introducci ó a la bioinformàtica roderic guigó i serra roderic.guigo@crgt
DESCRIPTION
Introducci ó a la Bioinformàtica Roderic Guigó i Serra [email protected]. Bioinform àtica, UPF Curs 2010-. US-EC Workshop on Marine Genomics, Washington DC fall 2010. Training the next generation of Biologists. Roderic Guig ó, [email protected] - PowerPoint PPT PresentationTRANSCRIPT
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Training the next generation of Biologists
Roderic Guigó, [email protected] for Genomic Regulation,
Barcelona
US-EC Workshop on Marine Genomics, Washington DC fall 2010
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Why “next generation biologists” should be trained differently than
biologists of previous generations?
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Why “next generation biologists” should be trained differently than
biologists of previous generations?
•The impact of technology– in the way we do Biology
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Technology is not new to Biology
In 1676 his credibility was questioned when he sent the Royal Society a copy of his first observations of microscopic single celled organisms. Heretofore, the existence of single celled organisms was entirely unknown … The Royal Society arranged to send an English vicar, as well as a team of respected jurists and doctors to Delft, Holland to determine whether it was in fact Van Leeuwenhoek's ability to observe and reason clearly (wikipedia)
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Two moments in the second half of the past century
1. Sequencing (Sanger et al)ACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACGGGGATGAGCTCAGGGGCCTCTAGAAAGATGTAGCTGGGACCTCGGGAAGCCCTGGCCTCCAGGTAGTCTCAGGAGAGCTACTCAGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCCAGCAGCAGGGGACTGGACCTGGGAAGGGCTGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCATGTGGACTAGGAGCTAAGCCACAGCAGGACCCCCACGAGTTGTCACTGTCATTTATCGAGCACCTACTGGGTGTCCCCAGTGTCCTCAGATCTCCATAACTGGGAAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTTAAAATGAGGACTGAATTAGCTCATAAATGGAAAACGGCGCTTAAATGTGAGGTTAGAGCTTAGAATGTGAAGGGAGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGAGGGGGTGTGGAATTTGAACCCCGGGAGAGAAAGATGGAATTTTGGCTATGGAGGCCGACCTGGGGATGGGGAAATAAGAGAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAACTGTTTGTGCTGGGATTAGGCTGTTGCAGATAATGGAGCAAGGCTTGGAAGGCTAACCTGGGGTGGGGCCGGGTTGGGGTCGGGCTGGGGGCGGGAGGAGTCCTCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGCGGGGCTTGCTCGGTTTTCCCCGCTTCTCCCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAAGCACACCCTGGGCCCCCTCTTCTTCTGCTGGTCTGTCCCCTGAGGGGAAAGCCCAGGTCTGAGGCTTCTATGCTGCTTTCTGGCTCAGAACAGCGATTTGACGCTCTGTGAGCCTCGGTTCCTCCCCCGCTTTTTTTTTTTCAGCCAGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCTATTCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCCGGCTAATTTTTTGTACTTTGAGTAGGGAAGGGGTTTCACTGTATTATCCAGGATGGTCTCTATCTCCTGACCTCGTGATCTGCCCGCCTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGAGCCTCCGCGCCCGGCCTCCCCATCCTTAATATAGGAGTTAGAAGTTTTTGTTTGTTTGTTTTGTTTTGTTTTTGTTTTGTTTTGAGATGAAGTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCTCCCAGGCTGGAGTTCAGTGGCTGGATCTCGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCGGAGTAGCTGGGACTACAGGAACATGCCACCACACCCGACTAACTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTGGAACTCCTG
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Two moments in the second half of the past century
2. mutliplexing, automating,…– Surveying many things at once– Surveying whole systems
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Biology is transitioning (at least partially)
from an “analytic” science: the real world
is disected in its elemental components in order to be comprehended
to “syntetic” science: the challenge is
the integration of globlal information on the living cell/individual/population/(eco)sytem.
From analytic to syntetic
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Biology, a science in which the effort has traditionally been directed towards data aquisition has become in a very short time a discipline in which the data is obtained with almost no human intervention, and the effort is turning towards data analysis.
