Programme

Sunday, 19 June

18:00–20:00 Registration & Installation help desk
18:00–20:00 Get Together with drinks and nibbles
Please see here for the teaching material - lectures and labs.

Monday, 20 June

08:30–09:15 Lecture 01 Introduction to Bioconductor (Martin Morgan)
09:15–10:00 Lecture 02 PCA and other low-dimensional embeddings (Levi Waldron)
10:00–10:30 Coffee break
10:30–11:15 Lecture 03 Statistical tests I (Wolfgang Huber)
11:15–12:00 Lecture 04 Regression I (Robert Gentleman)
12:00–13:00 Lunch break
13:00–13:30   Installation help desk
13:30–15:00 Lab 1 R and Bioconductor Basics (Martin Morgan)
15:00–16:30 Lab 2 R and Bioconductor Basics
16:30–17:00 Flashlight talks
  • Christian Scherhäufl
  • Luis Manuel Cervera Seco
  • Kai Faehrmann
  • Albert Fradera Sola
20:10–22:00 Evening session  
20:10–20:30   Beer and pizza will be provided
20:30–21:15 Demos
  • Interactive exploration and data quality assessment for matrix-shaped data with iSEE (Charlotte Soneson)
  • Using R/BioC with docker, singularity containers (Martin Morgan, Nitesh Turaga); bulker.io (Levi Waldron)
21:15–22:00 Discussion sessions

Tuesday, 21 June

08:30–09:15 Lecture 05 Basics of RNA-Seq (Davide Risso)
09:15–10:00 Lecture 06 Regression II (Charlotte Soneson)
10:00–10:30 Coffee break
10:30–11:15 Lecture 07 Single-cell RNA-seq: data properties, embeddings (Davide Risso)
11:15–12:00 Lecture 08 Distances, nearest-neighbour graphs and clustering (Vincent Carey)
12:00–13:30 Lunch break
13:30–16:30 Lab 3 End-to-end RNA-Seq workflow (Charlotte Soneson)
13:30–16:30 Lab 4 Single-cell transcriptomics (Davide Risso)
16:30–17:00 Flashlight talks
  • Daniel Fridljand
  • Anže Lovše
  • Martín González
  • Stephan Drothler
20:10–22:00 Evening session  
20:10–20:30   Beer and pizza will be provided
20:30–21:15 Demos / pitches
  • 5 min: Reproducible research and open science (Laurent Gatto, Charlotte Soneson)
  • 10 min: Shiny (Vincent Carey)
  • 10 min: Getting started with cloud computing (Martin Morgan, Nitesh Turaga); GPUs (Nitesh Turaga)
  • 10 min: HDF5 / large single-cell datasets (Davide Risso)
21:15–22:00 Group discussion sessions on the lawn / patio
  • ... participants suggestions welcome!
  • Reproducible research and open science (Laurent, Charlotte)
  • git, docker (Nitesh)
  • HDF5 / large datasets (Davide)
  • Cloud (Martin)
  • New / emerging technologies and their data analytical needs (Wolfgang)
  • Biggests challenges in biological data analysis (Vince)

Wednesday, 22 June

08:30–09:15 Lecture 09 Human Cell Atlas | Ontologies | Shiny (Vincent Carey)
09:15–10:00 Lecture 10 Statistical tests II (Wolfgang Huber)
10:00–10:30 Coffee break
10:30–11:15 Lecture 11 Group projects (Vincent Carey)
11:15–12:00 Lecture 12 Annotation Resources (Johannes Rainer)
12:00–13:30 Lunch break
14:00–22:30   Social programme: excursion to the mountains, dinner

Thursday, 23 June

08:30–09:15 Lecture 13 Mass spectrometry-based proteomics (Laurent Gatto)
09:15–10:00 Lecture 14 Visualization (Wolfgang Huber)
10:00–10:30 Coffee break
10:30–11:30 Lecture 15 Supervised machine learning (Robert Gentleman)
11:30–12:00 Lecture 16 Mass spectrometry-based metabolomics (Johannes Rainer)
12:00–13:30 Lunch break
13:30–16:30 Lab 5 Proteomics (Laurent Gatto, Johannes Rainer)
13:30–16:30 Lab 6 Multiple testing and FDR (Wolfgang Huber)
13:30–16:30 Lab 7 Multimodal data (Levi Waldron)
13:30–16:30 Lab 9 Annotation of untargeted metabolomics data (Johannes Rainer)
16:30–17:00 Flashlight talks

Friday, 24 June

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08:30–09:15 Lecture 17 (Generalized) Linear Models (Robert Gentleman)
09:15–10:00 Lecture 18 Immunoinformatics (Katharina Imkeller)
10:00–10:30 Coffee break
10:30–11:15 Lecture 19 Emerging topic
11:15–12:00 Lecture 20 Group projects (Vincent Carey)
12:00–13:30 Lunch break
13:30–16:30 Lab 5 Proteomics (Laurent Gatto, Johannes Rainer)
13:30–16:30 Lab 6 Multiple testing and FDR (Wolfgang Huber)
13:30–16:30 Lab 7 Multimodal data (Levi Waldron)
13:30–16:30 Lab 9 Annotation of untargeted metabolomics data (Johannes Rainer)
16:30   Closing remarks

Flashlight talks

Each talk 5 min + 2 min questions

Lecturers and Teaching Assistants

Vince Carey (VJC) Laurent Gatto (LG) Robert Gentleman (RG) Wolfgang Huber (WH) Julia Philipp (JP) Johannes Rainer (JR) Davide Risso (DR) Charlotte Soneson (CS) Martin Morgan (MM) Levi Waldron (LW) Constantin Ahlmann-Eltze (CAE) Simone Bell (SB) Nitesh Turaga (NT)