TBGRI
This presentation is the property of its rightful owner.
Sponsored Links
1 / 85

Biodiversity Informatics S. Sreekumar, Safeer PM, Biju CK, Raveendran M, PowerPoint PPT Presentation


  • 82 Views
  • Uploaded on
  • Presentation posted in: General

TBGRI. Biodiversity Informatics S. Sreekumar, Safeer PM, Biju CK, Raveendran M, Parvathy Sankar & Krishnan PN Bioinformatics Centre, Tropical Botanic Garden & Research Institute Palode, Thiruvananthapuram. E-mail:[email protected] Web site : www.tbgri.org www.bioinfotbgri.org.

Download Presentation

Biodiversity Informatics S. Sreekumar, Safeer PM, Biju CK, Raveendran M,

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Biodiversity Informatics

S. Sreekumar, Safeer PM, Biju CK, Raveendran M,

Parvathy Sankar & Krishnan PN

Bioinformatics Centre,

Tropical Botanic Garden & Research Institute

Palode, Thiruvananthapuram

E-mail:[email protected]

Web site : www.tbgri.orgwww.bioinfotbgri.org

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

What is Biodiversity

Biological diversity means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part. This include diversity within species, between species and ecosystems.

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Elements of Biodiversity

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Types of Biodiversity

Alpha diversity : The total number of species coexisting in a region

Beta diversity : As habitats change along climatic and topographic gradients, new species turn over takes place

Gamma diversity : High species turn-over rate with distances between sites of similar habitats

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Plant diversity in India and the world

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Animal diversity in India and the World

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • What are microorganisms

  • Organisms microscopic in dimensions, includes Viruses, Bacteria, Algae, Fungi and Protozoa

  • United States patent office includes plant and animal cells besides Viruses, Bacteria, Fungi and Protozoa

  • Microbes are patentable as per WTO and Indian patent laws

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Microorganisms in the world

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Microorganisms described in India

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • Biodiversity issues and profiles

  • Identifications

  • Quantifications

  • Distributions

  • Endemism

  • Hotspots and Warm spots

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • What are ‘Hotspots’

  • Areas having rich endemism and are facing extreme threat perception

  • Hotspot areas occupy about 8% of world geographical area but hold 46% of total world species

  • Includes major tropical forests, relict temperate mediterranean ecosystems

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • Hotspots versus agrobiodiversity

  • Hotspot centres do not include major and Vavilovian centres of origin and do not encompass major agrobiodiversity ecosystems of the world.

  • As a paradigm ‘Hotspot’ concept helps conservation of endemic and threatened tropical ecosystems and does not protect agrobiodiversity

  • The driving force for the evolution and domestication of wild species took place in the deforested woodlands and grasslands through human intervention and environmental determinism

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Biodiversity Hotspots

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Biodiversity Hotspots

TBGRI

Total endemic species 124,035 i.e., 46% of world species (270,000)

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • What are ‘Warm spots’

  • Areas holding vast genetic resources, predomesticates, agro-pastural woodlands and grasslands which are modified or co-evolved with man’s determinism and environmental stresses.

  • These warm spot areas are in or adjacent to the cradles of human civilisations.

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

India is one of the twelve mega diversity countries in the world

In India species richness is often accompanied by enormous genetic diversity found within individual species. This makes India one of the Vavilovian Centres of diversity and origin of about 167 crop plants and the primary or secondary centres of domestication of a few animals.

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Ecosystem wise, India has 42 vegetation types, 16 major forest types, 10 biogeographical zones and 25 hot spots of endemic centres

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

In India - about 5725 endemic taxa of angiosperm (33.5% of Indian flora)

Hot spots of endemic species in India

1. Andaman group of islands

2. Nicobar group of islands

3. Agasthyamala hills

4. Anamala - high ranges

5. Palni hills

6. Nilgiris-Silent Valley-Wyanad-Kodagu

7. Shimoga-Kanara

8. Mahabaleshwar-Khandala Ranges

9. Konkan -Raigad

10. Marathwada-Satpura

11. Torupati-Cuddappa-Nallamalai hills

12. Vizagapatanam-Ganjam-Jeypore hills

13. Southern Deccan (leeward side)

14. Chotanagpur Plateau

15. Kathiawar-Kutch

16. Rajasthan-Aravalli hills

17. Khasia-Jaintia hills

18. Patkoi-Manipur-Lushai hills

19. Assam

20. Arunachal Pradesh Himalaya

21. Sikkim Himalayas

22. Garhwal-Kumaon Himalaya

23. Lahul-Himachal Pradesh Himalaya

24. Kashmir-Ladak Himalaya

25. Nepal Himalaya

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • Hottest of hot spots in India

