High Performance Bioinformatics

Wednesday, 13 December 2017 (All day) to Friday, 15 December 2017 (All day)

This course is in English.

Description:

This course focuses on the development and execution of bioinformatics pipelines and on their optimization with regards to computing time and disk space. In an era where the data produced per-analysis is in the order of terabytes, simple serial bioinformatic pipelines are no longer feasible. Hence the need for scalable, high-performance parallelization and analysis tools which can easily cope with large-scale datasets. To this end we will study the common performance bottlenecks emerging from everyday bioinformatic pipelines and see how to strike down the execution times for effective data analysis on current and future supercomputers.

As a case study, two different bioinformatics pipelines (whole-exome and transcriptome analysis) will be presented and re-implemented on the supercomputers of Cineca thanks to ad-hoc hands-on sessions aimed at applying the concepts explained in the course.

Topics: 

NGS-data, big-data analysis, code parallelization, MPI, running a bioinformatics pipeline, large-scale sample datasets.

Target audience: 

Biologists, bioinformaticians and computer scientists interested in approaching large-scale NGS-data analysis for the first time.

Pre-requisites: 

Basic knowledge of python and command line. A very basic knowledge of biology is recommended but not required.
 

Target: 
Companies
Research Institutions
Universities
Area: 
Languages
Science
Length: 
3 dd

Next courses

Non sono previste edizioni di questo corso.

Any question?

For HPC and computer graphics courses, write to corsi.hpc@cineca.it

About CINECA

Cineca is a non profit Consortium, made up of 70 Italian universities, 5 Italian Research Institutions and the Italian Ministry of Education.

Today it is the largest Italian computing centre, one of the most important worldwide. With more seven hundred employees, it operates in the technological transfer sector through high performance scientific computing, the management and development of networks and web based services, and the development of complex information systems for treating large amounts of data.

It develops advanced Information Technology applications and services, acting like a trait-d'union between the academic world, the sphere of pure research and the world of industry and Public Administration. .

Visit the Cineca website