Computing

Introduction

Besides the biological aspects, the course will offer an intensive introduction to computing for biological research. We request that all students bring a laptop, although we understand that this may not be possible for some. We will rely mainly on Open Source software. Installation discs will be available, but in case you want to familiarize yourself with the tools beforehand, they are listed here.

Mac OS X, Windows or Linux are fine - all the key software is available for each platform. Macs and Linux systems are preferred.

During the course we will assemble a digital record of the trip (using HTML), including reports and photographs. This will be loaded to the web after the course. All students will be expected to contribute to this digital record.

Document preparation

We will use OpenOffice for all word processing, presentations and spreadsheets. OpenOffice heavily uses Java, so make sure you have a Java Runtime Engine (JRE) installed (all Macs have this pre-installed; for Windows, the OpenOffice package contains a JRE). For macs, there is a special version of openoffice called NeoOffice. If you want to use OpenOffice on a Mac, you will need to make sure X11 is installed (pre-installed on new versions of OS X, or on your OS X install disks for earlier versions).

Make sure you have a PDF viewer: Adobe Reader for all platforms, Preview on Mac, various (e.g., xpdf) for linux.

HTML authoring and viewing

We will learn to write HTML directly, so you will need a good text editor:

• PSPad (Windows)
• NotePadPlus (Windows)
• TextWrangler (Mac)
• Taco HTML editor (Mac)

However, you may also like to download a WYSIWYG HTML editor, such as NVu. OpenOffice can also save as HTML.

• Please install Firefox, even if you have IE or Safari installed.

Raster image manipulation and viewing

• The GIMP
• Any of a large range of viewers, e.g. Irfanview, Imgv, gThumb. See Wikipedia's comparison of image viewers.

Vector image creation

• Inkscape

Statistical analysis

• R. Probably the most powerful and comprehensive platform for statistics and modeling. A tool for life!
• Please also install these packages:
  • ade4
  • adehabitat
  • ape
  • bipartite
  • cocorresp
  • CTFS
  • eco
  • ecodist
  • fossil
  • gam
  • gdata
  • gpclib
  • gtools
  • labdsv
  • maptools
  • mgcv
  • picante
  • pixmap
  • RColorBrewer
  • Rcmdr
  • rgl
  • sp
  • spdep
  • splancs
  • tripack
  • vegan
  • VR
  • waveslim
  NOTE: the package build must match the version of R you have installed. In most cases, downloading the most recent R (e.g., 2.9.0) and the current package, as listed on the package pages, should work---try it to check.

Reference management

• JabRef

Phylogenetic analysis

• General tool and character reconstruction: Mesquite
• Phylogeny reconstruction: Phylip
• Tree viewing: Treeview, or Archaeopteryx