All programmes > Management of Large-Scale Omics Data

Management of Large-Scale Omics Data (B-KUL-I0U19A)

4 ECTSEnglish34 Second termCannot be taken as part of an examination contract
Fiers Mark (coordinator) |  Moreau Yves |  N. |  Fiers Mark (substitute)
POC Bioinformatics

Aims

Students will be able to design and use systems to store and serve large biological datasets, and to obtain disparate data from online resources. They will have an up-to-date view of technologies that are used for storing, exchanging, processing and querying of big datasets.

Previous knowledge

Students are required to have a basic background in the nature and characteristics of high-throughput technologies, basic scripting experience and basic insight in the concepts of relational database management. This background can be acquired through the following courses: Practical Computing for Bioinformatics (I0u30A), Database Management (I0D42B).

Order of Enrolment


This course unit is a prerequisite for taking the following course units:
I0U20A : Integrated Bioinformatics Project

Is included in these courses of study

Activities

2 ects. Management of Large-Scale Omics Data (B-KUL-I0U19a)

2 ECTSEnglishFormat: Lecture14 Second term
N. |  Fiers Mark (substitute)
POC Bioinformatics

Content

1. Introduction to Big Data for Omics
2. Workflow management systems
3. Data storage & visualization
4. Reproducible research

Course material

Lecture slides & recordings
Github
 

1 ects. Management of Large-Scale Omics Data: Exercises (B-KUL-I0V12a)

1 ECTSEnglishFormat: Practical14 Second term
N. |  Fiers Mark (substitute)
POC Bioinformatics

Course material

Lecture notes

Format: more information

Exercises accompanying OLA I0U19a

1 ects. Ethics of Big Data (B-KUL-I0W18a)

1 ECTSEnglishFormat: Lecture6 Second term
Moreau Yves
POC Bioinformatics

Content

  • Basic clinical research ethics
  • Informed consent
  • Confidentiality and privacy
  • Why does privacy matter? Non-discrimination. Right to be let alone (Warren & Brandeis).
  • GPDR research exemption. Secondary use.
  • Why is genomic data sensitive? Family relations. Medical information. Difficulty to anonymise.
  • Role of ethical committee
  • Role of data access of committee
  • Role of privacy commission
  • Threat scenarios: hackers, insurance companies, law enforcement, repressive government, etc.
  • Protecting privacy: IT security. Federated systems. Privacy spectrum.
  • Preventing over-regulation: opportunity cost.
  • Escalation. Whistleblowing.

Course material

Lecture slides

Evaluation

Evaluation: Management of Large-Scale Omics Data (B-KUL-I2U19a)

Type : Partial or continuous assessment with (final) exam during the examination period
Description of evaluation : Written, Presentation, Participation during contact hours
Type of questions : Open questions
Learning material : Course material

Explanation


Assessment for this course is based on the exam 7.5/20, an assignment 7.5/20 and participation in an ethics debate 5/20.