  • Eastern Himalayas

  • Western Ghats

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Western Ghats

Lying along the west coast of Peninsular India in the north-south direction from the mouth of Tapti river in Gujarat to Kanyakumari in Tamil Nadu. It forms a continuous series of hills except 30 km wide Pallakkad gap, which separate the Nilgiri hills from Anamali

Geographic position - 8o 20’ – 20o 40’ N Latitude

73o – 77o E Longitude

Length - 1600 km

Area- 1,00,000 km2

Altitude- 150 – 2695 m

Rain fall- 1000 – 7000 mm

Temperature - 5 – 10 oC to 25 – 30oC

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

Western Ghats – Peaks

Kalsubai - 1646 m

Banasuram- 2060 m

Vavulmala - 2339 m

Doddabetta - 2637 m

Devarmala - 1922 m

Anamudi - 2695 m

Agasthyamala - 1868 m

Bioinformatics Centre TBGRI


Western ghats vegetation types

Southern tropical thorn forest - 200 – 300 m

Southern tropical dry deciduous forest- 200 – 500 m

Grasslands of lower altitudes - 200 – 500 m

Southern tropical moist deciduous forest- 300 – 700 m

Tropical semi-evergreen forest - 500 – 800 m

Southern tropical wet-evergreen forest - 800 – 1500 m

Subtropical montane forest- above 1500 m

Grasslands of high altitudes- above 1500 m

Western Ghats – Vegetation types

TBGRI

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

Western Ghats – Floristic diversity

TBGRI

  • Angiosperms – 4000 sp.

  • Gymnosperms – 4 sp.

  • Pteridophytes – 350 sp.

  • Bryophytes – 400 sp.

  • Lichens – 550 sp.

  • Algae – 400 sp.

  • Fungi – 5500 sp.

Bioinformatics Centre TBGRI


Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

TBGRI

  • BIODIVERSITY AND ITS BENEFITS

  • Agriculture

    • Functioning ecosystem

    • Economic value- extractable products, fuels, medicines, materials for shelter, food and energy

    • Compounds, genes & species for industry

    • Ecosystems- climate regulation, hydrological and chemical cycles in soils

  • Recreation- social, ethical, spiritual, cultural and economic goods and services

  • Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Why rich biodiversity in India?

    TBGRI

    • Strategic position having connection with adjacent floristic regions

    • Vast stretch of geographic area of 329 m ha; 7500 km long coast line.

    • Diverse habitats – dry deserts, cold deserts, alpine, temperate, tropical habitats, wetland areas (4.1 million ha.), mangroves.

    • Diverse ecological conditions (High rainfall area, coldest place on earth etc.). Altitude varying from sea level to the highest mountain ranges of the world.

    • Gondawana connection.

    • Himalaya as an active speciation zone.

    • 12 biogeographic regions representing 3 basic biomes and 2 natural realms as identified by Udvardy (1975).

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Biodiversity use value

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Increase in the biodiversity from the appearance of the first organism

    • The increase has not been continuous

    • Present day biodiversity stands at an estimated 13.5 million species with only 1.75 million of these currently described

    • The present extent of biodiversity is contributed by only a relatively few groups of organisms

    • Human kind has been, and continues, to be, instrumental in the erosion of biodiversity

    • The biodiversity crisis may be current rather than imminent

    • Erosion of biodiversity varies from region to region

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Factors affecting Biodiversity – Direct / immediate causes

    • Exploitation of wild living organisms

    • Expansion of agriculture, forest and aquaculture

    • Habitat loss and fragmentation

    • Species introductions

    • Pollution of soil, water and atmosphere

    • Global climatic change

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Factors affecting Biodiversity – Indirect cause

    • Growth of human population

    • Human social organisation

    • Unscrupulous natural resource consumption

    • Global trade culture

    • Lack of strategy to value the environment

    • Inequity in ownership, management & flow of benefits

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Current global environmental trends

    • Unsustainable use of renewable resources

    • Increasing greenhouse gas emissions

    • Reduction in natural areas and biodiversity

    • Increasing use of chemicals

    • Escalating use of energy

    • Unplanned urbanization

    • Disruption of global biogeochemical cycles

    • (UNEP 1997)

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • International efforts

    • Biodiversity Conventions, Trade related intellectual property rights (TRIPS) and General agreement on tariffs and trade(GATT)-give guidelines and regulations for biological resource use.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Biodiversity Information management - Issues

    • Biodiversity information is very complex, voluminous and rapidly proliferating.

