Pre-arrival Instructions
Internet Access
- We will be accessing the internet during the course. There are wireless networks in St Anne's, and you will be given a temporary user name and password on the Oxford wireless network. However, a more convenient and longer-lived solution is to enrol in Eduroam at your institution (if this is available, which it will be for most UK and Europena universities. Consult your local network for instructions and sign up before the course.
BioCyc database access
The software we use during the course makes use of the BioCyc collection of databases, partial copies of which will end up on your laptop (see below). You should visit the BioCyc license page and complete the form there.
Install VirtualBox on your laptop
- You are expected to bring a laptop to the course; none will be provided. You will need about 3 Gb of disc space, and small netbook devices or similar may not be sufficiently powerful.
To simplify software installation and behaviour issues, we provide the software we use in the course as a 'virtual machine' to run on your computer (of whatever type) with VirtualBox virtualisation software. Please go to this page for instruction, but only go as far as getting VirtualBox installed.
Do not download ScrumPy.ova yet as we are still producing the version for this course. We will tell you when to do so, or else distribute it on the first day of the course. If things go wrong or do not seem to work, we will resolve them in the first practical session at the workshop.
If your laptop is running a Linux operating system, you may instead try installing ScrumPy according to the instructions. If it doesn't seem to work, we can look at that also in the first practical session.
Maths revision
For those of you whose maths is a distant memory, don't worry; we will try to explain the necessary concepts. We will, however, make reference to matrix and vector notation. If you want to prepare beforehand, take a look at these slides. If this leaves you puzzled, we may incorporate some tutorials on the maths early in the course.
Starting with Python
Our modelling software is a set of modules for the programming language Python (to be exact, Python 2). We will cover the basics that you need to know about Python during the practicals in the course. If, however, you are unused to computer programming, and would like to prepare for the course, you could take a look at these condensed instructions before the course. If you want to practise the language in advance of the course, then you may need to download Python for your computer's operating system to get started. Python is an interpreted language, so type python in a terminal/command window Control-D will exit from the Python interpreter.