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3rd East Asia
Bioinformation Network
Meeting

3rd EABN

An ASEAN-Plus-Three Project

 

ASEAN-Plus-ThreePLUS THREE

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2nd ASEAN-China Workshop

BioMedicalAsia2008

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2nd EABN 2007

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Yong Loo Lin School of Medicine

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Biochemistry NUS

AMBIS

APBioNet

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Bioinformation
3rd EAST ASIA
BIOINFORMATION NETWORK (3rd EABN) 2008
SINGAPORE

Friday, 18 April 2008
Venue: CIT Auditorium, Computer Centre Building, National University of Singapore

Resolutions

Draft Resolutions dated 18th April 2008 under review by circulation
Signed Resolutions

Reports, Policy and Planning Discussion Topics

Printable version


Bioinformatics Curriculum in Tertiary Education

Minimum skills guidelines specify the minimum set of skills required of a trained person in a specific discipline for a specific purpose.

Proposal EABN08/01 for:
Minimum skills required of biologists in bioinformatics and biocomputation (msrBIC)

Definition:
Minimum informatics and computational skills for Biologists (including those practitioners or trainees in various disciplines of biology and applied biology such as biotechnologists) define the minimum set of skills we need to inculcate in our trainees so that when they graduate from our institutions, they can become suitably qualified practitioners of the discipline for which they trained, specifically to be competent in essential aspects of bioinformatics and computational biology, theory and practical.

Curriculum and Syllabus Development:
From a clear definition of these minimum skills we wish to adopt, which we will have to review and revise from time to time to keep up with the latest scientific and industry demands, we can define curriculum and syllabus for our teaching and training of these individuals, evolve strategies for implementing the training of our lecturers and trainers, to the actual implementation of lectures, practicals and training of our students.

The actual implementation will require provisioning of various facilities such as computer clusters and affordable personal mobile computers, wireless or wired Internet broadband access, computational software and tools, database and other computing resources.

An East Asian minimum skills required of biologists in bioinformatics and biocomputation (East Asian msrBIC)

The following are proposed the minimum skill requirements of a biologist in informatics and computing.

All biologists graduating with an undergraduate degree in ASEAN countries should possess such informatic and computing skills.

Those institutions offering courses which do not have such curriculum or syllabus can seek help to incorporate them, send trainers to be trained in these skills to teach undergraduate and/or graduate students and provision for facilities and resouces to support this kind of training.

All university degree or diploma-holding biologists and practitioners of various biological disciplines should have these minimal basic skills.

Those who do not can be sent for training in locally organised educational courses or events, and international ones.

Proposal EABN08/02 for the regular refinement of the:
List of Minimum Skills Required (msrBIC)

  • Basic knowledge of how to use a computer and its operating system
  • Basic knowledge of how to use Internet applications such as Web browsers and downloading by file transfer
  • Knowledge of basic resources of biological information and search techniques
    • PubMed and Google Scholar and online journals for bibliographic information
    • Genbank, EMBL and DDBJ for nucleotide sequence data
    • Swissport/Uniprot for protein sequence data
    • wwPDB for structural coordinates
    • KEGG for pathway data
    • OMIM for genetic information
    • Miscellaneous databases
  • Knowledge of basic software tools and Web applications, and interpretation of results such as the following or their equivalent:
    • BLAST for sequence homology searches
    • PCR Primer Design and Plasmid drawing for molecular biology application
    • EMBOSS, GCG or Lasergene, Vector NTI software applications for sequence analysis and manipulation
    • CLUSTALW and MEGA for sequence alignment, phylogenetic inference and tree drawing

All ASEAN universities offering biological courses should benchmark themselves against the above basic standards. If they are lacking in any aspect, the necessary remedial action to implement course material and curricula should be started.

Courses envisaged for ASEAN designed for meeting these msrBIC standards include:

  1. Basic Introductory Curriculum in Bioinformatics for Lecturers
  2. Bioinformatics Curriculum in an Undergraduate Life Science Program/Course
  3. Practical Bioinformatics Curriculum in Bioinformatics for Graduate Students
  4. Implementation Plan in Group A, Group B and Group C countries, institutions or departments or courses or programmes
    1. Group D: No or litte molecular biology or biotechnology content and no msrBIC skillsets at all.
    2. Group C: Sufficient molecular biology or biotechnology content but insufficient to meet msrBIC.
    3. Group B: Already incorporated basic bioinformatics curriculum and meets msrBIC
    4. Group A: Already advanced in implementation of bioinformatics and computational biology curriculum and exceed msrBIC standards

Prequalification of institutions for scheduling for training

All ASEAN countries are to submit tertiary level course curriculum in biology and associated disciplines to benchmark against the msrBIC standards and be classified informally according to these categories for purposes of scheduling training and courses and these purposes only, and not for ranking or other measurements or assessment.

Annual reports of progress at each level of categorisation will be expected.

Certification exams or waivers can be subsequently discussed.