    • The biodiversity data can be categorised in to different types such as molecular sequences, gene diversity, individuals, species, higher taxa, population, habitats, ecosystems, biomes, etc.

    • Management of complex and voluminous data of biodiversity is very difficult.

    • Biodiversity data are scattered and not organised for further studies.

    • At present it is very difficult to get a comprehensive picture of the genetic wealth of our nation.

    • Application of Bioinformatics tools is the best solution to the above problems.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics ?

    Medicine

    Biology

    Bioinformatics

    Maths + Physics + Statistics

    Computer + Information technology

    Bioinformatics is an emerging field of science

    Bioinformatics evolved from the convergence of Biology, Computer science, Information technology, Mathematics, Physics, Statistics and Medicine.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics uses computational algorithms for database creation, data management, data warehousing, data mining and global communication networks.

    To understand the links between pieces of information from research areas such as molecular biology, structural biochemistry, enzymology, cell biology and physiology, bioinformatics uses computational power to catalog, organise and structure these pieces into biologically meaningful entities.

    These “entities” are reflection of the cellular organisation of life and its common denominator – that all life evolved from a common ancestral form.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics Definition ?

    Bioinformatics is an interdisciplinary field, therefore this newly emerging discipline has variously defined by different authors.

    “Bioinformatics is the design and development of computer based technology that support life sciences”

    Bioinformatics definition – Oxford English Dictionary

    (Molecular) bio –informatics: bioinformatics is conceptualising biology in terms of molecules (in the sense of physical chemistry) and applying “informatics techniques” (derived from disciplines such as applied maths, computer science and statistics) to understand and organise the information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applications.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Principles of Bioinformatics

    • The data produced by the thousands of research teams all over the world are collected and organised in databases specialised for particular subjects. Well known e.g., GDB, SWISS-PORT, Genebank and PDB.

    • Analyse the collected data by using computational tools/techniques

    • Development of appropriate computational software/tools for programming and analysing the biological data.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Sub-disciplines within Bioinformatics

    The development of new algorithms and statistics with which to assess relationships among members of large data sets.

    The analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures

    The development and implementation of tools that enable efficient access and management of different types of information

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Dr. Margaret Oakley Dayhoff (1925-1983) was a pioneer in the use of computers in chemistry and biology, beginning with her Ph. D thesis project in 1948.  Her work was multi-disciplinary, and used her knowledge of chemistry, mathematics, biology and computer science to develop an entirely new field, the Bioinformatics.  She is credited today as a founder of the field of Bioinformatics. 

    Dr. Dayhoff was the first woman in the field of Bioinformatics. 

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Applications of Bioinformatics

    TBGRI

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Schematic outlining how scientists can use bioinformatics to aid rational drug discovery

    TBGRI

    • MLH1 (human gene encoding a mismatch repair protein (mmr)) on short arm of chromosome 3.

    • Through linkage analysis and its similarity to mmr genes in mice, the gene has been implicated in nonpolyposis colorectal cancer.

    • from nucleotide sequence, the amino acid sequence of the encoded protein can be determined using translation software.

    • Sequence search techniques used to find homologues in model organisms, and based on sequence similarity, it is possible to model the structure of the human protein on experimentally characterised structures.

    • Docking algorithms design molecules that could bind the model structure, leading for biochemical assays to test their biological activity on the actual protein.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • The important applications of bioinformatics in biodiversity are:

    • The complex and voluminous data of biodiversity can be digitised for easy accession, analysis and interpretation.

    • It makes easy survey, documentation and measurement of biodiversity data.

    • Based on the available data, future biodiversity of a particular area can be predicted and model can be formulated by computational methods, thereby appropriate measures can be taken for its conservation and sustainable utilisation.

