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Concepts, historical milestones & the central place of bioinformatics in modern biology:. a European perspective. Overview. Where the term bioinformatics originated Where the ‘ modern ’ concept originated Some key events & folk Its place in ‘ the new biology ’. Origin of Bioinformatics.

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concepts historical milestones the central place of bioinformatics in modern biology
Concepts, historical milestones & the central place of bioinformatics in modern biology:

a European perspective

Teresa K.Attwood

University of Manchester

overview
Overview
  • Where the term bioinformatics originated
  • Where the ‘modern’concept originated
  • Some key events & folk
  • Its place in‘the new biology’

Teresa K.Attwood

University of Manchester

origin of bioinformatics
Origin of Bioinformatics
  • The origin of the term‘bioinformatics’ has been attributed to Paulien Hogeweg
    • Dutch theoretical biologist
  • She & colleague Ben Hesper coined the term in the early ‘70s, defining it as
    • “the study of informatic processes in biotic systems”
      • Hogeweg, P. (2011) The roots of bioinformatics in theoretical biology. PLoS Computational Biology, 7(3), e1002021
  • The term failed to gain traction for ~20 years

Teresa K.Attwood

University of Manchester

origin of bioinformatics1
Origin of Bioinformatics
  • The origins of the ‘modern’concept of bioinformatics are rooted in sequenceanalysis
  • Driven by the desire to
    • collect
    • annotate
    • & analyse sequence data
      • systematically (i.e., using computers)!

This concept of‘bioinformatics’was barely known pre 1990…

Teresa K.Attwood

University of Manchester

key milestones

GIVEQCCASVCSLYQLENYCN

Key milestones

FVNQHLCGSHLVEALYLVCGERGFFYTPKA

CSD

1950 1960 1970 1980 1990 2000 2010

insulin

ribonuclease

Dayhoff Atlas

margaret dayhoff 1925 1983
Margaret Dayhoff1925-1983
  • Pioneer of computer methods to compare proteins
    • & to derive evolutionary histories from alignments
  • Particular interest in deducing evolutionary connections from sequence evidence

Teresa K.Attwood

University of Manchester

margaret dayhoff
Margaret Dayhoff
  • Collected all the known protein sequences
    • made them available to the scientific community
  • In 1965, she compiled a book
    • Atlas of Protein Sequence & Structure

Teresa K.Attwood

University of Manchester

margaret dayhoff1
Margaret Dayhoff

“There is a tremendous amount of information regarding the evolutionary history and biochemical function implicit in each sequence andthe number of known sequences is growing explosively. We feel it is important to collect this significant information, correlate it into a unified whole and interpret it”

M.O.Dayhoff to C.Berkley, February 27, 1967

Strasser, B. (2008)

“GenBank – Natural history in the 21st century?”

Science, 322, 537-538

Teresa K.Attwood

University of Manchester

key milestones1
Key milestones

CSD

PDB

ARPAnet

Exam 1

What pernicious, life-changing development occurred in 1971?

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

ribonuclease

Dayhoff Atlas

Auto DNA sequencing

Auto protein sequencers

65

7

data overload in the usa
Data overload in the USA

“the rate limiting step in the process of nucleic acid sequencing is now shifting from data acquisition towards the organization and analysis of that data”

Gingeras, T.R. & Roberts, R.J. (1980)

“Steps toward Computer Analysis of Nucleotide Sequences,”

Science, 209, 1322-1328

Teresa K.Attwood

University of Manchester

data overload in the usa1
Data overload in the USA

“a centralized data bank [is] essential for the efficient use of nucleic acid sequence information”

C.Anderson, Minutes, 1980

Teresa K.Attwood

University of Manchester

data overload in europe
Data overload in Europe
  • While the US debated where to locate a new centralised resource, EMBL acted…
  • The 1st internationally funded, public ‘central’ nucleotide sequence database was thus European
    • the EMBL data library, Heidelberg
      • preceded the 1st release of GenBank by ~6 months

Attwood, T.K. et al. (2011)

Concepts, Historical Milestones & the Central Place of Bioinformatics in Modern Biology:

A European Perspective

In Bioinformatics - Trends & Methodologies, Intech Online Publishers,

Teresa K.Attwood

University of Manchester

data overload in europe1
Data overload in Europe
  • Copies of the EMBL data library & GenBank were being maintained in Cambridge
    • together with their search tools, etc.
  • An integrated system gave access to the dbs & tools
    • “this system is presently being used by over 30 researchers in 8 departments in the University & in local research institutes. These users can keep in touch with each other via the MAIL command”!

