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Nov 7, 2013 (3 years and 9 months ago)

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Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
1









and


















Joint Student and Supervisor Handbook for two related structured PhD programmes





Draft 2013





Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
2


Contents:













P
AGE


Introduction


3

1.

The objective of the programme
s







4

2.

Project choice and s
tudent control of project direction




5

3.

Each student is registered within a UCD School






7

4.

Supervision











9

5.

Doctoral Studies Panel and
Research and
P
rofessional Development plan

10

6.

Stage Transfer










12

7.

Candidacy Requirement
part A: Coursework






15

8.

Candidacy Requirement part B: Seminar and lab group participation


19

9.

Demonstrating/Graduate Teaching assistant






20

10.

Review of student’s balance

of work effort and direction




21

11.

Approximate schedule of events









21

12.

External conferences, workshops, placements





23

13.

Publications











24

14.

Thesis Production










25

15.

Thesis Examination










26

16.

Conflict Resolution for Students and
Supervisors





30

17.

PhD Symposium










31

18.

International Students









31

19.

Accommodation










33

20.

Student Health Services









33

21.

Applying for a PPS number










35

22.

University Facilities









36

23.

Useful web links










39








Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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3


This
h
andbook
is de
s
igned as a guide to completing
the
PhD in

Bioinformatics and Systems
Biology,
which includes students in Systems Biology Ireland,
and for those participating in
the Welcome Trust
PhD
Programme in

Computational Infection Biology.

I
t includes
policies
and requ
irements

for students based primarily at UCD
that may be subject to change over
subsequent years.

Some sections in the booklet will be relevant to only one of the degree
programmes
, as indicated where relevant
.


It is essential that each student
should
be aware of

these requirements, and proactively plan

his/her

activities in order to satisfy them.

If you require clarification about these

policies,
you should discuss them with your

supervisor, your

Doctoral Studie
s Panel
,
or
the PhD
Programme
Director
.


Bioinformatics and Systems
Biology:

Denis Shields
Denis.Shields@ucd.ie

Computational Infection Biology:

Geraldine Butler
gbutler@ucd.ie
.


The
program
me
s

are
managed by steering committee
s
:


Bioinformatics and Systems Biology

Denis Shields (PhD

programme

Director; School
of
Medicine and Medical Science
)
; Des
Higgins (School
of
Medicine and Medical Science), Padraig Cunningham

(School of Computer
Science and Informatics), Ted Cox (School of Mathematical Sciences), Emer Cunningham
(Graduate Studies, UCD), Boris Kholodenko (
School of Medicine and Medical Sciences and
SBI)
, Till Frank (School of Physics and SBI
)

and Cathal Seoighe (
School of Mathematics,
NUIG).


Computational Infection Biology

Geraldine Butler (School of Biomolecular and Biomedic
al Science
)
,

Denis Shields (School of
Medicine and Medical Science)
,

Steve Gordon (School of Agriculture, Food
S
cience
and
Veterinary Medicine
), Neil Ferguson

(School of
Biomolecular and Biomedic
al Science
), David
McHugh

(
School of Agriculture, Food
S
cience and Veterinary Medicine),
Brendan Murphy
(School of Mathematical Science),
Anthony Chubb

(School of Medicine and Medical Science)
.


Anthony Chubb

(
bioinfo@ucd.ie
) acts as administrator

and manager

for BSB and as one of
the administrative contacts for CIB.
Heather Wood (Heather.Wood@ucd.ie)

acts a
s
administrator

of the
CIB

programme.



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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4



1.

The objective
s

of the programme
s





Bioinformatics and Systems Biology


The objective is to establish a world
-
class structured PhD programme that takes in
graduates from diverse undergraduate disciplines
:
Mathematics,

Statistics, Biology,
Computer Science, Engineering, Chemistry, Physics
,
and provides them with
training

in the
inter
-
disciplinary area of Bioinformatics

and Systems Biology.


This programme will provide taught cou
rses to support cross
-
disciplina
ry training. A strong
focus on interdisciplinary supervision is
vital

to this programme, typically an experimental
(“wet”) and a computational (“dry”) supervisor. While
usually
the
essential
PhD skills are
dry,
generally
students will spend a minimum of 3
months in the laboratory. This has an
important formative component, familiarising “dry” students with the different research
culture in “wet” labs.




Computational Infection Biology


The objective is to provide a highly innovative thematic PhD programme in Computational
Infection
Biology that

will deliver graduates with expertise in biology and computational
modelling, ready to lead interdisciplinary research programmes within biomedic
al research,
bio
-
pharma and agri
-
food industries. The programme will offer projects in all areas of
infection biology from genomic analysis of pathogens, to drug discovery and investigation of
host/pathogen interactions.


The contribution and collaboration

of two supervisors is a key part of both programmes,
which have been developed within the framework of the UCD Graduate School’s established
procedures for structured PhDs. The programmes cater for the specific requirements of
students coming from very di
verse undergraduate backgrounds, and enables them to
acquire important interdisciplinary and transferable skills relevant to both their PhD research
and their future careers. Students are strongly encouraged to take transferrable skills
training (e.g. in
entrepreneurship and innovation) as the opportunities arise.





Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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5


Mentoring


We
have recently

initiat
ed

a mentoring system, whereby students from previous years
mentor new incoming students.
This
allows

existing students within the programme
s

to

p
rovide guidance to new students.


2.

Project choice and s
tudent control of project direction


Bioinformatics and Systems Biology
:

For students in this programme funded by the
IRCSET
Graduate Education Programme (GREP)

and for SBI students funded by Science Foundation
Ireland

scheme the funding is primarily attached to the student.
The student is encouraged
with consultation from
their Doctoral

Studies Panel
(DSP)
to regularly consider what
structure
of research best me
et the
ir own
training needs.
For example, the student may
choose to spend more time in the wet lab

than the minimu
m three months
.


Computational and Infection Biology
: During the first year, students wil
l work on two
rotation projects
. At the end of the
first year the student will choose a PhD project from
those provided. In general, students will have a free choice of projects. However, not all
supervisors wil
l offer a project in all years. The steering committee will make a decision if
there is competit
ion for the same project.

Projects will typically have two co
-
supervisors,
one from an experimental, and one from a computational background.


Rotation projects: At the beginning of the first year, students will choose two rotation
projects, one laborator
y
-
based and one bioinformatics/computational based.
One person will
generally supervise the projects
. The projects available are listed on the programme web
site, at
http://bioinfo
-
casl.ucd.ie/cib/
.

Students will be presented
with information to help make a choice during

an o
rientation day
in September
. We will attempt to match students to the project of their choice; however, it
is unlikely that any one supervisor will supervise more than one student
. The rotation
projects provide an opportunity to gain expertise in different areas. It is possible (and
indeed likely) tha
t many students will choose a different area for their final PhD project.


The current plan is that
Rotation 1

wil
l take place during

October



early February
, and
Rotation 2

from
mid
-
February


July
. You will also be taking taught modules during
this


Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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6


time (see section 7
). The final PhD project will therefore begin during the summer
at the
end of your first year
.


Budgets and consumable
s


Bioinformatics and Systems Biology


Each student that is funded

by IRCSET will get their fees paid for every year
, plus an annual
stipend

(set

up in year 1 for the full 4
years
).

They will also receive a personal budget for a
laptop/pc/mac plus

money for lab
consumables

and a budget for conferences
, plus a
nominal budget for work placements. It is the
responsibility

of each student to manage this
budget by producing copies of all expenses and giving them to
the programme
administrator
.

Details
of the budget available for students may vary depending on the
studentship, and
budgets

will be indicated to students on their arrival.
SBI SFI funded
students will get their fees paid every year and an annual stipend set up in year 1. Laptop

purchases

can be discussed with

Philip Smyth

(x6975)

in the Conway Institute.

Each SBI
student has a budget allocated for lab consumables, travel and work placement. It is the
responsibility of each student to manage their own budget and present copies of expenses
to both their supervisor and the SBI administrative officer. Travel expenses must be prior
authorised by the student’s supervisor also.


