Bioinformatics Growth in the Asian Region
20 years of Development
Tan Tin Wee
Founding Secretariat
Asia Pacific Bioinformatics Network
29th August 2009
HKU-Pasteur Research Centre - EMBO
Bioinformatics and Comparative Genomics Course
1
20 years: European Success Story
EMBO, EMBL, EMBnet, EBI
European Union
European Commission
European Molecular Biology Organisation
European Molecular Biology Laboratories
European Molecular Biology Network
European Bioinformatics Institute
2
Europe-Asia Comparison
Funds+Time+Cooperation+Culture
EU/EC funding
More than 20 years
EMBO – solid history
EMBnet – 20yr network of
national nodes in over 20
countries. Well interconnected
by GEANT2
Long time of high volume data
generation and bioinformation
creation
Know how to share and
cooperate
No such Asia governmental
body; may be APEC or ASEAN
GIW nearly 20yrs; A-IMBN 12
yrs; APBioNet 11yrs
A-IMBN – recent start 1997
APBioNet – bioinformatics
node formation still in
progress. Not well connected
network. Only national links;
last mile problems.
Recent growth in data volume
and bioinformation creation is
still new.
Asia still trying to learn how to
catch up
3
Organisational Comparison
EMBL DataLibrary
EBI
ECCB conference
EU/EC
EMBO
EMBL
EMBnet
EMBnet National
Nodes in Europe and
Other places
InCoB conf
-
A-IMBN
eIMBL
APBioNet
AASBi
APBC and
GIW conf
Asia Bioinformation
Institute ?
National Nodes? Not ready
ABC?
4
Parallel Growth of Biology and
Internet/IT in 20years
Mosaic
Web browser
World
Wide
Web
started
Web
2.0
Internet
widespread
Grid
Computing
Cloud
Computing
Internet2
???
Synergy
2000
1990
Genome
Project
Bacterial
Genomes
Start
emerging
Human
Genome
completed
IT
2020
2010
Human
Genome
completed
New
Gen
Seq
BIO
5
Bioinformatics in Singapore 90’s
1991 – Biocomputing Interest Group
1992 – Bioinformatics User Support – first Gopher, WAIS
server in Asia; hypertext web interface to bioinformatics
software
1993 – First biological World Wide Web site biomed.nus.sg
1995 – Planning the formation of the Bioinformatics Centre
(BIC) National Univ of Singapore
1996 – BioKleisli, BioPortal, integration projects
1997 – Bioinformatics Resource
1998 – BioMirror1 Project; APBioNet Formed
1999 – Remote solving of Xray structure of Bucandin
6
Bioinformatics outreach for Asia
in the ‘90s
Limited awareness
Limited recognition
Limited resources
Limited manpower
Mainly in Japan – GIW genome informatics
workshop; DDBJ
Sporadic efforts to introduce bioinformatics
Late 90s – emergence of bioinformatics groups
in Korea, Malaysia, China, Taiwan
Efforts by WHO (recently TDRs); ICGEBnet
formation (Trieste, Delhi); Pasteur’s efforts
7
Formation of APBioNet
Help ourselves
1997 APEC TEL WG survey – great
disparity of bioinformatics competence;
poor inter-Asian connectivity.
1997 EMBnet nodes in Asia – 2.
1998 APBioNet formation in PSB’98
Hawaii
1998 till today – network, education,
training, conferences, software, services
… awareness low, organisation weak…
8
APBioNet objectives:
Fostering the Growth of Bioinformatics and Allied
Disciplines in the Asia Pacific
Members from Australia, Bangladesh, Brunei Cambodia,
China, India, Indonesia, Japan, Korea, Laos, Malaysia,
New Zealand, Pakistan, Philippines, Russia, Saudi
Arabia, Singapore, Thailand, Vietnam and in North
America and Europe.
