June 23 - June 29

CSAMA 2013 Agenda Calendar
Sunday, June 23
Time: 5:00 PM - 6:00 PM
Summary: Installation Help Desk (1)
Time: 6:00 PM - 8:30 PM
Location: Main course site
Summary: Meet Together
Monday, June 24
Time: 8:30 AM - 9:15 AM
Summary: L01: Introduction to R and Bioconductor (MM)
Time: 9:15 AM - 10:00 AM
Summary: L02: Basics of high-throughput sequencing technologies and short read aligners (SA)
Time: 10:00 AM - 10:30 AM
Summary: Coffee break
Time: 10:30 AM - 11:15 AM
Summary: L03: Elements of statistics 1: t-test and linear model (RG)
Time: 11:15 AM - 12:00 PM
Summary: L04: What you still may want to know about microarrays (WH)
Time: 12:00 PM - 1:00 PM
Summary: Pause (no lunch served)
Time: 1:00 PM - 2:00 PM
Summary: Installation Help Desk (2)
Time: 2:00 PM - 3:15 PM
Summary: Tutorial1: R Intro, Part1. Note: Students taking the Advanced R Tutorial on friday, will instead do Lab 3 during this time.
Time: 3:15 PM - 3:30 PM
Summary: Coffe break
Time: 3:30 PM - 4:40 PM
Summary: Tutorial1: part II o Lab3 part II
Time: 4:40 PM - 5:00 PM
Summary: Wrap up
Time: 5:00 PM - 5:30 PM
Summary: Flashlight Session 1
Tuesday, June 25
Time: 8:30 AM - 9:15 AM
Summary: L05: Visualisation (VJC)
Time: 9:15 AM - 10:00 AM
Summary: L06: RNA-Seq 1: differential expression analysis and error models (SA)
Time: 10:00 AM - 10:30 AM
Summary: Coffee break
Time: 10:30 AM - 11:15 AM
Summary: L07: RNA-Seq 2: NB-GLMs, and application to alternative exon usage (SA)
Time: 11:15 AM - 12:00 PM
Summary: L08: Computing with genomic ranges, sequences and alignments (MM)
Time: 12:00 PM - 2:00 PM
Summary: Pause (no lunch served)
Time: 2:00 PM - 3:15 PM
Summary: Lab 1: Complete RNA-Seq workflow (from FASTQ to GSEA). Part 1
Time: 3:15 PM - 3:30 PM
Summary: Coffe break
Time: 3:30 PM - 4:40 PM
Summary: Lab1: Part 2
Time: 4:40 PM - 5:00 PM
Summary: Wrap up
Time: 5:00 PM - 5:30 PM
Summary: Flashlight Session 2
Wednesday, June 26
Time: 8:30 AM - 9:30 AM
Summary: L09: Elements of statistics 2: Classification and regularisation (1h WH)
Time: 9:30 AM - 10:00 AM
Summary: L10: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
Time: 10:00 AM - 10:30 AM
Summary: Coffee break
Time: 10:30 AM - 11:15 AM
Summary: L11: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
Time: 11:15 AM - 12:00 PM
Summary: L12: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
Time: 12:00 PM - 2:00 PM
Summary: Pause (no lunch served)
Time: 2:00 PM - 10:00 PM
Summary: Social Program
Thursday, June 27
Time: 8:30 AM - 9:15 AM
Summary: L13: Leveraging annotation and data integration: working with gene and genome annotations (MM)
Time: 9:15 AM - 10:00 AM
Summary: L14: eQTL / molecular-QTL analyses; integrative analysis of the Cancer Cell Line Encyclopedia (VJC)
Time: 10:00 AM - 10:30 AM
Summary: Coffee break
Time: 10:30 AM - 11:15 AM
Summary: L15: Elements of statistics 3: multiple testing and independent filtering (WH)
Time: 11:15 AM - 12:00 PM
Summary: L16: Emerging topic (TBC)
Time: 12:00 PM - 2:00 PM
Summary: Pause (no lunch served)
Time: 2:00 PM - 3:15 PM
Summary: Lab2: DNA-Seq analysis: from a human genome (subset of Illumina shotgun WGS) to annotated variants. Part 1
Time: 3:15 PM - 3:30 PM
Summary: Coffe break
Time: 3:30 PM - 4:40 PM
Summary: Lab2: RDNA-Seq analysis: from a human genome (subset of Illumina shotgun WGS) to annotated variants. Part 2
Time: 4:40 PM - 5:00 PM
Summary: Wrap up
Time: 5:00 PM - 5:30 PM
Summary: Flashlight Session 3
Friday, June 28
Time: 8:30 AM - 9:15 AM
Summary: L13: Gene set enrichment analysis (RG)
Time: 9:15 AM - 10:00 AM
Summary: L14: DNA Variant Calling (RG)
Time: 10:00 AM - 10:30 AM
Summary: Coffee break
Time: 10:30 AM - 11:15 AM
Summary: L15: Hilbert curve (SA) + Motifs, PWMs (MM)
Time: 11:15 AM - 12:00 PM
Summary: L16: Emerging topic (TBC)
Time: 12:00 PM - 2:00 PM
Summary: Pause (no lunch served)
Time: 2:00 PM - 3:15 PM
Summary: Tutorial2: Advanced topics in R - functional programming, parallelization, S4, debugging, writing packages
Time: 2:00 PM - 3:15 PM
Summary: Lab3: Annotation and visualization. Part 1
Time: 3:15 PM - 3:30 PM
Summary: Coffe break
Time: 3:30 PM - 4:40 PM
Summary: Lab3: Part 2
Time: 3:30 PM - 4:40 PM
Summary: Tutorial2: Part 2
Time: 4:40 PM - 5:00 PM
Summary: Wrap up

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