Resources in Support of Bioinformatics Curriculum to meet msrBIC

  1. Bioinformatics Software and Services
    1. Bioinformatics Server BioSlax Server software from ASEAN SCB Project on Bioinformatics Spin-off Company and Bio-Mirror Project
      1. Deployment Schedule
      2. Singapore's NUS (BioMirror 1999, APBioBox 2003, APBioKnoppix 2004 and BioSlax 2006)
      3. Malaysia's UPM (BioMirror 2004)
      4. Philippines's ASTI, DOST (BioMirror 2004)
      5. Thailand's KU (BioMirror 2004) and PSU (2006)
      6. Vietnam's IBT Bio-IBT (August 2007)
      7. Brunei, Indonesia, Lao PDR, Cambodia, Myanmar
    2. Bioinformatics Database Distribution Project
      P2P Project with KOBIC, PSU and NUS

  2. Bioinformatics Online Courses
    1. S* Alliance
    2. ASEAN Virtual Institute of Science and Technology (AVIST) Hypercourse in Bioinformatics
  3. Bioinformatics Lectures and Talks
    1. CanalAVIST project from ASEAN SCIRD and AIT, Thailand with support from TEIN2.


Bioinformatics Research Projects and Scientific Conferences

Group A and B countries and institutions shall be invited to participate in the following research projects

  1. Avian Influenza Database Project from the ASEAN Workshop on Reverse Genetics-based Vaccines for Avian Influenza: BIOTEC Thailand News Report aidb
  2. ASEAN-China Traditional Medicines (TCM) Informatics project
  3. Bioinformatics component of ASEAN-Japan OADB project (Pending Japan's decision on OADB)

They can be invited to send students and professors to present posters, software demos, oral papers and submissions for publication in conference proceedings and journals, at the following conferences:

  1. InCoB (more biological)
  2. APBC (more computing)
  3. ISMB (advanced)
  4. RECOMB (specialised)
  5. GIW (specialised)
  6. and other specialised conferences


Bioinformatics Activities

  1. BioWiki Competition by KOBIC (suitable for Groups C and D institutions for organisational involvement, but open to all individuals in A, B, C and D contexts)
  2. BioWorkflow Competition by Inforsense,Inc, Shanghai (suitable for A and B institutions and their staff and students)


Bioinformatics and Computational Biology Professional Affiliation

  1. The International Society for Computational Biology (ISCB) is currently the only organisation solely dedicated to the promotion of bioinformatics and computational biology and its professional practice.
  2. It is a "scholarly society dedicated to advancing the scientific understanding of living systems through computation"
  3. East Asia membership is not very high. We should encourage bioinformatics professionals in our region to contribute in service and achievement to the ISCB.
  4. The international society should reflect the increasing strength and growing influence of Asian bioinformatics through the increasing level of membership.
  5. The ISCB also has an affiliateship scheme that has strict criteria for national or regional bioinformatics and computational biology associations and societies to become officially associated by affiliation to ISCB.
  6. Asia bioinformatics societies and associations should be encouraged to form as practitioners in the countries increase in numbers and these organisations should be making plans to achieve the criteria set out in ISCB Regional Affiliateship and seek affiliation at the appropriate time.
  7. Proposal to encourage formation of national societies to form in China, Brunei, Cambodia, Lao PDR, Myanmar, Thailand, VietNam
  8. Proposal to encourage and facilitate existing national societies towards affiliation, i.e. Malaysian, Indonesian and Philippines bioinformatics and computational biology society to seek regional affiliation with ISCB.
  9. Proposal to support existing ISCB-affiliated societies/associations such as Korean KSBI, Japanese JSBI, Singapore AMBIS, to continue active participation in ISCB.
  10. Official affiliates can get special discounts on ISCB events, and get travel fellowships for their members to attend ISCB events like ISMB annual conference or RECOMB etc.


Bioinformatics and Computational Biology in Systems and Synthetic Biology

  1. Ground work for informatics and computational training for Systems Biology
  2. Ground work for informatics and computational training for Synthetic Biology


References

  1. Tan TW, Kiong D and Chang H. (1993) Computer Applications in Infectious Disease Research: an Asian biotechnology, biocomputing and bioinformatics network resource? In Proceedings of the Workshop on Biotechnology Approaches to Diagnosis, Prevention and Treatment of Infectious Diseases, Feb 24-27, 1993. Bangkok, Thailand.
  2. Ranganathan S., Subbiah S. and Tan T.W. (2002) APBioNet: The Asia Pacific regional consortium for bioinformatics. Applied Bioinformatics, 1(2) (2002), 101-105.
  3. Gilbert D., Ugawa Y., Buchhorn M., Tan T. W., Mizushima A., Kim H., Chon K., Weon S., Ma J., Ichiyanagi Y., Liou D., Keretho S., and Napis S (2004). Bio-Mirror project for public bio-data distribution. Bioinformatics, 20(April 2004), 3238-3240.
  4. Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan, Honghuang Lin, Tin Wee Tan (2008). Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Bioinformatics 24(2): 299-301.
  5. Y.P. Lim, J. Hg, P. Gardner, S. Ranganathan, S. Andersson, S. Subbiah, T.W. Tan, W. Hide, A. Weiss (2003). S Star's Trial Bioinformatics course: An online learning success. Biochemistry and Molecular Biology Education 31(1), 20-23.
  6. Bhak, J. http://bioinfra.net/index.php/BioP2P
  7. P2P Project http://everest.bic.nus.edu.sg/p2p
  8. Azureus program. Available: http://azureus.sourceforge.net/
  9. BioSlax distributions. Available: http://www.bioslax.com/
  10. APBioKnoppix2 distribution. Available: http://compaq.apbionet.org/apbioknoppix2
  11. CanalAVIST www.canalavist.org
  12. S* Life Science Informatics Alliance's Introductory Bioinformatics Course s-star.org



Previous updates: Last Updated: April, Feb 2008
First Created: 6 Feb 2008 Tan Tin Wee