MSC Bioengineering Handbook

MSc NTRE
in FOR
Bioengineering
BIOENGINEERING
Course Handbook 2012-2013
TRINITY CENTRE FOR BIOENGINEERING
Neural Engineering Cardiovascular Biomaterials Regenerative Musculoskeletal

Medicine
MSc in Bioengineering
Course Handbook 2012-2013
Dear M.Sc. Student, Dear Bioengineer,

This handbook is designed to provide you with information about the M.Sc. in
Bioengineering. You will find details about modules, assessment and examinations,
guidelines to conduct your research project and writing your dissertation as well as
outlining the roles of the supervisor and the student which will be useful to you during
your studies. There is also background information on the Faculty members and contact
details for course lecturers and administrative staff.
The M.Sc. in Bioengineering is a unique venture between Trinity College Dublin,

University College Dublin, the Royal College of Surgeons in Ireland and the National
College of Art and Design. The programme has many advantages. The most important
advantage is the student's experience of studying at all Institutions and interaction with
a wide range of academic and research staff whose focus is bioengineering.
Furthermore, the lecturers are experts in the topic in each institution, and the laboratory
facilities of all universities can be employed in practicals and laboratory exercises.
On behalf of all the lecturers and staff, I would like to wish you well in studying for your
M.Sc. in Bioengineernig. The Trinity Centre for Bioengineering has a long, experienced
history in providing biomedical engineering education. We have successfully graduated
hundreds of MSc in biomedical engineering who have all built on their postgraduate
opportunities for careers in academia, the medical device industry and medicine. We
wish you the same success as you embark on the MSc in Bioengineering this year.
If you have any questions or comments, please do not hesitate to contact us.
MSc in Bioengineering |
Professor Richard Reilly

Course Director M.Sc. in Bioengineering
1
TABLE OF CONTENTS
Welcome from course director 1
Table of Contents 2
Course Objectives 3
Course Structure, Annual Schedule & Dates of Examinations 4
M.Sc. Course Modules

Biomechanics 5
Basic Medical Science 7
Physiological Measurement 9
Rehabilitation Engineering (optional module) 12
Biomaterials 13
Neural Engineering (optional module) 15
Cell & Tissue Engineering (optional module) 16
Research Methods 17
Thesis 19
Faculty Members 34
Course Regulations 40
Recommended reading material 44

Careers in Bioengineering 45
Course Administrators 47
Campus Maps
TCD Campus Map 48
UCD Campus Map 49
NCAD Campus Map 50
1B
Trinity College Academic Year Structure 51
2
COURSE OBJECTIVES & LEARNING OUTCOMES
This programme aims to give a sound and broad basis in bioengineering. In particular,
we aim to provide engineers and scientists with the education needed to practice
bioengineering in the medical devices industry in Ireland.
Specifically the aims are:

To give students a broad understanding of the key subjects of bioengineering,
viz., biomechanics, biomaterials, bioinstrumentation, cell and tissue engineering,
neural engineering and rehabilitation engineering.
By way of case studies and assignments, to give students a familiarity with

bioengineering applied in the main surgical disciplines; e.g. orthopaedics,
cardiology, gastroenterology, ENT Surgery, neurology.
To give students a sound understanding of how to apply the scientific method to

research in an industrial or clinical context.
To give students the ability to exploit information technology for monitoring the
performance of medical devices or the health of patients through medical
devices.
To give students a knowledge of how the medical device industry is regulated

and of how to obtain acceptance of new products onto the market.
3
ANNUAL SCHEDULE & COURSE STRUCTURE
MODULE ECTS TERM LECTURE DATES EXAM MODULE

DATES COORDINATORS
MODULES
Biomechanics 10 Michaelmas 1 - 5 October 2012 10 Dec 2012 Dr Conor Buckley
Basic Medical Sciences 5 Michaelmas 5 October 7 Dr Aoife Gowran

December 2012
Physiological 10 Michaelmas 5 9 November 2012 12 Dec 2012 Prof. Richard Reilly

Measurement
Rehabilitation 10 Michaelmas 19 23 November 2012 14 Dec 2012 Prof David Fitzpatrick

Engineering*
Dr Kevin OKelly
Biomaterials 10 Hilary 14 - 18 January 2013 13 May 2013 Dr Ken Stanton
Dr Eamon De Barra
Research Methods 15 Hilary 18 22 February 2013 Dr Ciaran Simms
Neural Engineering* 5 Hilary 25 27 February 2013 15 May 2013 Prof Richard Reilly
Cell and Tissue 5 Hilary 5 8 March 2013 17 May 2013 Dr Conor Buckley
Engineering*
Dissertation 30 Trinity 30 August 2012

*Optional module
The Masters course consists of:
four modules of 10 credits each. A 10-credit module consists of an intensive week of 27
contact hours, followed by a period of up to four weeks during which the equivalent of a
further 40 hours of lectures, tutorials, and case studies will be presented by self-study.
three optional modules of 5 credits each. Students must take two of these three options.
a project worth 45 credits consisting of a 15-credit module on research methods and a
30 credit dissertation
Please note that while every effort will be made to keep to the module and examination dates
given in this handbook, they may be subject to change. We will endeavour to give as much
notice as possible where this occurs
4
M.Sc. COURSE MODULES BIOMECHANICS
Course Coordinator: Dr. Conor Buckley, School of Engineering, TCD

Module Dates: Monday 1 s t to F riday 5 t h Octo ber 2012
Module Objectives
To provide students with an understanding of the application of applied mechanics to the
solution of problems in biological systems, and also with the main technologies used to
reconstruct biological function.
Syllabus
This course is taught at TCD by one intensive week of 27 contact hours followed by four weeks
of self-study using self-learning assignments. The self-study will be used to deliver lecture
material, tutorial assignments, design exercises, and case studies. These will amount to 40
hours in total. Therefore the course will comprise 67 hours of formal teaching. Lectures take
place in Trinity College Dublin.
Assessment
Assessment will be by way of course assignments and a final examination. The exam makes up
60% of the total result with assignments and lab marks making up the other 40%.
Submission of assignments and labs via Blackboard
Final Examination: 10 December 2012 9.00am 12.00pm

5
M.Sc. COURSE MODULES BIOMECHANICS
Sample TIMETABLE
Day 1
(9.00-9.30) Opening remarks and introductions
(9.30-10.00) Welcome Coffee Reception
Lect. 1 (10.00-11.00) Physiological blood flow and function of the heart
Lect. 2 (11.00-12.00) Bone Fracture Healing & Repair
BREAK
Lect. 3 (13.00-14.00) Disease and degeneration of tissues
Lect. 4 (14.00-15.00) Soft Tissue Microstructures
Lect. 5 (15.00-16.00) Ligament tendon and muscle viscoelasticity
Lect. 6 (16.00-17.00) Musculoskeletal biomechanics
Day 2
Lect. 7 (9.00-10.00) Optimization and calculation of muscle forces
Lect. 8 (10.00-11.00) Pedestrian kinematics and injuries in collisions with vehicles
Lect. 9 (11.00-12.00) Introduction to injury biomechanics
Lect. 10 (12.00-13.00) Injuries to the head and spine
BREAK
Lect. 11 (14.00-15.00) Cardiovascular stents & Angioplasty catheters 1
Lect. 12 (15.00-16.00) Cardiovascular stents & Angioplasty catheters 2
Lect. 13 (16.00-17.00) Transcatheter heart valve technologies
Day 3
Lect. 14 (9.00-10.00) Medical devices: directives, regulations and standards
Lect. 15 (10.00-11.00) Risk analysis and risk management in medical devices
Lect. 16 (11.00-12.00) Tissue growth and adaptation
Lect. 17 (12.00-13.00) Bone Mechanics
BREAK
Lect. 18 (14.00-15.00) Injuries to the abdomen
Lect. 19 (15.00-16.00) Injuries to the long bones.
Lect. 20 (16.00-17.00) Cartilage mechanics
Lect. 21 (17.00-17.30) Pre-laboratory/Assignment briefing
Day 4
Lect. 22 (9.00-10.00) Bioacoustics
Lect. 23 (10.00-11.00) Biomechanics of the spine and intervertebral disc
Lect. 24 (11.00-12.00) Cardiovascular Biomechanics 1
Lect. 25 (12.00-13.00) Cardiovascular Biomechanics 2
BREAK
Lab Groups 1 & 3 (14.00-15.30)
Lab A: Damage and histology of compact bone
Lab Groups 2 & 1 (15.30-17.00)
Lab B: Poroelastic mechanical properties of cartilage tissue
Lab Groups 3 & 2 (17.00-18.30)
Day 5 Location: Printing House Hall
Lect. 26 (9.00-10.00) Bone and joint replacements - design and materials selection
Lect. 27 (10.00-11.00) Medical device innovation- From concept to patent to product
Lect. 28 (11.00-12.00) Hands on innovation in the medical devices sector
Lect. 29 (12.00-13.00) Mergers and acquisitions (M&A) in the medical device industry
BREAK
Lab Groups 4 & 6 (14.00-15.30)
Lab A: Damage and histology of compact bone
Lab Groups 5 & 4 (15.30-17.00)
Lab B: Poroelastic mechanical properties of cartilage tissue
Lab Groups 6 & 5 (17.00-18.30)
6
M.Sc. COURSE MODULES MEDICAL SCIENCES
Course Coordinator: Dr Aoife Gowran, School of Medic ine, TCD
Module Dates: Friday 5 t h October to Friday 7 t h December 201 2
Module Objectives
The course aims to give an introduction to human biology and disease, such that students can
appreciate the medical basis for scientific/technical procedures in diagnosis and treatment. A
basic understanding of terminology and practice is emphasised. The lecture series will outline
the physiology and anatomy of the main body systems and introduce the cellular basis of
systems. Some principles of disease conditions are mentioned. The objective of the specialist
lectures and hospital laboratory visits is to provide an insight into the role of various
technologies in the diagnosis and management of patients. Additionally they will show the
integration of basic sciences, technology and clinical medicine across the continuum of care.
Assessment
Assessment will be by way of a group presentation (50%) and a written assignment (50%).
Group Presentation: Students will be assigned to a group by the Module Co-ordinator for the
purpose of this assignment. Presentations should be no longer than 10 minutes and each
member of the group should participate in the oral presentation as well as the preparation.
Students should note that assessment of the presentation is based on content, presentation
techniques, ability to answer questions, timekeeping and participation in other groups talks (i.e.
asking questions). Furthermore each group will be assigned a mark out of 10 by each of the
other groups on the day (these scores will be averaged and are worth 10% of the presentation
mark). Presentations will be based on one topic chosen by the group and should have a high
level of relevance to their overall course of study. Presentations should include:
Anatomy and physiology of the relevant organ system
Signs and symptoms of disease
Causes
Investigations & Treatment
Information relevant to the students course of study
Individual Assignment: The assignment topic is self-assigned by an individual student and

