Algorithmen der Bioinformatik

BIOINF4399 Advanced Java for Bioinformatics

Title BIOINF4399 - Advanced Java for bioinformatics
Lecturers Prof. Daniel Huson, Caner Bagic, Anupam Gautam and Timo Lucas
Venue online, Thursday, 8:15-10:00, 
Problem sessions

Tutorial A: TBA
Tutorial B:  TBA

Tutorial C: TBA


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 and a final exam.

Language English
Links Ilias ALMA



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

Date Topic Assignments...
22.04.2021 1. Introduction Assignment 1
29.04.2021 2. Events and controls

Java test

Assignment 2

06.05.2021 3. Drawing stuff in 2D Assignment 3
20.05.2021 4. Drawing stuff in 3D Assignment 4
10.06.2021 5.  Meshes Assignment 5
17.06.2021 6. FXML and CSS



24.06.2021 7. Undo-redo Discuss project with tutor
01.07.2021 8. Concurrency Discuss project with tutor
08.07.2021 9. Animation Project due
15.07.2021 10. Web services Project improvements
22.07.2021 11. Streams and other stuff Project improvements
29.07.2021 Project presentations