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CSAMA 2017
15th edition

Bressanone-Brixen
June 11-16, 2017

Start (welcome reception and buffet):
Sunday, June 11, 18:30

Academic programme:
Monday 8:30 to Friday 17:00

Registration closed on May 14 2017

Lecturers

  • Jennifer Bryan, RStudio and UBC
  • Vincent J. Carey, Harvard Medical School
  • Laurent Gatto, University of Cambridge
  • Wolfgang Huber, European Molecular Biology Laboratory (EMBL), Heidelberg
  • Martin Morgan, Roswell Park Cancer Institute, Buffalo
  • Johannes Rainer, European Academy of Bozen (EURAC)
  • Charlotte Soneson, University of Zurich
  • Levi Waldron, CUNY School of Public Health at Hunter College, New York

Teaching Assistants

  • Simone Bell, EMBL, Heidelberg
  • Vladislav Kim, EMBL, Heidelberg
  • Lori Shepherd, RPCI, Buffalo
  • Mike L. Smith, EMBL, Heidelberg

Organized in collaboration with

Previous editions of CSAMA

About

The one-week intensive course Statistical Data Analysis for Genome-Scale Biology teaches statistical and computational analysis of multi-omics studies in biology and biomedicine. It covers the underlying theory and state of the art (the morning lectures) and practical hands-on exercises based on the R / Bioconductor environment (the afternoon labs). At the end of the course, you should be able to run analysis workflows on your own (multi-)omic data, adapt and combine different tools, and make informed and scientifically sound choices about analysis strategies.

The course is intended for researchers who have basic familiarity with the experimental technologies and their applications in biology, and who are interested in making the step from a user of bioinformatics software towards adapting or developing their own analysis workflows. The four practical sessions of the course will require you to follow and modify scripts in the computer language R. To freshen up your R skills, see below for some links.

Topics

  • Introduction to R and Bioconductor
  • The elements of statistics: hypothesis testing, multiple testing, regression, regularization, clustering and classification, parallelization and performance (machine learning), visualisation
  • RNA-Seq data analysis
  • Computing with sequences and genomic intervals
  • Working with annotation – genes, genomic features, variants, transcripts and proteins
  • Gene set enrichment analysis
  • Mass spec proteomics and metabolomics
  • Basis of microbiome analysis
  • Experimental design, batch effects and confounding
  • Reproducible research and workflow authoring with R markdown
  • Package development, version control and developer tools (incl. git, github, RStudio)
  • Working with large data: performance parallelisation and cloud computing

Course Structure

The course consists of

  • Morning lectures: 20 x 45 minutes: Monday to Friday 8:30 – 12:00
  • Practical computer tutorials in the afternoons (13:30 – 16:30)

Course Materials

Download the course materials for the labs.
Download the course materials for the lectures.

Computer Tutorials

You will work on the labs at your own pace in small groups with expert guidance (all lecturers from the morning sessions plus teaching assistants).

Participants are required to bring their own laptop with the most recent release versions of R (i.e. 3.4) and Bioconductor (i.e. 3.5) installed. If your computer’s hardware is sufficiently powered for ‘real work’, you will enjoy the course more. A WiFi network card is welcome to connect to our local network (course material), however, there are no reliable connections to the internet at the course venue.

Social Programme

One of the afternoons is for a joint cultural and outdoors activity. We plan a guided tour at one of the Brixen area’s impressive cultural / historical sites and, depending on the weather, a trip into the mountains, a (light) walk in the high-alpine area and delicious local dinner.

RossAlm

2:55 pmWe meet at “Casa della Gioventù” and walk 1 min to the bus waiting for us in Via Dante.
 
Please take the underpass to cross “Via Peter Mayr.”
 
The way to the bus stop in Via Dante

3:00 pmThe bus leaves towards the cable car for Mount Plose.

3:30 pmThe cable car takes us to the top of Mount Plose in about 20-30 min.

45-60 minHiking to RossAlm at 2200 m altitude.

6:00 pmSocial dinner at RossAlm.

