Program Study Plan

The required IECB classes are grouped into 3 Areas: Area 1) courses teaching fundamental skills in computational biology methods; Area 2) practical courses and workshops in specific application areas; and Area 3) tutorials in which published research illustrating the integrated use of experimental and computational approaches in biological investigation is discussed.

Area 1 and Area 2 activities organized by the CUSO/IIIème Cycle and the Swiss Institute of Bioinformatics-SIB are part of the regional and national educational activities sponsored by those organizations. Area 3 tutorials are organized by the IECB program together with the Doctoral School.

During the course of their graduate studies, IECB students are required to accumulate 6 ECTS credits from Area 1, 1.5 ECTS credits from Area 2 and 1 ECTS credit from Area 3. Apart from these required 8.5 ECTS credits, students are free to choose according to their interests, subject to IECB Steering Committee approval, to meet the 12 ECTS credits required by the Doctoral School. (Please note: the requirement is 4 credits at the end of the 1st year: 2 tutorials + 2 other).

Computational skills courses will focus on fundamental skills in statistics, database use and programming and will be offered at both basic and advanced levels. Students whose skill levels exceed those of the advanced courses will be exempt from these fundamental skills courses.

Please look also at: http://www.sib.swiss/training/upcoming-training-events

Advanced programming with R
Organized by the CUSO doctoral programs StarOmics and Ecology and Evolution
ECTS: 2 credits

Advanced Python
Organized by the CUSO doctoral program StarOmics in 2020

Advanced R
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 1 credit (exam)

Advanced statistics: Statistical modelling
Organized by the Swiss Institute of Bioinformatics-SIB

Bayesian statistics
Organized by the Swiss Institute of Bioinformatics-SIB

Best practices in programming
Organized by the Swiss Institute of Bioinformatics-SIB

Better coding practices
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 credit

Big data management for small/medium and large scale project - data stewardship
Organized by the Swiss Institute of Bioinformatics-SIB

Bioinformatics Algorithms
Organized by the UNIL Ecole Doctorale
ECTS: 3 credits (course + exam)

Biostatistics for non-statisticians: good practices, misuse and pitfalls
Organized by the Interuniversity Doctoral Program in Organismal Biology, Neuchâtel
11-12 January 2017, in Neuchâtel / 2-3 November 2017 in Lausanne
ECTS: 0.5 credit

Data wrangling and plotting with R (tidyr,dplyr,ggplot)
Organized by the CUSO (E&E program)
ECTS: 1 credit

De novo assembly and annotation
Organized by the Swiss Institute of Bioinformatics-SIB

First steps with R in life sciences
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5 (exam)

First steps with UNIX in life sciences
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 (exam)

Inside protein databases: bridging sequences and knowledge
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 (exam)

Intermediate R
Organized by the Swiss Institute of Bioinformatics-SIB
13-14 November 2017, in Lausanne
ECTS: 0.5 (exam)

Intermediate stats: data analysis in practice
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0,5 credit (exam)

Introduction to Biological Network Analysis
Organized by the Swiss Institute of Bioinformatics-SIB and the CUSO doctoral program StarOmics
ECTS: 0.75 credit

Introduction to high-performance computing (sciCORE cluster)
Organized by the Swiss Institute of Bioinformatics-SIB
21 October 2015, in Basel

Introduction to Markov models
Organized by the Swiss Institute of Bioinformatics-SIB

Introduction to Python - BioPython
Organized by the Swiss Institute of Bioinformatics-SIB

Introduction to statistics
Organized by the Swiss Institute of Bioinformatics-SIB

Joint Spring school bioinformatics and population genomics
Organized by the Swiss Institute of Bioinformatics-SIB and the CUSO (DPEE & StarOmics programs)
ECTS: 1.5

Machine learning for bioinformatics and computational biology
Organized by the Swiss Institute of Bioinformatics-SIB

Metabolomics: From data to publication
Organized by the Swiss Institute of Bioinformatics-SIB and the CUSO doctoral program StarOmics
ECTS: 0.75

Multivariate analysis for exploration and visualization of biological data
Organized by the Swiss Institute of Bioinformatics-SIB and CUSO DPEE program
13 November 2015, in Bern

Network analysis
Organized by the Swiss Institute of Bioinformatics-SIB

Parsing techniques for bioinformatics in Perl 6
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 credit

PhD course in Genomics Medicine
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 2 credits

Protein Bioinformatics: Sequence-Structure-Function
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 1 (exam)

Python for Life Scientists
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5 credit

SIB / SystemsX.ch Autumn School - Systems Modeling
Organized by the Swiss Institute of Bioinformatics-SIB
8-12 November 2015, in Schwarzenberg
ECTS: 2

Statistical genomics
Organized by the Swiss Institute of Bioinformatics-SIB

Statistics for Life Scientists
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 1 credit (exam)

Understanding regular expressions
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 credit

Using semantic web for faster (bio)-research
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5

The Practical Courses and Workshops will cover a broader range of topics.

Autumn School Machine Learning applied to Systems Biology
Organized by the Swiss Institute of Bioinformatics-SIB
 

Biochemical pathways and large scale metabolic networks
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 1.5 (without exam) or 2 (with exam)

Bioinformatics in the Chalet
Organized by the Swiss Institute of Bioinformatics-SIB
6-11 September 2015, in Le Grand Hotel, Chandolin

Chip-seq data analysis: from quality check to motif discovery and more - An introduction to the tools and databases of the EPD team
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 2 (paper presentation)

Exploring common and rare disease genetics with GWAS and NGS
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 1

High Performance Computing (HPC) in Life Science: Vital-IT infrastructure training
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25 (exam)

Introduction to Next Generation Sequencing (NGS)
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5

Introduction to transcriptomics
Organized by the Swiss Institute of Bioinformatics-SIB

Introduction to protein structure visualization and comparison using Swiss-PDB Viewer
Organized by the Swiss Institute of Bioinformatics-SIB

Ligand-protein docking, and computer-aided drug design
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5 (exam)

Practical introduction to SPARQL for biologists and informaticians
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.25

RNA-seq: From quality control to pathway analysis
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5

RNA-sequencing
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5 (exam)

Transcriptomics analysis: RNA-seq
Organized by the Swiss Institute of Bioinformatics-SIB
ECTS: 0.5 (exam)

Whole genome re-sequencing
Organized by the Swiss Institute of Bioinformatics-SIB

Information for the inscription with the Doctoral School: please use this link

Reasoning and Logic in Experimental and Computational Biology
ECTS: 1

Objective: Tutorial in the thematic field "Integrated Experimental and Computational Biology"
Modern, high throughput data generation methods allow the production of comprehensive data sets and thus a quantitatively unique analysis of many biological phenomena.
The tutorial "Reasoning and Logic in Experimental and Computational Biology" will aim at illustrating the unique conceptual approaches to appropriate experimental design, data analysis and data interpretation required when using high throughput methods.

Content: Presentation and discussion of published examples of the application of high throughput DNA sequencing and other genomic methods, applied to a range of different biological questions.

Evaluation: Students will be evaluated based on their participation in the faculty-moderated discussions.

Please note:
Each PhD student has to take part successfully to 2 tutorials during the first year. For the IECB, you have to attend to a second one, which you can choose on the list.