You are now starting the computer practicals of the course. The practical is split into several sessions, each designed to last a full calendar week. Each session comes with its own assignments, either text submissions in Studium or (group) presentations, these assignments need to be passed to complete this part of the course. Most exercises are done in groups and the final presentation is done in a group but all written assignments are graded per student.
IMPORTANT: The exercises are designed to work by booting the IBG computers into "Linux (EBC)" from where we will connect to an IBG server "Solander" which has all the tools needed set up. Working remotely on a server or cluster is a very realistic scenario for working as a bioinformatician. If you decide to use your own computers for logging in to Solander, you are doing that at your own risk. There might be parts of the labs that won't work that way. The TAs are present for the teaching part, not to help with IT issues caused by different computers, clients and operating systems.
Attendance to the lab sessions is not mandatory but highly encouraged. The TAs have other responsibilities outside of these sessions, so they will have limited possibilities to help you with questions. To receive credits for the labs, you need to submit answers to the assignments through Studium and give the final presentation.
Finally, the labs you are working with this year are new or have been substantially modified compared to previous versions of this course. We did our best to make them informative and interesting, and for them to run smoothly. We welcome any comments and suggestions for improvement - do not hesitate to write them down as we go along as you might have forgotten a lot of comments by the time you fill the course evaluation! This will be very helpful for the teachers and future students. Thank you!
The practical part of this course consists of six computer sessions (or labs), each lasting up to six hours. The overarching goals of these labs are to familiarize yourselves with modern bioinformatic tools and best practices, and to illustrate-by-doing the most important topics discussed in class. By completing all sessions and the final project, you will get a good idea of the work of bioinformaticians and biologists today. To improve the flow and the logic of each step in the bioinformatic workflow, we have designed most labs to be connected to each other; however, should you have troubles completing one lab, we will help you (for example by providing intermediate results) so you are not penalized for the following sessions.
Each session has six scheduled hours with the TAs in the computer rooms. At the beginning of first weekly session (per group X3A and X3B), the TAs will give a quick introduction to the content for the week.
The first session is for you to learn the basic tools that you will need for the entire course: the UNIX system and command line, work on a cluster, bash scripting etc.
From session 2 onwards, you will be working in groups and all exercises will revolve around one research question per group. In session 6, you will present your results to the rest of the class
Most exercises are done in groups including the final presentations. Every student still has to submit responses to the different assignments individually in Studium. This helps us to keep track of the progress and also enables us to see that all group members are actively involved in the work.