Course catalogue doctoral education - VT21

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Title Bioinformatics for cell biologists
Course number 2219
Programme Cellbiologi och genetik
Language English
Credits 1.5
Notes The course meets the requirements for a general science course.

Date 2020-09-14 -- 2020-09-18
Responsible KI department Institutionen för cell- och molekylärbiologi
Specific entry requirements -
Purpose of the course To increase the understanding of the basic principles of bioinformatics and to gain practical skills in bioinformatics analysis of sequence data.
Intended learning outcomes After the completed course, the students will be able to utilize basic bioinformatics resources and tools, apply and integrate current, advanced computational biology methods in their research, and to make use of publicly available genome-wide sequencing data sets.
Contents of the course The course covers the use of most common bioinformatics resources such as public data bases and tools for sequence analysis. Practical excercises and discussions bridge sequence analysis to cellular function.
Teaching and learning activities The learning activities on the course consist of lectures and practical computer excercises. In addition, the students will be supervised in the preparation of presentations on bioinformatics to benefit their own research.
Compulsory elements The computer excercises are obligatory. Absence from the obligatory moments is compensated according to the instructions of the course director.
Examination Formative examination with practical computer excercises. Summative oral examination in conjunction with the presentation of individual student projects.
Literature and other teaching material Articles and online resources which will be recommended during the course.
Number of students 8 - 8
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) start date of doctoral studies (priority given to earlier start date)
More information The course is given as practical and theoretical course in basic cell biology oriented bioinformatics. The course is organized as a full time intensive summer school Monday-Friday at the Medicinska Föreningen site "Solviken" in Värmdö. All course participants must bring their own laptop for the course practicalities with the following software pre-installed (or at least downloaded): Python, PyCharm, Java8, R and R studio. Links to all programs will be provided. Note that we will have very limited time to solve the installation problems. The focus will be the subset of the following topics (depending on the interest and skills of the attendees): Introduction to programming languages: R and python, minor attention to other languages. No prior knowledge of programming required. Access to major online databases, NCBI, Ensembl, UCSC. Using BioMart, GEO, GO resources. The sequencing techniques, sequencing data processing, alignments, variant calling, RNA-seq data analysis. Elements of DNA sequence analysis (motifs, k-mers, DNA barcodes). Making sense of gene lists. Methods of clustering, classification, visualization. Basic statistics and data presentation. Note that most course participants will be housed in shared rooms (several people per room). Participants must bring their own towels and sheets (sleeping bags not allowed). Basic campsite food will be provided breakfast, lunch and dinner. Toilets are simple campsite facilities, and there are no showers, however a sauna bath and the sea to swim in. For those who do not wish to overnight at the site, it is possible to commute on a daily basis, with buses leaving frequently from Slussen (total travel time from Slussen 40 minutes in one direction including a short walk). Indicate in your application if you are in possession of a tent, and if you are willing to stay in a tent for the four nights.
Additional course leader The main teachers will be Dr. Leonid Bystrykh and Dr. Victor Guryev from the University of Groningen.
Latest course evaluation Course evaluation report
Course responsible Matti Nikkola
Institutionen för cell- och molekylärbiologi

Matti.Nikkola@ki.se
Contact person Linda Lindell
Institutionen för cell- och molekylärbiologi
08-524 872 90
linda.lindell@ki.se

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