Introduction to Scientific Programming for Chemists

Owner	Bachelor Scheikunde (joint degree)
Coordinator	prof. dr. L. Visscher
Part of	Bachelor Chemistry (Joint Degree), year 3

Course manual 2019/2020

Course content

The course provides an introduction into scientific programming and scripting with the Python language. We start by covering the basics of programming: variables and operators, loops and conditional expressions, use of functions and libraries. We then pay attention to larger applications and data visualization. We end this part by discussing more advanced techniques in which the object-oriented features (classes, objects and methods, inheritance) that the Python language has to offer are used.

Examples will be taken from chemical research, mostly taking Python both as a programming language in its own right, but also discussing how python scripts can be used to glue together different existing scientific software tools to form sophisticated scientific modelling workflows.

For the latter purpose we also provide an introduction into the Unix operating system that is used in almost all scientific computing applications. Topics treated in this stage are: overview of hardware; operating systems; directories and files; file transfer; grep and regular expressions; editing with vi; sed and awk; shells and environment variables; running jobs via queueing systems.

 

Study materials

Literature

• C. Hill, 'Learning Scientific Programming with Python', Cambridge University Press, ISBN 978-1-107-42822-5 (or the e-book version).

• Hand-outs and online material

Other

• Students are expected to have a (not too old) laptop available for the self study part (or should be prepared to do this during working hours at  the VU computer rooms).

Objectives

• is familiar with the Unix operating system and its use in a research environment.
• is able to create small programs in the Python language and use the language to script scientific workflows.
• understands the basics of structured and object-oriented programming. 

Teaching methods

• Hoorcollege
• Zelfstudie
• (Computer)practicum
• Lecture
• Laptop seminar
• Computer lab session/practical training
• Self-study

Learning activities

Attendance

Programme's requirements concerning attendance (OER-B):

• Active participation is expected of each student in the course for which he is registered.
• If a student cannot attend an obligatory part of a programme's component due to circumstances beyond his control, he must report in writing to the teacher in question as soon as possible. The teacher, if necessary after consulting the study adviser, may decide to issue the student a replacing assignment.
• It is not allowed to miss obligatory parts of the programme's component if there is no case of circumstances beyond one's control.
• In case of participating qualitatively or quantitatively insufficiently, the examiner can expel a student from further participation in the programme's component or a part of that component. Conditions for sufficient participation are fixed in advance in the study guide and/or on Canvas.

Additional requirements for this course:

For the assignments it is compulsory to discuss them with the teaching assistants. Grades are only given after this discussion has taken place.

Assessment

Item and weight	Details
Final grade
0.5 (100%) Tentamen 1

Students will be assessed based via an exam (50%) and via the assignments handed in during the course (50%). For the Unix module, the grade will be passed / not passed. In case of not passed, a re-exam is offered. Having obtained a passing grade for Unix is a prerequisite for passing this course as a whole. The final grade is the average of the grades obtained for the assignments during the course and the exam.

All assignments should be made individually and grades are only final after a student has discussed his or her chosen program design with the teacher.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Processed course evaluations

Below you will find the adjustments in the course design in response to the course evaluations.

Contact information

Coordinator

• prof. dr. L. Visscher