The course wiki

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. Here, we will do all documentation using a DokuWiki. This is a simple to use and highly versatile Open Source wiki software with a clean and readable syntax. This will probably require some efforts in the beginning, but you will quickly get used to it. The DokuWiki not only helps to very rapidly and easily document your work but to also allows to work together with your peers, and makes it straightforward to link to information existing in the public domain.

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.

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.

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.

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.

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.