11

Bioinformatics Growth in the Asian RegionBioinformatics Growth in the Asian Region20 years of Development20 years of Development

Tan Tin WeeTan Tin WeeFounding SecretariatFounding Secretariat

Asia Pacific Bioinformatics NetworkAsia Pacific Bioinformatics Network

2929thth August 2009 August 2009HKU-Pasteur Research Centre - EMBO HKU-Pasteur Research Centre - EMBO

Bioinformatics and Comparative Genomics CourseBioinformatics and Comparative Genomics Course

22

20 years: European Success Story20 years: European Success StoryEMBO, EMBL, EMBnet, EBIEMBO, EMBL, EMBnet, EBI

European UnionEuropean Union

European CommissionEuropean Commission

European Molecular Biology OrganisationEuropean Molecular Biology Organisation

European Molecular Biology LaboratoriesEuropean Molecular Biology Laboratories

European Molecular Biology NetworkEuropean Molecular Biology Network

European Bioinformatics InstituteEuropean Bioinformatics Institute

33

Europe-Asia ComparisonEurope-Asia ComparisonFunds+Time+Cooperation+CultureFunds+Time+Cooperation+Culture

EU/EC fundingEU/EC funding

More than 20 yearsMore than 20 years

EMBO – solid historyEMBO – solid historyEMBnet – 20yr network of EMBnet – 20yr network of national nodes in over 20 national nodes in over 20 countries. Well interconnected countries. Well interconnected by GEANT2by GEANT2

Long time of high volume data Long time of high volume data generation and bioinformation generation and bioinformation creationcreationKnow how to share and Know how to share and cooperatecooperate

No such Asia governmental No such Asia governmental body; may be APEC or body; may be APEC or ASEANASEANGIW nearly 20yrs; A-IMBN 12 GIW nearly 20yrs; A-IMBN 12 yrs; APBioNet 11yrsyrs; APBioNet 11yrsA-IMBN – recent start 1997A-IMBN – recent start 1997APBioNet – bioinformatics APBioNet – bioinformatics node formation still in node formation still in progress. Not well connected progress. Not well connected network. Only national links; network. Only national links; last mile problems.last mile problems.Recent growth in data volume Recent growth in data volume and bioinformation creation is and bioinformation creation is still new.still new.Asia still trying to learn how to Asia still trying to learn how to catch upcatch up

44

Organisational ComparisonOrganisational Comparison

EU/ECEU/EC

- -

EMBOEMBO

A-IMBNA-IMBN

EMBLEMBL

eIMBLeIMBL

EMBnetEMBnet

APBioNetAPBioNet

ECCB conferenceECCB conference

AASBiAASBi

EMBL DataLibraryEMBL DataLibrary

EMBnet NationalNodes in Europe andOther places

EMBnet NationalNodes in Europe andOther places

Asia Bioinformation Institute ?

Asia Bioinformation Institute ?

EBIEBI

National Nodes? Not readyNational Nodes? Not ready

ABC?ABC?APBC andGIW conf

APBC andGIW conf

InCoB confInCoB conf

55

Parallel Growth of Biology and Parallel Growth of Biology and Internet/IT in 20yearsInternet/IT in 20years

Synergy

1990 2000 2010 2020

Genome Project

World WideWeb

started

MosaicWeb browser

New GenSeq

Web2.0

GridComputing

Human Genome

completed

Internetwidespread

BacterialGenomes

Start emerging

Human Genome

completed

BIO

IT

???

CloudComputingInternet2

66

Bioinformatics in Singapore 90’sBioinformatics in Singapore 90’s

1991 – Biocomputing Interest Group1991 – Biocomputing Interest Group1992 – Bioinformatics User Support – first Gopher, WAIS 1992 – Bioinformatics User Support – first Gopher, WAIS server in Asia; hypertext web interface to bioinformatics server in Asia; hypertext web interface to bioinformatics softwaresoftware1993 – First biological World Wide Web site biomed.nus.sg1993 – First biological World Wide Web site biomed.nus.sg1995 – Planning the formation of the Bioinformatics Centre 1995 – Planning the formation of the Bioinformatics Centre (BIC) National Univ of Singapore(BIC) National Univ of Singapore1996 – BioKleisli, BioPortal, integration projects1996 – BioKleisli, BioPortal, integration projects1997 – Bioinformatics Resource1997 – Bioinformatics Resource1998 – BioMirror1 Project; APBioNet Formed1998 – BioMirror1 Project; APBioNet Formed1999 – Remote solving of Xray structure of Bucandin1999 – Remote solving of Xray structure of Bucandin

