Admission requirements
This course is mandatory for and restricted to students who do the Minor ‘Computational approach to Disease Signaling and Drug Targets’ (CADSDT; the entire Minor or only Part 1), the Minor ‘Modern Drug Discovery’ (MDD) and the Elective Module ‘DSDT’. The same admission criteria apply to this course as for the respective aforementioned programs.
Description
Computational Thinking is an essential skill for the 21st-century. With data gathering and algorithm development by Big Tech in the news regularly, such thinking is not only useful to understand the mechanisms underlying specific observations, but it is also indispensable to develop and apply modern computational approaches to solve the many open problems in the area of (computational) drug research. An important part of computational thinking is the ability to write computer scripts that execute well-defined computational tasks.
In this course, we will explore examples of computational thinking in drug research. We will provide an introduction to programming in R. Moreover, we will discuss mathematical equations, limits, derivatives and graphs of functions, which will subsequently be applied in the mathematical modeling of biological networks. We will also build upon previous statistics courses and explore the use of linear models for statistical inference testing and how to apply this in R. A substantial part of the course will be hands-on training in writing your own computer programs in R, with applications in mathematical modeling and using data sets that are relevant in drug research. In addition, computational thinking is highlighted in the context of chemogenomics; we will discuss how machine learning is used in chemogenomics to discover new drugs, introduce techniques from this field, and study peer reviewed literature. Finally, we will bring these concepts together in a case study, where we will use these techniques on biomedical datasets.
Course Objectives
The student is able to:
Solve mathematical equations, calculate limits and derivatives and draw graphs of functions
Analyze one-dimensional (1D) differential equations by pen and paper and interpret output from such analysis
Program an R-script to analyze mathematical equations including 1D differential equations
Program an R-script to format and analyze a (drug related) dataset and visualize the data
Choose and perform statistical inference tests using linear models in R on data that often arises in drug research, and draw conclusions from these tests
Select and discuss the optimal approach from an array of computational methods, for a given chemogenomic use case
Timetable
You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have successfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.
MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).
For more information on MyTimeTable, watch the video or go the the 'help-page' in MyTimetable.
PLEASE NOTE
Always check the detailed schedule on the Brightspace module of each Course 2-3 weeks before the start of the Course for group-specific meetings, (intermediate) deadlines, etc..
Mode of instruction
Practical course, consisting of: lectures, demonstrations, pen&paper and computer exercises, literature research and a group assignment.
Assessment method
Students will be assessed on the following modalities:
A scripting test (30%)
Group data-analysis assignment (20%)
Exam (50%)
Total grade = 100%
In the written exam, a total of 60 points can be obtained, and the grade for the exam is determined by dividing the total number of obtained points by 6. Presence and active participation for the hands-on work during the course will be monitored and leads to a maximum of 6 points out of the 60 possible points on the written exam.
Reading list
Literature will be provided during the course.
Registration
Registration for the lectures and exam via uSis is mandatory.
Contact
Dhr. G. Burger, MSc