    • It helps to predict species invasions using ecological niche modeling.

    • The electronic information may serve as the raw material for augmenting future developments in all areas of biology.

    • The digital databases can easily provide the current status of the biodiversity of a particular area.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • The biodiversity extinction rate can be easily documented and theoretical studies and modeling can be formulated for its conservation on priority basis.

    • The computational analysis makes easy understanding of the phylogenetic relationship among the species/individuals.

    • Through internet biodiversity databases can be linked together and the information can be shared.

    • The researchers can easily identify the priority materials for their studies.

    • The potential indigenous material can be easily identified for biotechnological intervention.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics resources on the Web

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Recently several web sites providing biodiversity information

    • Biodiversity databases in the web can be broadly classified into the following groups

    • Global databases

    • Geographical, regional and national databases

    • Databases for specific taxonomic group

    • Government, scientific and advocacy organisations promoting biodiversity study

    • Other resources.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Global Databases

    SPECIES 2000

    TBGRI

    Established in 1994 by

    the International Union of Biological Sciences (IUBS), in co-operation with the Committee on Data for Science and Technology (CODATA) and the International Union of Microbiological Societies (IUMS).

    It was subsequently endorsed by the UNEP Biodiversity Work Programme 1996-1997, and associated with the Clearing House Mechanism of the UN Convention on Biological Diversity.

    • Enumerating taxonomic indexes of all known species of organisms

      (animals, plants, fungi and microbes) on Earth.

    http://www.sp2000.org

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Global Database

    TBGRI

    Global Biodiversity Information Facility (GBIF)

    A long term project of the International Organisation for Economic Cooperation and development, is building “ an interoperable network of biodiversity databases and information technology tools” the structure of which is summarized in the project’s business plan

    http://www.gbif.org/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Global Database

    The Tree of Life (ToL)

    TBGRI

    • Launched on 5 January 1996

    • The Tree of Life (ToL) is a collaborative effort

      of biologists from all over the world (21

      countries).

    • More than 4000 World Wide Web pages

      contained 948 pages, housed in seven

      computers on two continents.

    • Information about the diversity of organisms on Earth, their evolutionary history

      (phylogeny), and characteristics

    • Each page contains information about a particular group of organisms ToL

      pages are linked one to another hierarchically, in the form of the evolutionary

      tree of life. Starting with the root of all Life on Earth and moving out along

      diverging branches to individual species, thus illustrates the genetic connections

      between all living things

    http://tolweb.org/tree/phylogeny.html

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Global Database

    DEEP - GREEN

    TBGRI

    Phylogenetic and biodiversity data from published papers in interactive phylogenetic tree form

    Maintained by Green Plant Phylogeny Research Coordination Group, University & Jepson Herbaria, University of California, Berkeley

    http://ucjeps.herb.berkeley.edu/btyolab/greenplantpage.html

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    National Database - Mexico

    CONABIO

    National Commission for the Knowledge and Use of Biodiversity

    TBGRI

    • March 16th, 1992

    • An inter-ministerial commission, presided over by the Constitutional President of Mexico, and integrated by the heads of the State Ministries

    • Studies on the knowledge and use of biodiversity

    • Give assistance to government and other sectors

    • Disseminate knowledge on biological richness

    • Give continuity to international collaborative agreements and do public services.

    http://www.conabio.gob.mx/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    National Database – Costa Rica

    TBGRI

    • Established in 1989

    • Non-Governmental, non-profit, public interest organization of civil society that works in close collaboration with different Government Institutions, Universities, the private sector and other public and private organizations, both within and outside Costa Rica.

    • Generates information on the diversity of species and ecosystems found in the

      country. Has a collection of more than 3 million specimens of arthropods,

      plants, fungi and mollusks. It also generates information on the country’s

      different ecosystems.

    • In decision-making processes related to the protection and sustainable use of

      biodiversity

    • Creating greater awareness of the value of biodiversity

    • Computer tools to support the processes of generation, administration etc.

    http://www.inbio.ac.cr/en/default.html

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Geographical, Regional and National Databases

    TBGRI

    Nature serve

    • Non-profit conservation organization that provides the scientific information and tools needed to help guide effective conservation action.