Teresa K.Attwood

University of Manchester

key milestones2
Key milestones

PIR

EMBL, GenBank

CSD

PDB

ARPAnet

Internet

email

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

ribonuclease

Dayhoff Atlas

Auto DNA sequencing

Auto protein sequencers

568

65

859

7

enter amos bairoch
Enter Amos Bairoch
  • A crazy postgrad student in Switzerland
    • interested in space exploration & the search for ET life
  • His project was to develop s/w to analyse protein & nucleotide sequences
    • PC/Gene

Teresa K.Attwood

University of Manchester

amos bairoch
Amos Bairoch
  • Published his 1st paper in 1982
    • a letter to the BJ
  • Suggested use of checksums
    • “tofacilitate detection of typographical & keyboard errors”

Teresa K.Attwood

University of Manchester

amos bairoch1
Amos Bairoch
  • Why?
  • Alongside PC/Gene, he needed to supply a db
  • The Atlas wasn’t available electronically
    • typed in >1,000 protein sequences
    • some from the literature
    • most from the Atlas
      • by 1981, this was a large book, plus several supplements, listing 1,660 proteins

Teresa K.Attwood

University of Manchester

amos bairoch2
Amos Bairoch
  • In 1983, he acquired a computer tape of the EMBL Data Library
    • version 2, with 811 sequences
  • In 1984, he received the 1st available computer tape copy of the Atlas
    • (which became known as the PIR-PSD)
    • but… he disliked the PIR format

Teresa K.Attwood

University of Manchester

amos bairoch3
Amos Bairoch
  • So he converted the PIR database into the semi-structured format of EMBL
    • part manually & part automatically
  • The result was PIR+
    • & was distributed as part of PC/Gene (now commercial)
  • In summer 1986, he finally released the database independently of PC/Gene
    • to make it available to all, free of charge

Teresa K.Attwood

University of Manchester

amos bairoch4
Amos Bairoch
  • This new database was called Swiss-Prot
  • 1st released on 21 July 1986
    • the exact number of entries is unknown, as he lostthe original floppy disks!

Teresa K.Attwood

University of Manchester

amos bairoch5
Amos Bairoch
  • As part of his work on PC/Gene, he created another key database
    • diagnostic tool for characterising protein families
  • 1st released March1989, with 58 entries
    • this was PROSITE
  • Philosophy of his approach
    • coupling high quality data analysis with manual annotation

Teresa K.Attwood

University of Manchester

characterising protein families
Characterising protein families

PROSITE

[IVM]-[AS]-L-W-S-L-V2-L-A-[IV]-E-R-Y-[IV]3-C-K-P-M

PRINTS

Teresa K Attwood

University of Manchester

the burden of maintenance
The burden of maintenance
  • Database annotation…

Database

Maintenance

Nirvana

Database annotation

Teresa K Attwood

University of Manchester

amos bairoch s lament
Amos Bairoch’s lament

“It is quite depressive to think that we are spending millions in grants for people to perform experiments, produce new knowledge, hide this knowledge in often badly written text and then spend some more millions trying to second guess what the authors really did and found”

Bairoch, A. (2009)

The future of annotation/biocuration

Nature Precedings

Teresa K Attwood

University of Manchester

key milestones3
Key milestones

PRINTS

PROSITE

Swiss-Prot

PIR

EMBL, GenBank

CSD

PDB

ARPAnet

Internet

email

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

ribonuclease

Dayhoff Atlas

Auto DNA sequencing

Auto protein sequencers

568

65

859

7

3,900

global data overload
Global data overload
  • The number of sequences was growing
  • The number of structures was growing
  • The number of protein family signatures was growing

Exam 2

Two extraordinary developments had yet to take place. What were they?

