Mini-project: 60%
Each student will approach a staff and, in consultation with the staff, identify ways in which biocomputing tools can be applied to enhance the staff's research. This will be written up in an online report which will be assessed. The students are free to choose staff whose research will lend most mileage. The staff member will receive a copy of the report on how biocomputing and bioinformatics can actually improve and enrich their research. Staff need not be restricted to the Biochemistry Department.
Each student will identify a staff and the specific area of research. The most convenient will be the staff with whom the student is already doing a final year project. If this is not feasible, the student is free to approach another staff willing to participate in this project. In return, the staff will receive the report on how biocomputing and bioinformatics can actually facilitate their research.
Output:
Staff Name
Staff Position
Department/Research Centre/Institute
Title of Project
One-page Abstract of the research area and a statement of objectives specific
to the research area and the staff's research projects (avoid general statements,
abstracts should indicate specifically what the action items are)
Duration: One week
Report format:
Create a website on your NUSNET account.
Send the URL (e.g. http://everest.bic.nus.edu.sg/) where you
intend to create your webpages to tinwee@bic.nus.edu.sg
Include your email address, full name, and any other relevant information.
Design of Website
1. contents page should include the way you layout your report, including
your personal information, contact email etc.
2. links to next layer of webpages should be clearly indicated and systematic
3. add in necessary diagrams and graphics, which may be generated using various tools available on NUSNET and by FTP from the Internet.
4. all student's webpages will be linked from
http://everest.bic.nus.edu.sg/ by Dr Tan Tin Wee
Students are encouraged to learn from each other and keep track of
what other colleagues are doing, and to incorporate these new ideas into
theirs, creating a research collaboratory for collaboration, even though the
target subject area may be different.
5. Submission date : 1 week from project briefing.
Feedback
Within a few days, your website will be vetted and approved/rejected by
Dr Tan Tin Wee via email with feedback on how to improve the
objectives and goals. If the preliminary output is not up to quality,
you may be required to resubmit the preliminary work.
Once approval is given, you may proceed with achieving the goals you have
set out for the staff's research project.
2. Research Work
Based on your recently acquired knowledge about biocomputing and
bioinformatics from lectures and from journal papers/reviews, survey the
spectrum of wet-lab research work which your selected staff does. For
each sub-area, identify ways in which the new technology and tools can
enhance, improve the facility and quality of the research being carried
out. Identified material and tools should be gathered in a customised
webpage for your target staff. Please note that previous year's
students may have already laid the ground work for your project
this year. The work you do this year should be substantially different
from the previous year, and may build upon the work previously
carried out.
Example:
1. For instance, all researchers will need access to bibliographic
information. Your immediate work might be to identify all bibliographic
material available online which might help. This may include patent
information databases, and even biotech business and pharmaceutical
industries.
2. For researchers doing gene cloning, they will invariably need to
design PCR primers for example. You can survey the PCR primer design
software available.
3. For researchers doing sequencing, they will need help in sequence
acquisition, sequence annotation, sequence submission, tools and
software that assist in this process.
4. For all researchers, they need to keep up with some type of information
available online. For the specific research areas, students can create a
mini-Yahoo, the multibillion dollar company which acts like a one-stop
centre for any thing you wish to know. In this case, it should be a
one-stop web portal for your target researcher's access.
5. More enterprising students can request to create their webforms and
interface with biocomputing software to facilitate usage.
6. Students will be graded (for this part) on how well they set up the
customised website.
Duration: Two to three weeks after submission of preliminary work feedback
Output:
Two components will be required
1. Website of useful links to the researcher, including information
links, and tools, systematically classified. These weblinks are to be
clearly linked from the Report Homepage.
2. Write up report of researchers area of research, and for each area,
what sort of biocomputing tools and bioinformatics resources are
available.
Report should include methodology and the process taken to achieve the
report, as well as bibliographic references. Report is to be clearly
linked from the Report Homepage
Feedback:
Students are to keep tinwee@bic.nus.edu.sg informed of their progress
once a week by email.
Final Submission Date:
The miniproject will draw closure at a date informed by Dr Tan.
At this point, a copy of all websites will be generated and frozen for marking
and assessment.
However, students' copy of the online material can continue to be enhanced
further for the staff concerned, or directly handed over to the staff.
Presentation
Should time permit, we will arrange for a date for students to present
their case to staff involved and obtain feedback. This will not be
assessed.
Assessment
Students will be assessed based on their website.
a. quality of their report and recommendations
demonstrating comprehensiveness of scope, depth in selected areas,
accuracy and validity of recommendations, knowledge of biocomputing and
bioinformatics gleaned from course and from readings.
b. quality of their website
demonstrating competency in skills acquired during course,
As this will be an online submission, the homepage must contain all
information pertaining to the assessment, as well as contact email
should there be missing links or lost material that prevent a proper
assessment from being made.
Tan Tin Wee
12 Feb 2001
tinwee@bic.nus.edu.sg
References
Some selected references for you to start with, if you wish.
1. Stephens et al. (1998) Science 282 754- 759. Genome Sequencing of an
obligate intracellular pathogen of humans: Chlamydia trachomatis. (see
also commentary on p638 in the same issue. This is a classic example of
what can be deduced from a full genome sequence for a bacterium)
2. Bork et al. (1998) J. Mol. Biol 283 707-725. Predicting Function:
From genes to genomes and back. (this is a good paper to start from if
your target staff researcher has unknown gene sequence data that needs
to have function identified)
3. Ashburner M. and Goodman, N. (1997) Curr Opinion in Genetics and
Development 7 750-756. Informatics -genome and genetic databases. (for a
list of commonly used genetic databases)
4. Bono et al. (1998) Genome Research 8 203-210. Reconstruction of
amino acid bosynthesis pathways from the complete genome sequence. (for
some ideas of how bioinformatics can help if target staff has research
work dealing with some biochemical pathways)
5. Baker, P.G. and Brass, A (1998) Curr Opinion in Biotech 9 54-58.
Recent developments in biological sequence databases. (for some useful
introduction to biological sequence databases)
For referencing bibliography in your report, please use the standard
Harvard convention for standardisation, with complete name of article
included.
For referencing of web addresses, please make sure that you include the
author wherever possible, and the full URL website address with
directory path and file name. If possible, include the most relevant
home page of the referenced page in parenthesis.