S* Alliance Global Bioinformatics

Online Distance Education

Justin Choo*, Tan Tin Wee, Shoba Ranganathan* Presenter

Bioinformatics & Its Challenge

Rapid growth in past 3 years; rapidly evolving field

Few universities can offer the complete range of Bioinformatics courses

Lack of trained bioinformaticians in the Asia-Pacific region

What is S* ?

Founded in 2000, S* is a collaboration among 6 universities. 1 university joined.

To meet this challenge using distance learning technologies over advanced networks

Unified learning environment over the Internet freely accessible to everyone

S* Informatics Alliance

Karolinska Institutet

University Uppsala

University of the Western Cape

Stanford University

National University of Singapore

University of Sydney

South Africa

USA

Sweden

Singapore

Australia

University of California,San Diego

Goals of S*

Provide a GLObal Bioinformatics Unified Learning Environment (GLOBULE) made up of modular courses in the disciplines of bioinformatics, medical informatics and genomics

Provide accessibility to the highest possible quality of online courseware approved by the educators from the host institutions.

Develop an integrated modular learning environment that allows a student to select from both pre-requisite modules and advanced modules in order to build a comprehensive program.

History of S*

2000 - Sweden Stanford and Singapore agreement in Singapore - Meeting in Sweden: all founders involved

2001 - AGM in Copenhagen, 1st course 2002 – 2nd course 2002 - BioEd conference in Singapore,

AGM at NUS 2003 – UCSD joins, 3rd course, 4th course

Participants List

Geographic Distribution of Participants

0

100

200

1st Course

2nd Course

3rd Course

1st Course 26 21 7 10 7

2nd Course 65 12 18 32 24

3rd Course 180 41 15 41 8

AsiaAustrala

siaEurope America Africa

S* Course: Occupation

Occupation of S* Participation

6%

24%

7%

34%

4%

10%

8%3%

1%3%

Executives

Researcher/Scientist

Professor/Lecturer

Student

Manager

IT Professional

Engineer/Consultant

Homemaker

Health Care Related

Others

Course Pedagogy

A. Lectures

B. Discussion

C. Assessment

D. Tutorial (New)

E. Practical (New)

F. Course Feedback

Course Syllabus

1. Introductory Molecular Biology2. An Overview of the Computational Analysis of

Biological Sequences 3. Transcript Analysis and Reconstruction4. Comparative Genomics 5. Representations and Algorithms for

Computational Molecular Biology 6. Protein Structure Primer7. Protein Structure Prediction

Course Syllabus (cont.)

8. Protein Physics9. Genomics and Computational Molecular Biology

Genomics 10. Protein and Nucleic Acid Structure, Dynamics,and

Engineering 11. Proteomics12. Proteomes13. Structure Prediction for Macromolecular Interactions14. Protein - Ligand Modeling

Curriculum Cross-CheckEssential Curriculum 5- S* Course Curriculum

Molecular biology, cell biology, genetics

Provide an introductory and overview of the subject

Core Bioinformatics (protein , sequence alignment, protein modeling, threading, structure prediction)

There are still topics which S* will be covering in future. Some will be taught through short tutorials.

Computer science (programming, data structures/algorithms, database, AI, optimization)

Out of scope of S*, however, we are now trying to incorporate this into tutorial/practical sessions.

Statistics (probability theory, experimental statistical design and analysis, stochastic process)

Minimal. Will be looking into providing lecture on this topic.

Ethics (effects of technology on society, privacy and security issues)

This topic is often regarded informal. Currently, this is conducted among the participant in the discussion forum.

Delivery & Pedagogy Via the Integrated Virtual Learning Environment

developed @ NUS

Delivery & Pedagogy (cont.)

Video/Audio Lecture Presentation

Slides made available for reference and viewing

Email as the main communication tool Participant Course Coordinator Participant Teaching Assistant Teaching Assistant Course Coordinator

Sample Lecture

Sample Discussion Forum

Sample Assessment Session

Problems Encountered

Delivery format (video/audio)Made different quality video/audio encoding

files

Bandwidth problemSlow connection

Solution

Overcoming the bandwidth problem

- network of mirror sites

- MoU tie up with APBioNet

Pressing of CDs (to countries like Africa, Iran)

The S* Alliance Mirror Sites

University of Sydney,

Australia

Stanford

SANBI, South Africa

CSTNET+CERNE

T, China

Anna, Pune University, India

NUS, Singap

ore

UKM, Malay

sia

Mirroring and realtime lessons for Asia Pacific studentsMake use of APAN network infrastructure coordinated by APBioNet

