Introduction to Bioinformatics (UEB-UAT Bioinformatics Course - Session 1.1 - VHIR, Barcelona)
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This document provides an introduction to bioinformatics. It defines bioinformatics as the interdisciplinary field that develops methods for storing, organizing, and analyzing vast amounts of biological data generated by new technologies. It discusses the explosive growth of genomic and protein data. It also describes the roles and skills of bioinformaticians, including knowledge of biology, computer science, and quantitative disciplines. Finally, it outlines where bioinformatics is typically conducted, such as specialized centers and universities, and how it is usually done through online and open source solutions.
![WHAT DOES A BIOINFORMATICIAN KNOW?
17
• He/She must have “solid understanding” of
– Some biological discipline
• Biochemistry, Genetics,…
– Software development environments
• OS [Linux], Scripting languages [Perl, Java, R],
Databases [SQL], Web development [PHP, ASP,
Ajax…]
– Some quantitative discipline
• Mathematics, Statistics, Physics
At least two of the previous three!!
13/05/2014](https://image.slidesharecdn.com/bbr-1-140522075514-phpapp01/85/Introduction-to-Bioinformatics-UEB-UAT-Bioinformatics-Course-Session-1-1-VHIR-Barcelona-17-320.jpg)
Introduction to Bioinformatics (UEB-UAT Bioinformatics Course - Session 1.1 - VHIR, Barcelona)
- 1. Hospital Universitari Vall d’Hebron Institut de Recerca - VHIR Institut d’Investigació Sanitària de l’Instituto de Salud Carlos III (ISCIII) Bioinformàtica per la Recerca Biomèdica http://ueb.vhir.org/2014BRB Alex Sánchez alex.sanchez@vhir.org 13/05/2014 INTRODUCTION TO BIOINFORMATICS
- 2. We are drowning in information and starved for knowledge John Naisbitt Who on efficient work is bent, must choose the fittest instrument. Goethe (Fausto)
- 3. 1. What is Bioinformatics? ● The explosive growth of data ● The growth of GenBank ● Bioinformatics definition ● Bioinformatics and interdisciplinarity ● The scope of bioinformatics 2. What is a bioinformatician? ● What does a bioinformatician know? ● What does a bioinformatician do? 3. Where and how is bioinformatics done? ● Where is bioinformatics done? ● How is bioinformatics done? ● To know more… PRESENTATION OUTLINE 313/05/2014
- 5. THE EXPLOSIVE GROWTH OF DATA Hace ... Antes Ahora Nucleótidos 26 años (1982) 680338 pb (GenBank) > Miles de millones Proteínas 26 años 1500 300.000 DNA continuo 16 años 73 kb > 270 Mbases SNPs 16 años centenares 11 millones Genomas 11 años 0 organismos 1282 Organismos (mediados 2010) Expresión 10 años Limitado pocos genes Miles de estudios con miles de genes 513/05/2014
- 6. THE GROWTH OF GENBANK (1982-2000) 613/05/2014
- 8. BIOINFORMATICS • Born on the lookout for – the development of new technologies and – its application in the generation of huge amounts of data. • It is the interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. 813/05/2014
- 10. THE SCOPES OF BIOINFORMATICS • Information organization – Databanks and databases – Algorithms and exploitation tools • Analysis and interpretation of experimental results – Genome analysis and sequencing – Comparative genomics – Gene expression and transcription – Proteomics, protein-protein interaction • Systems biology modeling 1013/05/2014
- 12. ANALYSIS AND INTERPRETATION A G G G T T A T G C G C G A G A G T T C T G C T C G 1213/05/2014
- 15. IN SUMMARY… Data Knowledge Bioinformatics tools and resources 1513/05/2014
- 16. What is a bioinformatician? Environment, training, activities… of the bioinformaticians 1613/05/2014
- 17. WHAT DOES A BIOINFORMATICIAN KNOW? 17 • He/She must have “solid understanding” of – Some biological discipline • Biochemistry, Genetics,… – Software development environments • OS [Linux], Scripting languages [Perl, Java, R], Databases [SQL], Web development [PHP, ASP, Ajax…] – Some quantitative discipline • Mathematics, Statistics, Physics At least two of the previous three!! 13/05/2014
- 18. WHAT DOES A BIOINFORMATICIAN DO? 18 • Information management – Implementation and exploitation of local or online databases. – Installation and maintenance of web servers • Software development – Creation of local or web-based applications • Data analysis and exploitation – High Throughput and Next Gen Seq. data … 13/05/2014
- 19. Where and how is bioinformatics done? 1913/05/2014
- 20. WHERE IS BIOINFORMATICS DONE? 20 • Specialized centers – EBI, NCBI, EMBL… – INB, Plataforma Bioinformàtica de la UAB… • Bioinformatics services in research centers – UEB, UBB, BU… • Universities • Biotech companies • Pharmaceutical labs … 13/05/2014
- 21. HOW IS BIOINFORMATICS DONE? 21 • Usually, though not necessarily, it has “universal” purpose, to access a maximum number of users: – Often looking for online solutions – Often based on projects (more or less) open source and freely distributed * * It is not generalized at all – For instance, Ingenuity Pathways Analysis is not free but is quite good. 13/05/2014
- 22. TO KNOW MORE 22 • There are a lot of free courses and training activities: – EBI’s 2scan – NCBI’s tutorials – Local training courses • Introducción a la Bioinformática (Alex Sánchez, UEB/UB) • Invitació a la Bioinformàtica (Plataforma BioinfoUAB) • A great variety of rerefence books: • List of books on bioinformatics • Scientific Societies and Publications: – Bioinformatics, Briefings in Bioinformatics – International Society for Computational Biology 13/05/2014