77

Bioinformatics outreach for Asia Bioinformatics outreach for Asia in the ‘90sin the ‘90s

Limited awarenessLimited awarenessLimited recognitionLimited recognitionLimited resourcesLimited resourcesLimited manpowerLimited manpowerMainly in Japan – GIW genome informatics Mainly in Japan – GIW genome informatics workshop; DDBJworkshop; DDBJSporadic efforts to introduce bioinformaticsSporadic efforts to introduce bioinformaticsLate 90s – emergence of bioinformatics groups Late 90s – emergence of bioinformatics groups in Korea, Malaysia, China, Taiwanin Korea, Malaysia, China, TaiwanEfforts by WHO (recently TDRs); ICGEBnet Efforts by WHO (recently TDRs); ICGEBnet formation (Trieste, Delhi); Pasteur’s effortsformation (Trieste, Delhi); Pasteur’s efforts

88

Formation of APBioNetFormation of APBioNetHelp ourselvesHelp ourselves

1997 APEC TEL WG survey – great 1997 APEC TEL WG survey – great disparity of bioinformatics competence; disparity of bioinformatics competence; poor inter-Asian connectivity.poor inter-Asian connectivity.1997 EMBnet nodes in Asia – 2. 1997 EMBnet nodes in Asia – 2. 1998 APBioNet formation in PSB’98 1998 APBioNet formation in PSB’98 HawaiiHawaii1998 till today – network, education, 1998 till today – network, education, training, conferences, software, services training, conferences, software, services … awareness low, organisation weak…… awareness low, organisation weak…

99

APBioNet objectives:APBioNet objectives:Fostering the Growth of Bioinformatics and Allied Fostering the Growth of Bioinformatics and Allied

Disciplines in the Asia PacificDisciplines in the Asia Pacific

Members from Australia, Bangladesh, Brunei Cambodia, Members from Australia, Bangladesh, Brunei Cambodia, China, India, Indonesia, Japan, Korea, Laos, Malaysia, China, India, Indonesia, Japan, Korea, Laos, Malaysia, New Zealand, Pakistan, Philippines, Russia, Saudi New Zealand, Pakistan, Philippines, Russia, Saudi Arabia, Singapore, Thailand, Vietnam and in North Arabia, Singapore, Thailand, Vietnam and in North America and Europe.America and Europe.

1010

Members attend InCoB Members attend InCoB http://incob.apbionet.orghttp://incob.apbionet.org

International Conference on BioinformaticsInternational Conference on Bioinformatics

Annually since 2002: Bangkok, Thailand (200)Annually since 2002: Bangkok, Thailand (200)

2003: Penang, Malaysia (300)2003: Penang, Malaysia (300)

2004: Auckland, New Zealand (200)2004: Auckland, New Zealand (200)

2005: Busan, South Korea (300)2005: Busan, South Korea (300)

2006: New Delhi, India (1,000)2006: New Delhi, India (1,000)

2007: HongKong, China and Hanoi, Vietnam (300)2007: HongKong, China and Hanoi, Vietnam (300)

2008: Taipei, Taiwan2008: Taipei, Taiwan

2009: Singapore2009: Singapore

1111

APBioNet-ASEAN-ChinaAPBioNet-ASEAN-China11stst ASEAN China – 2004 Jingchu Luo Beijing ASEAN China – 2004 Jingchu Luo Beijing

22ndnd ASEAN-China – 2008 Singapore ASEAN-China – 2008 Singapore

33rdrd ASEAN-China – 2009 Shanghai (TCM ASEAN-China – 2009 Shanghai (TCM Bioinformatics and Systems Biology)Bioinformatics and Systems Biology)

1212

APBioNet Partners – East Asia APBioNet Partners – East Asia Bioinformation Network EABNBioinformation Network EABNSponsored by Korean Bioinformation NetworkSponsored by Korean Bioinformation Network

11stst EABN – Busan Korea 2005 EABN – Busan Korea 2005

22ndnd EABN – Thailand (NSTDA) 2007 EABN – Thailand (NSTDA) 2007

33rdrd EABN – Singapore (NUS) 2008 EABN – Singapore (NUS) 2008

1313

APBioNet PartnersAPBioNet Partners

ASEAN-IndiaASEAN-India– 11stst ASEAN-India Bioinformatics Workshop 2005 ASEAN-India Bioinformatics Workshop 2005– 22ndnd ASEAN-India Workshop 2006 ASEAN-India Workshop 2006