Each
UCD
IRCSET
and SFI
student
will

be set up on labstore within the Conway Institute
.
Y
ou will rec
eive your own
personal log on

labstore on the
Conway
intranet

(https://intranet.ucd.ie/conway/).

You should fill out the orange form
from
the Conway
Di
re
ctorate.
You can then purchase your equipment and collect it yourself from stores,
in
the basement
in the Conway.

For access to the Conway you will need a swipe card that will
be provided by
the directorate

once you have registered as a student within UCD.


Computational and Infection

Biology


Each student will receive an annual stipend and will have fees covered (EU

rate) for 4 years.
There is a small laboratory budget for year 1 and a larger one for years 2
-
4, which will be
controlled by the research supervisors

and the students
. There is also some support for
attendance at conferences. This will cover attendance at

1
-
2 major conferences for each
student. However, all students are encouraged to obtain support from other sources (such


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/Computational Infection Biology PhD programmes

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7


as scientific organizations), because the budget will not cover one conference per year.
Students can also apply to the steering commit
tee for funding to attend a specific tra
ining
programme or course (such as in entrepreneurship). There will be NO support for
purchasing a laptop
.


All students and supervisors will be set up with a labstore account in the Conway Institute
which will allow

you to purchase consumables. It is the responsibility of you and your
supervisor to ensure that spending stays within agreed budgets.


Travel cost for all students

All travel to conferences etc. must be agreed with your supervisor and the programme
director where appropriate. You will usually need to pay registration and flights in advance;
agreed costs will be refunded after the conference. You can claim a travel advance (up to
75%

of costs
) from your research account using form T2 available from
http://www.ucd.ie/bursar/forms.html
.
Keep ALL ORIGINAL receipts (registration, flights,
accommodation) and when you return you can claim a refund using form T1 or T3 from the
same site.
Travel costs (confer
ences and placements) will
only
be reimbursed
if

the planned expenses have been agre
ed in writing BEFORE

you register or
purchase flights/accommodation.

BSB students should obtain approval from Anthony
Chubb. CIB students obtain approval from Geraldine But
ler in year 1, and from their
PhD

supervisors in years 2
-
4. Flights can be booked using Club Travel (
pjames@clubtravel.ie
).
Club Travel
accept payment through lab
store
. You can buy directly from an airline (E.g.
Rya
nair or Aer Lingus) but you CAN
NOT use any other travel agency.


3.

Each student is registered within a UCD School


Bioinformatics and Systems Biology


Every

student on the programme has two supervisors

from the beginning
,

sometimes from
different schools

or different institutions
. The different
UC
D

schools include
d in the
programme include
:

Computer Science and Informatics
;

Mathematical Sciences
;

Medicine &
Medical Science
;

Biomolecular and Biomedical Science
;

Biology and Environmental Science
;

Public
Health
, Physiotherapy

and Population Science
.




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/Computational Infection Biology PhD programmes

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8


Supervisors are also drawn from the department of Molecu
lar and Cellular Therapeutics
(RCSI), the Institute of Neuroscience (TCD)
,

the Institute of Genetics (TCD)
, and the
departments of Mathematics and other
departments in NUIG
.


UCD
students will be registered to the major: PhD in Bioinformatics and Systems Biology
(CODE: X245)
and within the same school as your principal supervisor, though most projects
have joint supervisors sharing equal responsibility fo
r the student’s research.


Computational and Infection Biology


For your first year, every student will be registered

to the major PhD in Computational
Infection Biology

(CODE: FO19)

in the School of Biomolecular and Biomedical Science, under
the direction of Prof Geraldine Butler
.
At the end of

the first year you will choose a pr
oject
and two supervi
sors. You will then be registered within the same school as your principal
supervisor

(most projects have joint supervisors sharing equal responsibility for the student’s
research, but students are registered in only one school). Diffe
rent schools have different
requirements, for example for demonstrating, conflict resolution
,

etc.


Before

you begin your PhD there are a number of forms that have to be
completed. T
o get copies of these please make sure you contac
t Heather Wood
for CIB, and Ant Chubb for BSB.


1.

PhD Student Application for registration
.

2.

S
tudent
R
ecord information form
.

3.

Scholarship
A
uthorisation forms, p
ayroll set up form

and scholarship exemption
declaration forms found at
http://www.ucd.ie/registry/adminservices/fees/forms.htm
.

4.

Labstore access form
and Conway Institute access card form (both on the same
form)


Scholarship forms have

to be sent to
the Research Finance Office

before the 2
0
th

of the m
onth to get paid by the end of the next month.
It is important that these
forms are filled out

correctly and in your own hand
writing;

p
lease
consult
with
Heather
Wood or Anthony Chubb
before you send them
in
.



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/Computational Infection Biology PhD programmes

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For IRCSET
and Wellcome Trust
funded students,
Ant Chubb and Geraldine Butler

will look
after payment of fees each year
. The student has to
register each year by logging

onto SIS

web

(
https://sisweb.ucd.ie
)
. When your fees have been processed
go

to the student desk

in
the Tierney Building

to
collect

your student card.


4.

Supervision


UCD
Principal Supervisors



Should be a

permanent member of staff

OR a

member of the adjunct or visiting staff
of the University. Members of staff without an academic appointment cannot be
principal supervisors of
a
PhD

student



A full
-
time member of the academic staff on a temporary contract of

three years or
greater may act as Principal Supervisor with the approval of Head of School,
provided that there is a Co
-
Supervisor

who is a permanent member of staff



Should be a
n active researcher in the broad area of the student’s research topic,
with a
record of a peer
-
reviewed public
ation of international standing



Will n
ormally hold a doctoral degree and have experience in

supervising a doctoral
student.

The student is always registered to the School of the Principal supervisor.


The Co
-
Supervisor

The c
o
-
supervisor

can be from a different school within UCD or
(for the Bioinformatics and
Systems Biology programme)
fr
om Trinity College Dublin,
Royal College of Surgeons
,
or
NUIG
. The

co
-
supervisor

take
s

an active interest in the student’s progress and is a member
of their

DSP.


Supervisor responsibilities

The main duties and responsibilities of the Pri
ncipal Supervisor are as
:




To act as the main source of research supervision, mentoring, guidance and
advice
for the student throughout their research degree.



To meet regularly

with the student
(
at least once a month
)

in addition to regular
interaction.



To participate in the Doctoral Studies Panel (DSP).

Typically
the DSP

will comprise an
independent chair, the two co
-
supervisors and the student.



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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The co
-
supervisor will have an active role in specific aspects of the research undertaken or
in provision of technical advice or expertise.

For further information please refer to the Policy Document
‘Code of Practice for Supervisors
and Doctoral Students
’ which is

available at
http://www.ucd.ie/registry/aca
demicsecretariat/docs/researchs_code.pdf


5.

Doctoral Studies Panel and the
Research and Professional Development
Plan


Doctoral Studies Panels
(DSPs)
are designed to enhance the supervisor
-
student

relationship
and to ensure the quality of the research degree

student experience
. Records of the DSP
meetings are maintained as

part of the Research and Professional Development Plan
(RPDP). The DSPs will be assigned according to UCD’s recommendations.


Bioinformatics and Systems Biology

Prior to registration, students will have selected and been assigned a wet and dry lab
supervisor.
Additional member(s) of your Doctoral Studies Panel (DSP) will be
assigned
. The

chair of the DSP is chosen by
the management

committee, the School
where you
are registered is notified and then approves this panel.


Computation and Infection

Biology

For the first year, your nominal supe
rvisor is Prof Geraldine Butler.

Your

Doctoral
Studies Panel will
include the supervisors of your rotation projects
, and a
third
member assigned by the steering committee
. A new Doctoral Studies Panel will be
formed in year 2, and will include both project supervisors.


