Difference between revisions of "UNIL BSc course: Bioinformatics for Genomics 2022"
 
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* Schedule
 
* Schedule
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** 28 March 2022, 08:00-9:15: Lecture 1: "RNA-seq & DE" (Sven)
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** 31 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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** 31 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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** 31 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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** 4 April 2022, 14:00-15:00: 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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** 4 April 2022, 15:15-16:45: 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, 17:00-18:00: Tutorial 3: "More seq-data" (Daniel)
−
 
 
−
** 4 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Sven, Anneke, Alex, Daniel, Olga, Sofia, Michael)
 
  
 
** 5 April 2022, 8:00-9:30: Lecture 4: "Biological Networks" (Sven)
 
** 5 April 2022, 8:00-9:30: Lecture 4: "Biological Networks" (Sven)
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** 6 April 2022, 11:00-12:00: Final Session: "Wrap-up & feedback" (all)
 
** 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. 
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** 14 April 2022, 14:00-18:00: Flipped classroom: Bioinformatics exercises (Sven, Anneke, Alex, Sofia, Michael)
  
−
Additional lectures and tutorial will be given on April 5 and 6.
+
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.
  
 
* Lecture presentations:
 
* Lecture presentations:
−
** "RNA-seq & DE": [[Media:Lecture1.pptx | slides]]
+
** "RNA-seq & DE": [[Media:GGE2022_Lecture1.pptx | slides]]
−
** "Clustering": [[Media:Lecture2.pptx | slides]]
+
** "Clustering": [[Media:GGE2022_Lecture2.pptx | slides]]
−
** "More seq-data": [[Media:Lecture4.pptx| slides]]
+
** "More seq-data": [[Media:GGE2022_Lecture3.pptx| slides]]
−
** "Networks": [[Media:Lecture5.pptx | slides]]
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** "Networks": [[Media:GGE2022_Lecture4.pptx | slides]]
−
** "Advanced clustering": [[Media:Lecture3.pptx| slides]]
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** "Advanced clustering": [[Media:GGE2022_Lecture5.pptx| slides]]
  
 
* Exercise material:
 
* Exercise material:
−
** "RNA-seq & DE": [[File:Exercise1.zip]]
+
** "RNA-seq & DE": [[Media:GGE2022_Exercise1.zip | exercise]]
−
** "Clustering": [[File:Exercise2.zip]]
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** "Clustering": [[Media:Exercise2.zip | exercise]] | [[Media:Documents_from_tutorial_class.zip | extra material]]
−
** "Biclustering": [[File:Exercise3.zip]]
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** "Biclustering": [[Media:Exercise3.zip | exercise]]
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** "More seq-data": [[File:Exercise4.zip]]
+
** "More seq-data": [[Media:Exercise4.zip | exercise]]
−
** "Networks": [[File:Exercise5.zip]]
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** "Networks": [[Media:Exercise5.zip | exercise]]
  
 
* Recordings from previous year:
 
* Recordings from previous year:
 
** available on Moodle at: https://moodle.unil.ch/course/view.php?id=19549
 
** 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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