PFLS: Course Responsibilities and Grading

Table of Contents

Let’s talk about all the boring yet very important stuff first. It is extremely important you follow these instructions word-by-word, and make sure you understand all of them 100%. Please ask as many qeustions while we go through this document together at the beginning of the course as you need to feel that everything here is crystal clear ot you, and you are fully aware of your responsibilites and are comfortable with them :)

Course Responsibilities

The evaluation in this course will be based on five parts of a portfolio that we can divide into two major components:

  • The first major component is ‘class citizenship’ emails, described below in the section Part I (20% of your grade).
  • The second major component is ‘programming exercises’, described below in sections for Part II, III, IV, and V (80% of your grade).

Part I (20% of your grade) – Class Citizenship

Class citizenship emails will track your attendance and engagement to the course and will help the course director to have an overall understanding of the evolution of the course.

The class citizenship demands every participant to send a class citizenship email at the end of each day to meren@hifmb.de and sarahi.garcia@uol.de (and as in, sending the same email to both Meren and Sarahi).

The class citizenship email must be composed of two parts:

  1. A brief summary of the main concepts discussed during the day, interpreted by the attendee in their own words.
  2. A short question that is relevant to a concept or idea discussed during the lecture.

The last 10 minutes of every course day will be dedicated to writing the class citizenship emails, therefore the attendees will leave the class without having to remember doing it later. The class citizenship emails that are sent after the end of the class will not be taken into consideration as a mark of attendance.

The title of the class citizenship email must follow this pattern word-by-word where you will need to replace DD/MM/YY with the date, month, and the year (despite the simplicity of this request many students have failed to follow these instructions, so you are our last hope):

PFLS Citizenship: DD/MM/YY

The best class citizenship emails are those that are brief, genuine, and insightful. In an ideal world the emails should be no less than 50 words, and no more than 150 words. Please do not send notes you take throughout the class – your notes are for you, not for us. You should use the last 10 minutes of the day to gather your thoughts, and come up with a summary of what you can remember.

Here is an example class citizenship email:

Summary: Today we discussed what is phylogenomics, how phylogenomic trees are built, and why single-copy core genes are suitable for building phylogenomics trees. We also discussed the relationship between phylogenetics, phylogenomics, and pangenomics with respect to the fraction of genome used and the evolutionary distance that they can cover.

Question: Since phylogenomics and pangenomics are both useful for inferring evolutionary distances, it seems to me that integrating both methods in a systematic way would yield a more reliable tree. But it looks like the field only uses phylogenomics and pangenomics separately, is there a reason for that?

Part II, III, and IV (30% of your grade)

This part will be composed of three mini programming exercises that you will have to implement and return. Each programming exercise will provide you with explicit instructions regarding the nature of the data and question, and what the program is expected to achieve. You will use your learnings in the course to complete the programming tasks and submit the resulting source code.

Part V (50% of your grade)

This part will be composed of a single large programming exercise that will require you to orchestrate multiple programming tools and languages.

Grading

Grading scale:

Grade Threshold
1.0 95%
1.3 90%
1.7 85%
2.0 80%
2.3 75%
2.7 70%
3.0 65%
3.3 60%
3.7 55%
4.0 50%

For all grading related questions, please consult with Sarahi Garcia.