ScrumPy Metabolic Modelling Software
There are two options for installing ScrumPy:
If you are running a Linux operating system, such as Debian (8.0 or later) or Ubuntu (12.04 or later) download the latest version and refer to the earlier slides. ScrumPy can also be installed on other versions of Linux, depending on your technical knowledge - ask the instructors. Then jump to Getting started.
For all other operating systems, ScrumPy can be run as a virtual machine on your computer, provided you have about 7GB of free disk space. In order to do this you will first need to install virtualbox. For linux or mac we reccomend installing virtualbox from your standard repository (aka "App store"). Windows users can find it on the virtualbox website. Install VirtualBox, then follow the instructions below. If you use Windows, defragmenting your disk before proceeding will improve subsequent performance, though it's not essential.
Installing the ScrumPy virtual machine
Either copy the large (2.4GB) Wheezy_ScrumPy.ova file from the DVD or USB drive provided or patiently download it from our webserver.
Start VirtualBox on your computer. Select Import appliance from the File menu and choose the Wheezy_ScrumPy.ova file. Wait several minutes whilst this configures.
Wheezy_ScrumPy will appear on the VirtualBox Manager window. Select it and run it.
- If virtual box produces an error message at this point, you need to enable virtualisation in your machine's BIOS. Ask one of the demonstrators if this is the case.
Wait whilst Linux starts up. At the login screen, give your user name as scrumpy and password as SCRUMPY
Note
The virtual machine come with an ordinary root account (not sudo). The default password for this account is also SCRUMPY. Obviously these are extremely insecure, so having logged in for the first time it is important that you change both these passwords, especially if you use the machine on an institutional network.
Changing Passwords
Instructions to follow.
Getting Started
Open a terminal window. If you are running the virtual machine, click on Terminal under the Applications/Accessories menu item.
- Create a directory for your models.
mkdir instructions to follow.
Type ScrumPy, and it will start.