ScrumPy Metabolic Modelling Software

There are two options for installing ScrumPy:

Native Installation:

  1. If you are running a Linux operating system, ( Debian >=7.0, Ubuntu >=14.04, centos >=8) download the latest version and refer to the installation instructions. It is also possible to install ScrumPy on other versions of Linux, depending on your technical knowledge - ask the instructors. Then jump to Getting started.

ScrumPy in a Virtual Machine:

For all other operating systems, ScrumPy can be run in a guest virtual machine on your computer, provided you have about 7GB of free disk space. Note that the virtual machine includes a Linux operating system so that it is completely stand-alone.

In order to do this you will first need to install virtualbox. For linux or mac we recommend 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.

Instructions

  1. Copy the large ScrumPy.ova file from the USB drive provided onto your computer. It is also available for download from our server, but this will tale a long time and is not recommended.

  2. Start VirtualBox on your computer. Select Import appliance from the File menu and choose the ScrumPy.ova file. Wait several minutes whilst this configures.

  3. ScrumPy will appear on the VirtualBox Manager window. Select it and run it.

  4. 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.

  5. Wait whilst Linux operating system starts up. At the login screen, give your user name as scrumpy and password as scrumpy

Note

The virtual machine comes 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

  1. Open a terminal window. If you are running the virtual machine, click on Terminal under the Applications/Accessories menu item, or on the computer icon on the menu bar if it appears.

  2. Create a directory for your models.

  3. Type "ScrumPy", and it will start. Continue to the practical instructions for what to do next.