Teresa K.Attwood

University of Manchester

key milestones4
Key milestones

PRINTS

PROSITE

Pfam

InterPro

Swiss-Prot

TrEMBL

FlyBase

PIR

EMBL, GenBank

CSD

PDB

ARPAnet

Internet

email

www

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

H.sapiensgenome

C.elegansgenome

ribonuclease

Dayhoff Atlas

S.cerevisaegenome

HT DNA sequencing

H.influenzae genome

Auto DNA sequencing

D.melanogastergenome

Auto protein sequencers

568

65

859

7

2,423

3,900

105,000

slide28

Prosite

HAMAP

PIRSF

PRINTS

ProDom

InterPro

Gene3D

SUPERFAMILY

TIGRFAM

PANTHER

Pfam

Profiles

SMART

key milestones5
Key milestones

EMBnet

ELIXIR

NCBI

SIB

EBI

PRINTS

PROSITE

Pfam

InterPro

Swiss-Prot

TrEMBL

FlyBase

UniProt

ENA

PIR

EMBL, GenBank

CSD

PDB

ARPAnet

Internet

email

www

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

H.sapiensgenome

C.elegansgenome

ribonuclease

Dayhoff Atlas

S.cerevisaegenome

HT DNA sequencing

H.influenzae genome

Auto DNA sequencing

D.melanogastergenome

Auto protein sequencers

568

65

859

7

2,423

3,900

105,000

>500B

36.0M

key milestones6
Key milestones

EMBnet

ELIXIR

NCBI

SIB

EBI

PRINTS

PROSITE

Pfam

InterPro

Swiss-Prot

TrEMBL

FlyBase

UniProt

ENA

PIR

EMBL, GenBank

CSD

PDB

hundreds more

ARPAnet

Internet

email

www

1950 1960 1970 1980 1990 2000 2010

insulin

DNA sequencing

H.sapiensgenome

C.elegansgenome

ribonuclease

Dayhoff Atlas

thousands more

S.cerevisaegenome

HT DNA sequencing

H.influenzae genome

Auto DNA sequencing

D.melanogastergenome

Auto protein sequencers

billions more

568

65

859

7

2,423

3,900

105,000

>500B

36.0M

scary monsters

Red Line

Growth of EMBL since its inception

Scary monsters!

282 M

By2020, NGS & 3Gen technologies will be producing data a million times faster than the current rate

Green Line

Growth of manually annotated Swiss-Prot

35 M

540 K

84 K

Blue Line

Growth of PDB

the central place of bioinformatics in modern biology
The central place of bioinformatics in modern biology
  • Hopefully, this potted history speaks for itself
  • In the last 30 years, bioinformatics has given us
    • the first ‘complete’ catalogues of DNA & protein sequences
      • including genomes & proteomes of organisms across the Tree of Life
    • software to analyse biological data on an unprecedented scale
    • & hence tools to help understand
      • more about evolutionary processes in general
      • our place on the Tree of Life in particular
      • &, ultimately, more about health & disease
  • It isn’t a panacea, but its contribution has been huge

Teresa K.Attwood

University of Manchester

slide33

Recommended reading

Richon, A.B. A short history of bioinformatics (http://www.netsci.org/Science/Bioinform/feature06.html)

Bairoch, A. (2000) Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times. Bioinformatics, 16(1), 48-64.

Ashburner, M. (2006) Won for all – How the Drosophila genome was sequenced. Cold Spring Harbor Lab. Press

Strasser, B.J. (2008) GenBank – Natural history in the 21st century? Science, 322, 537-538.

Attwood, T.K., Gisel, A., Eriksson, N-E. & Bongcam-Rudloff, E. (2011) Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective

Teresa K.Attwood

University of Manchester

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