8:00 pmTime to leave! We walk back to the bus from RossAlm.

9:00 pmThe bus takes us back to Brixen.

Please pack/bring:

  • Solid footwear (ideal: hiking shoes or boots)
  • Jacket or warm sweater for the descent (it may get quite fresh)
Please note:
If you don’t attend the social programme, please let us know at the latest on Monday 12th June via email to simone.bell [at] embl.de

No Internet Access

Please note: The course venue does not provide stable internet access. The course provides a local network with the course material.


R BASICS

Programme

Sunday, June 11

17:00–18:00 Registration & Installation help desk
18:00–20:00 Get Together with drinks and nibbles

Monday, June 12

08:30–09:15 Lecture 01 Introduction to R and Bioconductor (MM)
09:15–10:00 Lecture 02 Computing with Sequences and Ranges (MM)
10:00–10:30 Coffee break
10:30–11:15 Lecture 03 Tabular data management (JB)
11:15–12:00 Lecture 04 Annotation resources (JR with MM)
12:00–13:00 Lunch break
13:00–13:30 Installation help desk
13:30–15:00 Lab 1 Introduction to Bioc (MM)
15:00–16:30 Lab 2 Use of Git and GitHub with R, RStudio,
and R Markdown (JB)
16:30–17:00 Flashlight talks

  • Tore Bleckwehl
  • Rosalba Giugno
  • Jan-Jaap Wesselink
  • Cristina Viéitez

Tuesday, June 13

08:30–09:15 Lecture 05 Basics of sequence alignment and aligners (CS)
09:15–10:00 Lecture 06 RNA-Seq data analysis and differential expression (WH)
10:00–10:30 Coffee break
10:30–11:15 Lecture 07 New workflows for RNA-seq (CS)
11:15–12:00 Lecture 08 Hypothesis testing (WH)
12:00–13:30 Lunch break
13:30–16:30 Lab 3 End-to-end RNA-Seq workflow (CS and WH)
Optional: Independent hypothesis weighting (WH)
16:30–17:00 Flashlight talks

  • Erica Valentini
  • Aurora Maurizio
  • Faris Naji
  • Daniel Weindl

Wednesday, June 14

08:30–09:15 Lecture 09 Multiple testing (WH)
09:15–10:00 Lecture 10 Linear models (basic intro) (LW)
10:00–10:30 Coffee break
10:30–11:15 Lecture 11 Experimental design, batch effects and confounding (CS)
11:15–12:00 Lecture 12 Robust statistics: median, MAD, rank test, Spearman, robust linear model (VJC)
12:00–13:30 Lunch break
13:30–22:00 Social programme: excursion to the mountains, dinner

Thursday, June 15

08:30–09:00 Lecture 13 Visualization, the grammar of graphics and ggplot2 (WH)
09:00–09:45 Lecture 14 Mass spec proteomics & metabolomics (LG and JR)
09:45–10:15 Coffee break
10:15–11:00 Lecture 15 Clustering and classification (VJC)
11:00–11:30 Lecture 16 Resampling: cross-validation, bootstrap, and permutation tests (LW)
11:30–12:00 Lecture 17 Analysis of microbiome marker gene data (CS)
12:00–13:30 Lunch break
13:30–15:00 Lab 4 Mass spec proteomics & metabolomics (LG and JR)
15:00–16:30 Lab 5 MultiAssayExperiment (LW)
16:30–17:00 Flashlight talks

  • Sylwia Czarnomska
  • Korbinian Bösl
  • Alessia Donato
  • Tine Descamps

Friday, June 16

08:30–09:15 Lecture 18 Gene set enrichment analysis (MM)
09:15–10:00 Lecture 19 Working with large-scale data (MM with VJC)
10:00–10:30 Coffee break
10:30–11:15 Lecture 20 Developer Practices, Writing functions (JB)
11:15–12:00 Lecture 21 Developer Practices, Writing packages (JB)
12:00–13:30 Lunch break
13:30–16:30 Lab 6 Graphics (WH)
13:30–16:30 Lab 7 Machine learning (supervised) (WH)
13:30–16:30 Lab 8 Large data, performance, and parallelization; large-scale efficient computation with genomic intervals (VJC, MM)
16:30 Closing remarks