Research and Professional Development planning is an integral part of the PhD programme.
The purpose of
such planning is to ensure that the student’
s work is clearly focused on
achieving their research and professional goals. This will play a major part in informing the
trajectory of
your

PhD research and in
your

training and development as a researcher.
These plans will also help the student develop key skills that will be invaluable for both their
current research and their future career prospects.


There are three main components to the RPDP:




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/Computational Infection Biology PhD programmes

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11


1.

Research Plan


This is to provide the student with a clear research focus and a
coherent research plan.

2.

Professional Development Plan


This is to enable the student to identify the skills
important to their research and career.

3.

Doctoral Studies Panel Meeting Record


A mandatory outcome of the DSP meetings
will be a formal record of the student’s research and professional plans and progress
to date. This will also inform the transfer assessment.


The RPDP forms are available for download from
http://www.ucd.ie/graduatestudies/currentstudents/rpdp/

CIB students will usually use the forms f
or

Science, and BSB students will use the forms for
Health Science.


Each student in the first year

will need to
attend an

initial

DSP meeting within one
-
three
months of starting,

to ensure that either (i) the two supervisors and the student clearly
understand the plan for the thesis work (Systems Biology and Bioinformatics) or (ii) the
student has chosen two rotation projects and is clear about the requirements for taught
modules

(Computational Infection Biology)
.
The
student is responsible for
convening
all DSP

meetings. For students in Systems

Biology and Bioinformatics
subsequent
meetings should
be held after

6 month
s and 12 months. For students in C
omputational and Infection Bi
ology,
meetings should he held after the first and second rotations.
The panel meetings should
discuss the development and progress of the student’s research and any training or
education needed for their research and further professional development.

All
reports need
to be signed by all DSP members,
clearly indicating that the DSP is happy with
progress to date
, or alternatively highlighting any reservations or p
otential reservations of
the DSP.
For CIB students, c
opies
(both a hard copy and an emailed PDF)
of all reports
should be sent to
Heather Wood, and for BSB students copies are sent to Ant Chubb.


Please note that all initial reports have to be submitted several months before
transfer to
S
tage 2 occurs. The
S
tage 2

transfer assessment usually occurs in
March of your second year
.



Each School has internal procedures
to consider

cases of (a)

serious problems (e.g.
personality conflicts) between a

student and her/his supervisory committee; (b) to decide a
course of action in case a student fails to satisfy any programme requirements.



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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12



It
is advisable that all students and supervisors familiarise themselves with UCD Code of
Practice for Supervisors
and Students

(section 4
), and the Code for Conflict R
esolution

(section 16)
.


Students are welcome to address any concerns to
the relevant
programme

director

(Denis
Shields or Geraldine Butler), who will advise them on the appropriate course of action.


6.

Stage Transfer


The
PhD programmes into two stages. Stage 1
is a period of research and skills
development where the student acquires the competencies required for independent
research in their area. Stage 2 is largely dedicated to carrying out a body of o
riginal,
publishable research required for a PhD.

Stage 1 studies normally comprise
s

90 credits so
that
a full time student
can

complete it

1n 12
-
18 months
. To progress in their doctoral
studies the student must undergo a Transfer Assessment

by an assessment panel
.


For students entering
the
programme
(s) between

September
and January,

PhD
S
tage
1
assessment

will take place
during March of your second year.



Assessment procedure


PhD Stage 1 Transfer


All fulltime students who registered for Bioinformatics and
Systems Biology

or the
Computational and Infection Biology
PhD between Sept
ember

and Jan
uary

must present for
PhD Stage 1 transfer assessment
sometime

in early

March
of the second year of study

(exact location and time of assessment will be emailed to you nearer the date).



Prior to this assessment copies of record forms
for
all

DSP meetings, signed off
by all
relevant participants,
must

be submitted to either Anthony Chubb (BSB) or Heather Woo
d
(CIB)
.



Students must also submit a written assessment report (work progress & thesis proposal)
document
.
This report will be given to the assessment panel. The criteria upon which the
candidates will be assessed are as follows



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13


1.

Are the aims of the
project clear?

2.

Has the student demonstrated an understanding of knowledge in the field?

3.

Is there evidence of progress made?

4.

Is there a clear research plan for the doctoral phase?


The report should be
at least five

but no more than
eight A4 pages
(excluding
references)

in length, (Times New Roman, 12pt, 1.5 spacing)
. It may contain figures
and tables. It
must

contain a research plan for the doctoral phase.
BSB
s
tudents
should
prepare a draft of the assessment report and present it along with the br
ief presentation
(see below) at their 12
-
month DSP.
CIB
s
tudents
should discuss their doctoral plan with
their two supervisors.
The
report
must be written to a good scholarly standard (within the
space constraints). The requirements will vary by area, but
a typical thesis proposal could
define precisely the prob
lem being addressed, the proposed solution, and the preliminary
results
that

demonstrate that the produced solution is viable, and a detailed plan for
completion.


In addition
the principal
supervisor

must submit

to the
programme a
dministrator
s

a
statement on the progress of the student within
S
tage
1 and recommendation on their
progression to
S
tage
2
, and the plans/progress on taught modules including transferable
skills, laboratory experien
ce, and industrial/academic placement
. This should also be signed

by the joint supervisor.


Students are to present for interview with the Assessment panel which will consist of at least
three members of academic staff in the university, assigned by the

relevant

steering
committee
s
.


Students will be asked to make a brief presentation (
no more than 5 min
ute
s
) and 4
slides maximum during which they will typically explain what the background to their project
is, what the main overall aims of the project
are, progress to date, and projected future
plans. This will be followed by questions and discussion with the student.



The decision on w
hether to upgrade/ transfer a student to
S
tage
2 of the PhD programme
will be made by the Assessment Panel. It will be

based on:



The quality of the Thesis Proposal



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General performance in the taught modules completed at this stage (but
not all modules will
need to be completed at this stage)



General performance in the rotation projects (for Computational and
Infection
Biology students).


Outcome of the Transfer Assessment:


The panel must make a recommendation after the assessments. The recommendation must
be one of the following:

1.

Satisfactory progress
-
transfer to PhD.

2.

Student would benefit from reassessment


present again in
3
-
6 months

3.

Work towards completion for the award of Masters Degree

4.

Termination

of Student’s registration


student to be awarded a certificate of credit
for any modules for which credit has been awarded.


After your Transfer Assessment has taken place a Transfer Assessment Review Meeting of
your DSP is held to discuss the recommenda
tions of your Assessment Panel. If the
recommendation is to progress to Stage 2, you will progress to the next phase of your PhD.
If the recommendation is other than for progression to Stage 2, the options recommended
by the Assessment Panel and the potent
ial for re
-
presenting to the next Assessment Panel
sitting of the will be discussed
with your DSP
.


Your transfer assessment reports will go to your relevant schools


Graduate School Board
meeting for approval and you will be notified shortly aft
er this me
eting of the outcome.


If you wish
,

you have the right to appeal a decision of the Assessment Panel. In the first
instance, an informal appeal should be made in writing to
the Director
. In the second
instance, an informal appeal should be made in writing
to your Head of School. In the third
instance, an informal appea
l should be made in writing to the College Graduate School
Board. In the event of an unsuccessful appeal at th
ese

level
s
, the student may apply to the
Assessment Appeals Office to formally app
eal the outcome of the transfer assessment.

Please contact the Dean of Graduate Studies (
http://www.ucd.ie/graduatestudies/infoforstaff/
)
for more information.





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7.

C
andidacy
Requirement part

A
: Coursework


UCD operates a credit
-
based system for accrediting modules acquired during the structured
PhD.
Students in both the
Bioinformatics and Systems Biology

and Computational and
Infection Biology

programme
s

are required to take

a minimum of
30 credits to be
accumulated at some stage dur
ing the PhD
.

It is recommended that most students take

35
credits
.
Where a student plans to depart from this, the DSP should contact the
Programme
Director
s

giving a justification.
Since a full year is 90 credits, that means
abo
ut a third of the
first year could

be taken up with coursework.
However it is not necessary that all credits are
obtained in year 1.
The table
on the following pages

indicates which modules are core
(required) and optional for the

programme
s
. Students
s
hould discuss with their principal
supervisor and Doctoral Studies panel which subjects are suitable for your PhD.