    • Nature Serve and its network of natural heritage programs are the leading source for information about rare and endangered species and threatened ecosystems.

    http://www.natureserve.org/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Database for Specific Taxonomic Group

    ICTVdB - The Universal Virus Database

    TBGRI

    The Universal Virus Database, ICTVdB, is authorised by ICTV (International Committee on Taxonomy of Viruses) and has been constructed by Cornelia Büchen-Osmond, from 1991-2000 in Bioinformatics Group, Australian National University, in consultation with ATCC and supported by NSF. In 2001 ICTVdB moved to the Biosphere 2 Center, the Western Campus of the Earth Institute, Columbia University of New York USA.

    Describe all viruses of animals (vertebrates, invertebrates, protozoa), plants (higher plants and algae), bacteria, fungi, and archaea from the family level down to strains and isolates. The lower levels of classification have important applications in medicine and agriculture, but also give insight into evolutionary trends.

    http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Database for Specific Taxonomic Group

    TBGRI

    Systematic Botany and Mycology Laboratory

    • Site of the U.S. Agricultural Research Service includes databases on taxonomy of vascular plants and fungi

    http://nt.ars-grin.gov/SBMLweb/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Database for Specific Taxonomic Group

    The European Register of Marine Species (ERMS)

    TBGRI

    • Created in 1998

    • Funded under the European Union MAST research programme

    • Authoritive taxonomic list of species occurring in the European marine

      environment.

    • Covers species of the kingdoms Animalia, Plantae, Fungi and Protoctista

      occurring in the marine environment.

    • Covers all the continental shelf seas of Europe, including the Mediterranean

      shelf, Baltic Seas and deep-sea areas

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Database for Specific Taxonomic Group

    TBGRI

    UNESCO-IOC Register of Marine Organisms (URMO)

    • Built and maintained by Jacob van der Land at the National Museum of Natural

      History, Leiden, the Netherlands.

    • Access to completed data sets is or will be provided by the Expert Centre for

      Taxonomic Identification (ETI). The register contains a number of 'global species

      databases' for exclusively, marine taxa

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Database for Specific Taxonomic Group

    TBGRI

    CephBase

    • Dynamic relational database-driven

      web site that has been online since

      1998.

    • Supported by the National

      Oceanographic Partnership Program

    • Located at the National Resource

      Center for Cephalopods at the

      University of Texas Medical Branch.

    • Provides taxonomic data, life history, distribution, images, videos, references and

      scientific contact information on all living species of Cephalopods (octopus, squid,

      cuttlefish and nautilus)

    • There are currently 1642 images, 146 video clips, 5900 ceph papers

    • CephBase currently has 64 collaborators.

    http://www.cephbase.utmb.edu/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Tools and Software for Integrating Online Biodiversity Data

    TBGRI

    Alice Software

    • 40 years combined experience

    • Engaged in project management and delivery

      of information management solutions with a

      focus on biodiversity, natural resources,

      conservation, ethno-botany and plant genetic

      resources.

    • Set of database tools  for managing  biodiversity data. 

    • To construct a framework, based upon a taxonomy understandable to

      biologists, for building rich a data content knowledgebase.

    • To create and publish a wide variety of databases of diverse content

      including monographic databases, species inventories, annotated checklists or

      identification keys.

    • Software for data capture and analysis, report generation, (e-publication) and

      data export into a variety of formats useful to biologists. 

    • Suitable for use by collaborative institutional projects or scientists working on

      their own.

    http://dialspace.dial.pipex.com/town/square/fd95/

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Government, Scientific and Advocacy Organisation Promoting Biodiversity Study

    TBGRI

    The National Biological Information Infrastructure (NBII)

    Broad, collaborative program to provide increased access to data and information on the nation's biological resources.

    Links diverse, high-quality biological databases, information products, and analytical tools maintained by NBII partners and other contributors in government agencies, academic institutions, non-government organizations, and private industry.

    http://www.nbii.gov/index.html

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Government, Scientific and Advocacy Organisation Promoting Biodiversity Study

    TBGRI

    Canadian Biodiversity Information Network (CBIN)

    • Coordinated and maintained by the

      Biodiversity Convention Office of

      Environment Canada

    • Provides efficient access, through the search

      icon, to biodiversity-related information from

      academia, industry, non-governmental

      organizations, and governments, on topics

      such as Canadian environmental activities,

      agreements, technologies, expertise etc.