Flashlight talks

Each talk 5 min + 2 min questions

Lecturers and Teaching Assistants

Simone Bell (SB), Jennifer Bryan (JB), Vincent J. Carey (VJC), Laurent Gatto (LG), Wolfgang Huber (WH), Vladislav Kim (VK), Martin Morgan (MM),  Mike Smith (MS), Johannes Rainer (JR), Lori Shepherd (LS), Charlotte Soneson (CS), Levi Waldron (LW).

Venue

We will welcome you on Sunday around 18:00h for a welcome buffet at the main site (1).

The main idea of this pre-course meeting is to meet each other in an informal environment, but you can also consider this as a course registration where we will give you all the course materials including the receipt of your payment.

Please note: there will be food and drinks to satisfy your hunger and thirst, and usually we move on into the town in smaller groups to enjoy the many beergardens and restaurants.

Conference sites

The following map is a very reduced one. You can have a big one in PNG format, or you can browse an interactive one from the web page of the Tourist Office in Bressanone-Brixen.

Conference sites (small map)

(1) Casa della Gioventù – main course site:

Casa della Gioventù is the place where both morning lectures and laboratory will take place, and it is also the place of the Welcome Buffet.

It is a building of the University of Padova, located in Via Rio Bianco 6, 5 minutes from the town center.

(2) Hotel Albero Verde (Grüner Baum):

It is a hotel were many of the participants usually stay.

(3) The railway station:

Where many of you will arrive.

Travel & Accomodation

How to get to Bressanone – Brixen

Bressanone (or Brixen) is in the bilingual province of Bolzano (Bozen) at 500 meters of altitude, in the Italian Alps, close to the Dolomites.


View Larger Map

By Train

Bressanone is on the international line between Munich (Germany) and Verona (Italy). Every train on this line stops in Bressanone. Moreover, there are many commuter connections from Innsbruck (Austria) and from Bolzano (Italy) to Bressanone.

The train from Verona P.ta Nuova to Bressanone takes about 2 hours, with frequent connections throughout the day. The train from Munich takes about 3.5 hours, with connections every 2 hours.

By Airplane

Several airports have good train connections to Bressanone:

  • Bolzano, Italy (BZO) 50 km (30 minutes by train)
  • Innsbruck, Austria (INN) 80 km (1 hours by train)
  • Verona, Italy (Valerio Catullo, VRN) 200 km
  • Munich, Germany (Franz-Josef Strauss, MUC) 260 km
  • Venezia, Italy (Marco Polo, VCE) 320 km
  • Milano-Linate, Italy (LIN) 330 km
  • Milano-Malpensa, Italy (MXP) 350 km

The closest large airport is Verona (Valerio Catullo) international airport. From Verona airport to the railway station Verona P.ta Nuova (see above) there are shuttle busses every 20 minutes from 6:30am to 11:35pm. From Verona to Bressanone it takes about 2 hours by train, and you have several trains per day (see above).

About Munich: please do not confuse Munich’s main airport (Franz-Josef Strauss) with Ryanair’s “Munich West” (Memmingen) – it is far out in the Allgäu, and it is not much fun coming from there by public transport; with a rental car, it may however be an option.

Hotel information

You need to make your reservation directly.

Hotel Gruener Baum (Albero Verde)

Please make your reservations yourself and ask for further information by sending an email to the following address: info@gruenerbaum.it or check their web site for the telephone number.

Hotel Goldene Krone

Please make your reservations yourself and ask for further information by sending an email to the following address: info@goldenekrone.com or check their web site for the telephone number.

Hotel Elephant

Please make your reservations yourself and ask for further information by sending an email to the following address: info@hotelelephant.com or check their web site for the telephone number.

Other accommodation

There also exist two youth hostel-like accommodations. These locations have low fares, and they can be considered as equivalent both for quality and location (Brixen is a small town). Please ask directly them if you need rooms (with or without bath, etc).