Accredited modu
les are available to assist you

in developing the knowledge and skills base
required to complete your PhD in the time re
quired
. It is recommended that
you identify the
modules most appropriate to your needs
in consultation with your supervisor

and DSP.


Please note that students taking modules in different colleges
should

contact
Anthony
Chubb or Heather Wood

to make sure
that we

have record
s
.
However, y
our performance
and grades
in taught modules will be
noted

in your final PhD transcript.


The course web sites
:
http://bioinfo
-
casl.ucd.ie/PhD/

provides

links to more information
about the modules that are listed below.




Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

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16


Bioinformatics and Systems Biology/Computational Infection Biology modules:


Module

School/
Institute

BSB

CIB

Who runs it

Semester

Credits

Module
number

Notes

Bioinformatics
Research
Seminars

Conway

C

C

Denis Shields

1&2

5

CNWY40070


Bioinformatics
Applications and
Databases

Comp Sci Inf

C

R
O

Anthony
Chubb

2

5

COMP50030


Molecules in
Medicine

Conway
Institute

C/
R


Clare
O’Connor

1

5

MDSA10240

for non
biologists

Basic Principles of
Cell
Biology

Conway
Institute

C/R


Paula Byrne

1

5

MDSA10180

for non
biologists

Introductory Statistics
using R for
computational
biologists

Math.
Sciences;
Comp

C

C

Michael
Salter
-
Townshend

1

2.5

STAT50010


Python Programming
for Computational
Biologists

Math.
Sciences;
Comp Sci Inf

C

C

Col
m

Ryan

1

2.5

COMP50050


Systems Biology

Mathematical
Science

C

R
O

To be
decided.

2

5

ACM40470


Online Research skills
CompBio

Conway
Institute

C

C

Anthony
Chubb

1

5

CNWY50030


Advances in Infection
biology

Veterinary
Medicine


C

Stephen
Gordon

2

5

VET40080


Communications and
Outreach

Comp Sci Inf

O


Bridget Kelly

1

5

COMP41380


Bioinformatics for
Computational
Scientists

Comp Sci Inf

O


Gianluca
Pollastri

2

5

COMP40400


Multivariate Analysis

Mathematical

Sciences

O

O

Claire
Gormley

2

5

STAT40150


Machine Learning

Comp Sci Inf

O


P
Cunningham

1

5

COMP30120


Bayesian Analysis

Math.
Sciences

O

O

Brendan
Murphy

1

7.5

STAT40390


Molecular
Neuroimmunology

Conway

O


Jana Haase

2

5

CNWY40110


Genomics and
Proteomics

SBBS

O


Jana Haase

2

5

BMOL30050

(limited
spaces)

Genomics
-

principles
and practical
applications

Conway


O

Brendan
Loftus

3

2.5

CNWY40150


Current Concepts in
Infection Biology

Veterinary
Medicine


O

Jennifer
Mitchell

1/2/3

5

VET40090


Advanced Research
Skills for Biological
Scientists

Conway


O

Giuliana Elia

2/3

5

CNWY40100


Introduction to
“omic” and advanced
imaging technologies

Conway


O

Giuliana Elia

2

5

CNWY40090


Conway Lecture and
Seminar series

Conway

O

O

Ollie Balcque

1/2/3

5

CNWY40010




Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
17


Additional modules that may be suitable for non
-
biologists

Plant and Animal
Genetics

SBES

O


Stefano
Mariani

2

5



Molecular Genetics
and Biotechnology

SBBS

O


Patrick
Caffrey

2

5



Potential transferable skills modules (or see Graduate
Certificate and Entrepreneurship)

Innovation and
knowledge part 1

Business
management

O


Prof F. Roche

2

2.5



Innovation and
knowledge part 2

Business
management

O


Prof F. Roche

2

2.5



NUIG module available by video conferencing

Probabilistic Models

in Molecular Biology

NUIG

O


Prof. Cathal
Seoighe

2






C
-

core; O
-

option; RO


recommended option.
Graduate Certificate in Innovation and Entrepreneurship

CIB students may participate in the courses designed for the Graduate Certificate and
Entrepreneurship at UCD/TCD. The first two modules are available as options taken in conjunction
with the 20 credits of core modules listed above. The entire certificate
(30 credits) may also be taken
over 2 years, in addition to the 25 credits of core modules. There is a charge per module;
however,
you can apply for a bursary to cover the entire costs. See details at

http://www.innovators.ie/p/whowewant

Opportunity
Generation and
Recognition (Core for
certificate)




Innovation
Academy


5


Available
to all
students

Creative thinking and
Innovation (Core for
certificate)




Innovation
Academy


10


Available
to all
students

http://www.ucd.ie/graduatestudies/coursefinder/taughtprogrammes/grad
-
cert
-
innovation/

Other modules
are

available for those who have taken the core modules. See web site for details.



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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18


Module levels

The first
number of the module code indicates module Level
.
Most

PhD students will find
Level 4+
(Masters
+

level) academic and research skills modules most useful. However, a
limited number of Level 1
-
3 may be appropriate in certain cases,
for example
if you need
to
learn something from outside your undergraduate discipline.


To find out about other modules available go
to:

http://www.ucd.ie/students/course_search.htm

Select the modules tab. Make sure to

select appropriate levels (if in doubt choose all of
1,2,3
,

4

and 5
) if using the search facility.
Modules provide information on timetabling
(subject to change) and on pre
-
requisites, which may help in identifying more basic courses
that you may choose
to attend first.


Computer science and informatics courses:

http://csimoodle.ucd.ie/moodle/


Module registration

Please make sure you register for
every module you participate in;

you will not be able to
retrospectively register for any modules.


If you wish to get permission to opt out of a core
module, for which you are automatically registered, contact
the programme director

seeking
permission as soon as possible. Note that if you do not withdraw in time, the module may
appear as a ‘
FAIL

in your PhD transcript detailing information on courses taken.
Online
registration is gradually being introduced for graduate modules. However, most still need
module registration forms.


Your Principal Supervisor
must sign the module registration form

(fo
r CIB students, forms
will be signed by G. Butler)
;
they

must also be signed by the module coordinator where the
module is from outside the student’s School.

To receive credit and register for each module Computational Infection Biology Students
should fill out the relevant form and give it to
Heather Wood
, Systems Biology Ireland
students should give it to Philip Smyth. All modules should be discussed with
your Principal
Supervisor as soon as possible.


If you
later
decide to withdraw from the module or to audit the module, you must inform
Heather Wood or Anthony Chubb

within six weeks of the commencement of the module.





Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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19


Taking Modules for Credit and

Auditing Modules:


You may opt to take a taught module for credit or to audit the module

(i.e. attend and
learn, but not be assessed)
. In either case, you will be expected to attend all classes and
associated seminars,
practicals
, etc., unless otherwise
agreed with the module coordinator.
Taking a module for credit involves undertaking all module assessments, while auditing a
module requires that you attend

all
classes
, labs etc

without an
y assessment.
If you would
like to audit a module, please first
discuss this with the module coordinator.


Modules at other Institutions


You should also use your RPDP to record details of any courses or modules you may take
outside of UCD.
Molecular Medicine Ireland

runs regular courses
(
www.MolecularMedicineIreland.ie

)
. To receive credit for any of these please discuss this
w
ith
your programme director
.


8.

C
andidacy Requirement
part
B:


Seminar
and lab group
participation


To encourage
your
communication
with
research groups

at UCD and to foster an awareness
of

and an interest in research
,

students are
required to



1.

Attend and contribute to
the
UCD Bioinformatics

and Computational Infection Biology

seminar series

throughout their PhD

(part of CNWY40070)

2.

To

attend
and take part in
the lab group meetings

of their host laboratories
.

3.

