MODELING AND COMPUTATIONAL METHODS IN BIOLOGY
MODELLI E METODI COMPUTAZIONALI PER LA BIOLOGIA
| A.Y. | Credits |
|---|---|
| 2021/2022 | 6 |
| Lecturer | Office hours for students | |
|---|---|---|
| Margherita Carletti | Always, after lesson time |
| Teaching in foreign languages |
|---|
|
Course with optional materials in a foreign language
English
This course is entirely taught in Italian. Study materials can be provided in the foreign language and the final exam can be taken in the foreign language. |
Assigned to the Degree Course
| Date | Time | Classroom / Location |
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| Date | Time | Classroom / Location |
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Learning Objectives
The course aims at providing students the basis of matematical modeling applied to Biology, both from a theoretical point of view via differential equations of various kinds, and from the numerical and computational point of view in order to simulate their solutions. The course is also meant to enable students catching the usefulness of and the criticism in the use of mathematical modelling in Life Sciences in order to describe complex phenomena and discuss possible scenarios.
Program
1. The basis of mathematical modeling
1.1 What is a mathematical model?
1.2 Characteristics of a mathematical model
2. Differential Equations and Differential Systems
2.1 Background to the concepts of derivative and integral of a function.
2.2. Ordinary Differential Equations and Cauchy problem (ODEs).
2.3 (Hints on) Delay Differential Equations (DDEs).
3. Differential modeling of biological processes
3.1 Models for popuation growth: Malthus, Verhulst, Gompertz.
3.2 Models for the spread of infections; SI, SIS, SIR, SI(R)S, SEIR. Applications to Covid-19 and other infectious diseases. Models including vaccination, if available.
3.3 Modeling bacteria-bacteriophage infections in marine environment (ODEs, SDEs).
3.4 The use of MATLAB for the simulation of the solutions of models introduced in 3.1 - 3.2 - 3.3.
Bridging Courses
Although not mandatory, having passed the exam of Mathematics is strongly recommended.
Learning Achievements (Dublin Descriptors)
Students should demonstrate:
D1. Thorough knowledge and non mnemonic comprehension of the treated issues.
D2. Capability of application of the concepts of derivative and integral of a mathematical function to modeling.
D3. Capability of justifying each equation in a model according to its biological meaning
D4. Capability of defending a thesis, making links among different studied issues, enhancing strength and weakness points of a mathematical model applied to Biology.
D5. Ability of using a rigorous scientific language in the exposition of the studied issues.
Teaching Material
The teaching material prepared by the lecturer in addition to recommended textbooks (such as for instance slides, lecture notes, exercises, bibliography) and communications from the lecturer specific to the course can be found inside the Moodle platform › blended.uniurb.it
Supporting Activities
None
Teaching, Attendance, Course Books and Assessment
- Teaching
- Frontal lessons
- Weekly check of uploaded material on the Moodle platform
- Attendance
Not mandatory
- Course books
Uploaded material on the Moodle platform; slides, scientific papers and useful links.
- Assessment
Oral examination consisting in:
Introduction and discussion of numerical results of one of the differential models studied during the academic year or a new one according to the student's choice. In this second case, the student HAS TO SEND TO THE TEACHER (margherita.carletti@uniurb.it), NOT LATER THAN 5 DAYS BEFORE THE EXAMINATION DAY, one or more scientific articles and/or other material useful to understand the biological problem and evaluate the student's presentation.
The maximun available time to the student for his/her discussion of the chosen model is 30 minutes.
Introduction and discussion of the chosen model can be done in any way (oral speech only, PPT slides ....), according to the student's preference.
- Disabilità e DSA
Le studentesse e gli studenti che hanno registrato la certificazione di disabilità o la certificazione di DSA presso l'Ufficio Inclusione e diritto allo studio, possono chiedere di utilizzare le mappe concettuali (per parole chiave) durante la prova di esame.
A tal fine, è necessario inviare le mappe, due settimane prima dell’appello di esame, alla o al docente del corso, che ne verificherà la coerenza con le indicazioni delle linee guida di ateneo e potrà chiederne la modifica.
Additional Information for Non-Attending Students
- Teaching
Weekly check on the Moodle platform.
- Attendance
Not mandatory
- Course books
Uploaded material on the Moodle platform; slides, scientific papers and useful links.
- Assessment
Same as ATTENDING STUDENTS.
- Disabilità e DSA
Le studentesse e gli studenti che hanno registrato la certificazione di disabilità o la certificazione di DSA presso l'Ufficio Inclusione e diritto allo studio, possono chiedere di utilizzare le mappe concettuali (per parole chiave) durante la prova di esame.
A tal fine, è necessario inviare le mappe, due settimane prima dell’appello di esame, alla o al docente del corso, che ne verificherà la coerenza con le indicazioni delle linee guida di ateneo e potrà chiederne la modifica.
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