should be based on a relevant area from their specific course of study. The student must
integrate information from the Basic Medical Sciences module into their chosen topic (20% of
the marks will be assigned this). The assignment should be no longer than 2 A4 pages of font
12 text, anything longer will be penalised. A maximum of 4 figures, flowcharts, tables etc., may
be included. Pass mark: 40%
Course Evaluation: We would appreciate if you could take some time at the end of the module
to complete the evaluation sheet which will be given to you. This information will help us
evaluate the course and hopefully improve it. The questionnaire need not be signed but it is
important that all questions are answered. Completed forms may be given to Dr Aoife Gowran
or your course co-ordinator at anytime.
7
M.Sc. COURSE MODULES
27B MEDICAL SCIENCES
Course Topics
Introduction
Cells, Tissues, Organs
Pathology
The Human Brain
Muscle
The Respiratory System
Circulatory System
Blood
Immune System
The Renal System
Bone and cartilage
Patient Investigation: St. Jamess Hospital
Diagnostic Imaging & Histopathology
The Endocrine System
Case Study of endocrine disorder: Diabetes
Gastrointestinal system
Case Study: Paediatrics
Case Study: Surgical Patient

Revision & preparations of presentations
Presentations and hand-in of individual assignments
8
M.Sc. COURSE MODULES PHYSIOLOGICAL MEASUREMENT
Course Coordinator: Prof. Richard Reilly

Module Dates: Monday 5 t h to F riday 9 t h November 20 12
Module Objectives
To provide students with a substantial knowledge of the theory, principles and applications of
instrumentation as applied to Biomedical Engineering and to introduce design methodologies of
medical instrumentation and devices.
At the end of this module it is anticipated that students will have obtained:
Describe the main element of the central nervous system.
Calculate ionic currents and voltages in cell membranes.
Derive models of action potential generation and propagation in excitable cells.
Specify the primary performance characteristics of transducers.
Explain the operation of the main transducers used in clinical medicine.
Outline and characterise an electrical equivalent model of a sensing electrode.
Analyse the characteristics of various amplifier configurations.
Analyse and evaluate the primary performance metrics of bioelectric amplifiers.
Analyse electrophysiological data with signal processing methods.
Explain the use of biomedical signal processing to aid clinical interpretation of data.
9
M.Sc. COURSE MODULES PHYSIOLOGICAL MEASUREMENT
Syllabus
This course is taught at TCD over one intensive week of 35 contact hours followed by four
weeks of distance learning using self-learning assignments. The distance learning will be used
to deliver tutorial assignments, design exercises, and case studies. These will amount to 40
hours in total. Therefore the course will comprise 70 hours of formal teaching.
Monday 5th Nov

8.30-9.00 Coffee and Refreshments
Lect. 1 Opening remarks and Introduction Richard Reilly
Lect. 2 Organization of the nervous system Sonja Hermann
Lect. 3 Bioelectric potentials and currents Sonja Hermann
Lect. 4 Action potential generation Sonja Hermann
BREAK
Lect. 5 Electrode Design Kevin OKelly
Lect. 6 Electrode Design Kevin OKelly
Lect. 7 Electrode Tissue Interfaces Richard Reilly
Tuesday 6th Nov

Lect. 8 Transducers types and characteristics I Martin Burke
Lect. 9 Transducers types and characteristics II Martin Burke
Lect. 10 Bioamplifiers I Martin Burke
Lect. 11 Bioamplifiers II Martin Burke
BREAK
Lect. 12 Measurement of Cardiac Function Richard Reilly
Lab. (Group 1) Bioinstrumentation Design Lab Martin Burke/Richard Reilly
Lab. (Group 2) Bioinstrumentation Design Lab Martin Burke/Richard Reilly
Wednesday 7th Nov

Lect. 13 Blood pressure measurement Martin Burke
Lect. 14 Oxygen measurement Richard Reilly
Lect. 15 Measurement of Knematics and Movement Isabelle Killane
Lect. 16 Electric Stimulation of biological tissue Richard Reilly
BREAK
Lab. (Group 1) Gait Analysis Hugh Nolan
Lab. (Group 2) Respiratory Function Shona DArcy/Martin Holmes
Thursday 8th Nov

Lect. 18 Biomedical Signal Analysis Ed Lalor
Lect. 19 Biomedical Signal Analysis Ed Lalor
Lect. 20 Biomedical Signal Analysis Richard Reilly
Lect. 21 Biomedical Signal Analysis Richard Reilly

BREAK
Lab. (Group 1&2) Matlab Introduction and Biomedical Applications Mick Crosse/James Sullivan
Friday 9th Nov

Lect. 22 Respiratory Physiology Richard Costello***
10
Lect. 23 Bioacoustics Henry Rice
Lect. 24 Patient Adherence in Medical Devices: a case study Shona DArcy
Lect. 25 Challenges and opportunities in wireless and global health Richard Reilly
BREAK
Shona DArcy and Martin
Lab. (Group 1) Respiratory Function Holmes
Lab. (Group 2) Gait Analysis Hugh Nolan
*** Royal College of Surgeons in Ireland and Beaumont Hospital
Assessment
Assessment will be by way of course assignments and a final examination. The exam makes up
60% of the total result with assignments and lab marks making up the other 40%.
Course assignments:
The assignments offered are as follows:
Medical Instrumentation (deadline Friday, 16th November 2012)
Data analysis (deadline Friday, 30th November 2012)
Needs analysis for Medical Instrumentation (deadline Friday, 6th December 2012)
Submission of assignments and labs: to June OReilly at [email protected]
Final Examination:
The exam will consist of two parts: all 12 questions in the first part must be answered, and any 3
of the 6 questions in part two must be answered.
Examination Date: Wednesday 12th December 2012 at 9.00am

11
M.Sc. COURSE MODULES REHABILITATION ENGINEERING
*optional module
Course Coordinator: Dr. David Fitz Patric k, University College Dublin
Module Dates: Monday 19 November to F riday 23 November 2012
Syllabus
This course consists of one week of lectures and lab activity, in addition to self-study. Students
will be based in UCD, Belfield and the National Rehabilitation Hospital (NRH) for this period.
The following is an indicative list of lecture topics:

Rehabilitation Engineering Contextual overview & historical background
Orthotics & prosthetic design
Analysis of Movement - Clinical gait and motion analysis
Wheeled mobility
Rehabilitation and assistive technologies
The following is an outline description of each 4-hour lecture/lab topic content:

1) Rehabilitation Engineering Contextual Overview:
The incidence and societal cost of injury and rehabilitation; Historical overview of the scientific
and technological field; Patient X a case study in the clinical problems posed for rehabilitation
engineering. Group assignment definition and discussion.
2) Movement Analysis & Prosthetic Design:
Introduction to gait analysis and applications. The technology - 3D kinematics, force plates,
electromyography. Data analysis and interpretation. Clinical outcome assessment with an
emphasis on rehabilitation.
3) Wheeled Mobility & Seating:
This module will introduce the scientific basis for the design and application of assistive
technologies in mobility and seating environments. The core technologies will be identified and
typical applications demonstrated.
4) Rehabilitation & Assistive Technologies:
This module serves as an introduction to the field of Assistive Technology. It provides students
with an overview of popular technologies available and outlines their use by and for people with
disabilities. This will provide students with an opportunity to get some "hands on" experience of
using a range of Assistive Technologies from Power Mobility, Environmental Controls,
Alternative and Augmentative Communication and alternate access to computers.
5) National Rehabilitation Hospital (NRH) - practical/laboratory activity:
Visit the UCD/NRH rehabilitation engineering research laboratory on the hospital campus in Dun
Laoghaire. Review of past and current rehabilitation engineering projects by the engineering
staff and some demonstrations. Presentations by Therapists (Physio, Speech, Occupational)
on the benefits of technology to their clients.
Assessment
5B
Assessment will be by way of course assignments and a final examination.
Course assignment:
Course assignment and lab report will account for 40% of the total result.
Final Examination: 14 December 2012. The exam will account for 60% of the total result.
12
M.Sc. COURSE MODULES BIOMATERIALS
Course Coordinator: Dr. Kenneth Stanton, University College Dublin
Module Dates: Monday 14 t h January to Friday 1 8 t h January 201 3
Course Lecturers: Dr. Alun Carr, U niversity College Dublin

Dr. Kevin OKelly, Trinity College Dublin
Module Objectives
At the end of this module, it is anticipated that students will have obtained a detailed
understanding of the composition and properties of the major classes of biomaterial used in
medical and dental devices. The required functionality for a range of synthetic implantable
biomaterials and how this relates to material choice for specific applications will also be
covered, as will the most common tissue and blood interactions with implanted biomaterials,
and issues associated with the use of surface modification methods to enhance the
biocompatibility of materials. Regulatory issues relating to current developments in second
generation biomaterials and standards associated with quality and safety will be included.
Syllabus
This course is taught at UCD and TCD over one intensive week comprising 30 contact hours
followed by four weeks of distance learning using self-learning assignments. The distance
learning will be used to lecture material, tutorial assignments, design exercises, and case
studies. These will amount to 40 hours in total. Therefore the course will comprise 70 hours of
formal teaching. The module will cover the following topics:
1: Introduction to Biomaterials
Overview of materials and the relationship between biomaterials and medical and dental devices.
2: Applications and Markets for Biomaterials

World-wide market for biomaterials, projections for developments in the uptake of biomaterials
(demographics, medical advances, etc.) and the clinical implications of biomaterials development.
3: Common Biomaterial Types

Metals, alloys, polymers, ceramics
4: Key Materials Issues in Biomaterials
5: Regulation and standards for quality and safety

FDA, EU - Medical Device Directives, GMP, ISO, CE marking.
6: Biomaterials in Medical Devices and Prostheses:

