Links

Some useful trypanosome links

This list is in no way supposed to be exhaustive, just some of the online resources that we go to most often. My apologies if you have been left out!

Gull lab - my ex lab.
Carrington lab - includes more trypanosome expression and tagging constructs.
Cross lab - lots of resources, protocols and information on growing trypanosomes, etc.
Clayton lab - more constructs for trypanosomes.
Horn lab - p2T7 derivatives and TrypanoFAN links. David Horn also maintains a great list of links to other trypanosome research labs.

GeneDB - curated pathogen (and other) genome resourses from the Wellcome Trust Sanger Centre.
TriTrypDB - genomic resourses with emphasis on integration of functional data. Part of EuPathDB family of databases developed by the labs of David Roos and Jessica Kissinger.
The T. brucei sequencing project based at the Wellcome Trust Sanger Centre.
TDR: tropical disease research - World Health Organisation site.
VSGdb - database of VSG sequences.

ImageJ - the fantastic Open Source image manipulation and analysis software. Free, runs on any operating system and includes 2 great scripting methods making the whole package very customizable (cf. our own macros). The functionality of ImageJ has been hugely extended by the development by users of sets of plugins. Anyone with an interest in microscopy should check out the ImageJ for Microscopy collection and the LOCI bioformats library.
μmanager - Open Source software package for control of automated microscopes/cameras developed by Ron Vale's lab.
IMOD - package of tools for 3D modelling and analysis of tomograms, EM serial sections and optical sections.
R - statistical programming project.
Sanger software - various bioinformatics tools. We particularly like artemis and ACT.
Staden package - relatively simple sequence assembler.
Dendroscope - nice interactive viewer for phylogenetic and rooted networks information.
ApE: A Plasmid Editor - cross-platform plasmid editor.

SourceForge - Open Source software archive. Loads of applications.
OpenOffice - Open Source alternative to Microsoft Office that everyone should have. (Win/OSX/linux)
Inkscape - scalable vector graphics application similar to Adobe Illustrator, only better! Old Illustrator figures can be opened directly (some) or by saving in SVG format. (Win/OSX/linux)
Bibus - bibliographic referencing software to replace EndNote - works with OpenOffice. (Win/linux)
Firefox - why run Explorer when Firefox is available? (Win/OSX/linux)
Okular - my personal favourite from the many available PDF viewers. I also really like the commandline PDF toolkit for all sorts of pdf-related manipulation. (linux)
VLC - powerful and nice multimedia player/server for most kinds of video/audio. FFmpeg is also a really good tool for converting/filtering video and audio. (Win/OSX/linux)
K3b - useful CD/DVD writer. (linux)
Linux Mint - why not go linux? This is our current favourite distro.