Supported by FAOBMB, IUBMB, UNESCO, local Supported by FAOBMB, IUBMB, UNESCO, local inst.inst.– APBioNet Workshop in Bogor, Indonesia 2000APBioNet Workshop in Bogor, Indonesia 2000– APBioNet Workshop in Malaysia 2000APBioNet Workshop in Malaysia 2000– APBioNet Workshop in Brunei, 2004APBioNet Workshop in Brunei, 2004– APBioNet Workhsop in Riyadh, Saudi Arabia 2005APBioNet Workhsop in Riyadh, Saudi Arabia 2005– APBioNet Workshop in Lahore, Pakistan 2006APBioNet Workshop in Lahore, Pakistan 2006– APBioNet Workshop in Hanoi, Vietnam 2007APBioNet Workshop in Hanoi, Vietnam 2007

1414

Top InCoB Papers have been Top InCoB Papers have been published since 2006published since 2006

www.bioinformation.net

http://www.biomedcentral.com/bmcbioinformatics/

1515

Steady Growth of Research Steady Growth of Research output in Asiaoutput in Asia

From Elsevier

1616

CitationsCitations

1717

Transformation Transformation in 2000sin 2000s

Build NetworkBuild NetworkBuild Database ResourcesBuild Database ResourcesBuild Computational ServicesBuild Computational ServicesDevelop training softwareDevelop training softwareHold training coursesHold training coursesCoordinate and organise conferences, Coordinate and organise conferences, workshops, meetingsworkshops, meetingsInject bioinformatics into curriculumInject bioinformatics into curriculumPolicy meetings at governmental and Policy meetings at governmental and intergovernmental levelintergovernmental level

1818

APAN and national RENsAPAN and national RENs

1997 Singapore Research & Education 1997 Singapore Research & Education Network (SINGAREN)Network (SINGAREN)

Today everyToday everycountry has country has NREN of NREN of some kind orsome kind orplans for oneplans for one

1919

TEIN 2 and TEIN 3TEIN 2 and TEIN 3

10M euros 10M euros

TransEurasian TransEurasian Information Information NetworkNetwork

2020

BioMirror since 1998BioMirror since 1998

http://www.bio-mirror.nethttp://www.bio-mirror.net//

2121

More Asian Databases emergingMore Asian Databases emerging

Original successful ones: DDBJ, KEGG, Original successful ones: DDBJ, KEGG, wwPDB (PDBj)wwPDB (PDBj)

Many more emerging but they are not Many more emerging but they are not sustainable e.g. ANTIMIC, SPDmod, sustainable e.g. ANTIMIC, SPDmod, EXINT, Xdom, etc.EXINT, Xdom, etc.

Growth in CJK - China Japan, Korea, Growth in CJK - China Japan, Korea, Taiwan.Taiwan.

2222

BioGridBioGrid

2323

BioGridBioGrid

Grid computing installable in three stepsGrid computing installable in three steps

Funded by International Development Funded by International Development Research Centre IDRC PAN-Asia Grant Research Centre IDRC PAN-Asia Grant 20022002

Azereus P2P database distribution system Azereus P2P database distribution system – Grant funded by IDRC in 2007-2009– Grant funded by IDRC in 2007-2009

- Thailand, KOBIC, NUS collaboration.- Thailand, KOBIC, NUS collaboration.

2424

APBioGrid ComputingAPBioGrid Computing

2525

BioWorldWideWorkFlowBioWorldWideWorkFlow

2626

BioWorldWideWorkFlowBioWorldWideWorkFlow

2727

BioWorldWideWorkflowGrid mtgBioWorldWideWorkflowGrid mtg

2828

Introducing WizFolio.comIntroducing WizFolio.com for bibliographic sharing and managementfor bibliographic sharing and management

To manage and share all the scientific papers you have read, and more, Just sign up and login!