9
Members attend InCoB
http://incob.apbionet.org
International Conference on Bioinformatics
Annually since 2002: Bangkok, Thailand (200)
2003: Penang, Malaysia (300)
2004: Auckland, New Zealand (200)
2005: Busan, South Korea (300)
2006: New Delhi, India (1,000)
2007: HongKong, China and Hanoi, Vietnam (300)
2008: Taipei, Taiwan
2009: Singapore
10
APBioNet-ASEAN-China
1st ASEAN China – 2004 Jingchu Luo Beijing
2nd ASEAN-China – 2008 Singapore
3rd ASEAN-China – 2009 Shanghai (TCM
Bioinformatics and Systems Biology)
11
APBioNet Partners – East Asia
Bioinformation Network EABN
Sponsored by Korean Bioinformation Network
1st EABN – Busan Korea 2005
2nd EABN – Thailand (NSTDA) 2007
3rd EABN – Singapore (NUS) 2008
12
APBioNet Partners
ASEAN-India
– 1st ASEAN-India Bioinformatics Workshop 2005
– 2nd ASEAN-India Workshop 2006
Supported by FAOBMB, IUBMB, UNESCO, local
inst.
–
–
–
–
–
–
APBioNet Workshop in Bogor, Indonesia 2000
APBioNet Workshop in Malaysia 2000
APBioNet Workshop in Brunei, 2004
APBioNet Workhsop in Riyadh, Saudi Arabia 2005
APBioNet Workshop in Lahore, Pakistan 2006
APBioNet Workshop in Hanoi, Vietnam 2007
13
Top InCoB Papers have been
published since 2006
http://www.biomedcentral.com/bmcbioinformatics/
www.bioinformation.net
14
Steady Growth of Research
output in Asia
From Elsevier
15
Citations
16
Transformation
in 2000s
Build Network
Build Database Resources
Build Computational Services
Develop training software
Hold training courses
Coordinate and organise conferences,
workshops, meetings
Inject bioinformatics into curriculum
Policy meetings at governmental and
intergovernmental level
17
APAN and national RENs
1997 Singapore Research & Education
Network (SINGAREN)
Today every
country has
NREN of
some kind or
plans for one
18
TEIN 2 and TEIN 3
10M euros
TransEurasian
Information
Network
19
BioMirror since 1998
http://www.bio-mirror.net/
20
More Asian Databases emerging
Original successful ones: DDBJ, KEGG,
wwPDB (PDBj)
Many more emerging but they are not
sustainable e.g. ANTIMIC, SPDmod,
EXINT, Xdom, etc.
Growth in CJK - China Japan, Korea,
Taiwan.
21
BioGrid
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BioGrid
Grid computing installable in three steps
Funded by International Development
Research Centre IDRC PAN-Asia Grant
2002
Azereus P2P database distribution system
– Grant funded by IDRC in 2007-2009
- Thailand, KOBIC, NUS collaboration.
23
APBioGrid Computing
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BioWorldWideWorkFlow
25
BioWorldWideWorkFlow
26
BioWorldWideWorkflowGrid mtg
27
Introducing WizFolio.com
for bibliographic sharing and management
To manage and share all the scientific papers
you have read, and more,
28
Just sign up and login!
Import From
Clipboard
Manual
Entry
Get Match
Direct PDF
Upload
Online
Search
Highly optimized
to PubMed
Colleagues
Import from
RIS
WizAdd
Direct Export
from Webpages
WizFolio Web 2.0
Organize
Folder, Flags, Tags,
Filters
Locate Full-Text
Articles (PDF)
WizCite
Seamless citation
generation with live
preview
Sharing of
References
Word 2003
Word 2007
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Bioinformatics on a Disk
APBioKnoppix 1 and 2
Tim Littlejohn’s BioLateral disks
LiveCD – Knoppix-based
Extension of BioKnoppix (Puerto Rico)
30
BioSLAX virtual desktops
BioSLax on CD
BioSLax on DVD
BioSlax on VMware
BioSlax on USB stick
(BioSlax on Youtube movie)
BioSlax with MokaFive and VMPlayer
31
Bioinformatics and
Databases in a Box: BioSLAX
Server
- 500 to 1Terabyte HDD Boxes
- Plus BioSlax Server LiveCD
- Tested in Institute of Biotechnology
(IBT) Hanoi, 2007/2008
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Institutional Support
ASEAN
ASEAN Dialogue Partners – China, India
KOBIC
ISCB
FAOBMB
IUBMB
UNESCO
Many universities
Many national
bioinformatics societies
33
S* Life Science Informatics Alliance
A thousand trained online
Online courses from 2001 to 2005
S-star council from Stanford, Sweden
(Uppsala/Karolinska), Singapore, Sydney, South
Africa, UCSanDiego
Mirror sites in 10 places
Secretariat in National Univ of Singapore.
