[BioEdu] How to teach bioinformatics into an isolated area?

[Tan Tin Wee]

Dear Karlo,

Since you are in Asia, and Philippines is part of the ASEAN,
I will answer your email with the following as authoritatively
as I can:

1. For the past 15 years, since the 1992 plan for a biocomputation
infrastructure and framework for ASEAN, we have formed APBioNet
(http://www.apbionet.org) in 1998 and the ASEAN Committee on Science
and Technology (COST)'s SubCommittee on Biotechnology has initiative
a plan of action to set up an infrastructure for supporting the
transformation of life science education to include not just
molecular biology but also computational aspects of biology
including bioinformatics.

2. To build the framework which Jeff Bizzaro has mentioned,
in 1996 to date, we have worked on building the APAN network
(http://www.apan.net) and the Transpac Project to create the
necessary advanced internet infrastructure for education and research
linking USA and Asia. Philippines now has the PREGINET and
other Asian countries have their equivalent. More recently,
we have completed TEIN2 (http://www.tein2.net) which sees
the >10M euro interconnection of Europe and Asian countries
as part of FP6. Going forward, we are working on building
the ASTRENA as part of the ASEAN plan of action for
the ASEAN Science and Technology Research and Education Network
Alliance.

3. ASEAN COST has also built ASEAN Virtual Institute of Science
and Technology over the past half a decade (www.avist.org) to
deliver online educational material including bioinformatics.
Separately, an global alliance of National Univ of Singapore
(where I am at) and Stanford, Uppsala, Karolinska, SANBI,
and Macquarie etc have come together in the past six years
to put online bioinformatics courses, particularly for developing
countries (see http://s-star.org). Introductory
Course materials are freely available for your use in teaching,
and every year, we try to organise an online course, which
includes online problem-based learning etc.

4. More recently, AVIST has participated in the development
of a project on delivering online teaching material in
its CANALAVIST project (Kanchana Kanchanasut, AIT).
In addition, for rapid dissemination
of databases, we have set up the BioMirrors project in 1998,
(Gilbert et al) http://bio-mirror.net
and for places with narrower bandwidth, the P2P dissemination
of biological datasets (IDRC PAN Grant 2006/7 to PSU Thailand)
O(http://incob.apbionet.org/incob07/tutorial3.shtml).
To facilitate bioinformatics software usage,
we have constructed the APBioKnoppix software
(http://www.apbionet.org/grid/apbioknoppix2/) as part
of the IDRC Pan Asia Network Grant (since 2002/2003)
and set up a second generation liveCD system (http://bioslax.com).
Last month, we set up two 500Gbyte Boxes plus a liveCD
Server Version of BioSlax and were able to set up a
fully operational bioinformatics node within half a day
(http://www.bio-ibt.ac.vn)
at the Institute of Biotechnology, Hanoi, as part of our
workshop funded by UNESCO-IUBMB-FAOBMB.
(http://incob.apbionet.org/incob07/hanoi.shtml)

Any remote location can teach bioinformatics using
this standalone liveCD for client-based software as well as
the server-based software with an FTP archive
of biomirrors and unzipped blastable databases,
for a near-complete solution for the classroom without
Internet access or having bandwidth constraints
(although it would be nice to have
full broadband internet access).

5. With regards to outreach training courses, you
may be pleased to note that for NCBI, they have been
running courses throughout the region.
Dr Chuong Huynh, Chuong (NIH/NLM/NCBI) huynh at ncbi.nlm.nih.gov
is actively spearheading this, including a WHO-TDR
programme. On my part, wearing my APBioNet hat, we have
been involved in courses in Malaysia, Indonesia, Thailand,
Philippines (ASTI), Lahore, Hyderabad, Beijing, Riyadh
over the past 10 years. Many countries now have their
own national nodes for bioinformatics support for endusers
and teachers like yourself. Please look out for these
at your nearest bioinformatics node.

In the Philippines, our key contacts include:
Denis Villorente (Director ASTI) early pioneer of the
   BioMirror Node and host to an early Bioinformatics workshop
   testing out the BioGrid and APBioKnoppix software
Gloria Despacio Reyes who initiated the NIMBUS project
You may like to seek them out for help.

6. Even more recently, we are exploring online pedagogical
techniques including online Problem Based Learning, Moodle and
of late, LAMS from LAMS international.
http://lams.bic.nus.edu.sg/.