2929

WizFolio Web 2.0

WizCiteSeamless citation

generation with live preview

Word 2003Word 2007

Import from RIS

Manual Entry

Get Match

Online Search

Highly optimized to

PubMed

WizAddDirect Export

from Webpages

OrganizeFolder, Flags, Tags, Filters

Sharing of References

Import From

Clipboard

Direct PDF Upload

Colleagues

Locate Full-Text Articles

(PDF)

3030

Bioinformatics on a Disk Bioinformatics on a Disk APBioKnoppix 1 and 2APBioKnoppix 1 and 2

Tim Littlejohn’s BioLateral disksTim Littlejohn’s BioLateral disks

LiveCD – Knoppix-basedLiveCD – Knoppix-based

Extension of BioKnoppix (Puerto Rico)Extension of BioKnoppix (Puerto Rico)

3131

BioSLAX virtual desktopsBioSLAX virtual desktopsBioSLax on CDBioSLax on DVDBioSlax on VMwareBioSlax on USB stick(BioSlax on Youtube movie)BioSlax with MokaFive and VMPlayer

3232

Bioinformatics and Bioinformatics and Databases in a Box: BioSLAX Databases in a Box: BioSLAX

ServerServer

- 500 to 1Terabyte HDD Boxes- Plus BioSlax Server LiveCD- Tested in Institute of Biotechnology(IBT) Hanoi, 2007/2008

3333

Institutional SupportInstitutional Support

ASEANASEANASEAN Dialogue Partners – China, IndiaASEAN Dialogue Partners – China, IndiaKOBICKOBICISCBISCBFAOBMBFAOBMBIUBMBIUBMBUNESCOUNESCOMany universitiesMany universitiesMany nationalMany nationalbioinformatics societiesbioinformatics societies

3434

S* Life Science Informatics AllianceS* Life Science Informatics AllianceA thousand trained onlineA thousand trained online

Online courses from 2001 to 2005Online courses from 2001 to 2005

S-star council from Stanford, Sweden S-star council from Stanford, Sweden (Uppsala/Karolinska), Singapore, Sydney, South (Uppsala/Karolinska), Singapore, Sydney, South Africa, UCSanDiegoAfrica, UCSanDiego

Mirror sites in 10 places Mirror sites in 10 places

Secretariat in National Univ of Singapore.Secretariat in National Univ of Singapore.

3535

LAMS Learning Activity LAMS Learning Activity Management SystemManagement System

3636

CENTRA for online PBLCENTRA for online PBL

3737

CanalAVIST and AVISTCanalAVIST and AVISTAsean Virtual Institute of Asean Virtual Institute of Science and TechnologyScience and Technology

CanalCanalAVISTAVIST will utilize the  will utilize the Trans Eurasia Information NetTrans Eurasia Information Network (TEIN2)work (TEIN2) to deliver lectures and  to deliver lectures and streaming VDO to members streaming VDO to members of of TEIN2TEIN2, ASEAN, Europe , ASEAN, Europe and Australia with H.263 to and Australia with H.263 to DVTS supported by an E-DVTS supported by an E-learning platform learning platform VCLASSVCLASS (see  (see http://http://www.vclass.netwww.vclass.net) ) by the Internet Education and by the Internet Education and Research Lab, Asian Institute Research Lab, Asian Institute

of Technologyof Technology

3838

WEBCB at InCoB2008 and 2009WEBCB at InCoB2008 and 2009

Workshop on Education in Bioinformatics Workshop on Education in Bioinformatics and Computational Biology 23and Computational Biology 23rdrd Oct 2008 Oct 2008 Taipei, TaiwanTaipei, Taiwan

http://trg.apbionet.org/webcb/http://trg.apbionet.org/webcb/

Curriculum DevelopmentCurriculum Development

AccreditationAccreditation

Testing – India Bioinformatics certification Testing – India Bioinformatics certification examination systemexamination system