To attend the weekly research seminars in the Conway Institute


The seminar series

(CNWY40070)

takes the format of a 1
-
hour session

(Mondays at 1pm)
,
with two talks of 20 minutes followed by 10 minutes discussion.
A
ll PhD students will be
required to
give
at least one

presentation

as part of this series

in their first year
(
typically
their as
sessment transfer

or rotation

presentation
)
.

You will choose whether this

presentation
comprises a literature review, a presentation of one or more key articles, or a
presentation of your research to date and issues around it to stimulate discussion around
your research area.




Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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20


This seminar presentation will be assessed by
the
supervisors, a
s part of the
CNWY40070
module, evaluating the ability to communicate the science clearly.




A
ll students are required to

regularly
attend
the seminar series.

Attendance at seminars
in
year 1
will be self monitored on a sign off sheet to be countersigned at end of each
semester by
the students’ supervisor. Students will grade each talk on intelligibility,
relevance, and interest, and indicate whether they asked any questions
: this is used in

planning and discussing the student’s own
needs with their supervisor,

in future planning of
future seminar serie
s, and finally contributes towards as
sessment of the CNWY40070
module.
In subsequent years students will be strongly encouraged to continue to provide
strong support for the seminar series by attending it, and will
typically
present
once in each
year (
either
own
research finding
s or general overview

of
a research area
)

as req
uested by
the Seminar Series organi
s
er.


9.

Demonstrating/Graduate Teaching Assistant


PhD students interested in advancing their teaching skills can do so by demonstrating

(acting as a teaching assistant)

in some
undergraduate modules.

Some schools (for
example the School of Biomolecular and Biomedical Science) require that all PhD students
take on some demonstrating, which is paid at an hourly rate. Students in the CIB
programme will not do any demonstrating in their first year. Students in Systems Biolo
gy
and Bioinformatics ma
y have opportunities

to demonstrate in an undergraduate semester 1

(Sept
-
Dec)

Bioinformatics

module

(MEIN30240).



Students interested in demonstrating
must attend an associated teaching course. Those
registered with the School of Medicine and Medical Science (or who wish to demonstrate
in
MEIN30240)

must attend a two
-
day workshop on demonstrating (Teaching in Higher
Education, MDCS41410) in early Septemb
er. The workshop will prepare demonstrators for
demonstrating and for preparing the entries to their teaching portfolios. The portfolios
including at least 15 hours of demonstrating need to be completed before assessment,
usually at the end of semester 1 o
r at the end of semester 2 for those who can't do 15h in
the first semester.

A similar module is available for those registered with the School of
Biomolecular and Biomedical Science

(BMOL40080)
, and there
are
other modules in other
schools

(BIOL40100, CHEM40340 and MATH40340)
.



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
21



10
. Review of student’s balance of work effort and direction


Bioinformatics and Systems Biology
:
The student should have
two
supervisors drawn

from
different disciplines; this is intended to maximize the student’s opportunities to develop over
the four years. It is a stipulation of the programme that students spend at least 3 months in
an experimental laboratory, and normally at least half of th
e research time should be on
non
-
laboratory

(
i.e.

computational) research. However, outside of these constraints, the
student has the opportunity to make a case to the supervisory panel to alter either the
balance of experimental and computational work, o
r the overall direction and project area.
Having been in the programme a student may have an interest in re
-
directing the focus of
their studies, given the availability of alternative supervisors and project areas within the
programme. (Such flexibility

wi
ll be limited for certain studentships that are funded from
particular granting agencies

e.g. SFI fundin
g to SBI

is inflexible in this regard
). Each student
should discuss this with their Doctoral Studies Panel in the first instance. Students s
hould
arrange to meet with the
Director (typically up to month 10) to discuss any requests for a
significant shift in their supervisory team and project direction, so that alternative
approaches may be investigated and planned prior to the month 12 Review.



Computational and Infection Biology:

There will be two formal reviews of the students’
progress during year 1, at the end of each rotation. Students are required to gain
experience both in the laboratory and using a bioinformatics/computational approach

during
this time. At the beginning of year 2, the student will likely choose a project that has
emphasis on either a laboratory or a bioinformatics approach. However, all students are
encouraged to use both approaches, and to alter the balance as the proj
ect develops.


1
1
. Approximate schedule

of events


Under the normal course of events, P
hD student

progress
shoul
d follow the following
schedule.


Bioinformatics

and Systems Biology Programme


Sept


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Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
22


Sept
-

Dec

Year 1


1 month Doctoral studies panel meeting.

Feb
-

May

Year 1

Doctoral Studies Panel 6 month review

May


June

Year 1

Review of student’s balance of work effort and direction

Sept
-
Dec
Year 2

Doctoral Studies Panel 12 month review

Mid Mar

Year 2

Assessment Meeting for Stage 1 to Stage 2 transition.

Aug
Year 2

Supplementary assessment for Stage 2 where appropriate

Oct
Year 2

Doctoral Studies Panel 24 month review

Oct
Year 3

Doctoral Studies Panel 36 month review

Jun
-
Aug


Year 4

Submit thesis


Computational Infection Biology


Sept Year 1

Commence studies

Sept Year 1

Choose rotation projects, and begin rotation 1

Oct


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Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
23


Coursework

is normal
ly completed in the first

two

year
s
,
but some modules may be taken at
a later stage depending on student needs.

Seminar
a
ttendance
and participation

continues throughout your

time

at UCD
.



1
2
.

External
conferences, workshops, placements


For most students there is adequate funding to attend 1
-
2 major international conferences
during your PhD.

You should plan th
ese

carefully, discussing with your supervisors from
both labs what upcoming meetings will be most beneficial, especially as many

important

meetings have abstract submission deadlines
many
months before the actual meeting.

You
should also consider obtaining f
inancial support from other sources, such as from scientific
organisations. Join any relevant organisations in your first year as a
PhD

student.


(a) Conferences and workshops

Students should aim early in their career to present at conferences, ideally orally
but
poster
presentations

are also appropriate
. Funding
from the Programme
s

to support attendance at
conferences is contingent on the student making a real effort to get a g
ood quality abstract
submission to the conference organizers before their deadline (often well in advance of the
meeting). A good quality abstract needs to be carefully reviewed
in advance of submission
by both supervisors.
The Virtual Institute of Bioinfo
rmatics, Eire (VIBE) meets about once a
year and provides a useful national forum to present results in a friendly environment
(
http://oscar.gen.tcd.ie/vibe/meet.html
).


(b) Placements

for students in Bioinformatics and Systems Biology

Students
can
benefit greatly from placements in academic or industrial laboratories abroad.
Su
ch placements
will be considered by
the committee

to be equivalent to

one module (5
credits) where students complete a
2
-
page
report submitted to their supervisor

and to
the
administrator

bioinfo@ucd.ie

on compl
etion of the work placement. Typically placements
may occur towards end of
2
nd

year and in the 3
rd

year of the PhD.

SBI has an exchange
program in place

with the Manchester Centre for Integrated Systems Biology (MCISB) and
students will be free to
take up a placement in the Manchester labs in their 3
rd

year.


Industry placements

Industry placements will be both national and international, in both the very specific areas
of PhD project interest (usually a longer term placement of 2
-
5 months), with shorter term


Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
24


national placements in companies employing computationally skilled PhDs

with a biological
background (e.g. in the clinical trials industry), aimed at future career planning. In placing
students, we will follow up our existing contacts in Irish based companies including
Illumina
,


Quintiles, Wyeth, Siemens, I
d
entigen, IBM, Ge
nable,
Opsona;

and companies abroad

including Astra Zeneca
, Merck
,
Pfizer

and Illumina
.


International laboratories.

