Collected below are links (organised by subject) to web-sites where more information about the programs refered to within these pages may be found. Where possible the "homepage" for the software and its author are provided. This is by no means a comprehensive list of resources, but it should get you started.
Before asking questions a quick search of the internet will often lead you to a credible answer (remember that the internet is not peer reviewed, so don't take everything at face value). A couple of very useful web-sites for general information are given below.
Google - Regarded as the 'best' search engine on the net. It pays dividends to read the advanced search section as this greatly enhances your ability to find what you are looking for.
Wikipedia - An Open (i.e. any one can submit) On-line Encyclopedia.
Scirus - A Science Specific search engine.
If there are any obvious ommissions, broken links, or you'd just like to comment on the site, feel free to email me.
Links have been divided into sections for ease of navigation, use the shortcuts below to find the appropriate section
This section contains links to various resources for Genetic Analysis. If you're unsure where to start looking for software I'd recommend the Rockefeller University Linkage Site.
G2D - Candidate Genes to Inherited Diseases proritises genes within a genomic region according to their function in relation to a given disease using data mining and gene sequence analysis.
gMap.net - Web-based interface for genome mapping run by the Wellcome Trust Centre for Human Genetics.
SNPtagger - a web-based interface for tagging SNPs from inferred haplotypes
Tagger - on-line haplotype tagging tool.
SNP Spectral Decomposition - A web-interface for correcting for multiple testing of SNPs in LD.
Genetic Power Calculator - A suite of on-line interfaces for performing Power Calculations for Genetic studies (with instructions).
Hard-Weinberg Equilibrium & Case-Control association tests - A web-site that allows you to test for Hardy-Weinberg equilibrium in cases and controls independently and test for association. Generates de Finetti diagrams (Cannings & Edwards 1968), and allows multiple SNPs to be tested simultaenously.
htSNP finder - Altman Lab, Stanford University
Another web-based interface for tagging SNPs - written in Java (Ke & Cardon 2003)
Listed below are a collection of web-sites that details courses (MSc's and week long courses) related to the area of Genetic Epidemiology and Statistical Genetics
University of Sheffield - MSc Genetic Epidemiology - Individual Modules may be taken by non-students.
Netherlands Institute for Health Sciences - a series of week long Spring Courses on gene mapping (GE03; GE04; GE05; GE06).
GENESTAT - a useful on-line resource for statistical genetics.
You can always get the results you were hoping for by visiting the E-Z-LOD score calculator.
Because so many people cringe when the word statistics is mentioned I thought I'd include a section with links to resources on the net that will help you overcome your fear.
GraphPad (Includes a link to download a .pdf version of the book Analysing Data with GraphPad Prism)
There are innumerable specialised statistical mailing lists spread across the internet. A few for specific software packages are mentioned below, and a number of software packages that you will encounter, such as Haploview or Merlin, have their own mailing lists aimed at informing users when new releases are available. Given below is a link to the Stat-Transfer web-site that lists a number of statistically orientated mailing lists.
<Statistical Software Discussion Lists - a list of mailing lists for discussion of statistical software, statistics in general and specific statistical techniques.
R mailing lists - mailing lists associated with the R statistical software including SIG's (Special Interest Groups).
Stata is a statistical package for managing, analysing and graphing data. It is a superb piece of software that will be able to carry out virtually any analysis that you require (and a load you won't ever use). It is written in such a way that users may write their own modules for it, so even if a particular statistical test is not available in Stata, you can (if so inclined) write your own program and make it available to other users via the Internet.
Stata really is an excellent program (although maybe a little expensive for the individual user). There is however one criticism I have of Stata and that is its fairly awkward to 'pick up'. Whilst all of the commands are fully documented, you really need to know which function you wish to use in order to find the syntax of the command and how to use it. The majority of commands are intuitvely named, but it can be daunting if you're starting off using it on your own. For this reason I've included the links below to on-line resources for learning how to use Stata.
There is also an excellent Stata mailing list for users to post questions and queries which they are unable to resolve themselves. I've found this to be a very useful resource when I've become 'stuck' using Stata. Other subscribers are very helpful, but please read and follow the guidelines listed on the Statalist FAQ. Details of how to subscribe, and post queries to the list are also documented.
R is a GNU project that aims to freely implement the S statsicial language (essentially it is a free version of S-Plus). It is widely used by researchers world-wide, and like Stata has an extensible language. As a consequence there are also a large number of user written programs which can be obtained from one of the CRAN mirrors (Comprehensive R Archive Network).
R-project - Home page for the R project, check out the documentation section.
R FAQs - Fairly obvious.
R News - A newsletter for R which includes useful hints and tops.
R - Contributed - User contributed documentation for R (okay they may well be secondary, but they're listed on the R website).
