CS 4490Z/4460Z - Thesis/Bioinformatics Thesis
Class time: 8:30 - 9:30am, Mondays, online.
(See later below for specific class meeting days)
Course Instructor
Instructor: Nazim Madhavji
Office: MC 381
Office Hours: emails, anytime
E-Mail: madhavji <at> gmail <dot> com
CS4490Z/4460Z
(For CS3380F/G/Z, please see later below)
This course provides
students with an opportunity to work on a project
outside a particular course setting, with a faculty
member at Western University as supervisor. The supervisor can be from any department at Western.
Supervisors from other universities will be considered
on a case-by-case basis but will require a Western professor as a proxy.
The topic of the project
can be in any field
covered by the Dept. of Computer
Science for CS4490Z
theses (and can include applications from subjects outside computer
science, e.g., engineering, law, and social sciences).
Students enrolled in bioinformatics (CS4460Z)
are expected to focus on topics from the health
domain.
The objective
of the course is to give the student an opportunity to undertake a project
which is less structured than assignments and/or which requires the student to apply knowledge
and skills learned
from many different
courses. It is also an opportunity for the
student to demonstrate skills in independent study
and research.
The
anticipated learning outcomes:
·
Student gets to experience how to conduct research. This
includes such issues as understanding the problem context; understanding
related literature; defining research questions; learning about research
methodologies to be used; executing the research
methodologies; creating a novel system or investigating a phenomenon from
observations or data; performing comparisons with related literature; drawing
conclusions; performing threat analysis; etc.
·
Experience with writing a research proposal, and with writing
a thesis.
·
If working with a supervisor from a non-computer science (CS)
area (e.g., health, sciences, social sciences, business, etc.) then the student
should experience inter-disciplinary research (e.g., creating or implementing a
new algorithm applicable to non-CS application domain).
·
Experience with presenting and defending one’s thesis.
The suffix Z
denotes that this course is an essay course, i.e., it has a significant writing
component. There are progress reports, final report, as well as a presentation
of the work accomplished as part of a “conference” at the end of the course.
Regulations
·
The
default measure is that projects will be carried out individually.
However, the Dept. reserves the right to take exceptional measures. Student
requests for group thesis will not be entertained.
·
Thesis supervisor can be changed only PRIOR to an
agreement is made with the supervisor. The supervisor-student relationship is
bound once the agreement has been made.
·
Supervisor selection is an asynchronous process. Any student
can contact any supervisor independently.
·
Student acceptance by a supervisor is the prerogative of the
supervisor; the course instructor will not interfere in that process.
·
The thesis topic can be changed (only with the same supervisor) any time PRIOR to the
submission of the thesis proposal, provided that:
§ there is
mutual agreement between the supervisor and the student
§ a new topic is openly communicated to the course
coordinator (me) BY THE SUPERVISOR in
writing.
However, note that the proposal deadline will *not* change.
·
There are other specific issues to do with physical presence
for final presentation, late submission, etc. These are not listed
here.
·
Further regulations (implicit or discovered in real-time):
There may be other issues that may crop up that are not
listed above. The course instructor reserves the right to make the final
decision on those issues and they may not be appealed.
Prerequisites
CS4490Z:
(2.0 courses
from: Computer Science 3305A/B, 3307A/B/Y, 3331A/B,
3340A/B, 3342A/B, 3350A/B; plus registration in the Honors Specialization in
Computer Science or the Combined Honors BSc Computer Science/Juris Doctor (JD) Program) or (2.0 courses from: Computer
Science 3305A/B, 3307A/B/Y, 3319A/B,
3331A/B, 3340A/B, 3357A/B; plus registration in the Honors Specialization in
Information Systems)
CS4460Z:
Computer
Science 3331A/B and 3340A/B; plus 1.5 courses from: Biochemistry 2280A, Chemistry 2213A/B,
Computer Science 3319A/B, 3346A/B; plus registration in an Honors Specialization in Bioinformatics.
