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Titel Bioinformatics for cell biologists
Kursnummer 2219
Program Cellbiologi och genetik
Språk Engelska
Antal högskolepoäng 1.5
Noteringar Kursen uppfyller kraven för en allmänvetenskaplig kurs.
Datum 2020-09-14 -- 2020-09-18
Kursansvarig institution Institutionen för cell- och molekylärbiologi
Särskild behörighet -
Kursens syfte To increase the understanding of the basic principles of bioinformatics and to gain practical skills in bioinformatics analysis of sequence data.
Kursens lärandemål 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.
Kursens innehåll 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.
Arbetsformer 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.
Obligatoriska moment 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.
Kurslitteratur och övriga läromedel Articles and online resources which will be recommended during the course.
Antal studenter 8 - 8
Urval av studenter 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)
Övrig 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.
Ytterligare kursledare The main teachers will be Dr. Leonid Bystrykh and Dr. Victor Guryev from the University of Groningen.
Senaste kursvärdering Kursvärderingsrapport
Kursansvarig Matti Nikkola
Institutionen för cell- och molekylärbiologi

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

Solnavägen 9

171 77
Stockholm