Basics
- Windows 10/8.x/7
- Mac
- Linux
- 1.3GHz or faster processor
- 2 GB RAM or greater
- 1024*768 screen resolution
- Java Runtime Environment 8 (or higher)
- R 3.4 (or higher) [optional]
MOG is freely available to download from http://metnetweb.gdcb.iastate.edu/MetNet_MetaOmGraph.htm. Click the download button, and then download the .zip file. Unzip the downloaded file to get a .jar file, this is the MOG program. MOG’s source code is available at https://github.com/urmi-21/MetaOmGraph/.
It’s a lot easier to get started with an existing project. So select and download a ready-to-go project from MOG [the same page that you download MOG from (http://metnetweb.gdcb.iastate.edu/MetNet_MetaOmGraph.htm)], there are several pre-compiled MOG projects to choose from. These are vetted projects, most containing public transcriptomics data of thousands of samples of RNA-Seq (from NCBI-SRA) or Affymetrix, and the sample metadata. Because we must rely on existing metadata we download from NCBI-SRA, the information about each sample is only as accurate and comprehensive as what the researchers entered. http://metnetweb.gdcb.iastate.edu/MetNet_MetaOmGraph.htm and download it.
IMPORTANT: Keep each of the three project files (the .mog file, the metadata file, and the data file) in the same directory [folder] (It is OK to add other files to the folder).
DOUBLE CLICK on the .jar file icon. After starting MOG correctly, MOG’s welcome dialog will be displayed on the screen.
Figure 2: MOG welcome dialog
With large data sets, more memory is needed for a few operations like PCA, t-SNE e.t.c, it is advised to run the MOG with more memory. This can be done either by running the command or by using the poweshell script provided along with the jar file.
- Open command prompt in windows and terminal in MAC.
- Navigate to the MOG directory in the command prompt/terminal using "cd" command or Copy the mog folder to the known location/directory and use "cd" to point the command line/terminal to the MOG jar file location/directory.
- Run the command: java -Xms4g -Xmx6g -jar mog-1.8.2.jar
mog-1.8.2.jar is the mog file, If you changed the file to a different name, give that file name instead of this. -Xms4g -Xmx6g: -Xms sets the initial memory and -Xmx sets the maximum memory. 4g represents 4 GB of initial memory, 6g represents 6 GB of maximum memory.
- Powershell : Powershell is required to use this approach. Download the powershell using the below provided links
- Windows: https://docs.microsoft.com/en-us/powershell/scripting/install/installing-powershell-on-windows?view=powershell-7.1#msi
- Mac: https://docs.microsoft.com/en-us/powershell/scripting/install/installing-powershell-on-macos?view=powershell-7.1#installation-of-latest-stable-release-via-homebrew-on-macos-1013-or-higher (recommended to use the homebrew i.e. brew install --cask powershell)
- Linux: https://docs.microsoft.com/en-us/powershell/scripting/install/installing-powershell-on-linux?view=powershell-7.1
Once the powershell is installed, double click on the "Mog_RunProvidingMoreMemory.ps1" file. It will prompt to enter the minimum and maximum memory(RAM) that you want to provide to MOG and MOG will start.
Verify that the powershell is installed correctly or not by typing "pwsh" in the terminal. If it is installed properly, you can find "PS" prepended to the line in the terminal like : PS /Users/xxxxx. Now, navigate to the MOG directory in the terminal using "cd" command or Copy the mog folder to the known location/directory and use "cd" to point the command line/terminal to the MOG jar file location/directory. Once you are in the mog folder, type "Mog_RunProvidingMoreMemory.ps1" in the terminal and it will prompt to enter the minimum and maximum memory(RAM) that you want to provide to MOG and MOG will start.
Multiple conflicting Java versions in MAC can create errors in starting MOG. To resolve this, follow the below steps:
- Open the terminal window (Press 'cmd' + 'space' to open spotlight search and type terminal, and press 'enter')
- Copy paste the below commands in the terminal to remove all the Java versions:
sudo rm -rf /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin sudo rm -rf /Library/PreferencePanes/JavaControlPanel.prefPane sudo rm -rf /Library/Application\ Support/Oracle/Java/ sudo rm -rf /Library/Java/JavaVirtualMachines - Go to https://java.com/en/ to download and install Java.
- MOG should now start without any problems.