Programming Course (MSc Bioinformatics)

Pascal Hirsch

News

Exam admission and registration

Written on 21.07.25 by Pascal Hirsch

Dear students,

all points of assignment sheet 5 for the students which were on the edge of getting the exam admission are entered into the CMS.
So, everyone can now see if they have passed the assignment sheets and got the exam admission or not.

If you've got the exam admission, please register… Read more

Dear students,

all points of assignment sheet 5 for the students which were on the edge of getting the exam admission are entered into the CMS.
So, everyone can now see if they have passed the assignment sheets and got the exam admission or not.

If you've got the exam admission, please register until July 25, 2025 for the "programming course - exam" / "Programmierkurs - Fachprüfung" in the LSF to take part in the exam.

Best regards,
Programming course team

Exam Information

Written on 08.07.25 by Pascal Hirsch

Dear students, 

please check the material section for the exam information.

• August 01, 2025, 12:30-14:30, Building E2.5, Room 0.01 (Günther-Hotz Lecture Hall)
• Best be there at least 15 min before the start
• LSF (de-)registration deadline one week before exam!
• Be able to show your… Read more

Dear students, 

please check the material section for the exam information.

• August 01, 2025, 12:30-14:30, Building E2.5, Room 0.01 (Günther-Hotz Lecture Hall)
• Best be there at least 15 min before the start
• LSF (de-)registration deadline one week before exam!
• Be able to show your passport / ID and student ID card
• Bring a black or blue pen. Do not use pencils or other colors.
• No electronic devices
• No documents or notes are allowed to be used.

Best regards,
Programming course team

Updated assignment 5 material

Written on 08.07.25 by Pascal Hirsch

Dear students,

we've updated the CMakeLists.txt in the assignment 5 material (see materials).
In before it was set up to use C++17 and we've updated it to use C++20.
So, if you want to use C++20 features you can replace your CMakeLists.txt with the new one, otherwise you can leave it as it is.

… Read more

Dear students,

we've updated the CMakeLists.txt in the assignment 5 material (see materials).
In before it was set up to use C++17 and we've updated it to use C++20.
So, if you want to use C++20 features you can replace your CMakeLists.txt with the new one, otherwise you can leave it as it is.

Best regards,
Programming course team

Tutorial 1 shift from July 08 to July 07

Written on 04.07.25 by Pascal Hirsch

Dear students,

the tutorial 1 next week will be shifted from July 08 to July 07 14:15 and will be held in E2.1, Room 0.07 (see timetable).

Best regards,
Programming course team

Today: Room change for tutorial

Written on 01.07.25 by Pascal Hirsch

Dear students,

because of a schedule conflict the tutorial today will be in Room 106. 

Exam overlap with Computational Methods for Epigenome Analysis

Written on 17.06.25 by Pascal Hirsch

Dear students,

for everyone taking part in the Computational Methods for Epigenome Analysis course of Prof. Fabian Müller, you still can take part in the Programming Course exam.
Just write Midhuna Maran (TA of the Computational Methods for Epigenome Analysis course) if you are taking part in both… Read more

Dear students,

for everyone taking part in the Computational Methods for Epigenome Analysis course of Prof. Fabian Müller, you still can take part in the Programming Course exam.
Just write Midhuna Maran (TA of the Computational Methods for Epigenome Analysis course) if you are taking part in both courses.

All the best,
Programming course team

Written on 06.06.25 by Pascal Hirsch

Dear students,

there will be no lecture or tutorial next week tuesday (June 10).

All the best,
Programming course team

Exam Dates

Written on 04.06.25 by Pascal Hirsch

Dear students,

we have set the dates and location for the exam and re-exam:

Exam: August 01, 2025, 12:30-14:30, Building E2 2, Room 0.01
Re-exam: September 11, 2025, 11:30-13:30, Building E2 2, Room 0.01

Don't forget to register in the HISPOS/LSF for the exams.

All the best,
Programming… Read more

Dear students,

we have set the dates and location for the exam and re-exam:

Exam: August 01, 2025, 12:30-14:30, Building E2 2, Room 0.01
Re-exam: September 11, 2025, 11:30-13:30, Building E2 2, Room 0.01

Don't forget to register in the HISPOS/LSF for the exams.

All the best,
Programming course team

Assignment 1 Grading

Written on 28.05.25 by Pascal Hirsch

Dear students,

your grading for the assignment 1 is now online and visible in the CMS.