Material choice implications based on device design; replacement of skeletal hard tissues;
cardiovascular implants and vascular grafts; dental implants; neural implants.
7: Improved Functionalisation of Biomaterials

Surface modification; controlled drug delivery systems.
13
M.Sc. COURSE MODULES BIOMATERIALS
8: Clinical Aspects of the Use of Biomaterials:

Biocompatibility and biomimicery; surfaces and surface interactions: tissue and blood
interactions; mineralisation and encapsulation.
9: Sterilisation and Packaging Considerations
10: Characterisation and Testing of Biomaterials:

Bulk analysis methods applied to the study of Biomaterials (XRD, FTIR, SEM/EDX, DSC, TGA,
DEA, etc.) Surface analysis methods applied to the study of biomaterials (XPS, SIMS, AES,
SERS, AFM/STM, etc.) Mechanical test: wear, friction, flexibility, fatigue, etc.
Lecture Topics
Lecture 1 Solids, crystallinity, defects, metals

Lecture 2 Solids, crystallinity, defects, metals and properties
Lecture 3 Solids, crystallinity, defects, metals and properties
Lecture 4 Polymers
Lecture 5 Ceramics
Lecture 6 Coatings
Lecture 7 Characterisation: X-ray Diffraction
Lecture 8 Characterisation: Thermal Analysis Techniques
Lecture 9 Characterisation: Spectroscopic Analysis Techniques
Characterisation: Electron Microscopy and Related
Lecture 10
Analyses
Lecture 11 Biological interfaces: biocompatibility/bioactivity
Lecture 12 Biological interfaces: biocompatibility/bioactivity
Lecture 13 Dental biomaterials
Lecture 14 Orthopaedic biomaterials (+ scaffolds and grafts)
Lecture 15 Cardiovascular biomaterials
Lecture 16 Neural biomaterials
Lecture 17 Functionalisation and drug delivery
Lecture 18 Functionalisation and drug delivery
Lecture 19 Regulatory Affairs
Lecture 20 Manufacturing and Clinical considerations
Assessment
Assessment will be by way of assignments and a final examination.
Course assignments
Each student will receive two assignments. Cumulative assignments will account for 40% of the
total marks.
Submission of assignments to Dr. Ken Stanton
Final Examination
The final examination consists of two sections, A and B. Two questions from each section (A
and B) and an additional question from either section giving a total of five questions must be
answered.
The exam will make up 60% of the total marks.
Examination Date: Monday, 13 May 2013.
14
M.Sc. COURSE MODULES NEURAL ENGINEERING
*optional module
Course Coordinator: Prof. Richard Reilly , Trinity College Dublin
Module Dates: Monday 25 to Wednesday 27 February 2013
Syllabus
The purpose of this module is to introduce students to the field of neural engineering from a
neuroscience perspective. Students will apply engineering principles to understand the
excitation of nerve and muscle, the generation of bioelectric signals and artificial stimulation of
biological tissues. Common methods of stimulating, recording and analysing neural systems will
be examined. The basic principles and methods studies will then be applied to examine specific
neuroscience applications of neural engineering, such as biomarkers for neurological and
neuromuscular disorders. This module will be based in Trinity College Dublin.
Introduction to Neural Engineering

Review of relevant physiology and anatomy
Electrical properties of neurons
Section 1 Monitoring Neural Activity
Monitoring neural activity: Bioelectric potentials and currents I
Monitoring neural activity: Bioelectric potentials and currents II
Action potentials
Implantable microelectrodes
Neural Spike trains and Analysis
Electroencephalography EEG
Electroencephalography EEG-II
EEG Recording and Analysis with application to Schizophrenia
EEG Recording and Analysis with application to Movement Disorders
Non-invasive Brain Machine Interfaces
Invasive Brain Machine Interfaces
Magnetic stimulation of biological tissues
Section 2 Replacing/Restoring Neural Function

Electric stimulation of biological tissues I
Electric stimulation of biological tissues II
Deep brain stimulation
Retinal and Visual Prostheses
Cochlear Implants and Auditory Prostheses
Assessment
Course Assessment will be by way of course assignments and a final examination.
Course Assignments:
Course assignment and lab report will account for 40% of the total result.
Submission of assignment and lab report to Blackboard
Final Examination: 15 May 2013 2 hour duration

The final examination will account for 60% of the total result.
15
M.Sc. COURSE MODULES CELL & TISSUE ENGINEERING
*optional module
Course Coordinator: Dr. Conor Buckley, School of Engineering, TCD
Module Dates: Tuesday 5 t h March to Friday 8 t h March 2013
Module Objectives
This module aims to provide students with the fundamentals of the current approaches and
technologies being adopted in the multidisciplinary field of Tissue engineering & Regenerative
Medicine, which aims to replace and generate new tissues through the combination of cells,
biocompatible materials and suitable biochemical and biophysical factors to improve or replace
biological functions that have been damaged through disease
Syllabus
This course is taught partly by self-study and partly by 2 days of lectures. There will be a total
of 15 hours formal teaching plus a 3-hour laboratory which will take place in the Parsons
Building, Trinity College for this period.
Examples of specific lecture titles are:
1) Tissue engineering & regenerative medicine principles
2) Advances in cartilage tissue engineering
3) Tissue engineering of the intervertebral disc (IVD)
4) Corneal tissue engineering and replacement
5) Stem cell biology
6) Cardiovascular tissue engineering
7) Bioreactor systems and design
8) Molecular biology techniques to analyse gene expression
9) Fundamentals of 3D construct technology
10) Biomaterials for scaffolds
11) Biomedical nanotechnology & systems
12) Mechanobiology- response of cells to mechanical forces
13) Nutrient transport
14) In vitro models of cell toxicity
Workshop: Introduction to practical tissue culture and analyses

Laboratory: Response of cells to mechanical forces
Assessment
Course Assessment will be by way of an independent learning assignment, laboratory report
and a final examination. The exam makes up 60% of the total result with assignment and
laboratory reports accounting for 40%.
Course Assignments:
Submission of assignment and lab report via Blackboard
Final Examination: 17 May 2013

The final examination will be two hours long. The exam will account for 60% of the total result.
16
M.Sc. COURSE MODULES RESEARCH METHODS
Course Coordinator: Dr. Ciaran Simms, TCD

Module Dates: Monday 18 to Friday 23 February 2013
Syllabus
This course is designed to provide a foundation for and complement the project work. The
course will be taught through a variety of approaches and by researchers from a range of
disciplines at TCD (main campus and St. James's hospital) and the National College for Art and
Design (NCAD). The course will be delivered through a series of lectures, seminars and
assignments designed to provide a foundation for research methods in biomedical engineering.
The following topics will be addressed:
ethics in research
business and entrepreneurship
guidelines for doing research in biomedical engineering
guidelines for writing a literature review, a research proposal and a dissertation
oral presentations
review of basic statistical methods for data analysis and referencing methods
aesthetics and ergonomics in Design
history of design and User-Centred Design
referencing systems
Learning Outcomes
At the end of this module, students will be able to apply appropriate research methods to
conduct research in the field of biomedical engineering. In particular, they will be able to
identify the principal ethical issues associated with their chosen research topic
identify the potential for commercialization of their research ideas
understand the processes for research in biomedical engineering
perform a literature review, write a research proposal and structure a dissertation
give an oral presentation on their project work
write a short paper based on their project work
use basic statistical methods for data analysis and hypothesis testing

understand the importance of aesthetics and ergonomics in engineering design

use an automatic referencing system within a word processing environment
17
M.Sc. COURSE MODULES RESEARCH METHODS
Component Marks Details Assessment by Estimated

(%) Student
hours
Research 10 5 page report on proposed project work; Thesis supervisor 40

Proposal
(template provided)
Industrial Design 20 Industrial Design module at NCAD NCAD 30
Ethical Issues 10 Students attend lectures in Ethical Issues in Thesis supervisor 20

Clinical Research, students answer
questionnaire on application to project work
(template provided); submitted as Appendix of
thesis
Statistics 20 Short course on Statistics Lab and case study 60
Innovation and 10 Evening seminar: talks from Business & Thesis supervisor 20
Entrepreneurship Industry; students answer questionnaire on
application to project work (template provided);
submitted as Appendix of thesis.
Oral Presentation 20 Midterm presentation with external examiner: 10 Course Director & 20
minutes presentation, 5 minutes questions External Examiner
Referencing Training Session in Endote (organised by TCD

Methods Training library)
Short Paper 10 Short Paper based on thesis work (template Thesis supervisor 40
provided); submitted as Appendix of thesis
39B
18
THESIS
Objec tives
The project forms the final part of the course. Members of staff within the Department propose
projects pertinent to their own research interests. Candidates are also encouraged to propose
their own projects, particularly in cases where the candidate has an industrial link. Each project
is supervised by an academic in the Trinity Centre for Bioengineering, Department of
Mechanical & Manufacturing Engineering and Department of Electronic and Electrical
Engineering. In some cases other academics (either within TCD or the other institutions
affiliated to the course) may also have a substantial involvement. Furthermore, additional
guidance may come from medical or healthcare professionals. In these cases, the project
usually sets out to solve a problem experienced by these healthcare professionals in the use of
a particular medical device.
Project titles will be issued and students will be allocated their project during Michaelmas term.
In Hilary term 2012, there will be a meeting at which each student gives a 10-minute
presentation to the External Examiner of the purpose of their work, and how they intend
achieving their goals followed by a five minute question and answer session. This allows all
candidates an overview of the work being carried out, and comments from staff and other
candidates can help determine the project objectives more clearly.
Projec t Titles
Here are some recent project titles undertaken by TCD M.Sc. students:
- Development of a pressure sensor for intra oral use
- Optimisation of coronary stem cell area
- Development of tissue-engineered collagen GAG fibrin heart valve constructs
- The influence of vehicle design on ground related injuries in pedestrian impacts
- Computational modeling of a production wheelchair for rear impact protection
- Anterior Knee Pain in Kneeling
- Computational modeling of Deep Brain Stimulation in Parkinsons Disease
- Strain fields in cell seeded agarose hydrogels using digital image correlation (DIC).
- Automatically Adapting Mattress for the Prevention of Pressure Sores and Ulceration
- Quantitative analysis of glycosaminoglycans (GAGs) and Type II collagen in
chondrocyte-seeded scaffolds
- Investigation of Biomechanics of Deformational Plagiocephaly (Flat Head Syndrome) in
Newborn Infants
- Optimisation of a novel biomimetic scaffold for bone healing
- Fracture Mechanics of Soft Tissues