7. For remote access to the Internet, I was once
chair of a remote satellite Internet project in Singapore
(1998) where we were part of the Japanese WIDE's AI3
(A triple I) project. The Japanese JCSAT3 satellite footprint
covers a large part of Asia including Philippines,
(http://www.ai3.net/) If you initiate a link with AI3
and WIDE, they would be interested in understanding how
to build a low-cost satellite groundstation in remote
areas of Philippines.
http://www.ai3.net/topology/index.html

8. If you are interested to link up with your local
representative to ASEAN on bioinformatics, you might
like to contact your ASEAN SCB focal point or Denis
or Gloria, or talk to Richard Bruskiewich at IRRI, Los
Banos. Note also that CGAIR also has its Crop-Improvement
Genomics programme under their Generation Challenge Programme.

9. Regarding your dream of teaching of  "Bioinformatics in some
isolated areas such as from the tribes that live in the mountains that
are uncivilized, those people who live in the rural areas etc"
it is a laudable vision which we will achieve one day, probably
after we sort out how to provision basic sustainable developmental 
programs such as Internet access to such remote places either from
the point of view of the Philippines network or from the perspective
of the eASEAN initiative, and probably after rural agricultural
programmes such as some of those which ASEAN SCB is involved in
come to fruition.

 From networking to databases to software and learning material
as listed above, I wish you all the best in your initiatives
to teach bioinformatics. When you do form your group, speaking
as the chair of the Affiliates Committee of the ISCB, the ISCB
would be interested to consider your official affiliation
with the International Society for Computational Biology,
to further the growth and transformation of 21st Century biology
into that which includes the computational and the informational
sciences.

bestrgds
Tan Tin Wee
--
Bioinformatics Focal Point and retired Chair, ASEAN Subcommittee on 
Biotechnology
Secretariat of Asia Pacific Bioinformatics Network apbionet.org
Secretariat of S* Alliance (s-star.org)
Chairperson, Education Committee, AVIST (avist.org)
Retired APAN director (apan.net)
Retired ASTRENA cochair 
(www.singaren.net.sg/apan/presentation/tinwee/astrena/astrena-APANOct97.ppt)
Advisor, Bioinformatics Centre (Resources), National Univ of Singapore
Co-Investigator, P2P project (http://everest.bic.nus.edu.sg/p2p/)
PI, BioSlax Project (http://bioslax.com)
Co-PI, APBioKnoppix project
Board Director, International Society for Computational Biology


J.W. Bizzaro wrote:
> 
> 
> Hi Karlo,
> 
> I haven't tried teaching people in remote areas, but I would assume that 
> the barriers to teaching bioinformatics in those areas are the same as 
> teaching anything on a computer.  You may have heard of the "One Laptop 
> Per Child" effort (http://laptop.org/).  That may be a good place to 
> start.  Those systems will run Linux, but there may be some issues to 
> installing certain applications on them (I don't think they have hard 
> drives).
> 
> This also brings up the issue of teaching bioinformatics at the 
> secondary level.  What would be a good curriculum for this?  I'm sure 
> that only very rarely would there be a course dedicated to the topic, 
> perhaps for honors students.  So, it's almost always taught as part of a 
> biology course.  What then could/should be taught in that limited time?  
> And, of all the software applications in bioinformatics, what would be 
> the easiest for high school students to learn?  Consider this: in remote 
> locations, you might as well forget about an Internet connection, so 
> visiting NCBI, etc. would be out of the question.
> 
> Cheers,
> Jeff
> 
> Karlo Claridades wrote:
>  > Hello everyone! I am Karlo Claridades,a third year from Bachelor of
>  > Secondary Education, and I'm from the Philippines.I am an aspiring high
>  > school teacher and I am specializing in biological science. I have seen
>  > the objectives and visions of Bioinformatics and I say that they are
>  > marvelous. Now, I want to gather some tips on how to teach
>  > Bioinformatics in some isolated areas such as from the tribes that live
>  > in the mountains that are uncivilized, those people who live in the
>  > rural areas etc. I have this urge to become a successful educator and
>  > more primarilly to help those who are uneducated and cannot be reached
>  > by the government and other educational institutions so I am posting
>  > this message.
>  > Thank You!    
>  >
> 
> --
> J.W. Bizzaro
> Bioinformatics Organization, Inc. (Bioinformatics.Org)
> E-mail: jeff at bioinformatics.org
> Phone:  +1 508 890 8600
> --
> 

-- 
Assoc Professor TAN Tin Wee :: Deputy Head, Biochemistry Dept :: Yong 
Loo Lin School of Medicine :: National University of Singapore :: Block 
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Assoc Professor TAN Tin Wee :: Master, Eusoff Hall :: National 
University of Singapore :: 10 Kent Ridge Drive, Singapore 119242 :: 
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