We will provide funding and logistical support towards
students
s
pending a period of time working in a laboratory abroad. We have an
agreement
to exchange students with the Systems Biology Programme
s

at Imperial College London

and
at
the
University of Manchester
. Student placements are best decided by the direction of
their research programme, and for this reason we anticipate that stud
ents will go to a
variety of locations and supervisors such as the following with which we have

previously
exchanged researchers on bioinformatics
-
related projects:


Alvis Brazma, EBI (Cambridge; microarray analysis)

Rob Russell, EMBL
-
Heidelberg
(oligopeptide structural bioinformatics)

Wolfgang Huber, EBI (tiling arrays)

Guy Perriere, University

of Lyons (Multivariate analysis)

John Quackenbush, Harvard School of Public Health (microarray analysis)

Laurent Duret, University of Lyons (molecular evo
lution)





(c) Placements for students in Computational Infection Biology

There
is no
support

for

placements for students in this programme. However, students may
apply to the steering committee for funds to attend suitable training programmes (such as
those
run

by FEBS) or to take modules in the Graduate Certificate in Entrepreneurship. The
Wellcome
Trust also prov
ides the possibility of a three
-
month policy internship at the
Academy of Medical sciences (London). These are awarded competitively in year 3
-
4 of the
PhD programme, and provide funding for an additional three months.


1
3
.
Publications

Publications in peer
-
reviewed journals are the internationally

recognised measure of the
standard and quality of your research work and are the “career currency” that you will be
evaluated on by future employers. Working with your supervisor, you should en
sure that on


Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

v4

Page
25


completion of Stage 2 of you
r

doctoral studies you have already published some of the work
carried out for your PhD and that the remaining publishable material has been submitted for
publication.


1
4
.
Thesis Production


In producing your thes
is you will work closely with your principal supervisor

and secondary
supervisor

to ensure that the research described and the way it is presented meets the
standards expected of a doctoral thesis.


A science
-
based thesis normally comprises:



Title



Statement of authorship and submission



Table of contents



Acknowledgements



Abstract (approximately 1 page long, stating succinctly what was done, what was
found and the implications)



Introductory chapter (the general context of the work as a whole i.e. a li
terature
review, with a statement of hypothesis and aims)



General methods/ information chapter (optional
-

e.g. a detailed description of the
methods used widely in the thesis
. Alternatively, each results chapter may have a
methods section.
)



Data chapters
-

usually each stands

alone with introduction, methods (including
methods of analysis), results and discussion, thus serving as a template for a
publication,
but also relating to other chapters.



General discussion (recapitulating the findings in the chapte
rs but in a broader
context, particularly in relation to other work, and overall implications, and
suggestions for further work)



Bibliography (using a sta
ndardised reference system e.g E
ndnote)



Appendices (optional), e.g. containing manuscripts, raw data,
computer software
you’ve developed etc.

It is strongly advised that students should consult literature on the writing skills required for
scientific papers and theses.
A limited bibliography is presented in below.


Suggested reading for writing scientific
theses and research papers



Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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26



Alley, Michael. 1996. The Craft of Scientific Writing. Third Edition. Springer. NewYork. 282p.
ISBN 0
-
387
-
947
-
66
-
3.
www.Springeronline.com


Gustavi, B. 2003. How to write and
illustrate a scientific pap
er. Cambridge University Press.
ISBN 0
-
521
-
53024
-
5. [UCD Library 8080665/GUS. 19.39]


More, Robert. 1998. How to Write. Tools for the Craft. University College Dublin Press.
Dublin. 165p. ISBN 1 900621 15 0.



When submitting
your thesis, your principal su
pervisor is required to sign a statement that
the thesis is ready for submission
.
If you are of the opinion that such a statement is being
unreasonably withheld, you can appeal in the first instance to the School Postgraduate
Studies Committee, the Graduate School Director and ultimately to the Academic Council
Standing Committee on Examinations.


All theses submitted by SMMS students must include a statement on plagiarism in
accordance with the School
’s policy on plagiarism. T
his policy can be obtained from the
school office.
Other schools may have or introduce similar requirements.
The UCD policy on
plagiarism is available from
http://www.ucd
.ie/registry/academicsecretariat/docs/plagiarism_po.pdf

PhD theses may be submitted providing

your fees are paid and your registration is current.
The fi
nal deadline for submission will be in late August of your final year.
For information on
submitting your thesis visit the
Assessment Unit
website at

http://www.ucd.ie/registry/assessment/info_stu.htm

1
5
. Thesis Examination

Thesis examination follows the regulations of the individual School and the UCD
Examinations Office. Typically students must have upgraded/transferred to
S
tage
2 of the
structured PhD programme

and

made satisfactory prog
ress as attested in their Annual
Re
ports. In summary
,

the thesis is evaluated by both an external and internal examiner. The
principal supervisor
may not be
an

internal examiner
.




Bioinformatics and Systems Biology
/Computational Infection Biology PhD programmes

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27


Thesis Examination

Your thesis will be examined by an Examination Committee comprising of an external
examiner
,

and one or two internal examiners
, and a chairperson
. The external examiner,
who must be a recognized expert in the field or research, has to be nominated by the
School, approved by the Graduate School and ratified by the Academic Council Executive
Commi
ttee. To maintain the independence of the examination process, your principal
supervisor cannot be an internal examiner. All examiners read and assess the thesis in
accordance with UCD guidelines which indicate tha
t examiners should give particular
attent
ion to:



The originality of the work described and the theories developed in the thesis



The candidate's familiarity with the published work of other authors in related areas



The candidate's ability to summarise the work of other authors and to synthesise a
theoretical framework within which to position the work described in the thesis



The candidate's prose style should be appropriate to the discipline, but clear, simple,
unambiguous writing, which is syntactically and grammatically correct
, is required of
all candidates



The methodology adopted by the candidate to address the research topic

o

Is it accurately and comprehensively desc
ribed? Is it appropriate to the topic?

o

Is the candidate aware of alternative methodologies which might have been

employed?

o

Is t
he candidate sensitive to any inherent weaknesses in the methodology?

o

Where a novel method has been developed, has it been tested and calibrated
appropriately?



Experimental Design



Presentation of the results of the research.

o

Are the results presented in a

clear, accessible way?

o

Are tables, figures or plates, where included, adequately annotated and
correctly referenced in the text?



Interpretation of Results:

o

Are the candidate's conclusions reasonable on the basis of the evidence
presented?

o

Has the signif
icance of the results been fully appreciated by the candidate?

o

Has the correct statistical analysis been employed (where appropriate) and
justifiable conclusions arrived at?

o

Have theories formulated on the basis of the results taken into account


Bioinformatics and Systems Biology
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28


relevant

findings published by other authors?

o

Has the candidate identified any weaknesses or lacunae in the evidence
adduced?



The bibliography

o

Is it comprehensive and up
-
to
-
date?

o

Are references to the published literature annotated accurately and
consistently i
n a recognised citation style?



Presentation of the thesis
-

is it free of typographical and other errors?

You will also be examined orally in a
viva voce
examination where you will be asked to
defend your work and conclusions (in the context of the criteria indicated above).


Some amendments to the thesis, often minor, are usually required. The report of the
examiners is considered by the Academic Council
Standing Committee on Examinations
(ACSCE). In the event of a recommendation by the examiners that a PhD degree not be
awarded you can submit a revised thesis for re
-
examination subject to the conditions set out
by the ACSCE. On submission, the revised the
sis must be accompanied by a statement from
your supervisor that the thesis has been revised under their supervision. You can also
appeal a decision of the ACSCE to the Assessments Appeals Committee.


PLEASE NOTE that your thesis is the property of UCD an
d all issues relating to
intellectual property are subject to the University’s practices and policies.


Thesis submission and examination procedures for Masters Theses are the same as those
described above except that an oral examination is not mandatory.
An oral exam can be
held on the request of the Head of School or of the examiners.


Research Ethics and Good Practice

The UCD Research Ethics Committee is tasked with reviewing and publicising best practice
designed to ensure that all research carried out

by UCD staff and students is done in a
professional manner and that such research complies with UCD’s ethical standards and
abides by relevant regulatory requirements.