34
LAMS Learning Activity
Management System
35
CENTRA for online PBL
36
CanalAVIST and AVIST
Asean Virtual Institute of
Science and Technology
CanalAVIST will utilize
the Trans Eurasia
Information Network
(TEIN2) to deliver lectures
and streaming VDO to
members of TEIN2, ASEAN,
Europe and Australia with
H.263 to DVTS supported by
an E-learning
platform VCLASS (see http://
www.vclass.net) by the
Internet Education and
Research Lab, Asian Institute
of Technology
37
WEBCB at InCoB2008 and 2009
Workshop on Education in Bioinformatics
and Computational Biology 23rd Oct 2008
Taipei, Taiwan
http://trg.apbionet.org/webcb/
Curriculum Development
Accreditation
Testing – India Bioinformatics certification
examination system
38
APBioNet Historical Milestones
1997: Bioinformatics survey of the region
1998: First Meeting at PSB Hawaii
1998: Endorsement by APEC TEL
1998: APBioNet as first project of APAN
1999: APAN-APBioNet BioMirrors Project
2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand,
Brunei
2002: InCoB conference series
2003: IDRC Grant for BioGrid software
2004: APBioKnoppix; later BioSlax (2006)
2004: ASEAN-China Bioinformatics Workshop
2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC
cooperation
2006: InCoB Conference publishes in BMC Bioinformatics; outreach to
Cambodia; Saudi Arabia; Pakistan; Vietnam
2007: IDRC grant for P2P dissemination of biomirror datasets;
CanalAVIST project
2008: 2nd ASEAN-China; 3rd East Asia Bioinformation Network; 7th
39
InCoB; BioSlax Server version; Dialogue with EMBnet.
What next?
Conferences, Workshops, Meetings
Training and Education
Network Infrastructure
Software
Mirror Services
…
Future?
40
Challenges ahead
Lack of curriculum transformation some Tier 1 universities
and none in Tier 2 and lower.
Lack of bioinformatics-enabled professors
Lack of institutional resources (network, expertise)
Lack of professional career framework
Lack of recognition and organisational support
Lack of recurrent or established financial support
Lack of bandwidth of older people, and lack of young people
and volunteers
Stimulate high impact research
Stimulate high impact resources and databases
Stimulate high impact software and services
Stimulate high quality education and graduates
41
What can we do strategically?
Be more actively involved in ISCB
Seek membership for our members in
EMBnet or its enlarged entity
E”xtended”MBnet
Facilitation of Research Grant funding
Support the ABC initiative
Support our colleagues in AASBi, APBC,
GIW etc.
42
Today’s Challenges for Asia and
Personal Genomics
BioInformation have and have-nots – big
disparity in capacities in different
institutions and cities of Asia
Lack of interoperability and
standardisation
Lack of Asia repositories – over reliance
on Western sources
Low to high level of knowledge in Asian life
scientists – big disparity
43
Personal Genomics
In 10 to 20 years, it will be common in the
West.
Asia will lag by at least 10 years
What will improve it?
– Education
– Positive Publicity
– Information infrastructure
– Standards and best practice
44
Role of Asian Bioinformation
Centers
Repository of public knowledge
– Stimulate private or proprietary knowledge
Promotion of standardisation and
interoperability
– Leverage on virtualisation, grid and cloud
Champion of bioinformation in our
institution, in our city, and in our country
– Education and awareness
– Scientific activism with our governments
45
New initiatives
Minimum Bioinformatics Skillsets for Life
science undergraduates/graduates
Minimum Information about a
Bioinformatics Investigation MIABi
AuthorID disambiguation
Deposition of datasets
What new areas of Research can we
compete in?
46
Origin of Species
200th Anniversary of Darwin’s birth
150th Anniversary of the
“Origin of Species”
Alfred Russel Wallace
Malay Archipelago
47
Origin of Life
48
From Religion: Logos
Old Testament of the Holy Bible:
Genesis 1:1 In the beginning God created the heavens and the
earth.
New Testament of the Holy Bible:
John 1: 1 In the beginning was the Word, and the Word was
with God, and the Word was God.
Logos (Greek, "word,""reason,""ratio"), in ancient and
especially in medieval philosophy and theology, the divine
reason that acts as the ordering principle of the universe.