- Redesign of a head restraint for rear impact protection of wheelchair occupants
- Optimisation of a multi layered scaffold to improve its potential for osteochondral defect
repair
7B
19
Guidelines for Thesis Report and Presentations
This section emphasises the Trinity Centre for Bioengineerings important regard for the acquisition of
communication skills. These notes will help you to develop those skills and that you will take pride and pleasure in
that development. You will find that you will not absorb all this information at a single reading. You should refer to
these notes whenever you are carrying out a significant piece of writing and especially when you are writing your
Thesis.
These instructions have been prepared to indicate to both thesis supervisors and students the expected standard of
report writing. It is likely that up to 20% of marks are lost by poor presentation of work. These notes are designed to
help students to avoid common faults and improve presentation of work. The advice can be applied to major theses
but also relevant to short reports and essays which may form part of in-course assessments.
Preparing a Synopsis
It is essential to prepare a detailed synopsis of any piece of written work which is likely to be more than one page
long. A synopsis helps the writer to see clearly what the main points are and to arrange the material so as to bring the
important points out. For the MSc thesis, the synopsis would show the order in which the material is to be presented,
some idea of the length of each section, what is to be included in each section and an indication of the location of
Figures, Tables and Plates.
There are two main objectives in preparing a synopsis:-

a) to produce a written document which can be discussed with the supervisor before a great deal of writing is done.
b) to help the writer to plan the work to the maximum effect
This is essential for large reports and is strongly recommended as a general practice.
A carefully produced synopsis can save hours of writing time and will allow alterations and additions. Work which is
not well-planned is likely to ramble and the main points will be lost.
Report Outline
Reports should be divided into the following standard sections:
1. Title Page
2. Abstract (Summary)
3. Acknowledgements
4. Contents Page
5. List of Tables
6. List of Figures
7. Introduction
8. Literature Review
9. Methods
10. Results
11. Discussion
12. References
13. Appendix
Very occasionally the nature of the material may require a different format. Students should consult
supervisors before deviating from the standard arrangement.
20
Scheduling
Literature Review should be written early in the project when you have read in detail journal articles in the project
area. The Literature Review will need to be brought up to date with new, more relevant papers as you research on
the project.
The Methods section should also be written very early in the project, after the Literature Review and polished later.
Results should be in the process of being written up during the experimental part of the project.
The Introduction is normally written last and is used to build the argument why the area of study is of interest and
importance in bioengineering.
Now follows a short discussion of the headings listed above.
Title Page
This page should include:
- Concise title (not more than 15 words) Should be informative. Abbreviations should be avoided
- Authors name
- Supervisors name
- Affiliation
- Date
- Degree for which thesis is being submitted
Abstract
- A short summary (usually one A4 sheet), which includes a brief outline of the aims of the study, the
methodology used, the main findings and the conclusions drawn.
- The abstract (not to exceed 250 words) should be clearly written and readily comprehensible to a broad
readership. The abstract should provide a concise summary of the objectives, methodology, key results, and
major conclusions of the study. It should be written in complete sentences, without explicit subheadings.
Contents page
- This should include chapter headings and details of sections within chapters, with page numbers.
List of Tables
- This should include details of all tables with page numbers.
List of Figures
- This should include details of all figures with page numbers.
Acknowledgements
- Acknowledge all those who provided support to you and your project (e.g., organisation, funding
body, supervisor, technicians).
- The Acknowledgements should be placed at the end of the text (before the references) except in
the MSc Thesis, when they should immediately follow the Title and Summary.
- As a matter of courtesy all staff mentioned should be given a title (Prof., Dr, Mr, Ms) and both
forename and surname. Only intimates should be referred to by first name only.
21
- Work contributed by others to your project must be acknowledged. Such a situation would arise
if, for example, stored samples generated by another researcher were used in the project or if the
nature of specific experiments to be included in the project dictated that they must be carried out
by an experienced researcher. The titles and names of such contributors and the precise nature of
their contribution must be included in this section in a clear statement of acknowledgement. An
omission of such an acknowledgement, where required, is plagiarism. Plagiarism, as
outlined elsewhere in this Handbook, is regarded by College as a serious offence and
the student concerned will be penalised.
- All the foregoing are preliminaries and should not be numbered with the main body of the text.
Instead, give preliminaries Roman numerals (i, ii etc.). The pages of the main text should be
numbered using Arabic numerals (1, 2, etc).
Introduction
- This should emphasise the importance of the research study and provide an overview of the key
concepts and questions posed. Therefore, the Introduction should include a statement of the
problem, research question or hypothesis, the objectives of the study, operational definitions of
term used and the background to the study.
Literature Review
- A summary of the background literature is necessary. You should aim to produce a detailed
overview of the current knowledge of the problem under study and outline a theoretical
framework or rationale as a basis for your study. It is important to critically analyse existing
literature on your research project.
- A clear statement of the problem and the immediate background as well as the aims of the project
and its relevance should be given.
Methods
- A clear account of all the experimental, materials, methods (including statistical analyses) and
experimental designs used must be given so that others can repeat the experiments. (The
anonymity of human subjects must be preserved, by using code numbers or letters.) In particular, it
should always be clear to the reader exactly what is being measured, and how many measurements
(or animals or subjects) there are in each value. Failure to do this will result in loss of marks. It may
be useful to clarify here the contribution of others to the practical work (see Acknowledgements).
- This section will provide a comprehensive explanation of the procedures used including details of
the following:
Overall design and justification of methods used.
A clear indication of the sample sizes used.
A detailed description of all experimental procedures; this should be sufficiently detailed
to allow replication.
A description of the instruments used.

An indication, if appropriate, of how published methods or available equipment was
modified for the current study.
An account of how data was analysed.
A sample of any questionnaire used, if appropriate.
A description of ethical issues for example, the process by which approval was obtained,
ethical issues in sample selection, data collection, publication of results etc.
22
Results
- This section, or sections should be a description and explanation of results using narrative, tables
and figures as appropriate. It should deal with facts and findings only, without interpretation (which
will be included in the Discussion).
- This is usually the most poorly-presented section of thesis and yet it one of the most important. The
reader must be led carefully through the results step by step. You should carefully consider the
order of the figures to be presented. The order of figures presented may or may not follow the
order the experiments were originally performed. You should consider which figures need to be
presented. The objective is not to include all your figures to simply show how much work you have
done, but to include those figures which are pertinent to the work. The main observations must be
brought out; it is NOT sufficient to present figures or tables and then leave the reader to work out
the conclusions (see later sections: Figures and Tables).
- Second-order variables. If you are using some transformation of the raw data, you should explain why
you are doing so and, if possible, what, if any, difference the transform makes. When results are
presented as % control, the absolute value of the control should be given in the Figure/Table
legend.
- Presentation of Statistics. This requires particular attention and is a skill which must be acquired.
Always state clearly what measure (mean, etc.) and what measure of variation (SD, etc.) is being
used. The number of observations (n) must be clearly stated and specifically given if SDs are used.
Do not give excessive numbers of decimal places; measures of variation should have one more
significant figure than the mean. It is important to clearly state the direction and magnitude of
the change observed. Do this first, and then give the result of any statistical tests used to determine
significance.
- Over-interpretation of results is a serious error. You must demonstrate that you understand the
significance of statistical testing. If a difference (or other statistical result, e.g. correlation) is not
statistically significant, you should not treat it as if it is. If you want to discuss a non-significant
trend in your results, make it clear that you know the difference.
Discussion
- This section should deal with discussion and interpretation of the data obtained and should include a
critical assessment of the data in the light of previous findings, speculation on the meaning of the
results obtained, analysis of the original hypothesis in the context of the findings, a discussion of
whether or not the findings support the hypothesis proposed and an assessment of the limitations of
the study. This should be concluded with a summary and conclusions and suggestions for further
research.
- This section often presents the most problems. In particular, it is often difficult to decide what
should go in the Discussion and what should go in the Results (see Preparation of a Synopsis, below).
A good guideline is When in doubt, put it in the Discussion, and leave the presentation of results
as uncluttered as possible.
- The Discussion will include the following.
Interpretation of the significance of your results.
A comparison of results (not forgetting control values) with those in the literature.
A discussion your results in context of the relevant literature.
A critical discussion of possible sources of error in the results. Critical means not only
listing the sources of error but also saying how important they are likely to be.
This list is by no means exhaustive and the categories will often overlap, but it should be helpful at the planning stage.
23
References
All cited references and only cited references should be included. The format used is the Harvard
referencing system.
Note that all references cited in text must appear in the list of references. General reading such as textbooks
should not be cited, unless you are using a figure or referring to a very specific point.
In the text
- When you make a scientific statement of fact, you must reference an original article with data to support this
fact (Smith et al., 1999).
- If there is only one author, quote the name only followed by the year the paper was published (Jones, 2000).
If there are two authors, use both names followed by the year the paper was published (Murphy & Quinn,
2001). If there are more than two authors, use et al. (always in italics with a full stop afterwards), which is
the Latin term for and others (Smith et al., 1999).
- If you want to reinforce the point and use several articles, they should be listed from the earliest to latest,
and separated by a semicolon (Smith et al., 1999; Jones, 2000; Murphy & Quinn, 2001).
- If you are quoting two articles by the same person in the same year, denote one as a and one as b. This is
done alphabetically according to the second author on the paper (Smith et al., 1999a; Smith et al., 1999b).
- When including the reference in the text, follow the following formats. Smith et al. (1999) have shown
that, It was shown by Smith et al. (1999) that.
Style of References
- Most journals use an abbreviated format for Journal titles. When abbreviating Journal titles make sure to
use the correct abbreviation. You can find the correct abbreviation of any journal on PUBMED
(http://www.ncbi.nlm.nih.gov/pubmed/). Some examples are as follows:
A = Ann Biomed Eng (single word journals are not abbreviated)
Annals of Biomedical Engineering = Ann Biomed Eng
Journal of Biomechanics = J Biomech
Journal of Neural Engineering = J Neural Eng
- Below is the reference style used by the IEEE Transactions on Biomedical Engineering. There are different
styles for journal articles, books, and book chapters as illustrated below.
Journal article
Cited in text as: (McMahon et al., 2008)
Cited in reference list as: McMahon LA, Reid AJ, Campbell VA, Prendergast PJ., Regulatory effects of mechanical strain
on the chondrogenic differentiation of MSCs in a collagen-GAG scaffold: experimental and computational analysis,
Ann Biomed Eng , 36, (2), p185 194, 2008.
Book
Cited in text as: (Simms and Wood, 2009).
Cited in reference list as: Simms CK and Wood DP (2009) Pedestrian and cyclist Impact - a Biomechanical Perspective,
Springer.
Chapter in a book
Cited in text as: (Lalor, 2009)

