Difference between revisions of "UNIL BSc course: Bioinformatics for Genomics 2022"

 
 
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* Coordinator: [[Sven Bergmann]]
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* Course aims:
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* [[Concept]]
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** Get to know some of the the bioinformatics methods necessary for genomic analysis
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* [[Useful tools]]
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** Use these methods on simple real cases
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* [[Dates and Deadlines 2022]]
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** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results
  
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* Projects
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* Prerequisites:
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** [[Retina Image Analysis]] (Michael)
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** Notions of genomics (gene, genome, transcriptome)
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** [[SNP minor allele frequencies and their functional implication]] (Anneke)
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** Basic statistics (what is a test, a p-value)
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** [[Heritability of BMI and other obesity measures]] (Sofia)
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** Basic literacy in R and/or Python.
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** [[Polygenic Risk Scores]] (Alex)
 
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** [[PascalX application: Marrying GWAS pairs]] (Daniel)
 
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** [[Analysing brain blood vessels through MRIs]] (Olga)
 
  
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* Supervisors
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* Teacher: [[Sven Bergmann]]
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** [[User:Michael|Michael]]
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* Assistants
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** [[User:Daniel|Daniel]]
 
** [[User:Anneke|Anneke]]
 
** [[User:Anneke|Anneke]]
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** [[User:Sofia|Sofia]]
 
 
** [[User:Alex|Alex]]
 
** [[User:Alex|Alex]]
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** [[User:Daniel|Daniel]]
 
 
** [[User:Olga|Olga]]
 
** [[User:Olga|Olga]]
  
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* [[Grading]]
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* Schedule
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* see also [[UNIL BSc course: Solving Biological Problems that require Math 2021]]
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** 31 March 2022, 08:00-9:15: Lecture 1: "RNA-seq & DE" (Sven)
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* [[How to upload files and edit your project page]]
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** 31 March 2022, 9:30-10:30: Tutorial 1: "RNA-seq & DE" (Anneke)
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** 31 March 2022, 10:45-12:00: Lecture 2: "Clustering" (Sven)
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** 4 April 2022, 14:00-15:00: Tutorial 2: "Clustering" (Alex)
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** 4 April 2022, 15:15-16:45: Lecture 3: "More seq-data" (Sven)
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** 4 April 2022, 17:00-18:00: Tutorial 3: "More seq-data" (Daniel)
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** 5 April 2022, 8:00-9:30: Lecture 4: "Biological Networks" (Sven)
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** 5 April 2022, 10:00-11:30: Tutorial 4: "Biological Networks" (Daniel)
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** 6 April 2022, 08:00-10:30: Lecture 5: "Advanced clustering" (Sven)
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** 6 April 2022, 11:00-12:00: Final Session: "Wrap-up & feedback" (all)
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** 14 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Sven, Anneke, Alex, Sofia, Michael)
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We will hand out simple bioinformatics exercises based on the tutorials. Students should work on these exercise until April 14 on which day we will do a 4h "Flipped classroom" where they can discuss these exercise with tutors. 
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* Lecture presentations:
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** "RNA-seq & DE": [[Media:GGE2022_Lecture1.pptx | slides]]
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** "Clustering": [[Media:GGE2022_Lecture2.pptx | slides]]
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** "More seq-data": [[Media:GGE2022_Lecture3.pptx| slides]]
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** "Networks": [[Media:GGE2022_Lecture4.pptx | slides]]
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** "Advanced clustering": [[Media:GGE2022_Lecture5.pptx| slides]]
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* Exercise material:
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** "RNA-seq & DE": [[Media:GGE2022_Exercise1.zip | exercise]]
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** "Clustering": [[Media:Exercise2.zip | exercise]] | [[Media:Documents_from_tutorial_class.zip | extra material]]
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** "Biclustering": [[Media:Exercise3.zip | exercise]]
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** "More seq-data": [[Media:Exercise4.zip | exercise]]
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** "Networks": [[Media:Exercise5.zip | exercise]]
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* Recordings from previous year:
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** available on Moodle at: https://moodle.unil.ch/course/view.php?id=19549

Latest revision as of 14:11, 6 April 2022

  • Course aims:
    • Get to know some of the the bioinformatics methods necessary for genomic analysis
    • Use these methods on simple real cases
    • Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results
  • Prerequisites:
    • Notions of genomics (gene, genome, transcriptome)
    • Basic statistics (what is a test, a p-value)
    • Basic literacy in R and/or Python.
  • Schedule
    • 31 March 2022, 08:00-9:15: Lecture 1: "RNA-seq & DE" (Sven)
    • 31 March 2022, 9:30-10:30: Tutorial 1: "RNA-seq & DE" (Anneke)
    • 31 March 2022, 10:45-12:00: Lecture 2: "Clustering" (Sven)
    • 4 April 2022, 14:00-15:00: Tutorial 2: "Clustering" (Alex)
    • 4 April 2022, 15:15-16:45: Lecture 3: "More seq-data" (Sven)
    • 4 April 2022, 17:00-18:00: Tutorial 3: "More seq-data" (Daniel)
    • 5 April 2022, 8:00-9:30: Lecture 4: "Biological Networks" (Sven)
    • 5 April 2022, 10:00-11:30: Tutorial 4: "Biological Networks" (Daniel)
    • 6 April 2022, 08:00-10:30: Lecture 5: "Advanced clustering" (Sven)
    • 6 April 2022, 11:00-12:00: Final Session: "Wrap-up & feedback" (all)
    • 14 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Sven, Anneke, Alex, Sofia, Michael)

We will hand out simple bioinformatics exercises based on the tutorials. Students should work on these exercise until April 14 on which day we will do a 4h "Flipped classroom" where they can discuss these exercise with tutors.

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