S Alliance Introductory Bioinformatics Online Course

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S Alliance Introductory Bioinformatics Online
Course

• Victor Tong, Richard Tan,
• Justin Choo and Tan Tin Wee
• Presenter and correspondent

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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 many regions of
  the world

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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

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S Informatics Alliance (since 2000)
WEBSITE http//s-star.org
Sweden
Karolinska Institutet
University Uppsala
USA
Stanford University
Singapore
University of California, San Diego
National University of Singapore
South Africa
Australia
University of Sydney
University of the Western Cape
Macquarie University
New candidate in negotiation Sao Paolo, Brazil
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Goals for Introductory Bioinformatics

• Provide free online material - for self
  learning- for teaching
• Provide a annual 3 month free online introductory
  bioinformatics course
• Experiment with new pedagogy and new curriculum
• 1st and 2nd Problem Based Learning module (2004
  and 2005)
• 1st Practical Hands-on course
• second one to be held in Lahore Pakistan (FAOBMB)
• Third one in Riyadh, Saudi Arabia (KACST)
• Develop software platform for practical
  bioinformatics
• Collaboration with APBioNet
• Produce APBioKnoppix2, a liveCD of bioinformatics
  open source software and others, ready to go.
• Identify good students

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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
• 2004 Macquarie University joins 5th course

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Luminary Lecturers Worldwide

• Anthony Weiss (Sydney, Australia)
• Betty Cheng (Stanford, USA)
• Douglas Brutlag (Stanford, USA)
• Jan-Olov Hoog (Karolinska, Sweden)
• Julie Mitchell (Wisconsin-Madison, USA)
• Lynn Ten Eyck (UC San Diego, USA)
• Marc Wilkins (Australia)
• Michael Levitt (Stanford, USA)
• Russ Altman (Stanford, USA)
• Shoba Ranganathan (Macquarie, Australia)
• S.Subbiah (Stanford, USA)
• Wei Liping (NexusGenomics, USA)
• Winston Hide (SANBI, South Africa)
• Kevin OBrien (Karolinska, Sweden)
• Mark Reimers (Karolinska, Sweden)
• Michael Waterman (Southern California, USA)
• Martti Tammi (Karolinska and NUS)

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Participants List
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(No Transcript)
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S Course Occupation
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Course Pedagogy

• Lectures
• Discussion
• Assessment
• Tutorial
• Practical
• Project PBL (New)
• Course Feedback

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Course Syllabus

• Introductory Molecular Biology
• An Overview of the Computational Analysis of
  Biological Sequences
• Transcript Analysis and Reconstruction
• Comparative Genomics
• Representations and Algorithms for Computational
  Molecular Biology
• Protein Structure Primer
• Protein Structure Prediction

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Course Syllabus (cont.)

• Protein Physics
• Genomics and Computational Molecular Biology
  Genomics
• Protein and Nucleic Acid Structure, Dynamics,and
  Engineering
• Proteomics
• Proteomes
• Structure Prediction for Macromolecular
  Interactions
• Protein - Ligand Modeling

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Curriculum Cross-Check
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Delivery Pedagogy

• Via the Integrated Virtual Learning Environment
  developed _at_ NUS

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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

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Sample Lecture
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Sample Discussion Forum
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Sample Assessment Session
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Problems Encountered

• Delivery format (video/audio)
• Made different quality video/audio encoding files
• Bandwidth problem
• Slow connection

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Solution

• Overcoming the bandwidth problem
• - network of mirror sites
• - MoU tie up with APBioNet
• Pressing of CDs (to countries like Africa, Iran)

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The S Alliance Mirror Sites
CSTNETCERNET, China
Stanford
Anna, Pune University, India
UCSD
Instituto de Inmunologia, Univalle, Colombia
SANBI, South Africa
UKM, Malaysia
NUS, Singapore
Quilmes National University, Argentina
University of Sydney, Australia
Mirroring and realtime lessons for Asia Pacific
students Make use of APAN network infrastructure
coordinated by APBioNet
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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

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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

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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
  SSTAR 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

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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

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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.

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PBL Session

• S is experimenting PBL sessions for second year
  running, using web-based collaboration platform
  IVLE (ivle.nus.edu.sg) and CENTRA
  (emeet.nus.edu.sg) and Skype.com.
• 2 Phases for PBL session over 12 weeks
• Phase 1 asynchronous session via IVLE discussion
  forums and submission of project proposals.
• Phase 2 synchronous/asynchronous sessions via
  CENTRA emeeting and IVLE discussion forums and
  project presentation/submission

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Pre-PBL Training for TAs

• Running PBL online as a PBL in itself for course
  coordinators and teaching assistants.
• Intensive asynchronous discussion and planning
• Education Office with team of three to six
  volunteer pedagogy experts led by Daniel Sze

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8 PBL topics for 160 students to choose from

• Semi-Automated Genome Annotation of Burkholderia
  pseudomallei
• Interaction of glycosmainoglycan(s) with the
  glial-derived neurotropic growth factor (GDNF)
  family ligands
• Comparing difference between 2 protein structures
  