Cited in reference list as: Lalor, E.C., Pearlmutter, B.A., & Foxe, J.J. (2009). Reverse correlation and the VESPA
method. In: Handy, T. C. (Ed.), Brain Signal Analysis: Advances in Neuroelectric and Neuromagnetic Methods, MIT
press.
The most important thing to remember when citing references is to be consistent.
24
Appendices
- This should include details of equipment and instruments used, details of software developed and, in some cases
tables of raw data. When appropriate, it should also include a copy of any questionnaire used.
- This should contain essential data and details of any other methods. Note that all entries in the Appendix must be
properly described in suitable legends. It is not inappropriate to repeat relevant statistical summaries in the
Appendix. All Tables in the Appendix must have fully descriptive titles so that they can be understood without
reference to the main text.
Figures and Tables

- These are a great deal of trouble to prepare and it is a pity to waste them for the sake of a little attention to
detail. All Figures and Tables must be numbered and have a descriptive legend, so that each can be understood
without reference to the text. Legends precede Tables and follow Figures. It may be desirable to include the
important observation or conclusion in the legend. All units of measurement and statistical parameters must be
identified. Axes on graphs and columns in tables must be labelled so that it is clear what each point or value
represents.
- Try to keep graphs uncluttered. Use conventional symbols of open and filled squares, triangles or circles.
Shading aids clarity in histograms. Tables should be as simple as possible. Try not to put all your results in one
huge Table because it is daunting for the reader.
- The commonest fault is failure to integrate Figures and Tables with the text. The reader must be guided and the
main points clearly brought out even at the cost of some repetition of material between legend and text. If
Figures or Tables are large it may not be possible to include the legend on the same page. In such cases, put the
legend on the facing page. If Figures, Tables or Plates (mounted groups of photographs) are brought together,
rather than being interspersed with the text, say so and tell the reader where they are. If it is necessary to put a
figure or table sideways in the text, it should be arranged so that is viewed from the right.
- You should avoid directly copy-pasting figures/mechanistic diagrams from elsewhere; you will not be awarded any marks for
using previously published figures/mechanistic diagrams. You are expected to take time to draw the major parts of such
figures/mechanistic diagrams that are most relevant to your research. If you do decide to copy a figure from somewhere else, or
modified it only a little, the original figure must be acknowledged (with reference in the legend and in the list) (see
Plagiarism).
Grades of Heading
Careful attention should be given to this point at the planning stage. Examples of the usual grades of heading are
given below with a short description of each in brackets). Use bold or italic type as shown.
HEADING: RESULTS [capitals in bold print, centred, no underline or stop]
Subheading: Electroencephalographic Analysis [Upper and lower case in bold print, centred, no stop]
Further subheading: EEG Feature Extraction [Upper and lower case in bold italic print, centred, no stop]
Word Processing
- There are some conventions which should be followed. Paragraphs should be created by leaving a blank line and not by
indenting. Do not put spaces before a punctuation mark because it might be carried over to the beginning of a new line.
- All punctuation marks should have only a single space after them, never before.
25
Spelling, English and Grammar
- Poorly written reports stem from poorly crafted sentences. Sentences that are long or poorly written can be
frustrating to read and will loose you a great deal of marks. You are expected to spend time on writing each and
every sentence in you thesis with care. Make sure you do not forget the basic rules of English. Use nouns, verbs,
adverbs, adjectives accordingly in each sentence. A common mistake is to make sentences too long. Keep
sentences short and simple as far as possible.
- Do not expect that the reader will remember what has been said in previous sentences. Make sure you clearly
spell out what is meant in each sentence, even if it means repeating yourself. Be specific and clear and avoid
being vague. Ideally each sentence should be self explanatory.
- Your supervisor will focus on the scientific content and is not expected to check spelling, to correct your English
or any mistakes in grammar. A spell check should be performed before handing documents to your supervisor
and before final submissions. Ask a colleague to read your report before handing any material to your supervisor
and before final submission. If your colleague does not understand what you have written, you should make
corrections before handing to your supervisor.
- Ensure the spell checker is set to English (UK) and not English (US) by using the Language option on the
Tools menu. Remember that you will still need to proof-read the final draft; the spelling checker will not find all
errors. Pay special attention to names and technical terms
- Here is a list of the correct forms of words that are commonly mis-spelled.
accommodate dependent (adj.)
occurred separate
loose (i.e. not tight) lose (i.e. mislay)
principal (i.e. main) principle (i.e. underlying tenet)
- UK English rather than US English forms should be used: e.g. fibre not fiber.
- Students t test should have a capital and apostrophe); the t should be italicised.
- Its should never be written in formal prose; always use it is. The possessive is its.
- Numbers less than eleven should be spelt in full unless they refer to specific units, e.g. '6 days', but 'six subjects.'
- Note that sec, 'h', 'min' [no stop] and 'd' are the abbreviations for seconds, hours, minutes and days,
respectively. The multiplier 'k' as in km (kilometre) is always lower case. The abbreviations for units never take
an 's-plural'.
Headers and Footers

Header can be used to insert space and/or a running title at top of each page; a Footer does the same at the bottom of
the pages.
Pagination
Should be checked as the last stage in preparing a manuscript. It is usual to adjust the text so that odd lines or parts of
lines do not appear at the beginning or end of a page. The adjustment may be done by inserting blank lines in
appropriate places or by using the Insert Page Break command. Word has a Control widows and orphans option
(see Format menu, Paragraph, Line & Page breaks tab). Remember to set the page style (Page Setup) and
printer type (via Chooser) before doing this and work from the beginning of the text.
26
Font Style
- Choose your font with care. Some fonts take up a lot of space and others may not be suitable for laser-printing.
Avoid fonts named after cities. Arial has been found to be a satisfactory, clear and reasonably compact font.
- Fonts are designed for different purposes and a font that is easy to read on a screen (e.g. Geneva) is not
necessarily suitable for body-text. Times is designed for narrow columns and does not look well in A4 pages and
should not be used. Times New Roman shares many of the characteristics of Times (compact, with a lot of white
space) but looks better.
Spacing
If a type-size larger than 10 pt is used, it is unnecessary to double-space. If you use 12 pt body text, 1.5 spacing may
be adequate. Check with your supervisor if in doubt.
Special Sorts
There are many special characters which will be useful to you, such as the degree symbol ( alt+k) and acute
accents or fada (alt+e, followed by the letter you wish to accent) and grave accents (alt+~, followed by the letter).
For Greek characters it is better to use the insert font function rather than using the font Symbol. This allows you to
change the font in the document and keep the Greek characters. If you use font Symbol and decide to change the font
in the document you will have to go back and individually change all the Greek characters back to Symbol font.
Preparing Material for PowerPoint

Students are required to make oral presentations - another important skill. PowerPoint presentation will be used.
Legibility. Anything less than 18 pt body text will be difficult to read. Headings should be about 24 pt. Use Arial font
to improve legibility. Times is not suitable for projection. Bolding the text is helpful too. Diagrams will usually need
to be enlarged. It is useless to merely copy pages from papers or books the print size will be neither big enough
nor dense enough.
Density. Five lines is the useful maximum per slide; and bullet points are better than continuous prose. If you are
tempted to put more on, think again.
Practice, Practice, Practice your talk: Avoid reading from your notes and from your slides. Are you trying to write your
speaking notes onto the slide? It is not good technique to simply read out what is on the screen. If you practice your
talk beforehand, you will not need to read from your notes.
Plagiarism:
Plagiarism is considered as academically fraudulent, and an offence against University discipline.
1. Plagiarism is interpreted by the University as the act of presenting the work of others as ones own work, without
acknowledgement. Plagiarism is considered as academically fraudulent, and an offence against University discipline.
The University considers plagiarism to be a major offence, and subject to the disciplinary procedures of the
University.
2. Plagiarism can arise from deliberate actions and also through careless thinking and/or methodology. The offence
lies not in the attitude or intention of the perpetrator, but in the action and in its consequences. Plagiarism can arise
from actions such as: a) copying another students work b) enlisting another person or persons to complete an
assignment on the students behalf c) quoting directly, without acknowledgement, from books, articles or other
sources, either in printed, recorded or electronic format d) paraphrasing, without acknowledgement, the writings of
other authors Examples c) and d) in particular can arise through careless thinking and/or methodology where
students: (i) fail to distinguish between their own ideas and those of others (ii) fail to take proper notes during
preliminary research and therefore lose track of the sources from which the notes were drawn (iii) fail to distinguish
27
between information which needs no acknowledgement because it is firmly in the public domain, and information
which might be widely known, but which nevertheless requires some sort of acknowledgement (iv) come across a
distinctive methodology or idea and fail to record its source. All the above serve only as examples and are not
exhaustive. Students should submit work done in co-operation with other students only when it is done with the full
knowledge and permission of the lecturer concerned. Without this, work submitted which is the product of collusion
with other students may be considered to be plagiarism. When work is submitted as the result of a Group Project, it
is the responsibility of all students in the Group to ensure, in so far as possible, that no work submitted by the Group
is plagiarised.
3. It is clearly understood that all members of the academic community use and build on the work of others. It is
commonly accepted also, however, that we build on the work of others in an open and explicit manner, and with due
acknowledgement. Many cases of plagiarism that arise could be avoided by following some simple guidelines:
a) any material used in a piece of work, of any form, that is not the original thought of the author should be fully
referenced in the work and attributed to its source. The material should either be quoted directly or paraphrased.
Either way, an explicit citation of the work referred to should be provided, in the text, in a footnote, or both. Not to
do so is to commit plagiarism
b) when taking notes from any source it is very important to record the precise words or ideas that are being used and
their precise sources
c) while the Internet often offers a wider range of possibilities for researching particular themes, it also requires
particular attention to be paid to the distinction between ones own work and the work of others. Particular care
should be taken to keep track of the source of the electronic information obtained from the Internet or other
electronic sources and ensure that it is explicitly and correctly acknowledged
4. It is the responsibility of the author of any work to ensure that he/she does not commit plagiarism.
5. Students should ensure the integrity of their work by seeking advice from their Lecturers, Course Co-ordinator,
Director or Supervisor on avoiding plagiarism. All Schools should include, in their handbooks or other literature
given to students, advice on the appropriate methodology for the kind of work that students will be expected to
undertake.
6. If plagiarism as referred to in Paragraph (2) above is suspected, the Director of Teaching and Learning
(Postgraduate) will arrange an informal meeting with the student, the students Supervisor or other appropriate
representative, and the academic staff member concerned, to put their suspicions to the student and give the student
the opportunity to respond.
7. If the Director of Teaching and Learning (Postgraduate) forms the view that plagiarism has taken place, he/she
must decide if the offence can be dealt with under the summary procedure set out below. In order for this summary
procedure to be followed, all parties noted above must be in agreement. If the facts of the case are in dispute, or if
the Director of Teaching and Learning (Postgraduate) feels that the penalties provided for under the summary
procedure below are inappropriate given the circumstances of the case, he/she will refer the case directly to the
Junior Dean, who will interview the student and may implement the procedures set out in Section 5 (Other General
Regulations).
8. If the offence can be dealt with under the summary procedure, the Director of Teaching and Learning
(Postgraduate) will recommend to the Dean of Graduate Studies one of the following penalties: a) that the piece of
work in question receives a reduced mark, or a mark of zero; or b) if satisfactory completion of the piece of work is
deemed essential for the student to rise with his/her year or to proceed to the award of a degree, the student may be
28
required to re-submit the work. However, the student may not receive more than the minimum pass mark applicable
to the piece of work on satisfactory re-submission.
9. Provided that the appropriate procedure has been followed and all parties above are in agreement with the
proposed penalty, the Dean of Graduate Studies may approve the penalty and notify the Junior Dean accordingly. The
Junior Dean may nevertheless implement the procedures set out in Section 5 of Calendar Part II on Graduate Studies
website(Other General Regulations).
Turnitin
Students must submit their thesis to TurnItIn which is the standard in online plagiarism prevention. It instantly
identifies papers containing unoriginal material from over 40 Million Student Papers, 12 Billion Web Pages, over
10,000 newspapers, Magazines & Scholarly journals and Thousands of Books. Turnitin allows educators to check
students work for academic integrity by searching for improper citation or potential plagiarism by comparing it
against continuously updated databases using the industrys most advanced search technology. Every Originality
Report provides instructors with the opportunity to teach their students proper citation methods as well as to
safeguard their students academic integrity. Turnitin is also web Based so compatibility between different computers
and operating systems isnt a problem.
TurnItIn can also be used for the following:

