The AP* Retreat, KLCC, Kuala Lumpur. Feb 28, 2010
Report on APBioNet
Asia Pacific Bioinformatics
Tan Tin Wee
Founding Secretariat
Asia Pacific Bioinformatics Network
1
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.
2
APBioNet
(Founded 1998)
1997 APEC TEL WG survey – great
disparity of bioinformatics competence;
poor inter-Asian connectivity.
1998 APBioNet formation in PSB’98
Hawaii; APBioNet as an APAN project
Focussing on country training courses
Network, education, training, international
conferences, software, database services
and publications
3
Achieved Global Recognition
2005: Official Affiliation with ISCB as Regional
Affiliate (International Society for Computational
Biology)
2008: Invited Presentation at 20th Anniversary of
the European Molecular Biology Network 2008,
Martina Franca, Italy.
2009: Invited Presentation at the Inaugural
Formation of the IberioAmerican Bioinformatics
Society, RIBio, Mexico.
4
Organisational Comparison with
other Regions
EMBL DataLibrary
EBI
ECCB conference
EU/EC
EMBO
EMBL
EMBnet
EMBnet National
Nodes in Europe and
Other places
InCoB conf
-
A-IMBN
eIMBL
ABC
APBioNet
AASBi
APBC and
GIW conf
Asia Bioinformation
Institute ?
National Nodes? A few who
are members of EMBnet
5
Regular AGMs at InCoB
http://incob.apbionet.org
International Conference on Bioinformatics InCoB
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 (300)
2009: Singapore (400)
2010: Tokyo Sep 26-28 (Waseda ICC)
6
Top InCoB Papers have been
published since 2006
http://www.biomedcentral.com/bmcbioinformatics/
www.bioinformation.net
7
Steady Growth of Research
output in Asia From Elsevier
IN 2010, at InCoB in Tokyo, we will publish top papers in six journals:
BMC Bioinformatics
BMC Genomics
Immunomics Research
IPSJ Transactions
8
APBioNet-ASEAN-China
1st ASEAN China – 2004 Jingchu Luo Beijing
2nd ASEAN-China – 2008 Singapore
3rd ASEAN-China – 2010 (TCM
Bioinformatics and Systems Biology
proposed)
9
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
10
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
11
Participation in APAN TEIN2/3
and national RENs
1997 Singapore Research & Education
Network (SINGAREN)
Today every
country has
NREN of
some kind or
plans for one
Bioinformatics
is a big user
12
BioMirror since 1998
http://www.bio-mirror.net/
13
Published paper in top bioinformatics
Journal (Gilbert et al, 2004)
14
BioGrid
15
Won Supercomputing SC’2003
Most Geographically Distributed
Project
http://www.psc.edu/publicinfo/sc2003/awards.ht
ml
16
“BioDataGrid”
APBioGrid
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.
17
Received Grant from IDRC/APNIC Pan Asia
Networking Grant and published paper in 2007
18
BioWorldWideWorkflowGrid mtg
19
Joint Collaboration with
WizFolio.com
for bibliographic sharing and management
To manage and share all the scientific papers
you have read, and more,
20
Just sign up and login!
Bioinformatics on a Disk
APBioKnoppix 1 and 2
Tim Littlejohn’s BioLateral disks
LiveCD – Knoppix-based
Extension of BioKnoppix (Puerto Rico)
21
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
BioSlax on Citrix Xen Cloud
22
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
23
Institutional Support
ASEAN
ASEAN Dialogue Partners – China, India
KOBIC
ISCB
FAOBMB
IUBMB
UNESCO
Many universities
Many national
bioinformatics societies
24
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.
25
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
26
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
27
Transformation
in past 10 years
Build on Networks
Build Database Resources
Build Computational Services
Develop training software
Hold training courses
Coordinate and organise conferences, workshops,
meetings
Inject bioinformatics into curriculum
Publication of special journal issues in more than 3
different journals
Policy meetings at governmental and intergovernmental
level
28
What next?
Conferences, Workshops, Meetings
Training and Education
EUAsiaGrid (FP7)
Cloud Computing Software
BioMirror2 database Services
MIABi – Minimum Information about a
Bioinformatics Investigation
AuthorID, DocID data deposition
Asian Bioinformation Centers
29
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
30
APBioNet Historical Milestones
1997: Bioinformatics survey of the region
1998: First Meeting at PSB Hawaii
1998: Endorsement by APEC TEL; 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
InCoB; BioSlax Server version; Dialogue with EMBnet.
2009: Formation of Asian Bioinformation Centers with A-IMBN
2010: InCoB 2010 conference in Tokyo
31