v2.0.0

Downloading and Installing BiMS

0) Prerequisites

BiMS needs Java and R (with the packages rJava, MALDIquant 1.6 and MassSpecWavelet 2.12) in order to work, so you will have to install them before start with this installation process.

You can find the installation files and instructions of this programs in their respective web pages:

Alternatively, once you have installed R, you can also run the following script to install the needed libraries:

							#Install rJava 
							install.packages("rJava")
							#Install MALDIquant
							install.packages( "MALDIquant", "MALDIquantForeign")
							#Install MassSpecWavelet 
							source("http://bioconductor.org/biocLite.R")
							biocLite("MassSpecWavelet")

1) Download

You have two options:

  • Download your BiMS copy from here (49 MB) and go to step 2.
  • Or you can download this Ubuntu 11.04 (32 bits) Virtual Machine (~1.5 GB) with a copy of BiMS and R with the neccesary packages already installed and configured. Run the virtual machine (you will need Virtual Box) and go to step 4.
If you have some trouble installing the BiMS VM, you can check our BiMS VM - Quick Installation Guide.

BiMS directory structure
Figure 1. BiMS file structure

2) Descompress

Decompress the downloaded file (you will need a ZIP decompressor).

Once decompressed you should have a directory structure like seen in Figure 1.

3) Configure

Before start working with BiMS you have to: (i) set R environment variables, (ii) include R shared libraries in LD_LIBRARY_PATH and (iii) set he directory holding the JRI shared library (libjri.so). If you are under a Windows envirnoment you have to edit the run.bat file. Otherwise, if you are under a Linux environment you have to edit the run.sh file.

Under Linux, the run.sh must look like:

							# Set R environment variables.
							export R_HOME=/usr/lib/R
							export R_SHARE_DIR=/usr/share/R/share 
							export R_INCLUDE_DIR=/usr/share/R/include
							export R_DOC_DIR=/usr/share/R/doc
							export R_LIBS_USER=${HOME}/R/i686-pc-linux-gnu-library/2.15

							# Include R shared libraries in LD_LIBRARY_PATH.
							export LD_LIBRARY_PATH=${R_HOME}/lib:${R_HOME}/bin

							# The directory holding the JRI shared library (libjri.so).
							JRI_LIB_PATH=${HOME}/R/i686-pc-linux-gnu-library/2.15/rJava/jri


Under Windows, the run.bat must look like:
							rem Set R environment variables.
							set R_HOME=C:\Program Files\R\R-2.15.1
							set R_SHARE_DIR=%R_HOME%\share 
							set R_INCLUDE_DIR=%R_HOME%\include
							set R_DOC_DIR=%R_HOME%\doc
							set R_LIBS_USER=C:\Users\hlfernandez\Documents\R\win-library\2.15

							rem Include R DLLs in PATH.
							set PATH=%PATH%;%R_HOME%\bin\x64

							rem The directory holding the JRI shared library (libjri.so).
							set JRI_LIB_PATH=%R_HOME%\library\rJava\jri\x64

4) Launch BiMS

In case you are under a Windows environment you have to execute the run.bat file. Otherwise, if you are under a Linux environment you have to execute the run.sh file.

Now, you can follow the BiMS tutorial in order to know to use BiMS.

Here you can found two MALDI-TOF MS datasets which can be used as input for BiMS.

Windows Wine dataset (raw)
Wine-Dataset.zip (28.1 MB)
Wine dataset (raw, in mzXML format) employed in Julio Dinis de Miranda et. al. 2012:
Direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine as a powerful tool for classification purposes
Nunes-Miranda JD, Santos HM, Reboiro-Jato M, Fdez-Riverola F, Igrejas G, Lodeiro C and Capelo JL (2012) Talanta 91: 72-76
Windows Cancer dataset (preprocessed)
Cancer-Dataset.zip (0.3 MB)
Cancer dataset (preprocessed) employed in R. López-Cortés et. al. 2012:
Fast human serum profiling through chemical depletion coupled to gold-nanoparticle-assisted protein separation.
López-Cortés R, Oliveira E, Núñez C, Lodeiro C, Páez de la Cadena M, Fdez-Riverola F, López-Fernández H, Reboiro-Jato M, Glez-Peña D, Capelo JL and Santos HM (2012) Talanta 100: 239-245.

Source code of BiMS is published in SourceForge and publicly available for download at https://sourceforge.net/projects/bims/