CRAN Task View: Genetics in R - A list of genetics related R packages maintained by Gregor Grojanc.
SimHap - A Java front-end (to an R backend) for performing simulation based haplotype analyses of populations (Registration required).
Bioconductor - An open source project for the analysis and comprehension of genomic data (based on R).
Follow the links below to find out more information about the Human Genome Project
CEPH Database - On-line access to CEPH genotypes.
There are hundreds of statistical mailing lists out there on the web (some of which are already listed above. Rather than attempt to regurgitate a lot of whats already been written I simply point you to the excellent list maintained by Stat/Transfer, which maintains a very comprehensive list of Statistical Software Lists and the page even allows you to manage to your subscriptions.
The internet is an invaluable source of information for bioinformatics (it may even be argued that bioinformatics would not be in its current state if it were not for the internet) and the web-sites and databases below are all freely available to search. You may have to register to use some of them, but thats free as well
BLAST2GO - a universal Gene Ontology annotation, visualization and analysis tool for functional genomics research.
On-line Mendelian Inheritance in Man (OMIM) - Repository for linkage and association of genes to disease.
PEDRo - a database for experimental proteomics data.
Perlegen - Web-site for the company Perlegen.
s*star.org - online bioinformatics tutorials
UCSC Genome Bioinformatics - Data from the Human Genome Project.
Here are a few online resources for learning more about how to use some of the bioinformatics resources that are available.
The Scriptome - Protocols for Manipulating Biological Data
On-line Encyclopedia for Genetic Epidemiology - online resource for Genetic Epidemiologists.
Listed below are links to various Journals covering areas such as General Science, Human Genetics, Molecular Biology, Immunology and Medicine
Journals relating to statistics in biology and medicine.
Other links that may be of use...
A list of upcoming conferences in genetics, genomics and proteomics is available.
The links below provide a starting point for those who are new to LINUX, there are a number of links to some of the more popular LINUX distributors, and a host of resources for learning the basics.
Gentoo Linux - an excellent way of generating a highly customised distribution (my GNU/Linux distribution of choice).
Slackware Linux - the original and best GNU/Linux distribution, in a word "simplicity".
SLAX - the best (IMHO) 'live' (i.e. bootable) Linux distrobution to date.
Debian Linux - lots of packages, and well supported.
Redhat Linux - if you just want to get a system up and running then use this.
DNALinux - a specialised distribution based on SLAX aimed at bioinformatics users.
For details of other Linux distributions then you should go to distrowatch.com
Further useful resources on LINUX, Cygwin (a UNIX shell for Windows, which I would highly recommend you use), and general information are below.
IBM developerWorks : Linux (includes the Technical Library).
A common question made by users of Windoze is "Is there a GNU/Linux version of program X which I use under Windoze?", and invariably the answer is yes. A list of alternative software packages can be found at Alternatives to Windows Software.
I find NewsGroups (also known as UseNet) to be an invaluable source of information and help when I have problems configuring LINUX (or software in general), and trying to use commands such as sed, and grep. You can use FreeAgent (Start -> Programs -> Internet Tools -> FreeAgent) to browse the various NewsGroups, or you can view mirrors at Google Groups. If you are going to post a NewsGroup, first read the advice given at How to Ask Questions the Smart Way. You may find your first few postings frustrating if you do not follow the advice given here, as you're likely to get responses along the lines of "Please provide more information", or "RTFM".
A batch of software that I'm using (read learning) how to use for work. The list includes the software as well as Tutorials and wiki's on how to use the software. Hopefully some will find this collection useful.
R - GNU implementation of the S statistical programming language.
Latex - A scientific documentation type-setting program.
lyx - A WYSIWYM front end to the Latex
The links below are a collection of software that I have 'discovered' over the years and which I find useful on a regular basis
MetaPad - An excellent feature rich replacement for NotePad, highly recommended.
Emacs - The GNU text-editor/work environment, provides a highly customizable work environment, with the ability to read/send email, calendar, syntax highlighting, directory editor, newsgroup reader, FTP and many more features (including a psychologist and games) included. Can be tricky to learn, but once you have, you'll never turn back. If your going to be using Emacs to edit lots of Stata Do-Files, then I would strongly recommend getting Bill Risings Emacs ado-mode
Emacs Wiki - A really useful wiki to the bewilidering array of options and uses of Emacs.
Irfan View - An excellent image and multi-media viewer, very useful for browisng collections of images, and for converting batches of files from one format to another.
Here is a list of some other useful/interesting links I have come across...
Nature Scitable an exellent resource for genetics and the life sciences.
fetchbook.co.uk - an online book price comparision that allows you to search and compare book prices.
The Genomic Dub Collective - A homage to Darwin's 'Origin of Species' with a roots reggae twist :-).