Peer Review: Students can review and respond to their classmates' work online and also encourages collaborative
learning and improving student writing
GradeMark: The ability to mark student work in a unique, paperless environment and view assessment over time
GradeBook: A tool that enables instructors to manage grades and assignments online
Student FAQs on Turnitin:
What if Turnitin finds text matches in my paper?
Turnitin determines if text in a paper matches text in any of the Turnitin databases. The service does not detect or
determine plagiarism an instructor needs to make that call based on the matches shown in the Originality Report.
Indeed, the text in the student's paper that is found to match a source may be properly cited and attributed. It is
recommended that instructors carefully review the Originality Report before making any determination of
plagiarism. Such determinations of plagiarism require human judgment, and instructors and students alike should
understand their institution's academic integrity policies before turning in written assignments.
Who can see my paper?
Only the instructor, and possibly a TA assigned to the course, can see a student's paper. If a match is found between
the student's paper and another student's paper, the instructor can request the matching paper from the other
student's instructor. That instructor then decides whether to share the matching paper depending on the
circumstances. The only exception to this rule is in the case of peer review assignments
Does Turnitin violate student copyrights?
No - student works are the property of the student, and are copyrighted and protected. iParadigms, LLC (the parent
company of Turnitin) makes no claim of copyright to any of the works submitted to the Turnitin system.
29
Withheld access (a stay)
Should an author of a thesis wish to withhold permission for the use of her/his work, a written application must be
made to the Dean of Graduate Studies at the time of submission of the thesis for examination. Such applications must
have the written support of the graduate student's Supervisor or Director of Teaching and Learning (Postgraduate),
must state the reasons for the request for a stay on access and must provide a contact address. The maximum length
of a stay is five years. During this period of withheld permission the thesis may be consulted, lent or copied only by
written permission of the author who is under an obligation to reply to all inquiries within a reasonable time.
THESIS SUBMISSION
Dissertation submiss ion date is 30 August 201 3
Submit two hard bound copies to the Course Administrator in Trinity Centre for
Bioengineering office. A copy must also be emailed to [email protected].
It is the duty of the postgraduate student to familiarise him- or her-self with College regulations in relation to
submission of theses. Please see thesis submission guidelines , these regulations are on the Graduate Studies website.
H H
The thesis must be put through turnitin (www.turnitin.com). The thesis must contain immediately after the title page
the declaration page (see sample page 2 below) signed by the author.
Note: Late submission could potentially result in a continuance fee being levied by the Graduate Studies Office
Dissertations should be written according to the style outlined below. Dissertations are assessed by academics who
may not be expert in the precise field of study. The style of the dissertation should be designed for that readership.
An external and internal examiner will be nominated and their names sent to the Dean of Graduate Studies in
consultation with the supervisor of the thesis. The thesis will be sent to these examiners. They may at this time
specify that they wish to examine the candidate by viva voce. Such an oral examination would be held in TCBE.
30
Sample Thesis
Cover
8B
Sample Page 1
Title
31
Sample Page 2
Declaration
32
The supervisor and the student TCD Students
An outline of the role of the supervisor has been provided by the TCD Graduate Studies Office:
The relationship between the supervisor and research student is a critical factor in determining the quality of the
postgraduate experience. Best practice leads to a relationship that may be described as mentoring on the part of
the supervisor and learning on the part of the student. For a successful collaboration between student and
supervisor, both parties have to recognise their own separate responsibilities. Due to the diverse demands of
different disciplines, it is not possible to legislate in detail across the whole academic range of college for the
practices that supervisors and students should follow. However certain general principles should be clearly
understood by all involved in postgraduate education. These are set out below.
Responsibilities of the supervisor

A research student is admitted by the Dean of Graduate Studies on the recommendation of the Director of
Postgraduate Teaching and Learning and course coordinator all of whom sign to this effect. The course
coordinator will assign each student to a supervisor for the duration of their research project.
The supervisor has a reactive and proactive role. He or she must be reasonably accessible to the student for
academic help and advice during progress of the research and particularly during preparation of the research
thesis; he or she has a duty to be in touch with progress of the research student's work and inform the student of
what is expected of him or her. In addition the supervisor should help student in the latter's dealings with
College officialdom and should be aware of College regulations as they affect postgraduates. Many of the cases
of poor relationships between research students and their supervisors stem from a differing interpretation of
what constitutes reasonable access. Supervisors need to recognize that the lack of adequate analysis of work
submitted to them, undue delay in its return, and refusal to make, or inability to keep, appointments, damage
the relationship with their students. Such inadequacies of supervision cannot be excused on the grounds of
pressure of other work.
Responsibilities of the student

Research student must keep in contact with his/her supervisor and advise the latter on progress of research.
He/she should submit written work or perform other academic exercises (for example contribute to seminars)
when requested by supervisor. When seeking the academic services of a supervisor, a research student must
acknowledge that the supervisor is likely to have other commitments and cannot be expected to drop everything
to attend to his/her needs. This is particularly important during period of preparation of research thesis;
supervisor and student should devise a timetable, which can be adhered to on both sides.
Additional points
1. Project supervisor will read one complete draft of literature review and project report prior to submission.
Do not expect your supervisor to read incomplete or multiple drafts of your work.
2. You should provide your supervisor with a draft of your literature review/project two weeks before
submission date, in order to leave plenty of time for them to read it, and for you to take on board any
suggestions that they may have for improvements.
33
FACULTY MEMBERS
Richard Reilly, BE, MEngSc, PhD, MIEI, MIEE, SMIEEE, FTCD Course Direct or
Professor Reilly is Principal Investigator in the Trinity Centre for BioEngineering, the Trinity College Institute of
Neuroscience and the Centre for Excellent in Ageing. The Professorship is a joint position between the School of
Medicine and the School of Engineering. His research expertise is the area neural engineering and biomedical signal
processing. He received his BE in Electronic Engineering 1987 and his MEngSc and PhD Degrees in Biomedical
Engineering in 1992 from University College Dublin. He was the 1999/2001 Silvanus P. Thompson International
Lecturer for the Institute of Electrical Engineers. In 2004 he was a Fulbright Scholar at the Cognitive Neuroscience
laboratory at the Nathan Kline Institute for Psychiatric Research New York. Professor Reilly is also the recent
Chairman of the Biomedical Engineering Division of the Institution of Engineers of Ireland. Professor Reilly was
Director of the Trinity Centre for BioEngineering from July 2008 July 2012. He recently served as Academic
Director of the TRIL Centre, a multi-institutional project on ageing and independent living. He is currently the
President of the European Society of Engineering and Medicine.
[email: [email protected]]
Kevin OKelly BSc(Berkeley) MEngSc(NUI) PhD(NUI) MA(TCD) CEng FRAMI

