Back
| Semester | fall semester 2020 |
| Course frequency | Every fall sem. |
| Lecturers |
Geoffrey Fucile (geoffrey.fucile@unibas.ch)
Alexander Kanitz (alexander.kanitz@unibas.ch) Torsten Schwede (torsten.schwede@unibas.ch) Mihaela Zavolan (mihaela.zavolan@unibas.ch, Assessor) |
| Content | Together with new measurement technologies, the use of computational and mathematical approaches that exploit modern information technology in the study of biological systems have brought about a deep transformation in the practice of molecular biology research. This course aims to train the students into the proficient use of programming in analyzing data derived from projects in life sciences. The format of the course includes 2 hour lectures, in which notions of software design and engineering will be discussed, and programming projects, done both in groups as well as individually. Group projects will come from various areas of life sciences (e.g. gene expression modeling and analysis, machine learning for sequence analysis, image analysis) and individual projects from the students’ areas of interest. The primary programming language is Python, a language broadly used in life sciences applications, but examples from other commonly used languages such as R and Matlab may also be included. |
| Learning objectives | By the end of the course, students should be comfortable with accessing and analyzing a wide variety of biological data. Concepts such as reproducibility, modularity, interoperability, and scalability will be emphasised. |
| Comments | Course registration is limited to 15 students. In the case of over-subscription to the course, selection will be based on the suitability of participants. |
| Weblink | Graduate Teaching Program |
| Admission requirements | Basic knowledge of computing systems, programming languages and algorithms are required. The course is focused on the widely used Python programming language in a UNIX context. Students should be comfortable with the material covered in basic tutorials in these languages, for example: https://edu.isb-sib.ch/course/view.php?name=UNIX_I http://learnpython.org/ https://www.codecademy.com/learn/python Students will require a sciCORE account, which can be requested with an email to scicore-admin@unibas.ch (please indicate the PI of your lab group). |
| Language of instruction | English |
| Use of digital media | No specific media used |
| Interval | Weekday | Time | Room |
|---|
No dates available. Please contact the lecturer.
| Modules |
Cycle E: Computational and Systems Biology (Master's Studies: Molecular Biology) Doctorate Biochemistry: Recommendations (PhD subject: Biochemistry) Doctorate Biophysics: Recommendations (PhD subject: Biophysics) Doctorate Cell Biology: Recommendations (PhD subject: Cell Biology) Doctorate Computational Biology: Recommendations (PhD subject: Computational Biology) Doctorate Genetics: Recommendations (PhD subject: Genetics) Doctorate Microbiology: Recommendations (PhD subject: Microbiology) Doctorate Molecular Biology: Recommendations (PhD subject: Molecular Biology) Doctorate Neurobiology: Recommendations (PhD subject: Neurobiology) Doctorate Pharmacology: Recommendations (PhD subject: Pharmacology) Doctorate Structural Biology: Recommendations (PhD subject: Structural Biology) Module Specialisation: Molecular Biology (Master's Studies: Nanosciences) Vertiefungsfächer Theorie und Vertiefungsfächer Biologie (Master's Studies: Computational Biology and Bioinformatics) |
| Assessment format | continuous assessment |
| Assessment details | Students must attend at least 80% of the sessions and actively contribute to discussion. Each student will develop, execute, and report the results of an independent project related to the computational methods discussed during the course. Ideally, students will develop their independent project around data from their own research. |
| Assessment registration/deregistration | Reg.: course registration, dereg: cancel course registration |
| Repeat examination | no repeat examination |
| Scale | Pass / Fail |
| Repeated registration | as often as necessary |
| Responsible faculty | Faculty of Science, studiendekanat-philnat@unibas.ch |
| Offered by | Departement Biozentrum |