    • Contains biodiversity-related information, including:

    • Canadian activities to implement the convention on Biological diversity and the

      Canadian Biodiversity strategy

    • Environmental technologies (ie. Products, services, processes), Data sources,

      Funding sources, Web sites, Upcoming events, Reference materials

    http://www.cbin.ec.gc.ca

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Other Resources

    Overview of Biodiversity Informatics

    TBGRI

    Launched on 18 September, 2000

    Focused on biological systematics and the work conducted in systematics collections (i.e., natural history museums)

    • Describes the subject areas in biological systematics, their interrelationships, and

      the important informatics projects in a given area.

      The subject areas are

      Taxonomic Names and Classification

      Taxonomic Character Data: Taxonomic Descriptions, Keys, and Phylogenetic Data

      Specimen Data and Species Distributions

      In each of these areas following details are discussed

      The nature and uses of the information

      How the data are captured and managed

      Status of data capture and management within the community (e.g., percent

      digitized)

      Significant projects for compiling data, developing software, etc.

    http://www.calacademy.org/research/informatics/sblum/pub/biodiv_informatics.html

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    Bioinformatics & Industrial Scenario

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industrial Scenario

    TBGRI

    Global Market

    • Current Biotechnology market range - $ 30-40 billion

    • Biotechnology growth rate 25 % per year

    • Bioinformatics constitute 8-10 % of total market size

      ie. about $ 2.5 billion

    • It is estimated that this will rise to about $ 5-6 billion

      by the end of this decade

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industrial Scenario

    TBGRI

    Major Bioinformatics Marketing Areas

    • Pharmaceuticals

    • Biotechnology

    • Industrial Biotechnology

    • Agricultural Biotechnology

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industrial Scenario

    TBGRI

    Major Bioinformatics Industry In The World Market

    Accelrys

    Compugen

    Celera Genomics

    IBM Life Sciences Solutions

    Incyte Genomics

    LION Bioscience etc.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industrial Scenario

    TBGRI

    Recently, it was reported that the rapid booming in bioinformatics industry has some negative effects.

    In fact, Bioinformatics as a science is still evolving. The underlying mathematical and algorithmic methods are still being developed. In this rapidly changing scenario, a company that aims to provide ‘standardised’ services will definitely fail. Only those companies that are contributing to the evolution of the subject itself, and generating their own intellectual property will survive in the long run.”

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industry Indian Scenario

    TBGRI

    Studies of International Data Corporation (IDC) – a major market research, analysis and consulting firm in the information field reported that India will be a potential star in bioscience field in the coming years

    India’s Strength

    • Bio-diversity

    • Human resources

    • Infrastructure facilities

    • Government’s initiatives

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics – Industry Indian Scenario

    TBGRI

    India’s Strength

    India is well placed to take the global leadership in genome analysis, as is in a unique position in terms of genetic resources. India has several ethnic populations that are valuable in providing information about disease predisposition and susceptibility, which in turn will help in drug discovery.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics Industry- Indian Scenario

    TBGRI

    • Currently more than 200 industrial firms in India are focusing their efforts in Bioinformatics.

    • In the global market current Indian contribution is small and is estimated to be Rs 80 crore only.

    • The Indian industries have been developing global products and quality services. Strand Genomics, SciNova Technologies, Mascon Life Sciences, Ocimum Biosolutions, Lab Vantage, VLife Sciences, Helix Genomics have come up with a suite of products which are gaining global acceptance

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics Industry- Indian Scenario

    TBGRI

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics Industry- Indian Scenario

    TBGRI

    Opportunities for IT companies in Bioinformatics

    • Effective utility of the various data sources and collation thereof

    • Developing better tools for data generation, data capture, and

      annotation

    • Developing and improving tools and databases for comprehensive

      functional studies including project management

    • Sharing of data and generating useful information from the

      database

    • Integration of heterogeneous information

    • Designing and developing a comprehensive solutions in assisting

      every process involved in biotechnology and drug discovery

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Bioinformatics Industry- Indian Scenario

    TBGRI

    Issues

    According to the industry people, mushrooming of bioinformatics institutes is creating a problem of finding talented and trained individuals in this industry. While many of them have a superficial knowledge and a certificate, India lacks true professionals in this area.  Therefore, generation of trained manpower and improving the quality of bioinformatics curriculum in our educational Institutions is become the need of the hour. Recently several industries have been made collaboration with R & D Institutions and such academia-industrial tie-up should hail break through in this sector

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Government Initiatives

    TBGRI

    • 1983

    • Formation of Task force on Bioinformatics by Dr. S.