See
http://www.ucd.ie/t4cms/REC%20Code%20of%20Good%20Practice%20in%20Research%2
0271010.pdf





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Penalties for plagiarism (i.e. passing off the work of others as the student’s own


for
example by failing to cite the source of material) and for fabrication of data

(i.e. fraud) are
severe. See


Activity

Timeline

Prerequisites

Selection and contacting of
External

Examiner (responsibility of
the supervisor)


4
-

6 months before submission


Extern must be someone
associated with a

University
outside the Republic of

Ireland.
The

name is submitted to the
School Postgraduate

Studies
Committee, to the
relevant
Graduate Committee and
ultimately

to the Academic
Council Executive Committee for

approval (ACEC meetings are
held 7 times a year)
.

Submit draft chapters /
draf
t thesis to supervisor
for review


If adequately
forewarned
, the
supervisor should attempt to turn
draft chapters around within a week
and the draft thesis in 2
-
3 weeks.


Schedule provisional date
for viva


Keep in mind the conferring
dates

because the final thesis must be
submitted at least 1 month in
advance.

Extern must have been
approved by the ACEC.


Complete supervisors
recommended corrections,
get thesis soft bound (3
copies)




Submit soft
-
bound thesis
with completed

forms to
Exami
nations Office in
Tierney

Building

Minimum 2
-
3 months prior to viva
(deadlines for submissions are for
fee purposes


see www.ucd.ie/fees/

Thesis submission dates
-

a) Outstanding fees, library
fines etc. must have been
cleared

b)
Examination forms must be


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30



Postgraduate studies)

signed by your supervisor

Hold viva. The time and
venue is the responsibility
of the

supervisor


Two hours is normal but it may be
longer (you won’t notice the time
going)

A good night’s sleep


you
already know what you need to

know!


Make
corrections
recommended by extern,
get thesis hard
-
bound and
submit
required copies

to
Examinations Office (
and
copies to the supervisors
)
.


a) There is a deadline for hard
-
bound thesis submission in order to
make the conferring date (about 1
month before conferring, see
www.ucd.ie/confer/
)


b) Thesis binding takes a minimum
of 24
-
48 hours and costs
about 4
0
euro each
-

you will need at least
4

copies

http://www.thesiscentre.ie/

You must submit:

a) the forms indicating the
result of the viva (written and
signed by the internal and
external examiners)

b) a le
tter from the internal
examiner stating that you have
addressed all the recommended
changes


Conferring


See www.ucd.ie/confer/ for dates


Hard
-
bound th
esis and letter
must have been
submitted to
Examinations Office



1
6
.
Conflict Resolution for Students and Supervisors


The relationship between the student and Supervisor is of vital importance to the s
uccess of
the Doctoral experience. As part of the doctoral support framework, a conflict resolutions
strategy is a necessary step towards ensuring the quality of education and training at UCD.
It is imperative for the minimisation of conflict and for good
practice in supervision
generally, that the roles and responsibilities of the student and supervisor are clearly
understood as detailed in The Code of Practice for Supervisors and Research Students. It is
important to recognise in addition that however fri
endly and supportive the relationship may
become, it is fundamentally recognised as academic and professional.


The following document deals spe
cifically with any issue that arises within the relationship of
the graduate research student and the supervisor
. The document will suggest the


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31


appropriate steps to take toward
s

conflict resolution in the context of university regulations,
guidelines and su
pport services.


It is the intention of the

document to discuss conflict resolution specifically within the
con
text of the student
-

supervisor relationship wit
h the aim of developing a cohesive
doctoral experience across the University. It is expected that both students and supervisors
contribute responsibly to the establishment and maintenance of a healthy workin
g
relationship.

http://www.ucd.ie/registry/academicsecretariat/conflictr.htm


1
7
.PhD Symposium

The PhD students

in the two programmes

have jointly
hosted

a symposium

each year
since

2010

called

Computation
al

Biology
for

Innovation
.


The aim is to bring together research in different areas of computational biology
and
infection biology
and provide an opportunity for students to showcase their work in an
interdisciplinary scientific environment. In addition, this event
is

an opportunity for students
to make their research known to leading companies in the field, and for the companies to
h
ave a chance to get to know the next generation of young Computational Biologists.

The

symposia consist of several sessions and have

presentations by PhD students and a
keynote speech by an internationally renowned speaker. All PhD students

doing research
in
Systems Biology and Bioinformatics and in Computational Infection Biology

are invited to
present
their research (oral or poster)
. The symposia are organized entirely by the PhD
students (including raising funding).


1
8
.
International Students

Immigration



All students from OUTSIDE the European Union (EU) or the European Economic Area
(EEA) must REGISTER IN PERSON after arrival at the GARDA NATIONAL IMMIGRATION
BUREAU.

Please see the IRISH NATIONAL IMMIGRATION SERVICE http://www.inis.gov.ie/
for full
details on application and registration procedures



Bioinformatics and Systems Biology
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Visa Requirements

The Irish Department of Foreign Affairs issues visas to citizens of certain countries who
wish to travel to Ireland. You can check whether citizens of your own country would nee
d
an entry visa by visiting the Irish Naturalisation and Immigration Service website.

Please note that students from the USA, Canada and Malaysia do not require entry visas to
Ireland. Students from these countries should skip to the section regarding Imm
igration
Requirements below.

Students who receive an entry visa must also register with immigration upon completion
of registration at UCD. See below for registration procedures.

Please see the www.inis.gov.ie
for full details on application procedures as these vary from
country to country.

Immigration Requirements and Procedures

All students from outside the European Union (EU), the European Economic Area (EEA), or
Switzerland must register in perso
n, following their arrival in Ireland, at the Garda National
Immigration Bureau (GNIB). The GNIB is located at 13
-
14 Burgh Quay, Dublin 2 (Tel: 616
7700). In order to register, a student needs to have the following documents
: ∙




Valid passport (and visa if

appropriate)



Valid UCD Student Card



Letter from the UCD Student Desk stating that you are a registered student and
indicating the start date and duration of your academic programme.



Evidence of fees paid to UCD (receipt)



Proof of sufficient funds: e.g
. current bank statement showing your name, a letter
of guarantee from parent or guardian indicating availability of sufficient funds, or a letter
from your sponsoring body confirming your financial status



Any other documents which may be requested by the

immigration authorities

Plea
s
e note that there is a €1
5
0 fee payable to the GNIB to register.

The cost of a multiple
entry visa is €100. Both
are needed

every year.

EU, EEA, or Swiss nationals, who are resident in Ireland to follow an approved academic
programme, are not subject to these immigration requirements.



Bioinformatics and Systems Biology
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1
9
.

Accommodation

UCD residence:
http://www.ucd.ie/residences/residences/glenomenaresidence/. You will
have to apply for rooms by using your student number and date of birth.
Please note that
postgrads and undergrads are mixed together.

Ch
eck out the following Web sites
:
-

www.daft.ie

www.findahome.ie

www.myhome2let.ie

www.unison.ie

Areas close to BELFIELD
are:
-

DUBLIN
4:
-
Ballsbridge, Donnybrook, Sandymount

DUBLIN
6:
-

Ranelagh, Rathgar, Rathmines

DUBLIN
14:
-

C
lonskeagh, Dundrum, Goatstown

DUBLIN COUNTY
:
-

Blackrock, Booterstown, Mount Merrion, Stillorgan


20
.
Student Health Services


The Student Health Service in UCD
-

Telephone: 716
-
3133
-

is located in the Student
Centre on the Belfield campus. If a student is worried about a health problem, they may
call to the Student Health Service, where the receptionist will make an appointment
for
them to see the appropriate officer.

There is no dental service attached to the Student Health Service and dental care is not
covered to a great extent even with a medical card. Dental treatment is relatively
expensive in Ireland and students are advi
sed to have a check
-
up before they leave home.
If dental treatment is required the Student Health Service can recommend a local dentist.

Health Insurance for EU Nationals


Students from EU Member States in possession of the European Health Insurance Card
(EHIC), which recently replaced the E111 and E128 health certificates, obtainable from
their own health authorities before departu
re, are entitled to

free emergency health
treatment in the public health system. Details are available at


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34


http://www.hse.ie/eng/services/Find_a_Service/en
titlements/EHIC/Visitors_to_Ireland.htm
l

Information on your entitlements as a visitor to Ireland under t
he EHIC system are given
on the website
www.ehic.ie

Please ensure that you obtain an EHIC card before you arrive in Ireland.

