ARCHITECTURES AND SYSTEMS FOR BIOLOGICAL DATA PROCESSING

International Teaching ARCHITECTURES AND SYSTEMS FOR BIOLOGICAL DATA PROCESSING

0622900005
DIPARTIMENTO DI INGEGNERIA DELL'INFORMAZIONE ED ELETTRICA E MATEMATICA APPLICATA
EQF7
DIGITAL HEALTH AND BIOINFORMATIC ENGINEERING
2021/2022



YEAR OF COURSE 2
YEAR OF DIDACTIC SYSTEM 2018
PRIMO SEMESTRE
CFUHOURSACTIVITY
324LESSONS
324LAB
Objectives
THE COURSE PRESENTS ADVANCED ASPECTS OF ARCHITECTURAL SOLUTIONS TO OBTAIN THE HIGH PERFORMANCE FOR INTENSIVE BIOLOGICAL DATA PROCESSING APPLICATIONS.

KNOWLEDGE AND UNDERSTANDING
UNDERSTANDING ADVANCED ASPECTS OF HIGH PERFORMANCE COMPUTING ARCHITECTURES, WITH PARTICULAR REFERENCE TO MULTIPROCESSOR PLATFORMS AND GENERAL-PURPOSE-GPU ARCHITECTURES.

APPLYING KNOWLEDGE AND UNDERSTANDING
DESIGN OF HIGH PERFORMANCE APPLICATIONS BASED ON THE ARCHITECTURES PRESENTED. USE OF LIBRARIES AND FRAMEWORKS FOR DISTRIBUTED COMPUTING, AND CPU / GPU PARALLELIZATION FOR THE EFFICIENT IMPLEMENTATION OF ALGORITHMS.
Prerequisites
THERE ARE NO SPECIFIC PROPEDEUTICS FOR THIS COURSE, ALTHOUGH IT IS STRONGLY RECOMMENDED, AT LEAST, TO FOLLOW THE COMPUTATIONAL GENOMICS COURSE.
Contents
INTRODUCTION TO ARCHITECTURE AND SYSTEMS FOR OMIC DATA ANALYSIS AND INTEGRATION (LECTURE / PRACTICE / LABORATORY HOURS 2/0/0)
PRINCIPLE OF COMPUTING ARCHITECTURES AND THEIR USE FOR COMPUTATIONAL GENOMICS: SHARED / DISTRIBUTED MEMORY, CLUSTER AND GPGPU (LECTURE / PRACTICE / LABORATORY HOURS 6/0/0)
SEMANTIC TECHNOLOGIES FOR THE REPRESENTATION AND INTEGRATION OF OMIC DATA: RDF, OWL AND SPARQL (LECTURE / PRACTICE / LABORATORY HOURS 4/4/0)
FRAMEWORK FOR DISTRIBUTED CALCULATION - APACHE ECOSYSTEMS (SPARK, FLINK, ARROWS) (LECTURE / PRACTICE / LABORATORY HOURS 6/4/0)
INTRODUCTION TO GPU PROGRAMMING WITH OPENACC (LECTURE / PRACTICE / LABORATORY HOURS 6/4/0)
PROJECT WORK (LECTURE / PRACTICE / LABORATORY HOURS 0/0/12)