From data acquisition to data analysis
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April 21, 2023 10
DNA microarrays
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Sequencing Evolution/Revolution
1990: thousand bases/day
2000: million bases/day
2010: billion bases/day
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• 2008: Major genome centers can sequence the same number of base pairs every 4 days
• 1000 Genome project launched
• World-wide capacity dramatically increasing
Further Evolution of Large-scale Genome Sequencing
• 2000: Human genome working drafts
• Data unit of approximately 10x coverage of human– 10 years and cost about $3 billion
• 2009: Every 4 hours ($25,000)
• 2010: Every 14 minutes ($5,000)
• Illumina HiSeq2000 machine produces 200 gigabases per 8 day run (BGI have ordered have 128)
Slide from Paul Flicek. EBI Bioinformatics Advisory Council
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la llei de Moore
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Within individual ecosystems
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Within individual ecosystems
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Within individual ecosystems
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq and nucleosome positioning• RNA sequencing as a proxy to the cell’s
phenotype
![Page 23: Introducci ó a la Bioinformàtica Roderic Guigó i Serra roderic.guigo@crgt](https://reader035.vdocuments.us/reader035/viewer/2022062500/56815275550346895dc0a548/html5/thumbnails/23.jpg)
Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq, nucleosome positioning, …• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq, nucleosome positioning, …• RNA sequencing as a proxy to the cell’s
phenotype
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Sequencing challenges
• Sequencing to survey dynamics of ecosystems• Metagenomes
– Ecosystems (enviromental, individual)
• Other species genomes• Reference Human Genome• Individual genomes• Individual meta-genomes• Within individual genomic diversity• Sequencing as the read-out of experiments
– Chip-Seq, nucleosome positioning, …• RNA sequencing as a proxy to the cell’s
phenotype
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ACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACGGGGATGAGCTCAGGGGCCTCTAGAAAGATGTAGCTGGGACCTCGGGAAGCCCTGGCCTCCAGGTAGTCTCAGGAGAGCTACTCAGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCCAGCAGCAGGGGACTGGACCTGGGAAGGGCTGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCATGTGGACTAGGAGCTAAGCCACAGCAGGACCCCCACGAGTTGTCACTGTCATTTATCGAGCACCTACTGGGTGTCCCCAGTGTCCTCAGATCTCCATAACTGGGAAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTTAAAATGAGGACTGAATTAGCTCATAAATGGAAAACGGCGCTTAAATGTGAGGTTAGAGCTTAGAATGTGAAGGGAGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGAGGGGGTGTGGAATTTGAACCCCGGGAGAGAAAGATGGAATTTTGGCTATGGAGGCCGACCTGGGGATGGGGAAATAAGAGAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAACTGTTTGTGCTGGGATTAGGCTGTTGCAGATAATGGAGCAAGGCTTGGAAGGCTAACCTGGGGTGGGGCCGGGTTGGGGTCGGGCTGGGGGCGGGAGGAGTCCTCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGCGGGGCTTGCTCGGTTTTCCCCGCTTCTCCCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAAGCACACCCTGGGCCCCCTCTTCTTCTGCTGGTCTGTCCCCTGAGGGGAAAGCCCAGGTCTGAGGCTTCTATGCTGCTTTCTGGCTCAGAACAGCGATTTGACGCTCTGTGAGCCTCGGTTCCTCCCCCGCTTTTTTTTTTTCAGCCAGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCTATTCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCCGGCTAATTTTTTGTACTTTGAGTAGGGAAGGGGTTTCACTGTATTATCCAGGATGGTCTCTATCTCCTGACCTCGTGATCTGCCCGCCTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGAGCCTCCGCGCCCGGCCTCCCCATCCTTAATATAGGAGTTAGAAGTTTTTGTTTGTTTGTTTTGTTTTGTTTTTGTTTTGTTTTGAGATGAAGTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCTCCCAGGCTGGAGTTCAGTGGCTGGATCTCGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCGGAGTAGCTGGGACTACAGGAACATGCCACCACACCCGACTAACTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTGCCTGCTTCAACCTCCCAAAGTGCTGGGATTACAGACGTGGGCCACCGCGCCCGGCTGGGAGTTAAGAGGTTTCTAATGCATTGCATTAGAATACCAGACACGGGACAGCTGTGATCTTTATTCTCCATCACCCCACACAGCCCTGCCTGGGGCACACAAGGACACTCAATACACGCTTTTCGGGCGCGGTGGCTCAAGCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGTACATGAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAACTAGCCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGTGACACAGCGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATACACGCTTTTCCGCTAGGCACGGTGGCTCACCCCTGTAATCCCAGCATTTTGGGAGGCCAAGGTGGGAGGATCACTTGAGCCCAGGAGTTCAACACCAGACTCAGCAACATAGTGAGACTCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGCCACACACCTGTGGTCCCAGCTACTCAGAAGGCTAAGGCAGGAGGATCGCTTAAGCCCAGAAGGTCAAGGTTGCAGTGAACCACGTTCAGGCCACTGCAGTCCAGCCTGGGTGACAGAGCAAGACCCTGTCTGTAAATAAATAACGCTTTTCAAGTGATTAAACAGACTCCCCCCTCACCCTGCCCACCATGGCTCCAAAGCAGCATTTGTGGAGCACCTTCTGTGTGCCCCTAGGTACTAGCTGCCTGGACGGGGTCAGAAGGAACCTGAACCACCTTCAACTTGTTCCACACAGGATGCCAGGCCAAGGTGGAGCAACCGGTGGAGCCAGAGACAGAACCCGACGTTCGCCAGCAGGCTGAGTGGCAGAGCGGCCAGCCCTGGGAGCTGGCACTGGGTCGCTTTTGGGATTACCTGCGCTGGGTGCAGACACTGTCTGAGCAGGTGCAGGAGGAGCTGCTCAGCCCCCAGGTCACCCAGGAACTGACGTGAGTGTCCCCATCCCGGCCCTTGACCCTCCTGGTGGGCGGCTATACCTCCCCAGGTCCAGGTTTCATTCTGCCCCTGCCACTAAGTCTTGGGGGCCTGGGTCTCTGCTGGTTCTAGCTTCCTCTTCCCATTTCTGACTCCTGGCTTTAGCTCTCTGGAATTCTCTCTCTCAGTTCTGTTTCTCCCTCTTCCCTTCTGACTCAGCCTGTCACACTCGTCCTGGCGCTGTCTCTGTCCTTCACTAGCTCTTTTATATAGAGACAGAGAGATGGGGTCTCACTGTGTTGCCCAGGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCACCTCGCCTCCCAAAGTGCTGGGAATAGAGACATGAGCCACCTTGCTCGGCCTCCTAGCTCTTTCTTCGTCTCTGCCTCTGCTCTCTGCGTCTGTCTTTGTCTCCTCTCTGCCTCTGTCCCGTTCCTTCTCTCTTGGTTCACTGCCCTTCTGTCTCTCCCTGTTCTCCTTAGGAGACTCTCCTCTCTTCCTTCTCGAGTCTCTCTGGCTGATCCCCATCTCACCCACACCTATCC
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In summary
• Intrinsec symbolic/computational nature of biological (genomic) data
• Emphasis in synthesis (rather/in addition to analysis)
• Exponential data production– Separated from human intervention
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bioinformàtica
Articles a Medline amb la paraula clau Bioinformatics.
any # articlesfins el 1990 0
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bioinformàtica
Articles a Medline amb la paraula clau Bioinformatics.
any # articlesfins el 1990 01990-1994 15
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bioinformàtica
Articles a Medline amb la paraula clau Bioinformatics.
any # articlesfins el 1990 01990-1994 151995-1999 823
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bioinformàtica
Articles a Medline amb la paraula clau Bioinformatics.
any # articlesfins el 1990 01990-1994 151995-1999 8232000-2004 7827
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bioinformàtica
Articles a Medline amb la paraula clau Bioinformatics.
any # articlesfins el 1990 01990-1994 151995-1999 8232000-2004 78272005-2008 18822
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Bioinformatics, Genomics, Systems Biology in Medline
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bioinformatics 14,100,000
chemoinformatics 226,000
astroinformatics 195
neuroinformatics 364,000
socioinformatics 610
geoinformatics 506,000
meteoinformatics 48
econoinformatics 441
ecoinformatics 160,000
Bioinformatics
Google search: X-informatics (11 juny, 2007)
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Engineering and biology: increasingly interconnected• Improved technologies to survey Biological
Systems– NGS and the like [technological fluency]
• Engineering of Biological Systems– Medicine– New and modified biological systems
• Using Biology to build non-biological systems– DNA computing
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Biology has changed and it is changing
•Quantitative thinking•Ability to attack unanticipated problems
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Biology requires quantitative thinking
• Statistics • Mathematics• Computer Science• …
and programming skills (unix)
• The ability to interrogate data, and to models systems
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dues idees • La biologia, una disciplina en la que l’esforç ha estat
tradicionalment dedicat a l’obtenció de les dades, ha esdevingut en poc temps una disciplina en la que les dades s’obtenen de manera gairebé automàtica, i l’esforç s’ha desplaçat cap a l’anàlisi de les dades.
• La Bioinformàtica més que un altre (sub) disciplina de la Biologia (com ara la bioquímica, la genètica, la botànica, …) és una disciplinea que permea tota la Biologia; és una manera de fer Biologia; en molts casos, la única manera de fer Biologia.
• Molts processos biològics poden ser entesos com a computacions gairebe sensu stricto.