ComputingAndSoftware

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.

Statistical analysis

• R. Probably the most powerful and comprehensive platform for statistics and modeling. A tool for life! (http://www.r-project.org).
  • Windows. Install R-2.3.1-win32.exe (or newer). Please also install these packages (or newer): CTFS_1.00, cocorresp_0.1-3, pixmap_0.4-4, eco_2.2-1, rgl_0.66, RColorBrewer_0.2-3, ecodist_1.01, sp_0.8-18, gam_0.96, spdep_0.3-25, Rcmdr_1.1-7, gdata_2.1.2, splancs_2.01-17, VR_7.2-27.1, gpclib_1.3-3, tripack_1.2-10, ade4_1.4-1, gtools_2.2.3, vegan_1.8-2, adehabitat_1.4, maptools_0.5-12, waveslim_1.5, ape_1.8-3, mgcv_1.3-17.

PDF preparation and viewing

• Open Office. Version 2.0.2 or newer. (http://www.openoffice.org)
• Adobe Acrobat Reader

HTML authoring

We will learn to write HTML directly. However, you may also like to download a WYSIWYG HTML editor, such as NVu (http://www.nvu.com)

• PSPad (Windows) (http://www.pspad.com)
• Taco HTML editor (Mac) (http://tacosw.com)

Image manipulation and viewing

• The GIMP (www.gimp.org)
• Any of a large range of viewers, e.g. Irfanview, Imgv, gThumb, ShowImg?... (see http://en.wikipedia.org/wiki/Comparison_of_image_viewers)

Reference management

• Jabref (http://jabref.sourceforge.net)