All the best,
Programming course team

Assignment1: Automatic Tests

Written on 22.05.25 by Pascal Hirsch

Dear Students,

we've uploaded the automatic tests (including the secret tests) from assignment1 to the material section.
https://cms.sic.saarland/prog_bi_25/materials/ -> Assignment 1: Automatic Tests

It contains a folder with the input and solution files along with a text file… Read more

Dear Students,

we've uploaded the automatic tests (including the secret tests) from assignment1 to the material section.
https://cms.sic.saarland/prog_bi_25/materials/ -> Assignment 1: Automatic Tests

It contains a folder with the input and solution files along with a text file "test-commands.txt" which contains the commands to test your code yourself.

Best regards
Your Programming Course-Team

New Revision: Assignment1 Material: test_files

Written on 06.05.25 by Pascal Hirsch

Dear Students,

there were some mistakes in the line endings of the test files in the Assignment1 Material, so the cmp function will detect these and report a difference.
We've uploaded a corrected version with the correct line endings
Please download and replace the files in the test_files… Read more

Dear Students,

there were some mistakes in the line endings of the test files in the Assignment1 Material, so the cmp function will detect these and report a difference.
We've uploaded a corrected version with the correct line endings
Please download and replace the files in the test_files folder.
No other files were changed.

Best regards
Your Programming Course-Team

Additional Tutorial Slot

Written on 17.04.25 by Pascal Hirsch

Dear students,

we've added an additional tutorial slot for thursdays 14:15-15:45.
You can freely choose a tutorial slot without any additional registration.
Both slots will cover the same content, so you should only go to one of them.

Tuesdays, 14:15-15:45,  Building E2.1 Room 001, Tutor: Ian… Read more

Dear students,

we've added an additional tutorial slot for thursdays 14:15-15:45.
You can freely choose a tutorial slot without any additional registration.
Both slots will cover the same content, so you should only go to one of them.

Tuesdays, 14:15-15:45,  Building E2.1 Room 001, Tutor: Ian Diks
Thursdays, 14:15-15:45,  Building E2.1 Room 001, Tutor: Dmitrii Tsybulkin

All the best,
Your Programming Course-Team
Show all

Programming Course (MSc Bioinformatics)

General Information
In this course we will teach programming in C++. This course is not intended to serve as an introduction for general programming. We expect that the Bioinformatics Master students taking this course are already proficient in programming.
Since this course is intended for Bioinformatics Master students, these students will be prioritized in case we have too many participants.

Credit Points
This course is credited with 5CP for Bioinformatics (master) students.
Computer Science students can get either 5CP or 6CP (if they decide to do some extra work, like an additional assignment, short seminar, or small project).

Lecture dates:

  • Lectures will take place on Tuesday, 12:15-13:45, Building E2.1 Room 001
  • The first lecture takes place on April 15, 2025.

Tutorial dates:

  • Tutorials / Office Hour will take place on Tuesday from 14:15-15:45 and Thursdays from 14:15-15:45, Building E2.1 Room 001
    • Both tutorial slots will cover the same content, so you should only go to one of them.
    • You don't need to register for a slot, you can choose freely.
    • We will alternate between regular Office Hours and actual Tutorial sessions where we discuss the assignment sheets
  • The first tutorials take place on April 22, 2025 and April 24, 2025.

Registration for the lecture:

  • Please register for the course in the CMS to take part in the lectures and exercises.
    • Course registration deadline in the CMS is April 21, 2025 at 23:59

Registration for the exam:

  • To take part in the exam, you need to register additionally in the LSF.

To obtain a certificate you need to:

  • register in the LSF
  • successfully complete assignment 0
  • obtain at least 50% of points in the assignment sheets
  • pass the exam

Exam:

  • August 01, 2025, 12:30-14:30, Building E2 2, Room 0.01
  • Registration Deadline in the LSF: July 25, 2025

Re-exam:

  • September 11, 2025, 11:30-13:30, Building E2 2, Room 0.01
  • Registration Deadline in the LSF: September 04, 2025

Course Material

  • Lecture slides and assignments, as well as a discussion forum can be found in our CMS.
  • Your code should be hosted on our Gitlab. Accounts and repositories are going to be created for students being enrolled for the course.

Recommended Literature

  • For Beginners:
    • Stroustrup: Programming — Principles and Practice Using C++
    • Breymann: C++ programmieren (German only)
  • Advanced Reading:
    • Meyers: Effective Modern C++
    • Stroustrup: The C++ Programming Language
    • Stroustrup: A tour of C++ (3rd edition)
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