3939

APBioNet Historical MilestonesAPBioNet Historical Milestones1997: Bioinformatics survey of the region1997: Bioinformatics survey of the region1998: First Meeting at PSB Hawaii1998: First Meeting at PSB Hawaii1998: Endorsement by APEC TEL1998: Endorsement by APEC TEL1998: APBioNet as first project of APAN1998: APBioNet as first project of APAN1999: APAN-APBioNet BioMirrors Project1999: APAN-APBioNet BioMirrors Project2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand, Brunei2000: Involvement in S* Alliance; outreach start to Malaysia, Thailand, Brunei2002: InCoB conference series2002: InCoB conference series2003: IDRC Grant for BioGrid software2003: IDRC Grant for BioGrid software2004: APBioKnoppix; later BioSlax (2006)2004: APBioKnoppix; later BioSlax (2006)2004: ASEAN-China Bioinformatics Workshop2004: ASEAN-China Bioinformatics Workshop2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC cooperation2005: Affiliation with ISCB; ASEAN-India Cooperation; KOBIC cooperation2006: InCoB Conference publishes in BMC Bioinformatics; outreach to 2006: InCoB Conference publishes in BMC Bioinformatics; outreach to Cambodia; Saudi Arabia; Pakistan; VietnamCambodia; Saudi Arabia; Pakistan; Vietnam2007: IDRC grant for P2P dissemination of biomirror datasets; CanalAVIST 2007: IDRC grant for P2P dissemination of biomirror datasets; CanalAVIST projectproject2008: 22008: 2ndnd ASEAN-China; 3 ASEAN-China; 3rdrd East Asia Bioinformation Network; 7 East Asia Bioinformation Network; 7thth InCoB; InCoB; BioSlax Server version; Dialogue with EMBnet.BioSlax Server version; Dialogue with EMBnet.

4040

What next?What next?

Conferences, Workshops, MeetingsConferences, Workshops, Meetings

Training and EducationTraining and Education

Network InfrastructureNetwork Infrastructure

SoftwareSoftware

Mirror ServicesMirror Services

……

Future?Future?

4141

Challenges aheadChallenges aheadLack of curriculum transformation some Tier 1 universities Lack of curriculum transformation some Tier 1 universities and none in Tier 2 and lower.and none in Tier 2 and lower.Lack of bioinformatics-enabled professorsLack of bioinformatics-enabled professorsLack of institutional resources (network, expertise)Lack of institutional resources (network, expertise)Lack of professional career frameworkLack of professional career frameworkLack of recognition and organisational supportLack of recognition and organisational supportLack of recurrent or established financial supportLack of recurrent or established financial supportLack of bandwidth of older people, and lack of young people Lack of bandwidth of older people, and lack of young people and volunteersand volunteersStimulate high impact researchStimulate high impact researchStimulate high impact resources and databasesStimulate high impact resources and databasesStimulate high impact software and servicesStimulate high impact software and servicesStimulate high quality education and graduatesStimulate high quality education and graduates

4242

What can we do strategically?What can we do strategically?

Be more actively involved in ISCBBe more actively involved in ISCB

Seek membership for our members in Seek membership for our members in EMBnet or its enlarged entity EMBnet or its enlarged entity E”xtended”MBnetE”xtended”MBnet

Facilitation of Research Grant fundingFacilitation of Research Grant funding

Support the ABC initiativeSupport the ABC initiative

Support our colleagues in AASBi, APBC, Support our colleagues in AASBi, APBC, GIW etc.GIW etc.

4343

Today’s Challenges for Asia andToday’s Challenges for Asia andPersonal GenomicsPersonal Genomics

BioInformation have and have-nots – big BioInformation have and have-nots – big disparity in capacities in different disparity in capacities in different institutions and cities of Asiainstitutions and cities of AsiaLack of interoperability and Lack of interoperability and standardisationstandardisationLack of Asia repositories – over reliance Lack of Asia repositories – over reliance on Western sourceson Western sourcesLow to high level of knowledge in Asian Low to high level of knowledge in Asian life scientists – big disparitylife scientists – big disparity

4444

Personal GenomicsPersonal Genomics

In 10 to 20 years, it will be common in the In 10 to 20 years, it will be common in the West.West.

Asia will lag by at least 10 yearsAsia will lag by at least 10 years

What will improve it?What will improve it?– EducationEducation– Positive PublicityPositive Publicity– Information infrastructureInformation infrastructure– Standards and best practiceStandards and best practice

4545

Role of Asian Bioinformation Role of Asian Bioinformation CentersCenters

Repository of public knowledgeRepository of public knowledge– Stimulate private or proprietary knowledgeStimulate private or proprietary knowledge

Promotion of standardisation and Promotion of standardisation and interoperabilityinteroperability– Leverage on virtualisation, grid and cloudLeverage on virtualisation, grid and cloud

Champion of bioinformation in our Champion of bioinformation in our institution, in our city, and in our countryinstitution, in our city, and in our country– Education and awarenessEducation and awareness– Scientific activism with our governmentsScientific activism with our governments

4646

New initiativesNew initiatives

Minimum Bioinformatics Skillsets for Life Minimum Bioinformatics Skillsets for Life science undergraduates/graduatesscience undergraduates/graduates

Minimum Information about a Minimum Information about a Bioinformatics Investigation MIABiBioinformatics Investigation MIABi

AuthorID disambiguationAuthorID disambiguation

Deposition of datasetsDeposition of datasets

What new areas of Research can we What new areas of Research can we compete in?compete in?