49
Tao (道, pinyin: dào (help·info) ) is a concept
found in Taoism, Confucianism, and more
generally in ancient Chinese philosophy. While
the character itself translates as 'way', 'path', or
'route', or sometimes more loosely as 'doctrine'
or 'principle', it is used philosophically to signify
the fundamental or true nature of the world. The
concept of Tao differs from Western ontology,
however; it is an active and holistic conception of
the world, rather than a static, atomistic one.
50
From Physics:
Mass-Energy Equivalence
Mass–energy equivalence was proposed in Albert Einstein's 1905
paper, "Does the inertia of a body depend upon its energy-content?",
one of his Annus Mirabilis ("Miraculous Year") Papers.[2] Einstein
was not the first to propose a mass–energy relationship, and various
similar formulas appeared before Einstein's theory with incorrect
numerical coefficients and an incomplete interpretation. Einstein was
the first to propose the simple formula and the first to interpret it
correctly: as a general principle which follows from the relativistic
symmetries of space and time.
S. Rainville, J.K. Thompson, E.G. Myers, J.M. Brown, M.S. Dewey, E.G. Kessler Jr., R.D. Deslattes, H.G.
Börner, M. Jentschel, P. Mutti, D.E. Pritchard. 2005. A direct test of E = mc2. Nature. Dec. 22, 2005
51
52
From Chemistry
Dmitri Ivanovich
Mendeleev
On March 6, 1869, Mendeleev made a
formal presentation to the Russian
Chemical Society, entitled The
Dependence between the Properties of the
Atomic Weights of the Elements, which
described elements according to both
atomic weight and valence.
Principles of Chemistry
(1868-70)
53
Periodic Table of Elements
54
The Standard Model in particle
physics
At present, matter and energy are
best understood in terms of the
kinematics and interactions of
elementary particles. To date,
physics has reduced the laws
governing the behavior and
interaction of all known forms of
matter and energy, to a small set of
fundamental laws and theories. A
major goal of physics is to find the
"common ground" that would unite
all of these theories into one
integrated theory of everything, of
which all the other known laws
would be special cases, and from
which the behavior of all matter
and energy could be derived (at
least in principle) (Wikipedia)
55
Two Dimensional Pattern of
Basic Sound as the basis of
Spoken Language
Sanskrit grammarians of
ancient India, who had
created astonishingly
sophisticated theories of
language based on their
discovery of the twodimensional patterns in basic
sounds
The tabular form of the
Sanskrit letters is due to the
two parameters (point of
articulation and aspiration)
as the basis of the spoken
sounds
56
From Linnaeaus
Taxonomy
Binomial Nomenclature
57
Claude Bernard 1813-1878
Homeostasis
Milieu interieur is the key process
with which Bernard is associated.
He wrote, "La fixité du milieu
intérieur est la condition d'une vie
libre et indépendante" ("The
constancy of the internal
environment is the condition for a
free and independent life").
Compare with Traditional Chinese
and Traditional Indian Ayuvedic
Medicine - Balance
58
What new metaphors for “the
New Biology”?
In 1623 Galileo crafted a famous metaphor that is still often cited by
scientists. Nature, he wrote, is a book written in "the language of
mathematics". If we cannot understand that language, we will be
doomed to wander about as if "in a dark labyrinth". (Crease, 2006)
The most important lesson to be found in Galileo's image is the need
to keep developing and revising the metaphors with which we speak
about science
59
On “Bioinformatics is Dead”, “I think we
are just at the beginning of something
more dramatic” John Quackenbush 2009
Information
Coded Information –
Need to build a concept of
Information
Need to measure it
Pierre-Henri Gouyon (2009)
60
Semantic Web or Semiotics?
Semiotics, also called semiotic studies or semiology, is the study
of sign processes (semiosis), or signification and communication,
signs and symbols, both individually and grouped into sign systems.
It includes the study of how meaning is constructed and understood
three branches:
Semantics: Relation between signs and the things they refer to,
their denotata.
Syntactics: Relation of signs to each other in formal structures.
Pragmatics: Relation of signs to their impacts on those who use
them.
Semiotics is frequently seen as having important anthropological
dimensions, for example Umberto Eco proposes that every cultural
phenomenon can be studied as communication.
61
The Origin
of Information
From the origin of species to the origin of encoded information in
living things
From Observational Science to Experimental science to Informational
Biological science
Future of Bioinformatics – the information in “bio” logical organisms
Looking at organisms as information perpetuating agents
Is this the theoretical biology of the future?
What is the language to be used? Mathematics? Ontologies?
62