The top left corner of the screen holds the index of the pages that belong with this course element:
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Figure Help-1. The course index lists the pages that you should visit during this course. Just start with the top one (in this example figure that is introduction), and work your way down the steps (in this example figure: data, SRS, ...., Alignment).. |
Immediately below the course index you find the support pages:
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Figure Help-2. The second block of left-hand column options is called "Miscellaneous". In this block you find pointers to (this) HELP page, files you need to download if you run the course at another location than the classroom, the slides of the seminars that were given as part of this course, a small dictionary with bioinformatics terms, and anything your teacher added as miscellaneous material. |
The third block in the right-hand column is labelled "Useful links", and that describes the content reasonably well.
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Figure Help-3. The third block of left-hand column options is called "Useful links". In this block you find pointers to web pages, databases, servers, etc., that we expect you might need at some moment. The content of this block depends very much on your teacher, and on the actual course. In a course to teach how to use BLAST you can expect here links to one or more BLAST servers, for example. |
The last block in the right-hand column is labelled "Author(s)", and that describes the content reasonably well.
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Figure Help-4. The fourth block of left-hand column is called "Author(s)". In this block you find pointers to author(s) responsible for this (part of) the course, and some further acknowledgments, if needed. |
Pages and parts of pages have a background colour. These colours have the following meaning:
Brown is used as the background of navigation pages, pages with pointers, etc. |
Orange is used on the top of many pages. It gives the main message of that step in the course. |
This yellowish colour is used for the core of the course. These pages you should read/study. |
Gray is used for support pages. These pages you can read, but do not have to. Gray pages can hold tables from which you look-up data needed to work out certain exercises. You might also have realized that this HELP page has a gray background :-) |
Obviously, other backgrounds are used for services outside this course. Many modelling-course related pages and a few services, for example, use this background pattern. |
Throughout the course you will find several hyperlinks. A normal word in the middle of a page can be hyperlinked to the CMBI-wiki. The CMBI-wiki is not like the real Wikipedia that it tries to explain everything perfectly and extensively, but rather tries to give you a very short hand-waving explanation that will allow you to place the term in the context of the course you are working on.
The NOOTs are notes for teachers. Only the teacher of the course gets the password needed to look at those notes. These notes can contain explanations about the choice of examples, answers to questions often asked by students, metaphores that can help with teaching.
LINKs hold background material that can help the students. Sometimes LINKs hold many pages of look-up material, sometimes they hold a small extra explanation about a topic we know students do not always immediately understand.
Questions are almost always followed by a hyperlinked Answer. The teacher has the password to get to those answers, and it is up to the teacher how he/she deals with the passwords. The teacher can in principle decide to give each question its own password...
Most pictures are hyperlinked to something. Often they are hyperlinked to the same picture, but at the normal scale so that the picture is less blurred; sometimes to the same molecule but then rotating, sometimes to a whole interactive session of some kind or another.
Well, except for the small toy sequences, each exercise one day was completely real. However, in most cases we have reduced the number of sequences to a handful, we have removed the most horrific residue numbering problems, etc. But the tools and the principles which we teach are used every day by hundreds of thousands of scientists all over the world to solve the problems arising in their science in their labs.