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
[email protected] 13/05/2014
INTRODUCTION TO BIOINFORMATICS
We are drowning in information and starved for knowledge
John Naisbitt Who on efficient work is bent, must choose the fittest instrument.
Goethe (Fausto)
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
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What is Bioinformatics?
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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
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THE GROWTH OF GENBANK
(1982-2000)
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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.
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BIOINFORMATICS AND INTERDISCIPLINARITY
Mathematics Statistics
Computer Science Informatics
Biology Molecular biology
Medicine
Chemistry
Physics
Bioinformatics
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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
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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
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INTEGRATIVE BIOINFORMATICS
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IN SUMMARY…
Data Knowledge Bioinformatics tools
and resources
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What is a bioinformatician?
Environment, training, activities… of the bioinformaticians
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WHAT DOES A BIOINFORMATICIAN KNOW?
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• 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!!
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WHAT DOES A BIOINFORMATICIAN DO?
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• 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
…
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Where and how is bioinformatics done?
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WHERE IS BIOINFORMATICS DONE?
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• Specialized centers – EBI, NCBI, EMBL… – INB, Plataforma Bioinformàtica de la UAB…
• Bioinformatics services in research centers – UEB, UBB, BU…
• Universities • Biotech companies • Pharmaceutical labs …
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HOW IS BIOINFORMATICS DONE?
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• 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.
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TO KNOW MORE
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• 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
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