Modelling and Simulation

Course manual 2020/2021

Course content

The course provides a detailed introduction to simulation and modelling techniques commonly used in the earth and natural sciences. The course is primarily intended for students from the Future Planet Studies bachelor’s program but is equally useful for those wishing to apply simulation and modelling techniques in related fields. Students in this course are required to have had experience in basic programming in Matlab, and acquaintance with classical mathematical models in geo-ecosystems or related fields such as ecology and/or evolution.

Study materials

Literature

• Suggested reading material will be provided together with the weekly assignments. This material is not necessary for completing the worksheets, it will be provided as extra enrichment and/or extra support.
   

Syllabus

Practical training material

• On Mondays weekly assignments (6) will be published with the hands on activities the students need to carry out that week.
   

Software

• Matlab

• Students will need to bring their personal laptops to the lectures, to the practicals and to the exam.  
  Matlab needs to be installed before the first lecture!
   

Other

Objectives

• The students will be acquainted with a range of simulation and modelling techniques, including differential equations and agent-based models; by the end of the course, students will be able to decide which of these is most appropriate for addressing a specific scientific problem.
• The students will develop practical expertise in the process of abstracting real systems into different modeling frameworks; by the end of the course, students will be able to translate a true scientific question into a model.
• The students will gain hands-on simulation exercises; by the end of the course, students will be able to translate a model into a computer simulation.
• The students will gain experience carrying out critical and creative scientific research with models and simulations; by the end of the course, students will be able to analyze a scientific problem by confronting different assumptions and abstractions in their simulations. 

Teaching methods

• Hoorcollege
• Laptopcollege
• Zelfstudie

Simulation and modelling in natural sciences require both skills (i.e., programming, developing algorithms, and solving equations) and techniques (i.e., the ability to recognise what is important and needs to be represented in the model, and what can and should be left out). Because this is a course designed for beginners, focus is given to both aspects— the technical side of constructing models and the ability to identify appropriate degrees of abstraction. 

Because there is no absolute set of rules that can universally be prescribed for insuring successful modelling results; students will be confronted with realistic and concrete hands-on modelling exercises throughout the course through which they can gain proficiency in the process of abstracting real systems into models and other practical expertise relevant to modelling and simulation. This will also support the development of each student's personal understanding and intuition, providing them with foundations for critical and creative problem solving in the natural sciences through simulation and modelling.

Learning activities

Attendance

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

• Participation in fieldwork is compulsory and cannot be replaced by assignments or other courses.
• In case of practical sessions, the student is obliged to attend at least of 90% of the sessions and to prepare himself adequately, unless indicated otherwise in the course manual. In case the student attends less than 90%, the practical sessions should be redone entirely.
• In case of tutorials/seminars with assignments, the student is obliged to attend at least 7 out of 8 seminars and to prepare thoroughly for these meetings, unless indicated otherwise in the course manual. If the course has more than 8 seminars, the student can miss up to 1 extra meeting for every (part of) 8 tutorials/seminars. If the students attends less than the mandatory tutorials/seminars, the course cannot be completed.

Additional requirements for this course:

• Attendance in the lectures is required unless special approval for absence has been given.
• Practical lessons: each student needs to be present and well prepared for at least 90% of the practical classes. In case the student missed more than 10% of the practical classes, he/she has to re-take the practical unless the exam committee decides on providing a practical-replacing assignment.
• In special cases, a student can receive an exemption for (part of) the obligatory components of a course. The exam committee judges the requests for an exemption.
• Students who have completed their weekly assignment and submitted it before the practical of Wednesday that week, have permission not to attend the Wednesday practical that week, unless students have explicitly been asked to be present that Wednesday (announcements will be posted on Canvas)

Assessment

Student final grade will be based on the score of the final exam and on the 6 assignments handed in by the students throughout the course.  The final grade will be based on a weighted average between the assignments submitted throughout the course (1/3) and the final exam (2/3): the score of the exam cannot be less than 4.5, and the assignments will only be included in the final grade if: a) the exam mark falls between 4.5 and 5.5, and b), if the final grade after inclusion of the assignments is higher. In such cases the final grade will never be higher than 6.0.

Assessment diagram

Students that were enrolled in the course in previous years

For students that are enrolled in the course for the 2nd/3rd/etc. time, it is still mandatory to complete all components

Inspection of assessed work

Contact the course coordinator to make an appointment for inspection.

Up to 20 working days after the announcement of the result students have the right to inspect their work. Students can make an appointment with the course coordinator, Dr. Artzy-Randrup at Yael.Artzy@UvA.nl

Assignments

Work assignment #1

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

Work assignment #2

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

Work assignment #3

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

Work assignment #4

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

Work assignment #5

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

Work assignment #6

• The assignment has to be submitted individually, students are allowed to discuss with each other but they must not provide final solutions or scripts to each other. 

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

Timetable

The schedule for this course is published on DataNose.

Additional information

Early requirements:

1) Experience with basic programming in Matlab 

2) Software and personal laptop:  Students will need to bring their personal laptops to the lectures, practical’s and the exam. Matlab needs to be installed before the first meeting (for assistance see below). 

FNWI offers licenses for MATLAB, including instructions for both Windows and Mac, as well as software support:

• Downloading Software: Software can be downloaded from www.datanose.nl/byod
• Support for software installation and other issues contact: laptops-fnwi@uva.nl. 
• Borrowing a laptop: FNWI students can rent a laptop at the library desk. The laptops include MS Office and Adobe Acrobat. You are allowed to install your own software on the device. The laptop comes with a laptop bag, charger, mouse, lock and HMDI-cable. Documents and software are deleted after return.

Last year's course evaluation

From 2013-2014, we have chosen to provide students with a better understanding of quality assurance by means of the table below. That is why we take a brief overview of the student evaluation and the resulting actions to improve the course.

Teacher's comment:

Some of the students felt they had fallen behind already in the early stages of the course and found it difficult to get back on track. To address this, I removed a two-week section of the course (the last two weeks of the course that were devoted to Cellular Automata). Instead I added two weeks to the beginning of the course as an extended introduction so students have more time to gain experience and confidence with the basic building blocks of the course are required for the later stages of the course. I also refreshed and reorganised all the remaining sections of the course accordingly,  as well as replacing some of the earlier material that had not been from my area of expertise with case studies that are. The removal of the CA block should be helpful for the students in itself since this implies that student can focus on one type of modeling approach (i.e., based on differential equations), decreasing the risk of confused or overload by multiple modelling approaches. 

Another addition is that at the end of each week students will have access to a self-assessment form with simple exercises and/or questions they can practice on. 

Finally, some students felt they could use more 1-1 support from the TA's. The course this year is smaller in size that it was last year, while still maintaining the same number of TA's. Hopefully the students will feel they have sufficient support this year.  They are always welcome to schedule an appointment with me outside of class hours, and I am also available during practicals  to answer questions. Indeed, most students commented that I was easily approachable and always took time to explain patiently,  I encourage the students to do so if for example they feel they are falling behind or for another reason.

Contact information

Coordinator

• dr. Yael Artzy-Randrup

Course coordinator:
       Dr. Yael Artzy-Randrup (Yael.Artzy@UvA.nl)

Teaching assistants: 
      Emma Polman, Caper Borgman and Walter van Dijk