schedule.md

Schedule

The course schedule consists of 1 afternoon (Tuesday) and 3 "full" days (Wednesday - Friday) in the first two weeks, with 1.5 days in the last week.

The "full days" run from 09:00 - 17:00, with a break from 12:00 - 13:30.

Conceptually, mornings are predominantly related to introductions, presentations and discussion of the previous days, and are afternoons reserved for independent work on the examples and tasks.

Introduction, File Formats & Genome Browsers (Michael Baudis)

2018-09-18 (Tue), 13-17

• general introduction into the topic (slides)
• schedule adjustment
• guidance about course room and computer use (Tina Siegenthaler)
• reading:
  • 1000 Genomes paper
  • The sequence of sequencers paper
• tasks:
  • Genome Storage Space & Cost, e.g. required for 1000 Genomes
    • WES & WGS
    • Different file formats
      • SAM
      • BAM
      • VCF
      • FASTA
    • Associated costs
    • Cost factors
    • Raw Storage costs

2018-09-19 (Wed), 09-17

• reference genome resources
• reading:
  • "Genomics made easier"
  • UCSC genome browser tutorial
• exercise: UCSC tutorial
• Answer for UCSC tutorial, genelist, genelist_canonical
• genome editions and coordinates
• reading:
  • segment_liftover article
• exercise: genome liftover

2018-09-20 (Thu), 09-17

• Annotating genome variants
• reading:
  • HGVS Recommendations (not for details, though)
  • dbVar "Overview of Structural Variation" (link)
  • info slides from the morning session
• Literature review and discussion

2018-09-21 (Fri), 09-17

• Associating variants with phenotypes and diseases (focus on cancer…)
  • Use of variant databases and annotation tools (CiVIC, OncoKB, ClinGen, arrayMap…)
• info slides from the morning session
• Hands-on analysis of genome data
  • copy number segmentation tutorial Reference publication
  • plink tutorial
  • variant <-> disease mapping exercise

Tools & Programmatic Solutions (Izaskun Mallona)

• SIB Swiss Institute of Bioinformatics tutorial on UNIX
• Unix slides
• Genomic formats slides
• Exercises

2018-09-25 (Tue), 13-17

• How are UCSC Genome Browser data stored? Why?
• Genomics data management: automation
  • Computer basics: plain text files, Unix terminal
  • Reproducibility
  • Systems set up (data download and software installs)

2018-09-26 (Wed), 09-17

• Unix for bioinformatics
  • Chapter 1: What is UNIX
  • Chapter 2: The UNIX filesystem
  • Chapter 3: UNIX shell - first steps
  • Chapter 4: UNIX shell - filesystem commands
  • Chapter 5: UNIX shell - working with files

2018-09-27 (Thu), 09-17

• Overview of the standard genomics data formats (I)
  • FASTA
  • FASTQ
  • SAM
  • BED
• Basic file processing for bioinformatics
  • awk, cut

2018-09-28 (Fri), 09-17

• Overview of the standard genomics data formats (II)
  • GFF/GTF
  • BEDgraphs
  • Wiggle files
  • VCFs
• Indexed genomic data formats
• Exercises

Genome Variants to Modified Proteins (Elif Ozkirimli Olmez)

2018-10-02 (Tue), 13-17

• Protein Structure Slides
  • Protein Data Bank PDB
• Literature
  • Bhattacharya R, Rose PW, Burley SK, Prlić A (2017) Impact of genetic variation on three dimensional structure and function of proteins. PLOS ONE 12(3): e0171355.
  • Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., et al. (2017). Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine, 23(6), 703–713.
  • Studer, R. A., Dessailly, B. H., & Orengo, C. A. (2013). Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochemical Journal, 449(3), 581–594.
• Protein Structure Analysis Task

2018-10-03 (Wed), 09-17

• Go over the protein structure analysis task from Tuesday. All of you did a great job!
• Uniprot slides
  • Uniprot
  • Gene Ontology, GO
• Uniprot introduction video, Uniprot Feature viewer video
• Uniprot activity
• Alignment slides
• Afternoon activity

2018-10-04 (Thu), 09-17

• We start at 9:30
• Oct 4 slides
• Oct 4 activity

2018-10-05 (Fri), 09-17

• Morning: Presentations on your protein
  • Biological relevance of your protein
  • Experimental details/methods
  • 2 key findings
  • Position of mutations on protein structure (structure figure)
  • Discussion
• Afternoon: BLAST task

Review, feedback & test (Michael Baudis)

• 2018-10-09 (Tue), 13-17 (slides)
  • Ontologies for metadata annotations (very brief introduction)
  • Privacy, security, society - implications of availability & possible re-identification of genome data
    • long range familial identification
    • principles of Beacon-style re-identification attack
    • "ease" of field sequencing (MinIon etc.)
• 2018-10-10 (Wed), 09-14:30
  • preparation/recap time in the morning
  • Written exam (13:00 - 14:30)
    • multiple choice and free questions