4747

Origin of SpeciesOrigin of Species

200th Anniversary of Darwin’s birth150th Anniversary of the “Origin of Species”

Alfred Russel WallaceMalay Archipelago

4848

Origin of LifeOrigin of Life

4949

From Religion: LogosFrom Religion: LogosOld Testament of the Holy Bible:Old Testament of the Holy Bible:Genesis 1:1 In the beginning God created the heavens and the Genesis 1:1 In the beginning God created the heavens and the earth.earth.New Testament of the Holy Bible:New Testament of the Holy Bible:John 1: 1 In the beginning was the Word, and the Word was John 1: 1 In the beginning was the Word, and the Word was with God, and the Word was God.with God, and the Word was God. Logos (Greek, "word,""reason,""ratio"), in ancient and Logos (Greek, "word,""reason,""ratio"), in ancient and especially in medieval philosophy and theology, the divine especially in medieval philosophy and theology, the divine reason that acts as the ordering principle of the universe.reason that acts as the ordering principle of the universe.

5050

TaoTao ( (道道, , pinyinpinyin: : dàodào ( (helphelp··infoinfo) ) is a concept ) ) is a concept

found in found in TaoismTaoism, , ConfucianismConfucianism, and more , and more generally in ancient generally in ancient Chinese philosophyChinese philosophy. While . While the character itself translates as 'way', 'path', or the character itself translates as 'way', 'path', or 'route', or sometimes more loosely as 'doctrine' 'route', or sometimes more loosely as 'doctrine' or 'principle', it is used philosophically to signify or 'principle', it is used philosophically to signify the fundamental or true nature of the world. The the fundamental or true nature of the world. The concept of Tao differs from Western concept of Tao differs from Western ontologyontology, , however; it is an active and however; it is an active and holisticholistic conception of conception of the world, rather than a static, the world, rather than a static, atomisticatomistic one. one.

5151

From Physics:From Physics:Mass-Energy EquivalenceMass-Energy Equivalence

Mass–energy equivalence was proposed in Mass–energy equivalence was proposed in Albert EinsteinAlbert Einstein's 1905 's 1905 paper, "Does the inertia of a body depend upon its energy-content?", paper, "Does the inertia of a body depend upon its energy-content?", one of his one of his AnnusAnnus Mirabilis Mirabilis ("Miraculous Year") Papers. ("Miraculous Year") Papers.[2][2] Einstein Einstein was not the first to propose a mass–energy relationship, and various was not the first to propose a mass–energy relationship, and various similar formulas appeared before Einstein's theory with incorrect similar formulas appeared before Einstein's theory with incorrect numerical coefficients and an incomplete interpretation. Einstein was numerical coefficients and an incomplete interpretation. Einstein was the first to propose the simple formula and the first to interpret it the first to propose the simple formula and the first to interpret it correctly: as a general principle which follows from the correctly: as a general principle which follows from the relativistic symmetriesrelativistic symmetries of of space and timespace 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

5252

5353

From ChemistryFrom Chemistry

Dmitri Ivanovich Dmitri Ivanovich MendeleevMendeleevOn On March 6March 6, , 18691869, Mendeleev made a , Mendeleev made a formal presentation to the formal presentation to the Russian Chemical SocietyRussian Chemical Society, entitled , entitled The The Dependence between the Properties of the Dependence between the Properties of the Atomic Weights of the ElementsAtomic Weights of the Elements, which , which described elements according to both described elements according to both

atomic weightatomic weight and valence. and valence.

Principles of Chemistry Principles of Chemistry (1868-70)(1868-70)

5454

Periodic Table of ElementsPeriodic Table of Elements

5555

The Standard Model in particle The Standard Model in particle physicsphysics

At present, matter and energy are At present, matter and energy are best understood in terms of the best understood in terms of the kinematics and interactions of kinematics and interactions of elementary particles. To date, elementary particles. To date, physics has reduced the laws physics has reduced the laws governing the behavior and governing the behavior and interaction of all known forms of interaction of all known forms of matter and energy, to a small set of matter and energy, to a small set of fundamental laws and theories. A fundamental laws and theories. A major goal of physics is to find the major goal of physics is to find the "common ground" that would unite "common ground" that would unite all of these theories into one all of these theories into one integrated theory of everything, of integrated theory of everything, of which all the other known laws which all the other known laws would be special cases, and from would be special cases, and from which the behavior of all matter which the behavior of all matter and energy could be derived (at and energy could be derived (at least in principle) (Wikipedia)least in principle) (Wikipedia)

