Introduction to Bioinformatics (M413)
Martin Reczko - Alexandros Dimopoulos
The course introduces students into the basic concepts of bioinformatics. It starts with a general overview of the various fields of bioinformatics and introduces dynamic programming as a solution to the sequence comparison problem (1). Next, a first introduction to the GNU / Linux operating system and the hands on use of basic command-line commands (CLI) as well as bash scripting is given. In addition, basic bioinformatics command line programs such as bedtools, vcftools, samtools, etc. are presented and used (2+3). Students are then familiarized with the programming language R, the use of IDE RStudio and the basic tools provided by the Bioconductor repository (4+5). Next, detailed examples of
NGS bioinformatics analysis and pipelines are explained for:
- RNAseq (quality control, gene expression analysis) (6),
- denovo assembly (both on the genome and transcriptome level) (7)
- ChipSeq, ClipSeq and (8)
- variant calling (exome sequencing example using GATK) (9)
Finally, the concept of flux balance analysis and genomic scale metabolic and macromolecular expression models is introduced (10). Each student will also present a recent scientific paper containing a bioinformatics application (11+12) and perform autonomously a selected data analysis with the methods introduced in the lecture within a small project conducted at the end of the course (13). Throughout the course, each student has access to her/his personal virtual machine with all necessary tools installed to conduct hands on exercises, assignments and the final project.
(numbers in brackets indicate the courses week)
Less
The course introduces students into the basic concepts of bioinformatics. It starts with a general overview of the various fields of bioinformatics and introduces dynamic programming as a solution to the sequence comparison problem (1). Next, a first introduction to the GNU / Linux operating system and the hands on use of basic command-line commands (CLI) as well as bash scripting is given. In addition, basic bioinformatics command line programs such as bedtools, vcftools, samtools, etc. are presented and used (2+3). Students are then familiarized with the programming language R, the use of IDE RStudio and the basic tools provided by the Bioconductor repository (4+5). Next, detailed examples of
NGS bioinformatics analysis and pipelines are explained for:
- RNAseq (quality control, gene expression analysis) (6),
- denovo assembly (both on the genome and transcriptome level) (7)
- ChipSeq, ClipSeq and (8)
- variant calling (exome sequencing example using GATK) (9)
Finally, the concept of flux
The course introduces students into the basic concepts of bioinformatics. It starts with a general overview of the various fields of bioinformatics and introduces dynamic programming as a solution to the sequence comparison problem (1). Next, a first introduction to the GNU / Linux operating system and the hands on use of basic command-line commands (CLI) as well as bash scripting is given. In addition, basic bioinformatics command line programs such as bedtools, vcftools, samtools, etc. are presented and used (2+3). Students are then familiarized with the programming language R, the use of IDE RStudio and the basic tools provided by the Bioconductor repository (4+5). Next, detailed examples of
NGS bioinformatics analysis and pipelines are explained for:
- RNAseq (quality control, gene expression analysis) (6),
- denovo assembly (both on the genome and transcriptome level) (7)
- ChipSeq, ClipSeq and (8)
- variant calling (exome sequencing example using GATK) (9)
Finally, the concept of flux