TOTAL LECTURE / PRACTICE / LABORATORY HOURS 24/12/12
Teaching Methods
THE COURSE (48H OF LESSONS, EXERCISES AND LABORATORY ACTIVITIES) IS CHARACTERIZED BY A DYNAMIC SETTING, WHICH INCLUDES THE ANALYSIS OF REAL SYSTEMS, INFRASTRUCTURES AND ALGORITHMS WITH THE ACTIVE PARTICIPATION OF STUDENTS WHO WILL PERFORM IN DEPTH ANALYSIS OF THE PROGRAMS AND SOLUTIONS ADOPTED FOR BUILDING PIPELINES FOR OMIC DATA ANALYSIS DURING THE PROJECT WORK.
IN PARTICULAR, THE EDUCATIONAL ACTIVITIES WILL INCLUDE LESSONS (24 HOURS), EXERCISES (12 HOURS) AND LABORATORY (12 HOURS) WHICH INCLUDES PART OF THE DEVELOPMENT OF THE PROJECT WORK. TO DEVELOP THE PROJECT, STUDENTS WILL APPLY THE KNOWLEDGE ACQUIRED TO IMPLEMENT AND DEPLOY ON SPECIFIC HARDWARE ARCHITECTURES ALGORITHMS USED FOR ANALYSIS OF OMIC DATA (SEQUENCE ALIGNMENT, GENOME ASSEMBLY, VARIANT CALLING). EDUCATIONAL ACTIVITIES WILL BE SUPPORTED BY THE USE OF THE UNIVERSITY E-LEARNING PLATFORM TO FACILITATE AND STIMULATE DISCUSSION AND DEBATE AMONG STUDENTS, AS WELL AS FOR NOTIFICATION AND DISTRIBUTION OF EDUCATIONAL MATERIAL.
Verification of learning
THE FINAL EXAM IS AIMED AT ASSESSING THE KNOWLEDGE AND OVERALL UNDERSTANDING OF THE CONCEPTS PRESENTED IN THE COURSE, THE ABILITY TO APPLY SUCH KNOWLEDGE TO IDENTIFY THE MOST SUITABLE COMPUTING INFRASTRUCTURE FOR THE EXECUTION OF SPECIFIC APPLICATIONS AND THE ABILITY TO COMMUNICATE THE IMPLEMENTED PROJECT. (COMMUNICATION SKILLS).
THE EXAM CONSISTS OF A PRACTICAL PART AND AN ORAL TEST (INTERVIEW). THE PRACTICAL PART CONSISTS IN THE DEVELOPMENT OF A PROJECT WORK TO BE CARRIED OUT IN GROUPS (2-4 STUDENTS) ON THE TOPICS PROPOSED AT THE BEGINNING OF THE COURSE. THE ORAL EXAM CONSISTS IN THE PRESENTATION OF THE RESULTS ACHIEVED DURING THE DEVELOPMENT OF THE PROJECT WORK. EVERY MEMBER OF THE GROUP EXHIBITS HIS CONTRIBUTION TO THE IMPLEMENTATION OF THE PROJECT TOGETHER WITH A DISCUSSION ON THE IMPLEMENTED ALGORITHMS AND THE ACHIEVED RESULTS.
IN THE FINAL EVALUATION, EXPRESSED WITH A SCORE OF 30/30, THE PRACTICAL PART WILL WEIGH FOR 65% AND THE ORAL EXAMINATION FOR 35%. THE PRAISE (30/30 CUM LAUDE) WILL BE ASSIGNED TO STUDENTS WHO WILL DEMONSTRATE A FULL MASTERY OF ALL THE MAIN METHODOLOGICAL AND TECHNOLOGICAL ASPECTS ADDRESSED IN THE COURSE AND HOW THESE CAN BE USED FOR THE IMPLEMENTATION OF SOLUTIONS IN SPECIFIC APPLICATION DOMAINS, TOGETHER WITH THE IMPLICATIONS ARISING FROM THEIR USE.
Texts
THE DIDACTIC MATERIAL FOR THE STUDY OF ARCHITECTURE, FOR THE EXERCISES AND LABORATORY ACTIVITIES, WILL BE PROVIDED BY THE TEACHER.

SUPPLEMENTARY TEACHING MATERIAL WILL BE AVAILABLE ON THE UNIVERSITY E-LEARNING PLATFORM (HTTP://ELEARNING.UNISA.IT) ACCESSIBLE TO STUDENTS USING THEIR OWN UNIVERSITY CREDENTIALS.
More Information
THE COURSE IS HELD IN ENGLISH
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