BIODICA Navigator: GUI for Independent Component Analysis for BIg Omics Data

BIODICA Navigator is a user-friendly environment for computation of independent components for omics data, using stability analysis and computing the optimal number of the components from their stabilities, and performing analyses for interpreting the results of ICA application.

BIODICA can work as Graphical User Interface (GUI) or in the command line mode.

BIODICA can use two computational cores for computing ICA: one (default) using Python and one using MATLAB.

Installation

For installing BIODICA Navigator

1. clone the repository into a local folder, with all files. Make sure that the name of the local folder does not contain spaces and hypens: otherwise, certain functions won't work. Do not use the name "BIODICA-master" which will be suggested by GitHub after downloading the repository!

2. check that the Java is installed. Java 1.8 or later version is required.

3. BIODICA Navigator uses Python implementation of ICA by default. For using it, one has to make sure that python command can be run from the command line and that stabilized-ica Python package is installed and accessible.

4. in case of using MATLAB ICA implementation (currently, it is of interest only for historical and compatibility reasons), the following instruction must be followed:

   4a) run install.bat (Windows) or install.sh in the root folder (this will copy the MATLAB RunTime binaries).

   4b) if you can use docker (recommended) for performing Matlab computations (then MATLAB or binaries are not required and no configuration of MATLAB Runtime is needed) then execute first

   docker pull auranic/biodica
   

   and change

   UseDocker = true
   

   in the config file.

Running BIODICA Navigator interface

Launch the BIODICA GUI by executing

java -jar BIODICA_GUI.jar

Running BIODICA from command line

To list all options for the command line use, execute

java -cp BIODICA_GUI.jar BIODICAPipeLine

Look at few examples of BIODICA command line use in cmdline_examples folder.

Tips and tricks:

It is not necessary to re-compute the ICA decomposition each time. Application of different procedures is possible for the results computed earlier, or even for the decompositions computed not with BIODICA. For example, the toppgene analysis can be launched by executing

java -cp BIODICA_GUI.jar BIODICAPipeLine -config config -sfile [path_to_metagene_file] -dotoppgene