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The course wiki

Documentation

Within this course, we will do quite a number of analyses and in silico experiments. Similar to the work in the wet lab, it will be necessary for you to document your work thoroughly. So far, you were probably used to document your work in a lab notebook. Switching now to an on-line documentation using a DokuWiki might be, therefore, a bit tedious in the beginning. However, we strongly encourage you to use this system, as it helps to very rapidly and easily not only to document your work, but to also interconnect it with the work of your peers, and with information existing in the public domain.

The course wiki

We have set up the course contents and all related information in the form of a DokuWiki. You will find the information about how to log-in into the DokuWiki here. Take the time to read the information, explore the links we provide, and, if it deems appropriate, also extend the WIKI by adding information. You are free to create and edit any page in the student area within this WIKI. Once you save your changes, you will be listed as a contributor and your name will be linked to the new version of the document. You can undo changes by returning to an old version of the page and saving this as the active one. To do so, just click on the clock symbol to the right of the wiki window.

WIKI editors and syntax

There is a plethora of information within the WIKI and in the web about how to format text in a WIKI, how to add links to media and web pages, how to input tables, and so forth. Per default, we have only one editor active, the DWedit. This allows you to have full control of the both source code and formatting of your wiki page, however, you need to remember the correct syntax.

CKG text editor

CKG text editor

In addition to the DWedit, which is something for purists, there are also WYSIWYG editors1), such as the CKG text editor. These editors seem to make life pretty easy, because it gives you the feeling of working with something like Microsoft word. You can copy and paste text and images, create and format tables with clicking buttons, and the like. However, the CKG editor will put formatting information into your source code, which makes things a bit messy. Moreover, it places pasted images somewhere in your system under automatically generated names, which makes it difficult to really organize your WIKI. Thus, if you want to have full control over how your text looks like and where pages and data is stored, we suggest to work with DWedit.

Adding wiki pages

In addition to editing page contents, you can also add pages. To control this addition of pages a bit, we have reserved one namespace, studentarea, for this. Just imagine this as a directory, where you can add new information. At the start page of this namespace, you will find a menu add new page, which you can use for this purpose. Give the new page a meaningful name. Don't use whitespaces, and keep in mind that capitalisation will be ignored. Put in the information you have in mind, save it, and it will appear in the Sitemap menu. You can then start linking to this information.

Deleting wiki pages

You have no permission to delete any pages. So, once you have created a page, it will stay there until the admin decides to delete it. However, of course you can delete page contents.

Course WIKI and Protocol

For the completion of the module, you will have to hand in a protocol. To avoid any confusions, a protocol has to fulfill the following criteria

  1. Introduce the scientific background of the project including relevant references
  2. Specify the research question, if applicable
  3. Provide materials and methods to an extent that allows others – including yourself a year or so later – to reproduce your work
  4. the results of your analysis
  5. a brief discussion
  6. has to be submitted as a single pdf to the course organizers. :!: A link to the DOKUWIKI will not be accepted as a protocol

If it deems appropriate, you can distribute the individual work packages in the project across different chapters in your protocol. Note, only the scientific work packages need to be covered in the protocol. The basic modules that serve to make you familiar with the computer infrastructure, the bash and the like can be skipped here.

The protocol is fundamentally different from the documentation of the project progress as it is reflected in your DOKUWIKI. However, if your project documentation is organized in the appropriate way, you can use large parts of it for your protocol.

1)
what you see is what you get