About CSAMA

The summer school 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 summer school will require you to follow and modify scripts in the computer language R.

Topics

The programme covers a wide range of topics, including but not limited to:

Introduction to R and Bioconductor
Elements of statistics: visualization, regression, PCA and other low-dimensional embeddings, statistical tests incl. multiple, classification / supervised machine learning
RNA-Seq data analysis – bulk and single cell
Spatial omics
Working with annotation – genes, genomic features, variants, transcripts and proteins
Mass spectrometry based proteomics and metabolomics
Immunobioinformatics
Experimental design, batch effects and confounding
Reproducible research and workflow authoring with R markdown
Package development, version control and developer tools

Summer School Structure

The format consists of:

Morning lectures: 20 x 45 minutes: Monday to Friday 8:30-12:00h
Practical computer tutorials in the afternoons: Mon, Tue, Thu, Fri 13:30-16:30h
Flashlight talks by participants: Mon, Tue, Thu 16:30-17:00h
Evening sessions: Monday and Tuesday 20:30-22:00h
A hike in the mountains: Wed 14:00-22:00h

Teaching Materials

All lecture slides and workshop material will be made available during the summer school and will remain available after the event.

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 and Bioconductor installed: R-4.2.x and Bioconductor 3.15 installed (details will be provided). Please make sure that your computer’s hardware is sufficiently powered (>=8 GB RAM, >20 GB free disk space) and that you have administrator rights. Please set up your computer beforehand; internet connections at the venue can occasionally be slow and unreliable.

One of the afternoons is for a joint cultural and outdoors activity. We plan a trip into the mountains with a (light) walk in the high-alpine area, weather permitting, and delicious local dinner.

Timetable


14.00h	We 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.”

14:15h	The bus leaves towards the cable car for Mount Plose.
14:45h	The cable car takes us to the top of Mount Plose in about 20-30 min.
	45-60 min Hiking to RossAlm at 2200 m altitude.
18:00h	Social dinner at RossAlm.
20:00h	Time to leave! We walk back to the bus from RossAlm.
21:00h	The bus takes us back to Brixen.

Please pack/bring:

Solid footwear (ideal: hiking shoes or boots)
Warm sweater/fleece and rain jacket for the descent (it can get quite fresh)