      Ramachandran

    • Dr. N. Seshagiri: Chairman of the Task force

    • 1986

    • Department of Biotechnology established

    • 1987

    • Biotechnology Information System Network (BTISnet)

    • 1st grant of Rs. 13.38 crores by DBT towards setting up of

      National Infrastructural facility on Bioinformatics

    • 1988

    • Establishment of the first 9 DIC’s in India

    • 1989

    • Onwards establishment of DIC sub-centres

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Government Initiatives

    TBGRI

    Current Status of BTISnet

    DICs - 10

    Sub DICs - 48

    COEs- 5

    Apex Centre - 1

    Port Blair

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Government Initiatives

    TBGRI

    Priority Areas of the Centre

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Human Resource Development

    TBGRI

    Educational Programs in Bioinformatics

    PhD. Programs

    • Jawaharlal Nehru University

    • Pune University

    • National Institute of Immunology

    • Indian Institute of Science, Bangalore

    • Madurai Kamaraj University, Madurai

    • Bose Institute, Kolkatta

    • Anna University, Chennai

    • TBGRI, Thiruvananthapuram

    • National Brain Research Centre

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Human Resource Development

    TBGRI

    Educational Programs in Bioinformatics

    M.Tech. Programs

    • Indian Institute of Information Technology

      (IIIT), Allahabad

    • International Institute of Information

      Technology, Hyderabad

    • Sathyabama Institute of Science and

      Technology

    • SASTRA (Deemed University), Thanjavur

    M.Phil. Programs

    • University of Kerala

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Human Resource Development

    TBGRI

    Educational Programs in Bioinformatics

    M.Sc. Programs

    • Pune University

    • University of Calcutta

    • Bharthiyar University

    • Bharatisadan University

    • Tamil Nadu Agricultural University

    • Jamia Millia Islamia University

    • Banasthali Vidayapith, Rajasthan

    • Amity Insitute of Biotechnology

    • Periyar University

    • University of Madras

    • University of Allahabad

    • University of Mysore

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Human Resource Development

    TBGRI

    Educational Programs in Bioinformatics

    Post Graduate Diploma

    • Jawaharlal Nehru University

    • Calcutta University

    • Madurai Kamaraj University

    • Pondicherry University

    • Pune University

    • Banashali Vidyapith

    • Tamil Nadu Veterinary and Animal Science University

    • University of Hyderabad

    • University of Kashmir

    • Institute of Bioinformatics and Applied Biotechnology

      (IBAB), Bangalore

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Conclusion

    TBGRI

    • Bioinformatics is evolved as a supporting discipline within

      biological science which offers the computational power to the

      storage, retrieval, analysis and interpretation of biological

      data.

    • Since last 10-15 years it has attained explosive growth and

      flourished well as an industry in the global market.

    • Considering the factors like rich biodiversity, human

      resources and infrastructure facility, India has great

      opportunities in this sector.

    • Government of India has recognized the potential of

      bioinformatics from its beginning and established a nation

      wide computer linked network system for promoting the R & D

      and industrial growth in the country.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Currently the Indian contribution in the global market from this

    • sector is only about Rs. 80 crore per annum.

    • One of the major problems in India is the lack of

      professionals in this area. Although educational

      courses in Bioinformatics are mushrooming now-a-days

      students are not professionally trained.

    • In the light of this, generation of trained manpower and

      improving the quality of Bioinformatics curriculum in

      our educational courses attained special attention.

    • It is observed that if industry and government work

      together and promote academia industrial collaboration

      India will become the forerunner in the global scenario

      in this filed.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    TBGRI

    • Indian has blessed with rich biodiversity which provides

      the raw material (says gene) for imminent

      biotechnological revolution of the country. But till date,

      our genetic diversity is not properly evaluated and

      documented.

    • Therefore, documentation and analysis of our

      biodiversity data would lead a great impact in the

      economic growth of our nation.

    Bioinformatics Centre TBGRI


    Biodiversity informatics s sreekumar safeer pm biju ck raveendran m

    Conserve and Sustainably Utilize Biodiversity

    Thank you


  • Login