5656

Two Dimensional Pattern of Two Dimensional Pattern of Basic Sound as the basis of Basic Sound as the basis of

Spoken LanguageSpoken LanguageSanskrit grammarians of Sanskrit grammarians of ancient India, who had ancient India, who had created astonishingly created astonishingly sophisticated theories of sophisticated theories of language based on their language based on their discovery of the two-discovery of the two-dimensional patterns in basic dimensional patterns in basic soundssoundsThe tabular form of the The tabular form of the Sanskrit letters is due to the Sanskrit letters is due to the two parameters (point of two parameters (point of articulation and aspiration) articulation and aspiration) as the basis of the spoken as the basis of the spoken sounds sounds

5757

From LinnaeausFrom Linnaeaus

TaxonomyTaxonomy

Binomial NomenclatureBinomial Nomenclature

5858

Claude Bernard Claude Bernard 1813-18781813-1878

HomeostasisHomeostasisMilieu interieur is the key process Milieu interieur is the key process with which Bernard is associated. with which Bernard is associated. He wrote, "La fixité du milieu He wrote, "La fixité du milieu intérieur est la condition d'une vie intérieur est la condition d'une vie libre et indépendante" (libre et indépendante" ("The "The constancy of the internal constancy of the internal environment is the condition for a environment is the condition for a free and independent life"free and independent life"). ). Compare with Traditional Chinese Compare with Traditional Chinese and Traditional Indian Ayuvedic and Traditional Indian Ayuvedic Medicine - BalanceMedicine - Balance

5959

What new metaphors for “the What new metaphors for “the New Biology”?New Biology”?

In 1623 Galileo crafted a famous metaphor that is still often cited by 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 scientists. Nature, he wrote, is a book written in "the language of mathematics". If we cannot understand that language, we will be mathematics". If we cannot understand that language, we will be doomed to wander about as if "in a dark labyrinth". (Crease, 2006)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 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 to keep developing and revising the metaphors with which we speak about science about science

6060

On “Bioinformatics is Dead”, “I think we On “Bioinformatics is Dead”, “I think we are just at the beginning of something are just at the beginning of something more dramatic” John Quackenbush 2009more dramatic” John Quackenbush 2009

InformationCoded Information –Need to build a concept of InformationNeed to measure itPierre-Henri Gouyon (2009)

6161

Semantic Web or Semiotics?Semantic Web or Semiotics?

SemioticsSemiotics, also called , also called semiotic studiessemiotic studies or or semiologysemiology, is the study , is the study of sign processes (semiosis), or signification and communication, of sign processes (semiosis), or signification and communication, signs and symbols, both individually and grouped into sign systems. signs and symbols, both individually and grouped into sign systems. It includes the study of how meaning is constructed and understood It includes the study of how meaning is constructed and understood three branches:three branches:SemanticsSemantics: Relation between signs and the things they refer to, : Relation between signs and the things they refer to, their their denotatadenotata. . SyntacticsSyntactics: Relation of signs to each other in formal structures. : Relation of signs to each other in formal structures. PragmaticsPragmatics: Relation of signs to their impacts on those who use : Relation of signs to their impacts on those who use them. them. Semiotics is frequently seen as having important anthropological Semiotics is frequently seen as having important anthropological dimensions, for example Umberto Eco proposes that every cultural dimensions, for example Umberto Eco proposes that every cultural phenomenon can be studied as communication. phenomenon can be studied as communication.

6262

The OriginThe Originof Informationof Information

From the origin of species to the origin of encoded information in From the origin of species to the origin of encoded information in living thingsliving thingsFrom Observational Science to Experimental science to Informational From Observational Science to Experimental science to Informational Biological scienceBiological science

Future of Bioinformatics – the information in “bio” logical organismsFuture of Bioinformatics – the information in “bio” logical organismsLooking at organisms as information perpetuating agentsLooking at organisms as information perpetuating agents

Is this the theoretical biology of the future?Is this the theoretical biology of the future?What is the language to be used? Mathematics? Ontologies?What is the language to be used? Mathematics? Ontologies?