Universitat Internacional de Catalunya

Introduction to Bioinformatics

Introduction to Bioinformatics
6
13489
2
Second semester
OB
BASIC HEALTH INFORMATICS TOOLS
Main language of instruction: English

Other languages of instruction: Catalan, Spanish

Teaching staff


Questions will be answered in person before or after class, or via e-mail.

Teachers:

Introduction

With the continuous generation of massive amounts of biomedical data on a daily basis, whether from research laboratories, clinical labs or private companies. We need to improve our ability to understand and analyze the data in order to take full advantage of its power in scientific discoveries and patient care. For non-bioinformaticians, “handling” big data remains a daunting task. 

This course is designed to cover the most basic bioinformatic skills that anyone in the biomedical field should know.

Pre-course requirements

To follow this class, previous knowledge in genetics, biomolecules and molecular biology is needed. Additional experience with the use of computers, web browsers and the internet and use of spreadsheets software is highly recommended.


Objectives

The goal of this course is to acquire a general view of basic bioinformatic tools in biomedical research and clinical practice. 

  • To obtain a global vision of the impact of data and how biology and biomedicine are changing.
  • To understand bioinformatics as a transversal tool to multiple disciplines.
  • To know and master the main available public biological databases in biomedical research.
  • To introduce basic knowledge of programming languages and their relevance in modern biology.

Competences/Learning outcomes of the degree programme

Basic skills

  1. Ability to understand, develop and apply computational workflows to solve complex biological problems.
  2. Understand how data-driven research is done.
  3. Communicate in a clear and accurate manner the process and results of their work.

General skills

  1. Use the most important bioinformatic resources in biomedical research. 
  2. Ability to independently identify and use the appropriate bioinformatic tools relevant to each biological compound and process. 

Transversal skills

  1. Develop the ability of organization and planning appropriate to the moment.
  2. Use the internet as a means of communication and a source of information.
  3. Know how to communicate, make presentations, and write scientific papers.
  4. Develop the ability of problem solving.

Learning outcomes of the subject

By the end of the course, students will:

  1. General knowledge of available biological databases and how to use them.
  2. General Knowledge of programming and programming languages.
  3. Generate scientific communications that entails the use of bioinformatic tools.

Syllabus

  • Unit 1: Introduction to Computational Biology

  • Unit 2: Biological Databases

  • Unit 3: Basics of programing

  • Unit 4: Bioinformatic tools for Genetics

  • Unit 5: Bioinformatic tools for RNA

  • Unit 6: Bioinformatic tool for Proteins

  • Unit 7: Molecule-protein Interactions

  • Unit 8: Bioinformatic tools for gene editing

Teaching and learning activities

In person



Lectures: Presentation of theoretical topics and technical aspects by the professor.

Clinical cases or case methods (CM): Presentation of a real or hypothetical situation in small groups. Students will work alongside the professor to solve practical questions. The teacher intervenes actively and, if necessary, contributes new knowledge. 

Practical sessions: In small groups, students will be assessed in their ability to independently use the tools presented in the lectures and CM. 

Virtual Education (VE): Online material that the student can consult from any computer, at any time and that will contribute to the self-learning of concepts related to the subject.

Evaluation systems and criteria

In person



1) Student in first call:
  • Final exam: 20%
  • Case method solution: 50% (5 blocks of 10% each)
  • Practical solution: 30% (6 sessions (5% session))
The teaching staff reserves an extra 10% of the mark to award it for subjective arguments such as: involvement, participation, respect for basic rules, etc.     2) Students in the second call or later: the same criteria as in the first call. The grade of any of the approved parts will be saved.
General points to consider about the evaluation system:
1) In all parts of the subject, a minimum grade of 5 must be obtained to be able to average with the other parts and the average must be higher than 5. The final exam will be a test with four options answer, where +1 will count for successes and -0.33 for errors.
2) Case methods will be assessed with assignments for each syllabus block. Each block has between 2-3 sessions and you will need to attend all the sessions of each block to be able to hand in the corresponding work later and get the assessment mark. Non-attendance or any CM as well as the non-presentation of the work before the corresponding deadline, will mean a 0 in the corresponding percentage. For each block it is 10% and there are up to 5 blocks that will end up adding up to 50% of the subject.
3) The practices will be evaluated with work that will be done on site at each practice. The work must be handed in before leaving the classroom. Non-attendance or non-presentation of the work during the corresponding practice will result in a 0 for the corresponding percentage. Each practice adds up to 5% up to a total of 6 practices that add up to 30%.
4) Class attendance:
  • Regular attendance at all classes is recommended.
  • Attendance is not mandatory, but non-attendance or not handing in assignments on time may affect the student's grade. The evaluated cases will be averaged proportionally.
  • The expulsion of a student from any of the classes will have a negative impact on the evaluations.

5) In the awarding of honours, special consideration will be given to candidates for their participation in the different methodologies of the subject, as well as respect for the basic rules.
6) Improper use of electronic devices, such as cell phones, tablets or laptops, may result in expulsion from class. Improper use is understood as the recording and broadcasting of both students and teachers during the different lessons, as well as the use of these devices for recreational and non-educational purposes.

Bibliography and resources

  1. Applied Bioinformatics, 2nd Edition. Springer (2018). ISBN: 978-3-319-68299-0
  2. Biomedical Informatics, 4th Edition. Springer (2014). ISBN:  978-1-4471-4473-1
  3. Fundations of Programming Languages. 2nd Edition. Springer (2017). ISBN: 978-3-319-70789-1
  4. Bioinformatics with Python cookbook, 2nd Edition ISBN-10: 1789344697
  5. H. Wickham. R packages. O'Reailly, Sebastopol, 2015.

Evaluation period

E: exam date | R: revision date | 1: first session | 2: second session:
  • E1 22/05/2023 16:00h
  • E2 27/06/2023 A12 11:00h