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

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TBA
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* Course aims:
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** Get to know some of the the bioinformatics methods necessary for genomic analysis
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** Use these methods on simple real cases
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** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results
 +
 
 +
* Prerequisites:
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** Notions of genomics (gene, genome, transcriptome)
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** Basic statistics (what is a test, a p-value)
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** Basic literacy in R and/or Python.
 +
 
 +
* Teacher: [[Sven Bergmann]]
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* Assistants
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** [[User:Daniel|Daniel]]
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** [[User:Anneke|Anneke]]
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** [[User:Alex|Alex]]
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** [[User:Olga|Olga]]
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* Schedule
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** 28 March 2022, 08:00-9:15: Lecture 1: "RNA-seq & DE" (Sven)
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** 28 March 2022, 9:30-10:30: Tutorial 1: "RNA-seq & DE" (Anneke)
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** 28 March 2022, 10:45-12:00: Lecture 2: "Clustering" (Sven)
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** 29 March 2022, 08:00-9:00: Tutorial 2: "Clustering" (Alex)
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** 29 March 2022, 09:15-10:45: Lecture 3: "More seq-data" (Sven)
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** 29 March 2022, 11:00-12:00: Tutorial 3: "More seq-data" (Daniel)
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** 4 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Anneke, Alex, Daniel, Olga)
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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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On 28/29 March we present the core material of this module. We will hand out simple bioinformatics exercises based on the tutorials. Students should work on these exercise until April 4 on which day we will do a 4h "Flipped classroom" where they can discuss these exercise with tutors. 
 +
 
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Additional lectures and tutorial will be given on April 5 and 6.
 +
 
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* Lecture presentations:
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** "RNA-seq & DE": [[Media:Lecture1.pptx  | slides]]
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** "Clustering": [[Media:Lecture2.pptx | slides]]
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** "More seq-data": [[Media:Lecture4.pptx| slides]]
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** "Networks": [[Media:Lecture5.pptx | slides]]
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** "Advanced clustering": [[Media:Lecture3.pptx| slides]]
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* Exercise material:
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** "RNA-seq & DE": [[File:Exercise1.zip]]
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** "Clustering": [[File:Exercise2.zip]]
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** "Biclustering": [[File:Exercise3.zip]]
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** "More seq-data": [[File:Exercise4.zip]]
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** "Networks": [[File:Exercise5.zip]]
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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

Revision as of 22:10, 23 March 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
    • 28 March 2022, 08:00-9:15: Lecture 1: "RNA-seq & DE" (Sven)
    • 28 March 2022, 9:30-10:30: Tutorial 1: "RNA-seq & DE" (Anneke)
    • 28 March 2022, 10:45-12:00: Lecture 2: "Clustering" (Sven)
    • 29 March 2022, 08:00-9:00: Tutorial 2: "Clustering" (Alex)
    • 29 March 2022, 09:15-10:45: Lecture 3: "More seq-data" (Sven)
    • 29 March 2022, 11:00-12:00: Tutorial 3: "More seq-data" (Daniel)
    • 4 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Anneke, Alex, Daniel, Olga)
    • 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)

On 28/29 March we present the core material of this module. We will hand out simple bioinformatics exercises based on the tutorials. Students should work on these exercise until April 4 on which day we will do a 4h "Flipped classroom" where they can discuss these exercise with tutors.

Additional lectures and tutorial will be given on April 5 and 6.

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