Antirequisites: Computer Science 3380F/G/Z, 4460Z (if taking 4490Z),
4470Y, 4480Y, 4490Z (if taking 4460Z)
Note: Unless
you have either the prerequisites for this course or written special permission
from your Dean to enroll in it, you may be removed from this course and it will
be deleted from your record. This decision may not be appealed. You will receive no adjustment to your fees in the event that you are
dropped from a course for failing to have the necessary prerequisites.
CS3380F/G/Z
This is a supervised study involving a research paper,
or the design of or development of a software project.
Antirequisite(s): Computer
Science 4460Z, 4480Y, 4490Z.
Prerequisite(s): Permission
from the department, plus: Computer
Science 2212A/B/Y and registration in the Specialization or Major
in Computer Science. To be permitted into this course, the student must have
found a topic and a willing departmental supervisor before the end of the add period.
Regulations
active for this course mirror those listed under cs4490/cs4460 above.
There are no required texts for this course. One suggested reference,
available in the university library, is:
·
Dawson, Christian W., Projects in
Computing and Information Systems: a Student’s Guide, Second
Edition; Pearson Education Limited, 2009.
Course Webpage and OWL
The CS4490Z/CS4460Z/CS3380F/G/Z webpage is accessible
through the departmental website. Class and project information and
announcements will be posted on OWL. You are responsible
for reading this information on a regular basis.
Computing Facilities
Each student will have access to an account on the
Computer Science Department senior undergraduate computing facility, GAUL. In accepting the
GAUL account, a student agrees to abide by the department's Rules of Ethical
Conduct
Note: After-hours
access to certain Computer Science lab rooms is by student card. If a student
card is lost, a replacement card will
no longer open these lab rooms, and the student must bring the new card
to the Systems Group. Likewise, if a student card ceases to provide access
where it should, it should be brought to the Systems
Group as well.
We may need to send e-mail
messages to the whole class, or to students
individually. E-Mail will be sent to the UWO e--mail address
assigned to students
by Information Technology Services
(ITS), i.e. your e-mail address
@uwo.ca. It is each student's responsibility to read this e-mail on a frequent
and regular basis, or to have it forwarded to an alternative e-mail address if preferred.
See the ITS
website for directions on forwarding e-mail.
However, you should note that e-mail at ITS (your
UWO account) and other e-mail
providers may have quotas or limits on the amount of space they can use. If you let your e-mail
accumulate there, your mailbox may fill up and you may lose important e-mail from your instructors. Losing e-mail that you
have forwarded to an alternative e-mail address is not an excuse for not
knowing about the information that was sent.
Wherever you receive e-mail,
be sure to configure your spam filter to allow e-mail from the instructor's e-mail address given above.
Otherwise, important messages
could get trapped
by your spam filter and missed. This is also not an excuse for not knowing
about information that has been sent.
Classes Schedule and Projects
There will be classes only as announced (typically on
OWL) by the instructor. It is anticipated that most of
the communication between students and the course instructor will be done by
email or in person.
Due dates for various deliverables and the weights are indicated in the table below.
(Note: schedule
subject to change)
Date |
Activity/Event/Deliverables |
Weight % |
14
Sept., 2020 |
CLASS:
Course introduction. |
|
As
scheduled |
CLASSes:
Project briefing by the supervisors. |
|
30
Sept. |
Supervisor
Chosen |
|
(As announced) |
CLASS:
Thesis proposal explained. (What
and how, etc.) |
|
|
Thesis/project
proposal. *** |
5 |
2-8
Nov. |
Reading
Week A Term |
|
21 |
Progress
Report 1.*** |
5 |
4
Jan., 2021 |
Start
of new of the B term |
|
13-21
Feb, 2021 |
Reading
Week B Term |
|
26
Feb. |
Progress
Report 2.*** |
10 |
29
Mar. |
All project documentation, software
artefacts (such as design, test cases, program code, etc.),research
results are to be delivered to the supervisor. Without this delivery, a mark
of zero will be given for the course. |
|
29
Mar. |
Final
Report.*** |
40 |
As
scheduled |
Presentation.*** |
40 |
5 Apr. |
End of Classes |
|
|
|
|
*** EXTREMELY IMPORTANT:
(1) All deliverables
(proposal, Reports 1 and 2, and Final Report and Presentation) are mandatory. A
course grade of zero will be recorded if there are any missing deliverables.
