GSMS Course Registration

All GSMS courses

Only GSMS PhD students (including BCN PhD students) can participate in these courses. Use your P-number to register (ask your Personnel Office).

For registration please go to Upcoming courses.

Course: Genome Data for beginners and advanced

 

 

Summary: Online genome databases are rapidly expanding and are already central to the biological and medical research. Such massive amount of information needs basic understanding of how to find the data of interest and what to do with those data. In this course students will practice with data retrieval from GEO, UCSC, Encode, ENSEMBL and other web sites. Basic introduction will be given to RNAseq, ChIPseq, as well as to genomic (promoter) motifs and gene ontology tools. Students will be introduced to basic programming in Python, R and few other script types. The course will include exercises with data retrieval, processing, and basic elements of analysis. Statistical evaluation of the obtained results will be discussed as well.

 

Learning outcomes: 

 

                   ·  Understanding the sources of genome data and approaches for data analysis

 

                   ·  Understanding the principles of R and Python packages use for genome data analysis. Basic knowledge of using and writing scripts in R and Python.

 

                   ·  Understanding basics of the experimental design and statistical robustness of the data sets.

 

        Assumed pre­knowledge A good understanding of molecular biology and genetics. Having experience with programming can be helpful, but is not required.

 

        Equipment Personal laptop with 8 GM RAM, preferably Mac or Linux. Windows can be used, but with limitations. R (with R-studio) and Python3 (with Pycharm) can be preinstalled, or will be installed during the course.

 

        Compulsory literature No

 

        Recommended Articles and online resources will be recommended during the course

 

        Exam
100% participation required, final assignment required

 

 

        Date, Time  Approximately 7 seminars 3 hours each, end October-November 2018.

 

 

EC (without exam)

1

Course coordinator

  • Leonid Bystrykh, PhD

Language

English

Contact person

Maaike Bansema, m.h.bansema@umcg.nl

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