These notes are intending for people working through the Exercises in genetic linkage analysis, and it is assumed that the exercises will already have been installed correctly so that they will run smoothly on your system - this means that the correct files and directory structures will have been set up, and that the necessary programs will have been installed correctly and will be conveniently available.
The exercises consist of HTML pages and related files which should be available locally (it is not intended that the exercises should be run from their native web site). You should be provided with the pages as files on a machine local to you and you should view them with a standard HTML browser such as Netscape while you work through them. It is very helpful if you also have a print-out of these pages available as hard copy, since this can be easier to refer to. However you should not rely entirely on reading the hard copy because then you will miss out on helpful tips which are provided as hypertext links. If you are following the exercises from a print-out, then whenever you get stuck or there is something you don't understand make sure that you look at the relevant section with the browser to see if there are any helpful links. See that the contents page of these exercises is saved as a bookmark in your browser so that you can always get back to it easily.
When you view these pages with an HTML browser you will see that some of them have hot links within the text. The main thing to say is DO NOT USE THESE LINKS. Actually, that is a slight exaggeration - you can use the links sometimes, but only if you really need to. Only use the links if you do not understand something and you think that the link may provide an explanation. However just following links around "because they are there" will mean that you quickly get lost and confused. Some links are intended to explain the basics of doing fundamental things such as running a program, and others link between entries in data files and explanations about what these entries mean, but try to read the explanation carefully first and only start using the links if you are uncertain about what is meant or how to do something. If you do follow a link like this then click on the Back button of your browser to return to where you were in the exercise.
At the end of each exercise are links to the contents page and the next exercise - you should use these so that you can work through the exercises in turn.
Assuming that the exercises have been set up correctly, if you start with the first exercise and work steadily through then you should find that all the data files you need are either provided originally or else will have been produced in the course of earlier exercises. However, if you leave out certain exercises or corrupt the data files you need then you should be able to use your browser to download the necessary data files for each exercise. Links to these files are included at the top of the HTML page for the exercise, so if any files are missing or become corrupted then just use these links to download the files to the directory in which you are running the exercises. (To do this using the Windows version of Netscape, hold down the shift key and then click on the link to the file. Other browsers may have other procedures for downloading files.) The files originally required for the exercises are stored in a subdirectory called original of the directory where the HTML files are kept. Modified versions of these files and files newly created in the course of some exercises are kept in a subdirectory called edited. Provided the exercises have been set up correctly, the links will automatically point to the right files. If ever you are working through an exercise and you get completely stuck and can't see what's wrong, then one thing to try may be downloading new copies of all the files you need for the exercise, using the links at the top of the page, and starting again.
It intended that the exercises are performed in a multi-tasking environment - either Windows or X. You should have your HTML browser running throughout, and you will also need to run example programs and a text editor. Some of these will run as independent applications and others will run from a DOS or Unix prompt. You should be able to have all the relevant programs running simultaneously and be able to switch between them in order to refer to the exercise notes and compare them with the program inputs and outputs as they run. Under Windows you switch between applications by using Alt-Tab, Control-Esc, (Windows 3.x) or the task bar (Windows 95+), but how this is done with X will depend on your own X server. Generally you should only have one copy of each program running at once, although sometimes you may wish to have more than one operating system shell (MSDOS or Unix) running simultaneously.
Read through the notes carefully and try to follow what they say. Text that you need to enter or actions you need to perform are generally written in bold, while things that you read such as program output are generally in italics (although other things are in italics too). Compare what is written in the notes with what you see in the data files, and make sure that modified data files appear exactly as shown in the notes before attempting to use them. Don't forget that if things do go badly wrong you should be able to download replacement copies of the data files using the browser.
The exercises are only intended to give you a little practical experience of some of the programs available. Thus they provide practically no theoretical explanation of the method or results. Nor do they provide any instructions on how to use the programs apart from what you need to run the exercises - if you intend to use any of the programs in any other capacity it is essential that you study their accompanying documentation.
These notes are written with the aim of being as flexible as possible with regard to the system on which the exercises can be performed, although they were originally targetted at a Microsoft Windows 3.11 environment. Explicit instructions are given for Windows 3.x and Unix, and only minor modifications would be needed for other versions of Windows. It is hoped to provide explicit instructions for other systems in due course, but inevitably there may be occasional differences between the letter of the instructions and what actually needs to be done.
It is also the intention to add notes and supplementary files which will allow users who cannot or do not wish to use particular programs to still be able to work through similar exercises using alternatives.
If you have any difficulty working through an exercise, the first thing to do is to read the notes very carefully to see that you have followed the instructions exactly. Also take a look at the instructions on running individual programs, which are available as links practically everywhere a program is run in the course of an exercise. These tips include things like making sure you are in the correct directory, making sure the necessary files exist in that directory, seeing that the files contain the correct information and so on. If you cannot work out what is going wrong, then try downloading new copies of the files necessary for the exercise (by using the links at the top of the exercise) and working through again from the beginning.
If you cannot discover the problem then, in the first instance, please contact the person responsible for setting up and maintaining the programs on your site, but feel free to contact me directly if necessary. Also please let me know if you find anything in the notes which is incorrect, unclear or confusing. There is a link at the bottom of each exercise which lets you email me directly.
Assuming that the exercises are set up correctly on your system, begin by having a quick look through the sections titled How to use operating system commands, How to run programs and Overview of file types used in exercises before moving on to the first exercise titled Setting up a simple two-point analysis using LINKAGE. The first two sections contain useful tips which are designed to be accessed as links from the exercises, but it is worth having a look at them to get some feel of what is in them before starting the exercises. You can always get to a particular exercise from the the contents page, and to move through the sections in turn, just follow the links at the bottom of each section.
Exercises in genetic linkage analysis
All material copyright (C) Dave Curtis 1996-2000
dcurtis@hgmp.mrc.ac.uk