|Title||BIOINF4399 - Advanced Java for bioinformatics|
|Lecturers||Prof. Daniel Huson, Caner Bagci, Anupam Gautam and Timo Lucas|
|Venue||online, Thursday, 8:15-10:00,|
|Problem sessions|| |
Tutorial A: Wednesdays, 8:15-10:00
Tutorial C: Wednesdays, 8:15-10:00
This course is intended for MSc students in bioinformatics and medical informatics.
Students in other programs will be admitted if space permits.
Grades will be based on the quality of a software project that you will undertake in this course.
This course will cover the following topics:
- Java 8 and JavaFX 8
- Version control using GitHub
- Design patterns such as MVC
- Concurrent programming in Java
- GUI design, animation and 3D graphics using JavaFX
- Java web services
- Unit testing
All topics will be taught in the context of a bioinformatics project.
We will write a lot of code, so a keen interest in programming is essential.
This is not an introduction to Java, you must already know Java to participate in this course. There might be a test at the beginning of the course to determine whether you have sufficient knowledge of Java to participate in the course.
Assignments and tutorials
Weekly assignments are handed out in class and are posted on this webpage. In the second half of the course, you will work on a project and the resulting code will be the basis of your grade.
We will setup GitHub-classrooms to work with.
We will discuss how to hand in your first assignment in the lecture on 22.4. Please enroll in the course using Ilias.
Tutorials will start in the week of 29.4.
In the second part of the course you will work on a bioinformatics software project.
In the past, there was one topic for all students to work on. This time, we might try providing a number of different topics for people to work on.
The following time-table is only an outline and is subject to changes
|22.04.2021||1. Introduction, scene graph||Assignment 1|
|29.04.2021||2. Events and controls|| |
|06.05.2021||3. FXML and SceneBuilder||Assignment 3|
|13.05.2021||4. Model View-Presenter, 5. Properties and binding||Assignment 4|
|20.05.2021||6. Shapes, 7. Mouse interaction||Assignment 5|
|27.05.2021||8. Drawing in 3D, 9. Meshes||Assignment 6|
|10.06.2021||10. Web client, 11. JSON|| |
|17.06.2021||12. Services and concurreny|| |
Discuss project with tutor
|24.06.2021||13. Animation||Discuss project with tutor|
|01.07.2021||14. Undo-redo||Discuss project with tutor|
|08.07.2021||15. Streams||Project due|
|15.07.2021||16. Web server||Project improvements|
|22.07.2021||17. Other topics||Project improvements|