Practical Course in Bioinformatics / Software lab

Location: MTZ Seminar Room, Pauwelstr, 19; 3rd Floor, Corridor B room 3.04.

Dates: Monday 9:30-12:30 (starting 18.04.2016)

Language: English

Prerequisite (desirable): Introduction to Bioinformatics

Credits: 7 (10 with extra work)

Lecturers: Ivan G. Costa

Evaluation: 20% protoypes / 60% final project / 20% presentation

Campus Description:  Bioinformatik Praktikum 

We will cover the usage and development of bioinformatic methods for analysis of next generation sequencing data. The lab task will be based on the implementation of a full bioinformatics pipeline including: integration of low-level analysis tools (i.e. short sequencing aligner), development of a method for high level analysis (i.e. detection of Single-nucleotide polymorphism) and generation of a biology friendly interface for simple operations (web interface). We will provide real data as disease vs. normal individuals as case studies to be analysed by students.

Schedule:

18.04.2016 – Introduction to Next Generation Sequecing Problems

25.04.2016 – Practical Example – NGS of Regulatory Genomics Data   |   Installation & Practical Script

02.05.2016 – Introduction to RGT,  Genomic File Formats  |  Installation & Practical Scripts

09.05.2016 – Project Description

17.05.2016 to 11.07.2016 – Project Development (Weekly)

04.07.2016 – Final Presentation: Algorithms/Optimization Group | Database/Interface Group

 Relevant Material:

Online course from EBI. Only these lectures are of direct interest:

• What is Next-Generation DNA Sequencing
• Key tasks in sequence analysis

Online courses:

• From Implanted Patterns to Regulatory Motifs (Lessons 1 to 3)
• Genomics Data Science