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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 | 2020-05-04 -- 2020-05-08 | 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 - 15 |
| 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 full time at Karolinska Institutet Solna campus. 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. |
| 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 |