• Ligand-Receptor Interactions in Drug Discovery
  depends on ligand docking software
• Comparative genome analysis of Pseudomonas
  species
• PCR primer design from the multiple sequence
  alignment of protein
• Structure-Function relationship of Proteins
• Protein Splicing

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Example PBL Topic 1 Semi-Automated Genome
Annotation of Burkholderia pseudomallei

• Melioidosis is a endemic disease prevalent in
  south-eastern Asia and northern Australia
  caused by Burkholderia pseudomallei... This PBL
  aims to address the general issue of genome
  annotation... More needs to be known about
  host-pathogen interactions during the disease
  process... How many such genes found in this
  pathogen? What can be known about host-pathogen
  interactions based on genome annotation of this
  bacterium? How can bioinformatics help in
  facilitating this kind of research?

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Role Change

• In PBL, theres 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

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PBL Session

• S is currently experimenting PBL session using
  web-based collaboration platform Centra
  emeeting (http//emeet.nus.edu.sg)
• Consideration/Issues to resolve
• How to accommodate so many participants
• Will participants with slow connection able to
  access ?

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Sample emeeting Session
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Online Delivery Mechanism

• Consider and want to explore various advanced
  networking technologies particularly on video
  conferencing software.
• e.g. AccessGridTM
• http//www.accessgrid.org/

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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.

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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
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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.

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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

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Issues Consideration

• Infrastructure (high speed network,
  connection/bandwidth)
• Cost of setting up
• Location of set-up
• Manpower required
• Technical competency

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Poster/Conf. Presentation

• Daniel Man-yuen Sze et al.  Prediction of
  potential T-cell epitopes generated through
  post-translational splicing. The third asia
  pacific bioinformatics conference, Singapore,
  January 2005, Poster.

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Feedback from Participants

• It was an all new experience for me to
  participate in an emeeting.This way of
  interaction really helped me learn things faster
  and assess the problem specifically.
• All the encouragement from our facilitator and
  his guidance made us focus our thinking in one
  direction and also motivated us to work in teams.
  
• I would say emeet provides us live interaction
  with the facilitator and participants making
  learning easier and faster. it is really nice and
  exciting to be apart of a new learning system.in
  a group it is very nice that people can share
  knowledge across countries.
• The first e-meet was the exciting experience. It
  had built a classroom like atmosphere on net. I
  had never imagined anything like that before.

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1st S Practical Hands-on

• 11-17 June 2005
• Participants from Singapore, India, Pakistan,
  Saudi Arabia
• LiveCD APBioKnoppix linux OS
• Interrogating BioDatabases
• Unix scripting, BLAST, MSA (Clustal/Treeview)
• Buildling Web databases (Apache/MySQL)
• Molecular Visualisation (Rasmol/Pymol) and
  homology modelling (Modeller)
• Etc

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Operational issues

• Complete solutions for teaching hands-on
• Client APBioKnoppix2 LiveCD
• Server Proteus Bioinformatics Computing Platform
• Low-cost complete solution for setting up
  teaching laboratories
• FPGA accelerated PC from sponsored from
  Progeniq.com

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Complete bioinformatics infrastructure in a
single box

• Over 200 common bioinformatics applications from
  APBioKnoppix
• Web front end for user friendly application
  access
• Automatic database updating
• FPGA acceleration for compute power of over 100x
  normal PCs

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Benefits

• convenient set up of bioinformatics labs
• for research and teaching labs
• One portable shoulder bag server box provides
  entire server infrastructure needed
• together with a stack of APBioKnoppix LiveCDs.
• low cost
• basic solution costs from USD 1,000
• scalability
• scales up for future compute power requirements
• additional accelerated algorithms

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Future ideas I

• APBioKnoppix3 using Knoppix 4 with USB boot, and
  a larger footprint than a CD.
• Combined with PHP for a full LAMP.
• Built in Mediawiki for self-learning blogging.

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Future Ideas 2

• BioMoodle
• Open source framework for replacement of
  proprietary IVLE system
• Reusable course material based on a
  Wikipedia-style contributed basis
• Environment where experts can hold their own
  workshops on an ad hoc or scheduled basis.
• Create virtual communities of learning.
• Partner with Willy Valdivia and Virtual
  Conference in Bioinformatics and Genomics to
  share content, and build training material around
  the excellent talks given by top bioinformatics
  people worldwide.

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Future Ideas 3

• Develop question and answer bank
• Run certification courses in conjunction with
  ISCB.

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Contact Information

• Emails
• A/P Tan Tin Wee
• Secretariat
• tinwee_at_bic.nus.edu.sg

S Web Site http//www.s-star.org S
Secretariat secretariat_at_s-star.org S Mailing
Address BioInformatics CenterDept of
Biochemistry, MD710 Kent Ridge
CrescentSingapore 119260Tel [phone]Fax
65-778-2466
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End Of Presentation