School of CSE - Details Needed for New Course Proposal

Course Title: Representations and Algorithms in Bioinformatics

Proposer: Bruno Gaeta

Rationale Why is the new course being proposed?

This course replaces BINF3001 in the revised bioinformatics
program, and consolidates the elements of BINF2001 and BINF3001
that are targeted at computer scientists who want to work in
bioinformatics. While this course would be core in the revised
bioinformatics program, the change of emphasis and prerequisites would
make it suitable as an elective for CSE students without requiring
biology prerequisites

What are the academic objectives?

The emphasis of the course is on the computational representation
of biological concepts and the use of algorithms to analyse the
represented biological data. Although the focus of the course is
on the use of these methods to analyse biological data, the methods
presented can also be applied to other domains.

Which programs/stage does it serve?

Bioinformatics programs (3647, 3755, 3756, 3757,
Bioinformatics/Commerce) in 3rd year or equivalent, as well as other
CSE programs (CE, CS, SE) as elective.

Why can the same objectives not be achieved with existing courses?

The current bioinformatics courses (BINF2001/3001) are suited
exclusively for bioinformatics students as they assumed knowledge both
in biology and computing. This makes them unavailable for students
in other programs which still would find part of the courses relevant
to their studies.

How does the proposed course relate to other courses?

BINF3010 and BINF3020 replace BINF2001 and BINF3001 and re-arrange
content between these two courses so they become suitable for
life science and computing students respectively, in addition to
bioinformatics students.

This course could also be offered as a postgraduate version suitable
for MIT/MCIT/PhD students, as a replacement for BINF9010 which is
currently targeted at a mixed audience and suffers as a result.

What overlap is there?	If there is any overlap, why is this
justified/not a problem?

Stakeholders and Consultation Who are the potential stakeholders,
who was consulted about the proposal (inside the School as well as
outside), what was the result of that consultation?

External stakeholders are mainly the school of BABS, who has been
consulted

Enrolment Impacts Likely enrolment (with justification), and impact
on enrolments of other courses.

The new courses should have an increased enrolment compared to
current BINF courses as they would be open to students outside the
bioinformatics program and would have less prerequisites.

Justification of Prerequisites (or lack thereof)

The course assumes programming skills (for assignments) and a
fundamental knowledge of data structures and algorithms.

Any Courses this is Replacing, and Why?

BINF3010/3020 replace BINF2001/3001

Delivery and Assessment Anything noteworthy about delivery mode,
assessment (with justification).

Handbook Entry

Textbooks/References

Syllabus Indicative syllabus / overview of contents (at a level of
detail well beyond that of the handbook entry)

String matching algorithms String alignment by dynamic programming
Fast heuristic string alignment Progressive and iterative multiple
sequence alignment Tree building algorithms Hidden Markov models
and associated algorithms Computational representations for sequence
families (PSSMs, profile-HMMs) Clustering and classification methods
Optimisation heuristics (hill-climbing etc) RNA structure prediction
(dynamic programming, SCFGs) Biological networks Causal modelling Open
source development environments in bioinformatics Special hardware
architectures in bioinformatics


Effect on School Resources:

1. Who is proposed to teach the proposed new course,
   and what impact would this have on their planned/current allocation?

Coordinated by Bruno Gaeta or Mike Bain, with guest lecturers from BABS
(and CSE if any volunteers)

2. What sort of tutorial component is proposed, if any?

Tutorial every week or every second week

3. What is the likely impact on lab utilisation (this relates
   to assignment and project work as well as scheduled labs?

Compared to BINF3001, the lab component would be reduced

4. Any other resource needs? E.g. special print/disk quota, access to
   servers, access to special machines, special labs.