The EHIC card covers you for

a temporary stay, and for

emergencies.
Students may have
entitlement to a Medical Card under EU regulations provided they have documents from a
competent institution

in another Member State stating they are still insured in that state, or
are a dependent of an insured worker.

This medical card, which can be obta
ined from the
local Health Service Executive in Dublin (Health Centre Headquarters, Vergemount Hall,
Clonskeagh, Dublin 6, opening hours 9.00 to 1.00 and 2.15 to 5.00 Monday to Friday, tel:
+353
-
1
-
269 8222) entitles students to free health care, including
visits to the local doctor,
all necessary in
-
patient and out
-
patient treatment in public hospitals and drugs and
treatment prescribed. If you obtain a medical card, you should ensure that the doctor in
your area, with whom you are registering, is a member
of the GMS (General Medical
Service) scheme.



Health Insurance for Non
-
EU Nationals


It is recommended that non
-
EU nationals coming to UCD should have private medical
insurance. If you have obtained private medical insurance in your home country please
ensure that it is valid in Ireland. However, under Irish law, non
-
EU students who will be
resident in Ireland for a minimum of one year are eligible for public hospital treatment
under the same conditions as an Irish citizen, though non
-
EU students staying

less than
one year are not. For full details on this contact the International Student Adviser
.

Private Health Insurance


You may prefer to obtain private health insurance, which will cover you for in
-
patient care
in private and public hospitals (depend
ing on the plan). These are offered by several
companies (Aviva Health,
Laya

Healthcare, Vhi Healthcare

etc.
). The best place to start is


Bioinformatics and Systems Biology
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35


with the statutory

regulator, the H
ea
l
th Insurance Authority, at
http://www.hia.ie
.

The
cheapest pl
ans cost about €450
-
500

a year.

Please note that medical cover does not begin immediately with these insurance schemes
.

There is a "waiting per
iod" of 26 weeks. Therefore,
they are not recommended

to students
coming to UCD for short periods.

21
.

Applying for a P
ersonal
P
ublic
S
ervice

number

You will need a Personal Public Service (PPS) number to get paid, to open a

bank

account,
and to access public services. You cannot get a PPS number before you arrive in Ireland.
You can find details at
h
ttp://www.citizensinformation.ie/en/social_welfare/irish_social_welfare_system/personal_public_service_number.html

To apply,
you will need to
contact your local office of the
D
epartment of Social Community
and Family Affairs
, which depends on where you live
,
see
http://www.welfare.ie/EN/Pages/default.aspx


Proof of identity is a vitally important aspect of the
registration procedure and must be
established before a PPS Number is allocated. Documents presented may be held for
authentication. The following are th
e prescribed documents to accompany a PPS Number
application:


Bring along the following when applying
for your PPS

number





Irish National

UK
Citizens


EU / EEA
citizens


Non
-
EEA nationals


Birth
Certificate /
Passport

Birth Certificate

(long
form) AND
photographic evidence
(passport or driving
licence)

Passport /
Birth
Certificate


Passport /
National ID
Card

Passport /

GNIB card

Proof of
address


Evidence of
Irish
Address

Evidence of
Irish
Address

Evidence of Irish
Address

Do Not Bring:



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36




Baptismal Certificates



Employment identity cards / personal letters



Photocopies of certificates / documents



Expired documents

Evidence of an address might include:



Household utility bill



Official letter / document



Financial statement



Property lease or tenancy agreement



Verified employer's letter

Note: All documents
must show the applicants name and address

2
2
.

University Facilities

Library

The modern and well
-
stocked central library is located within the building opposite the lake
in Belfield.
The Health Science library is located in the Health Science Buildin
g;

please note
that you need your student card to enter.
There are also smaller libraries around the
campus. The library catalogue can be searched online at
www.ucd.ie/~library



IT SERVICES

Please visit :

http://ww
w.ucd.i
e/itservices/onlineitguide10
-
11/

for information on

how to receive your UCD e
-
mail address

Any official UCD e
-
mail sent to students will be addressed to their UCD Connect
address
.



UCD E
-
mail address

UCD registered students are automatically given

a UCD network username and password
when y
ou register with the University. If you have forgotten your details, contact the
Helpdesk at ext. 2700.
It is advisable that you register your new laptop/mac with UCD IT
services.

UCD has very powerful computing clusters. Two are Phaeton (UCD) and Irish Centre for
High
-
End Computing (Stokes
-
ICHEC). Accounts in these clusters can be obtained

by filling


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the forms at
http://telescope.ucd.ie/app_forms/accounts/

once the students have their
personnel number. (You can request your personnel number from H
uman
R
esources.
)


The official

email address will be maintained in each student'
s record, from which
distribution lists are compiled. Students can arrange to have their
UCD Connect account
redirected

to another address or service provider but students should note that it is the
student's responsibility to ensure that this alternate mailbox is viable.

UCD IT Services will never ask for your username and password or any personal credentials
by email. F
or more information on 'phishing' emails
visit
IT Security pages

UCD has very powerful computing clusters. Two are Phaeton (UCD) and Irish Centre for
High
-
End Computing (Stokes
-
ICHEC). Account in
these clusters can be obtained

by filling
the forms at
http://telescope.ucd.ie/app_forms/accounts/

once the students have their
personnel number.


Security and Safety Awareness on Campus


UNICARE is a University service designed to enhance the security of property and
the
personal safety of students, staff and visito
rs on the UCD Belfield campus. The programme
operates through the combined efforts of students, staff, the local Gardaí, the Buildings and
Services Department and various groups within UCD.


24 Hour Confiden
tial Emergency Line



Internal Telephone No: 7999



E
xternal Telephone No: 716 7999


You should use the UNICARE number to call for emergency assistance or to report any
issues regarding personal safety and security of property on campus, e.g. an
accident/emergency, fire, theft, reporting suspicious or troublesome persons or reporting an
incident you may have witnessed.

The UNICARE emergency line is operated 24 hours a day and assistance will be
provided immediately in response to your call. UNICAR
E red emergency phones
are located throughout the Belfield cam
pus.


Student Welfare




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If students find themselves in any difficulties, be it personal, medical or financial, help
should be sought from the supervisor or any other member of staff. The university also has
a wide range of support services. Please see
http://www.ucd.ie/advisers/
/
http://www.ucd.ie/stuhealth/Counselling.html/

http://www.ucd.ie/chaplain/



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39


2
3
.

Useful li
nks


PhD

Bioinformatics and
Systems Biology

http://bioinfo
-
casl.ucd.ie/PhD/

Computational Infection Biology

http://bioinfo
-
casl.ucd.ie/cib/

Systems Biology Ireland

http://www.ucd.ie/sbi/


Graduate studies
Documents

and Policies

http://www.ucd.ie/graduatestudies/infoforstaff/


General regulations for the degree of
Doctor of Philosophy


http://www.ucd.ie/registry/academicsecretariat/docs/academic_r.pdf


P
rogression in Doctoral Programmes including

Stage 1 Transfer Assessment

http://www.ucd.ie/registry/academicsecretariat/docs/doctoralp_po.pdf


Code of Practice for Supervisors and Doctoral Students

http://www.ucd.ie/registry/academicsecretariat/docs/researchs_code.pdf


Policy on
Plagiarism

http://www.ucd.ie/registry/academicsecretariat/docs/plagiarism_po.pdf


Split
-
site Arrangements for PhD and other Graduate Research Students

http://www.ucd.ie/reg
istry/academicsecretariat/docs/splitsite_po.pdf


Student Complaint Policy and Procedures

http://www.ucd.ie/registry/academicsecretariat/docs/complaints_po.pdf


Code of Practice for Conflict Resolution for Supervisors and Research Students

http://www.ucd.ie/registry/academicsecretariat/conflictr.htm





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