (stand alone version):
     
  1. Login with your Windows user account. If you install MicrobeMS from the Windows administrator account the MicrobeMS installation routine will copy the main configuration file microbems.opt into a directory (C:\User\Administrator\Documents\MATLAB) which is not accessible when working later with your normal Windows user account!
  2.  
  3. Download and unzip the MicrobeMS installer microbems.v.0xx.setup.zip (see above)
  4.  
  5. Start microbems.v.0xx.setup.exe and follow then the instructions of the installation routine
  6.  
  7. The license file genkey.gen is not included in the installation package. To register for a free license please send an e-mail with your name and the name of the institution you are working for to the address lasch@microbe-ms.com
  8.  
  9. Copy the license key into the root directory of MicrobeMS (this is usually C:\program files(x86)\MicrobeMS\MicrobeMS, note that adminstrator rights may be required)
  10.  
How to install MicrobeMS pcode?
 
  1. Create an additional directory '\mass' in the existing toolbox directory structure of your Matlab installation. The complete path to the toolbox directory should be similar to
    'C:\program files\Matlab\R2014a\toolbox\matlab\mass' (may vary!) with C:\program files\Matlab\R2014a equaling the variable 'matlabroot'. You can check this variable by typing
     
      >> matlabroot
     
  2. at the Matlab command prompt. Note that the directory 'C:\program files\Matlab\R2014a\toolbox\matlab' should contain additional subdirectories such as \winfun oder \timefun.
     
  3. Unpack now the zip archive 'pcode-microbems-v0xy.zip' and copy all files into the new subdirectory ...\mass
  4.  
  5. Start Matlab and enter at the command prompt
     
      >> edit pathdef
     
  6. The editor will now load the file 'pathdef.m'. Add a new line with the complete path to the MicrobeMS pcode toolbox
     
      matlabroot,'\toolbox\matlab\mass;',...
     
  7. Save pathdef.m
  8.  
  9. Restart Matlab
  10.  
  11. To run MicrobeMS call the file 'mass.p' by typing
     
      >> mass
     
  12. Don't forget to copy your personal license key 'genkey.gen' (see above) into the directory '{userpath}\Matlab' (usually C:\User\YourUserName\Documents\Matlab, or alternatively in to the toolbox directory ...\mass!
  13.  
License Conditions
 
You are using the program at your own risk. We not take any responsibility for damages, problems etc. resulting from use of this program. We also does not give any warranty for bug-free operation, fitness for a particular purpose or the appropriate behavior of the program.
The software is provided 'AS IS'. For your personal use you can make copies and run as many instances as required, but it is not allowed to further distribute this software.
 
View the complete license agreement
 
If you do not accept all of the terms of this agreement, you shall have no right to download or use the MicrobeMS software.
 
All trademarks mentioned are property of their owners.
 
How to obtain a license?
 
Once you have accepted all terms of the license agreement you can download a free version of MicrobeMS. In order to run MicrobeMS an additional license key file ('keygen.gen') must be obtained.
 
In case of the pcode toolbox edition of MicrobeMS the key should be copied either into the directory '{userpath}\Matlab' (usually C:\User\YourUserName\Documents\Matlab), or directly into the toolbox directory ...\mass.
 
The license key for the stand-alone version should be copied into the root directory of MicrobeMS which is usually C:\program files (x86)\MicrobeMS\MicrobeMS (note that adminstrator rights may be required).
 
The individual license key is NOT included in the MicrobeMS installation package and will be send to you only on request. Please e-mail your request together with your name and an institutional address to the following e-mail address: lasch@microbe-ms.com.
 
What are the differences between the stand-alone and the Matlab pcode toolbox releases of MicrobeMS?
 
There are no functional differences between both software editions.
 
Relevant Publications Useful Links:
 
  1. What are the benefits of Microsoft Windows x64 Editions
  2. Link to The Mathworks:
  3. What are the benefits of 64-bit MATLAB versus 32-bit MATLAB?
  4. What is Matlab pcode? What is the difference between MATLAB code and P-code in MATLAB?


MicrobeMS - A Matlab Toolbox for Analysis of Microbial MALDI-TOF Mass Spectra

MicrobeMS Homepage

[ Publisher Details  |  Contact: lasch@microbe-ms.com  |  Copyright (c) 2004-2017 Peter Lasch. All rights reserved.]