You are required to complete a project related to the content of the on-site part of the course. You have the choice to either suggest a project to the teachers (which should be approved before you start your project) or to make a selection among the suggested projects below.

In the end of your project, you will describe the outcome of the project in a brief report.  Also, you will share the code and data with the teachers, in a format that can be executed by the teacher. Typically you will use github and jupyter notebook for communicating your results to the teacher.

List of potential projects:

  1. Recreate Figure 5A-F of the Paper Geyer et al. Paper. Also, perform a set of ANOVAs where you usepatient number as a blocking variable, and use BMI, HDL, LDL, Cholesterol, Triglyceride resp. HOMA as explanatory variables. Try to answer the question if you find more significantly regulated blood plasma proteins using the ANOVAs than using the correlation analysis.
  2. Analyze the CHO-cell growth data according to the instructions in the assignments (Point 1-6). Also, cluster the proteins using single linkage hierarchical clustering, using e.g. seaborn, to see if you see that the proteomes with proximity in time also end up close in the dendrogram.
  3. Analyze the Pathology Atlas (TCGA) Data according to the instructions.
  4. Implement a program that makes global sequence alignments with affine gap penalties. An algorithm that do so for you is described in these slides page 26 and onwards.