(2) Please note that final
report date and presentation date (TBA) are FIXED without exception (only
university exception applies). THESE ARE (or will be) FIRM DATES. Failing
to deliver these on the due date will result in the course grade of zero marks;
no exception will be made.
(3) Presentations: All
presentations will be online. (Details to be accounced via OWL.) Please make sure that you are able
to present your thesis at the scheduled date and time. No employment reasons,
family trips, or other reasons that preclude you from making your presentation
will be acceptable.
Late Submissions or Presentations
About the Project Deliverables
Submission of Deliverables
(i) the
supervisor and
(ii) the course instructor on
the OWL site.
Ethical Conduct
Scholastic offences
are taken seriously and students are directed to read
the appropriate policy, specifically, the definition of what constitutes a
Scholastic Offence, at the
following Web site: http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf.
Plagiarism: Students
must write their essays and assignments in their own words. Whenever students
take an idea, or a passage from another author, they must acknowledge their
debt both by using quotation marks where appropriate and by proper referencing
such as footnotes or citations. Plagiarism is a major academic offence. Please note, however, that students
are not allowed to make use of the work of others
unless explicitly instructed to do so in the description of an assignment.
All projects are to be exclusively your own work. You
may discuss approaches to problems among yourselves; however, the actual
details of the work (coding, documentation, etc.) must be an individual effort. Incidents that are judged to be the result of academic dishonesty will be reported to
the Undergraduate Chair. The selection of penalty to be applied is up to the Chair, with consultation of the
instructor.
The standard departmental penalty for assignments that
are judged to be the result of academic dishonesty is,
for the student's first offence, a mark of zero
for the assignment, with an additional penalty equal to the weight of the
assignment also being applied. You are responsible for reading and respecting
the Department of Computer Science's policy on Scholastic Offenses. and Rules
of Ethical Conduct.
The University of Western Ontario uses software for
plagiarism checking. Students may be required to submit their written work and
programs in electronic form for plagiarism checking.
All required papers may be subject to submission for
textual similarity review to the commercial plagiarism detection software under
license to the University for detection of plagiarism.
All papers submitted for such checking will be included as source documents in
the reference database for the purpose of detecting
plagiarism of papers subsequently submitted to the system. Use of the service
is subject to the licensing agreement, currently between The University of
Western Ontario and Turnitin.com (http://www.turnitin.com/).
Accessibility Statement
Please contact the course instructor if you require
material in an alternate format or if you require any other arrangements to
make this course more accessible to you. You may also wish to contact Services
for Students with Disabilities (SSD) at 661-2111 x 82147 for any specific
question regarding an accommodation.
Support Services
Learning-skills counsellors
at the Student Development Centre (http://www.sdc.uwo.ca) are ready to
help you improve your learning skills. They offer presentations on strategies for
improving time management, multiple-choice exam preparation/writing, textbook
reading, and more. Individual support is offered
throughout the Fall/Winter terms in the drop-in Learning Help Centre, and
year-round through individual counseling.
Students who are in emotional/mental distress should
refer to Mental Health@Western (http://www.health.uwo.ca/mental_health)
for a complete list of options about how to obtain help.
Link to policy on Accommodation
Consideration for Student Absences
www.uwo.ca/univsec/pdf/academic_policies/appeals/Academic_Consideration_for_absences.pdf
(which
includes a link to the Student
Medical Certificate)
The website for Registrarial Services is http://www.registrar.uwo.ca.
Link to services provided by
the University Students’ Council: http://westernusc.ca/services/