Kevin O Kelly is Associate Professor in the School of Engineering, Trinity College Dublin. He obtained a double
degree in Mechanical Engineering and Materials Science from the University of California, Berkeley in 1986, and an
MEngSc and a PhD from University College Dublin in 1988 and 2000. He was Senior Project Engineer at AMT
Ireland (1988-1993) and a Newman Scholar at UCD (1993-1996), before joining the staff at Trinity College Dublin.
He is a Chartered Engineer, a Member of the Institution of Engineers of Ireland, and a Fellow of the Royal Academy
of Medicine of Ireland. He is also President of the Section of Bioengineering of the Royal Academy of Medicine in
Ireland. Dr OKelly served as Deputy Director of the Trinity Centre for Bioengineering from 2002-2012.
[Email: [email protected]]
Ciaran Simms, BA, BAI, PhD, FTCD
Ciaran is a Lecturer in the Department of Mechanical and Manufacturing Engineering, and a Principal Investigator of
the Trinity Centre for Bioengineering at Trinity College Dublin. His research interests are in injury biomechanics
(with a focus on vulnerable road user safety), soft tissue mechanics (with a focus on passive muscle behaviour) and
medical device design.
David Taylor, MA (Cantab), PhD (Cantab), ScD (Cantab), FTCD, FIEI, CEng
Professor of Materials Engineering, School of Engineering and also a Principal Investigator in the Trinity Centre for
Bioengineering, Trinity College, Dublin. He has a PhD from Cambridge University in Materials Science and a CEng
from the Institute of Engineers of Ireland. He is the editor in chief of the Journal of the Mechanical Behavior of
Biomedical Materials. His research interests lie in the prediction and analysis of failure in materials and components,
including human bone and biomaterials as well as engineering materials.
Daniel Kelly, BA, BAI, MSc, PhD
Associate professor (Mechanical Engineering - Bioengineering) in Trinity College, Dublin and Director of Trinity
Centre for Bioengineering. Daniel Kelly received his BAI degree in 1999 and his PhD degree in 2004, both from the
University of Dublin, Trinity College. After receiving his doctorate he moved into industry, working as a research
and development engineer for a medical device company producing coronary and peripheral angioplasty catheters and
stents. His research interests are in the area of computational and experimental mechanobiology, focusing on the
applications this emerging discipline is having on cartilage tissue engineering and the design and pre-clinical evaluation
of next generation
34
FACULTY MEMBERS
medical devices and implants. In 2008 he was the sole recipient of the President of Ireland Young Researcher Award
to fund a research program investigating the mechanobiology of mesenchymal stem cells for articular cartilage repair.
In 2009 he received a Fulbright Award to take a sabbatical position as a Visiting Research Scholar in the Department
of Biomedical Engineering at Columbia University, New York. In 2010 he was awarded a European Research Council
Starter Grant of 1.5 million to develop novel mesenchymal stem cell based therapies for articular cartilage repair.
Brian OConnell, BDS, PhD, FACP, FTCD

Professor of Restorative Dentistry in the School of Dental Science and a Principal Investigator in the Trinity Centre
for Bioengineering. Prior to his appointment to Trinity College he was Head of the Gene Regulation and Expression
Unit at the National Institute for Dental and Craniofacial Research in Bethesda, USA. Prof OConnells current
research includes the differentiation of mesenchymal stem cells and the early events around implant healing. He is
also involved in collaborative projects on the development of novel implant surfaces.
Fergal J. O'Brien, BA, BAI, PhD, CEng, MIEI

Associate Professor in Anatomy in the Royal College of Surgeons in Ireland and Adjunct Associate Professor in
Bioengineering in Trinity College Dublin and Principal Investigator in the Trinity Centre for Bioengineering. He
heads one the largest tissue engineering/regenerative medicine research groups in Ireland. His research focuses on
bone mechanobiology and osteoporosis, the development of novel scaffolds for tissue engineering and the influence of
biophysical stimuli on stem cell differentiation. He is a reviewer for over 30 scientific journals, grant reviewer for
agencies in Europe (FP7), UK, Australia, USA and Ireland as well an Editorial Consultant for the Journal of
Biomechanics and Associate Editor (Tissue Engineering) for the Journal of the Mechanical Behavior of Biomedical
Materials. He has been awarded a number of scientific honours including a Fulbright Scholarship (2001),
Orthopaedic Research Society, New Investigator Recognition Award (2002), Science Foundation Ireland, President
of Ireland Young Researcher Award (2004: 1.1 million), Engineers Ireland Chartered Engineer of the Year (2005)
and a European Research Council Investigator Grant (2009: 2 million).
Henry Rice, BE, MA, PhD, CEng, MIEI, FTCD

Associate Professor of Mechanical Engineering at Trinity College where he has lectured since 1985. He is currently
Head of Discipline of Mechanical & Manufacturing Engineering. He is a specialist in both numerical and experimental
aspects of Acoustics and Vibration. One of his interests includes middle-ear vibro-acoustics where he has developed
links with the Kungliga Tekniska Hogskolan and the Karolinska Institute, Stockholm and the Mater Hospital, Dublin.
Adriele Prina-Mello, PhD, MBEMS, MEBEA

Research Fellow of Trinity College at the CRANN-SFI Trinity Nanoscience Laboratory. He holds a PhD in
Bioengineering from Trinity College and a full degree in Material Science and Engineering from Politecnico di Torino
(Italy). His research interests are in Nanotechnology, Biophysics, Biomagnetism and Cellular Engineering. His main
research work is focused on the understanding of the adaptative mechanisms of living cells and tissue when subjected
to external stimuli. He is also interested in clinical and experimental biomechanics and biomaterials. In CRANN, Dr.
Prina Mello also works as advisor in Nanoscience and Nanotechnology standard and policy in Ireland.
35
FACULTY MEMBERS
Aoife Gowran, BSc, PhD
Dr. Gowran graduated from The Dublin Institute of Technology in 2003 with a BSc (Hons) in Biochemistry and
Molecular Biology. In 2008 she graduated with a PhD in Neuroscience from the University of Dublin, Trinity
College. Her early research indentified that the psychoactive component of cannabis, delta-9-tetrahydrocannabinol
induces apoptosis (cell death) in the immature brain and that cannabis like substances, called endocannabinoids which
are naturally present in the body, protect brain cells from dying when given a toxic insult. Following her PhD Dr.
Gowran worked as a Postdoctoral Research Fellow at Trinity College Institute of Neuroscience where she continued
her research on the effects of endocannabinoids on the differentiation, survival and migration of Mesenchymal Stem
Cells (the precursors to bone and cartilage etc.). In 2010, Dr Gowran was appointed a lectureship in the Department
of Physiology and is continuing to research the potential of endocannabinoids to provide neuroprotection in
Alzheimers disease. [email: [email protected]]
Clive Lee, PhD, MD, ScD (Dubl), FRCSI, FRCSEd, CEng, FIEI, HRHA
Clive Lee is Professor of Anatomy at the Royal College of Surgeons in Ireland and Visiting Professor of Biomechanics
and Tissue Engineering at Trinity College Dublin. He is currently Chair of the Executive Committee of the Trinity
Centre for Bioengineering. He is a Chartered Engineer, past President of the Section of Bioengineering of the Royal
Academy of Medicine in Ireland (2000-02) and past President of the European Society for Engineering and Medicine
(2003-07). He was awarded the Fulbright Medal in 2003, the Samuel Haughton Silver Medal, and his ScD for
published work, in 2010. He is on the Editorial Boards of Technology & Health Care and the Journal of the
Mechanical Behavior of Biomedical Materials. He is currently Honorary Secretary of the Anatomical Society and
Chair of the Life Sciences Committee of the Royal Irish Academy, which he also represents on the Biosciences
Steering Panel of the European Academies Science Advisory Council. His research interests and Publications are in
microdamage and bone remodelling related to osteoporosis and functional anatomy. [email: [email protected]]
Garrett Lyons, MA, MSc, FRSA

Senior Lecturer (retired officially 2010) of Mechanical & Manufacturing Engineering, Trinity College, Dublin. He has
over forty years experience in various fields of engineering research and engineering design. His interest in
bioengineering grew out of design work for the development of assistive devices for the disabled. His current
research interests are in impact biomechanics and the properties of human skeletal muscle and other soft tissues.
Conor T. Buckley, BA, BAI, PhD, MIEI

In 2011 Dr. Buckley was appointed lecturer in Biomechanics and Tissue Engineering in the Department of
Mechanical and Manufacturing Engineering, Trinity College Dublin. On completion of a PhD degree in 2007 in the
area of scaffolds and bone tissue engineering, Dr. Buckley worked as a senior postdoctoral fellow in the fields of
cartilage regenerative medicine and mechanobiology- developing new strategies, medical devices and techniques for
stem cell based repair. In 2009, Dr. Buckley was awarded an SFI fellowship to work in the mesenchymal stem cell
group at the Leeds Institute of Molecular Medicine, UK focusing on isolation, enrichment and characterisation of
mesenchymal stem cells (MSCs) from different tissue sources for regenerative medicine purposes. His current main
research area focuses on the development of strategies to regenerate the intervertebral disc (IVD). Other research
areas include design and development of bioreactor based systems, cartilage tissue engineering, nutrient micro-
environments, biomaterial interactions and 3D scaffold construct technology. [email: [email protected]]
Wilfrid J. Higgins, BE, MBA, MSc, CEng, FIEI

Visiting Lecturer in the Department of Mechanical Engineering and a Principal Engineering Advisor in the Health
Service Executive. He is Chairman of the Scientific Advisory Committee on Medical Devices, Irish Medicines Board.
He is a chairman of the NSAI Health Care Standards Consultative Committee and represents Ireland at the Advisory
36
FACULTY MEMBERS
Board for Healthcare Standards in Europe. He is a member of the ETCI TC10 Committee and chairs the wiring rules
sub-committee. His research interests are in medical device regulation and standards, risk analysis, and health
technology assessment. [Email: [email protected]]
David FitzPatrick, BA, BAI, DPhil

Senior Lecturer and Head of the School of Engineering: Electrical, Electronic & Mechanical, at University College
Dublin. Following his BAI (TCD, 1985) in Mechanical Engineering, he received his D.Phil degree from the
University of Oxford in 1990 for doctoral work entitled Mechanics of the Knee Joint. Following a period of nine
years within the orthopaedic industry, he joined UCD in December1998. He is currently responsible for the design of
bioengineering curricula at undergraduate level and also contributes to post-graduate taught masters courses. He is
Director of the Bioengineering Research Centre within Mechanical Engineering and is a principal research contributor
and Board member within the Trinity Centre for Bioengineering, University of Dublin. His primary research
interests are in the fields of musculoskeletal modeling and anthropometrics, medical device design and design process
methodologies.
Madeleine Lowery, BE, PhD

Lecturer in Electrical and Electronic Engineering in the School of Electrical, Electronic and Mechanical Engineering,
University College Dublin. Before joining UCD, she spent five years as a post-doctoral researcher and then research
scientist in the Dept. of Physical Medicine and Rehabilitation, Northwestern University and the Rehabilitation
Institute of Chicago. Her research involves the exploration of nerve and muscle activity through a combination of
mathematical modelling and experimentation to improve our understanding of neuromuscular activity in healthy and
diseased states.
Kenneth Stanton, BSc MSc PhD CEng CSci MIMMM MIoN