Quilmes National University, Argentina

Instituto de Inmunologia,

Univalle, Colombia

UCSD

Strength Of The Course

Online content allow anytime-anywhere access

Presented by world renowned experts from different institutions

Made available to a broad audience Well-organised User friendly system

Advantages Member organizations do not need to

wait until experts in all domains of bioinformatics are hired (if at all possible)

Re-usable courseware Easily updated content Uniformity of curriculum and evaluation Globally accessible education

Feedback To think that a world-class, web based education with such

valued lectures is brought to your desk free of cost is impossible elsewhere. The course was wonderfully well managed. Our requests and problems were quickly and well attended to. I had a great time doing this course and thank the S*STAR team whole heartedly for making me a fortunate participant with this fantastic experience.

~ Naidu Ratnala Thulaja, Singapore

I think it is a very useful course, it is exactly what it says it is: an introduction to bioinformatics. It covers nicely major topics and provides enough information in order for us to understand what bioinformatics is all about. I enjoyed it very much and I am even a bit sad it is over. Thank you very much! ~ Patricia Severino, Romania

Feedback (cont.) Pretty good. A few rough edges but I'm sure you'll work

them out over time. I really enjoyed it. Most of the lectures were very well presented and the participants in the forums helpful. I'm very impressed at the amount of work that has obviously gone into setting up the course. ~ Alan Wardroper, Thailand

The international participation of the lecturers and students. The relevance of the field of bioinformatics in meeting the biomedical needs of today. The level of communication provided by the IVLE system enhanced learning considerably. The range of professional and academic background of students. The technical support provided by SStar was rapid and efficient to queries.

~ C.A.O. IDOWU, England

Problem-Based Learning (PBL)

Started at McMaster University Medical School over 25 years ago

Encourages hand-on and critical thinking. Its hands-on approach is particular suited for bioinformatics where many of the skills require practical execution and the problems encountered are generally open-ended.

PBL encourages : acquisition of critical knowledge. problem solving proficiency; problems tackled are generally open-ended. self-motivated learning. team participation.

Role Change

In PBL, there’s a fundamental change in the role played by the participants.a facilitator guides the entire session.a scribe records the entire session.some participants field questions; others try to

brainstorm and provide answers. There will not be student-teacher relationship,everybody is treated equally. Focus is on peer learning

PBL Session

S* is currently experimenting PBL session using web-based collaboration platform – TWiKi (http://twiki.org)

Consideration/Issues to resolve :How to accommodate so many participantsHow to host so many TWiKi pageWill participants with slow connection able to

access ?

Online Delivery Mechanism

Consider and want to explore various advanced networking technologies particularly on video conferencing software. e.g. AccessGridTM

http://www.accessgrid.org/

AccessGridTM

It is a suite of resources including multimedia large-format displays, presentation and interactive environments, and interfaces to Grid middleware and to visualization environments.

Developed by the Futures Laboratory at Argonne National Laboratory and deployed by the NCSA PACI Alliance, it is now used over 150 institutions worldwide with each institution hosting one or more Access Grid (AG) node.

Each node employs high-end audio and visual technology needed to provide a high-quality compelling user experience.

Immersive Learning

Enable group-to-group interactions across the Grid.

Activities such as large-scale distributed meetings, collaborative work sessions, seminars, lectures, tutorials, and training are made possible.

Fig 1: Controlling Audio/Visual Quality

Fig 2: Group-to-Group Live Interaction

Benefits

Reduce the costs and time of traveling. Enable live lecture presentation by the

prominent lecturers. Allow bi-direction interactive discussion forum Conduct virtual seminars and workshops Empower group-to-group collaboration work.

Example

National University of Singapore (NUS) - Singapore-MIT Alliance (SMA) lecture were beamed across twelve time zones from a classroom in MIT to a classroom at NUS

live, "virtual classroom" spanned continents, linking students half a world apart over Internet2

Issues & Consideration

Infrastructure (high speed network, connection/bandwidth)

Cost of setting up Location of set-up Manpower required Technical competency

Contact Information

Emails Justin Choo

Course Coordinator justin@bic.nus.edu.sg

A/P Tan Tin Wee Secretariat tinwee@bic.nus.edu.sg

A/P Shoba Ranganathan Chairman shoba@bic.nus.edu.sg

S* Web Site :http://www.s-star.org

S* Secretariat :secretariat@s-star.org

S* Mailing Address :BioInformatics Center

Dept of Biochemistry, MD710 Kent Ridge Crescent

Singapore 119260Tel: +65-774-7149

Fax: +65-778-2466

End Of Presentation