Hello! In this very first note I would like to show you, step-by-step, how to install NeuroDebian – a Linux distribution for neuroscientists – on Windows using virtual machine. This is the best option if you want to learn how to use tools available in NeuroDebian but you don’t want to bother about installing and configuring Linux which, for the first time, may be a bit painful and would cost a lot of your precious time which could be better used for learning some fascinating neuroscientific stuff instead.
If you already have Linux – and more specifically Debian or Ubuntu – adding NeuroDebian functionality to it is very easy and you should not bother with installing NeuroDebian as a standalone system. In fact NeuroDebian is mainly a repository of neuroscience applications and adding it to your system is only two command away: follow instructions here.
If you are still here and want to install NeuroDebian on virtual machine then – let the show begin!
1. Introduction
To understand what we will do in a minute you should know what Virtual Machine (VM) is. Shortly speaking it is a program which emulates a computer and let you do almost everything which you could do with a real one inside this emulator. Let’s assume, that your computer is running Microsoft Windows – we call it a host system. Virtual Machine runs on a host system and allow you to install many guest systems – which runs on Virtual Machine. Now it may seem a little bit messy, but surely it will become more clear when we will bring theory into action.
Before you begin downloading and installing stuff make sure that your system is powerful enough to handle virtual machine. Because it will have to run two operating systems at once you will need at least 1 GB of RAM memory. Processor is not so important here but if your current system is running to slow for you than expect the guest system to run even slower. To make yours computers life easier turn off all not necessary programs while running Virtual Machine to free resources that it will need. You will also need at least 3 GB of space on your hard drive to store file with your guest system and the longer you use it and more programs you install on it – the larger this file gets.
Still here? Let’s begin!
2. Downloading
First we need to download virtual machine software – the emulator. One of the best comes from Oracle, is open source and is called Virtual Box and we will use it. It runs on all major versions of Windows, Linux and Mac. You can download it here: https://www.virtualbox.org/wiki/Downloads. Choose version appropriate for your system, probably the one for Windows. If you prefer other virtual machine (like VMware) you can also use it, but it must support *.ova files.
The second file we will need is NeuroDebian itself. You could download image of NeuroDebian and install it from scratch on virtual machine just like you would do it on your “real” computer, but there is much easier way. We will download image of already installed and configured system which we will load directly into Virtual Box. depending on your operating system you will have to download 32 bit version or 64 bit version. Most probably your Windows is 32 bit, but you can check it by clicking with right mouse button on “My computer” icon on desktop and selecting “properties”.
If you are experiencing problems with downloading NeuroDebian image – your connections hangs up and your download finishes before downloading entire file (which happened in my case) you can use some kind download manager – for example Flashget.
Lets check: now you should have two file downloaded somewhere on your computer: Virtual Box setup program (probably called VirtualBox-4.1.8-75467-Win.exe) and NeuroDebian image file (probably called NeuroDebian_6.0.5_i386.ova). If this is correct, let’s go to the next step and install Virtual Box!
3. Installing Virtual Box
Run setup file and follow instructions.
4. Importing NeuroDebian image into Virtual Box
Now that you have Virtual Box installed, *.ova files should be associated with it, so clicking on previously downloaded file NeuroDebian_6.0.5_i386.ova should import it into VirtualBox. You can also choose option “Import Appliance” from “File” menu in VirtualBox, as shown on picture below.
1. Choose "Import Appliance" from "File" menu
Now follow the steps shown on pictures below and described in captions below.
2. Click on "Choose"
3. Locate image file you downloaded in previous step
4. Change memory available to virtual machine to half the size of your computer's memory.
5. If you want to change localization of files were VirtualBox will store your guest system - you can do it here
6. Wait until image will be imported
5. Running imported NeuroDebian
Now that you imported downloaded NeuroDebian image select it on the left panel of Virtual Box and click “Run” on the left-top side of the screen. It should run a NeuroDebian in a new window.
7. Select imported system on the left panel and click "Start"
If everything works fine after a while you should see NeuroDebian desktop in a new Window. You can use it like a normal program – for example you can use your clipboard to copy and paste between your host system and NeuroDebian . You can also run it in a full-screen having a feel of standalone operating system.
Important detail to know is your username and password which are already set up for you:
user: brain
password: neurodebian
You will need them to install any new software or to change system settings. I recommend to change them, at least password. To do so: in NeuroDebian click System -> Preferences -> About me -> Change Password. In newly opened window type in current password (as mentioned above: “neurodebian”), click Authenticate and type your new password twice.
After first start NeuroDebian will show you welcome message and will ask you about updating your system. You can do it, although it may take some time depending on speed of your internet connection.
8. Neurodebian running in VirtualBox
To shut it down just choose “System -> shutdown” in NeuroDebian menu. In case NeuroDebian hangs or form some other cases you want to emulate pushing “power” or “reset” button you can do it by choosing appropriate options from “Machine” menu of VirtualBox window (the one in which NeuroDebian desktop is visible). There you can also “pause” the virtual machine – programs running on it will pause probably freeing some of your computers resources. Probably the most useful option from “Machine” menu is “close” -> “save the machine state” which enables you to save the state of virtual machine, close VirtualBox or even your computer and restore the guest system on virtual machine anytime you want.
6. Setting up shared folders
Sometimes you will need to transfer some files from your host system (ex. Windows) to the guest system (ex. NeuroDebian). The easiest way to do so is to set up a shared folder. Doing so is very easy and makes chosen folders on your host system accessible to your guest system just like if they were there. In other words, after setting a shared folder, you will see selected folder from the host system in the guest system and you will be able to write and read files to in it from both systems.
To add a shared folder:
- Open VirtualBox manager window
- Go to choose a desired virtual machine on the left panel
- Click on “Settings”
- Chose “Shared folders” – the last option on the left side of settings window
- Click on the small icon of folder with plus sign on it on the right side of the window or click with right mouse button in the “folder list”
- Select “Auto-mount” option
- Chose folder on host system you would like to share by clicking on the arrow right to “Folder Path” -> “Other” and localizing desired folder in the opened dialog window (shown on picture below).
- In “Folder name” you can give a name under which the folder will be visible in the guest system.
9. Setting shared folder
Now, that you have set shared folder in the VirtualBox settings you can run (or reset, if it’s already running) the guest system. The shared folder is visible under folder “Media” in main system folder. To go there click on “Computer” icon on the desktop, then “File system” -> “Media” and your folder should be there under the name you have given to it or under an original name in host system, with prefix “sf_” added. Now you can use it just like any other folder and any changes made to it in the guest or host system will be visible in the both of them.
More on using NeuroDebian and Virtual box soon!
Cognosco ergo sum 