Lecturer in Advanced Materials at the UCD School of Electrical, Electronic and Mechanical Engineering. Following
his BSc in Materials Science (UL, 1995) and an MSc in Physics (London, 1996) he obtained a PhD for his work on
biomedical glass-ceramics (UL, 2000). He formerly held a lecturing post at the University of Limerick where he
taught biomaterials on the MSc Biomedical Engineering course. His research is primarily concerned with bioceramics,
crystallisation of inorganic solids and biological interactions between nano-particles and nano-structured surfaces.
Edmund Lalor, BE MSc PhD

Edmund Lalor received the B.E. degree in electronic engineering from University College Dublin, Ireland in 1998
and the M.Sc. degree in electrical engineering from the University of Southern California in 1999. After periods
working as a silicon design engineer for a Dublin-based company and a primary school teacher for children with
learning difficulties, Ed joined MIT's Media Lab Europe, where he worked from 2002-2005 as a research scientist
investigating brain-computer interfacing and attentional mechanisms in the brain. This research led to a PhD in
biomedical engineering which was completed through UCD in 2006. Subsequently, he spent 2 years in New York
working as a postdoctoral research fellow in the Cognitive Neurophysiology Laboratory at the Nathan Kline Institute
for Psychiatric Research and as an adjunct assistant professor in the City College of New York. He returned to a
position as an IRCSET Government of Ireland Postdoctoral Research Fellow based at the Institute of Neuroscience
and the Centre for Bioengineering in Trinity College Dublin in 2008. Following a brief stint at University College
London's Institute of Ophthalmology, he returned to Trinity College Dublin as an Ussher Lecturer in 2011.
37
FACULTY MEMBERS
Bruce Murphy, BA PhD

Dr Bruce Murphy is deputy director of the Trinity Centre for Bioengineering and a lecturer in Biomedical
Engineering at the Department of Mechanical and Manufacturing Engineering. Prior to this position he directed a
vascular medical device design group at NUI Galway. One of the technology outputs from this group has been
licensed into a start-up biomedical company based in Galway. He won the Entreprise Ireland One to Watch Award in
2009. Research interests are mitral valve regurgitation, local therapeutic delivery to diseased blood vessels, force
focused angioplasty and vascular tissue engineering.
John Gleeson, BA, BAI, PhD

Dr. Gleeson is a Principal Investigator and Project and Business Development Manager in the Tissue Engineering
Research Group, headed by Prof. Fergal OBrien, in the Royal College of Surgeons in Ireland. He is a graduate in
mechanical engineering from Trinity College Dublin (2001) and received his PhD in 2006, investigating the effect of
early stage primary osteoarthritis on bone composition and mechanical properties. His current role involves the
development and commercialisation of novel tissue engineering medical devices for the repair and regeneration of
bone and osteochondral tissue. Dr. Gleesons research interests include bone and cartilage mechanobiology,
biomaterials, osteoarthritis and orthopaedic tissue engineering and he was shortlisted for the 2009 Roche Researcher
of the Year award, recognising young investigators excellence in life sciences research.
38
COURSE REGULATIONS
The complete set of regulations is set out in the University Calendar. Copies are held in the College Library,
Enquiries Office, and all academic and administrative offices. A copy can be purchased in the Library Shop. Some of
the more relevant sections are summarised in the following sections.
Attendance, non -satisfac tory attendance and course work

Please note the following extract from the university calendar: For professional reasons, lecture and tutorial
attendance in all years is compulsory in the School of Engineering. Attendance at practical classes is also compulsory.
All students must fulfill the requirements of the Course Committee with regard to attendance and course work.
Students whose attendance or work is unsatisfactory in any year may be refused permission to take all or part of the
annual examinations for that year. Where specific attendance requirements are not stated, students are non-
satisfactory if they miss more than a third of a required course in any term.
At the end of the teaching term, students who have not satisfied the Department, School or Course Committee
requirements may be returned as non-satisfactory for that term. In accordance with the regulations laid down by the
University Council non-satisfactory students may be refused permission to take their annual examinations and may be
required to repeat their year.
Further details on the academic regulations concerning attendance, non-satisfactory attendance and course work are
given in the University Calendar on the Graduate Studies website.
Please note that you must attend the particular tutorial and laboratory sessions to which you have been assigned.
Collaboration, individual work & plagiarism

It is important to realise that the submitted work must be your own, and not taken verbatim from the internet or
other sources. To do so may be plagiarism, which is a serious offence.
Plagiarism is, simply put, the act of presenting the work of others as your own without acknowledgement. The last
two words are crucially important. The advancement of knowledge in any field relies heavily on the work of peers
and previous workers. Formal acknowledgement of their contribution not only gives them due credit for their work
but adds to the strength of your results and arguments. The regulations governing plagiarism are presented in the
calendar and you should read them. In summary, plagiarism can arise from actions such as:
- Copying another students work.
- Enlisting another person or persons to complete an assignment on the students behalf.
- Quoting directly, without acknowledgement, from books, articles, or other sources, either in printed,
recorded or electronic format.
- Paraphrasing, without acknowledgement, the writings of others.
5B
39
COURSE REGULATIONS
Results
Students are required to pass all modules of the course. Pass mark is 50%. TCD does not award grades to M.Sc.
degrees.
Postgraduate Diploma in Bioengineering

Candidates who do not proceed to the dissertation, or who have failed their dissertation but have passed all the
required modules and research methods module, may, on the recommendation of the examiners, be awarded a
Postgraduate Diploma in Bioengineering. Both the examinations and the dissertation are subject to external
moderation. Any student awarded the postgraduate diploma automatically forfeits the possibility of being awarded
the M.Sc. at any later stage.
Regulations for re -checking/remarking of Examination Scripts

i) All students have a right to discuss their examination and assessment performance with the appropriate members of
staff as arranged for by the Course Coordinator. This right is basic to the educational process.
ii) Students examination performance cannot be discussed with them until after the publication of examination
results.
iii) To obtain access to the breakdown of their results students should make a request to the Course Coordinator.
iv) Having received information about their results and having discussed these and their performance with the Course
Coordinator and the appropriate staff, students may ask that their results be reconsidered if they have reason to
believe:
- that the grade is incorrect because of an error in calculation of results,
- that the examination paper specific to the students course contained questions on subjects which were part
of the course prescribed for the examination, or
- that bias was shown by an examiner in marking the script.
In the case of the above, the request should be made to the Course Coordinator.
Once an examination result has been published it cannot be amended without the permission of the Course
Coordinator.
Commendation for Projects

The Course Committee, in consultation with the External Examiner, may award a commendation for projects of
exceptional merit.
Should you have any queries regarding regulations and guidelines that apply to postgraduate students at Trinity,
please consult the Graduate Studies website http://www.tcd.ie/Graduate_Studies or Part 2 of the University
H H
Calendar which can be viewed http://www.tcd.ie/calendar/part2/ This Calendar contains all information
H H
concerning graduate studies in Trinity College, Dublin.
Commencements
All candidates for conferral in April 2014 must apply to the Proctors Office. All registered postgraduate students
expecting to be conferred with a higher degree in the current academic year, are annually invited by email, to make
application to the Proctors Office. The invitation includes provision of all the information necessary to make
application. Candidates are advised that closing dates are very strictly adhered to, and late applicants will not be
admitted to the selected ceremony; however, they may be admitted to the next available commencement session. A
Commencements fee is applicable to all making application for conferral. Further information about the application
process is available here.
40
COURSE REGULATIONS
Class Descriptors
The following Descriptors are given as a guide to the qualities that assessors are seeking in relation to the grades
usually awarded. A grade is the anticipated degree class based on consistent performance at the level indicated by an
individual answer. In addition to the criteria listed examiners will also give credit for evidence of critical discussion of
facts or evidence.
Guidelines on Grades for Essays and Examination Answers
Mark Criteria
Range
90-100 IDEAL ANSWER; showing insight and originality and wide knowledge. Logical,
accurate and concise presentation. Evidence of reading and thought beyond
course content. Contains particularly apt examples. Links materials from lectures,
practicals and seminars where appropriate.
80-89 OUTSTANDING ANSWER; falls short of the ideal answer either on aspects of
presentation or on evidence of reading and thought beyond the course. Examples,
layout and details are all sound.
70-79 MAINLY OUTSTANDING ANSWER; falls short on presentation and reading or
thought beyond the course, but retains insight and originality typical of first class
work.
65-69 VERY COMPREHENSIVE ANSWER; good understanding of concepts supported
by broad knowledge of subject. Notable for synthesis of information rather than
originality. Sometimes with evidence of outside reading. Mostly accurate and
logical with appropriate examples. Occasionally a lapse in detail.
60-64 LESS COMPREHENSIVE ANSWER; mostly confined to good recall of
coursework. Some synthesis of information or ideas. Accurate and logical within a
limited scope. Some lapses in detail tolerated.
55-59 SOUND BUT INCOMPLETE ANSWER; based on coursework alone but suffers
from a significant omission, error or misunderstanding. Usually lacks synthesis of
information or ideas. Mainly logical and accurate within its limited scope and with
lapses in detail.
50-54 INCOMPLETE ANSWER; suffers from significant omissions, errors and
misunderstandings, but still with understanding of main concepts and showing
sound knowledge. Several lapses in detail.
45-49 WEAK ANSWER; limited understanding and knowledge of subject. Serious
omissions, errors and misunderstandings, so that answer is no more than
adequate.
40-44 VERY WEAK ANSWER; a poor answer, lacking substance but giving some
relevant information. Information given may not be in context or well explained, but
will contain passages and words which indicate a marginally adequate
understanding.
35-39 MARGINAL FAIL; inadequate answer, with no substance or understanding, but
with a vague knowledge relevant to the question.
30-34 CLEAR FAILURE; some attempt made to write something relevant to the
question. Errors serious but not absurd. Could also be a sound answer to the
misinterpretation of a question.
0-29 UTTER FAILURE; with little hint of knowledge. Errors serious and absurd. Could
also be a trivial response to the misinterpretation of a question.
41
COURSE REGULATIONS
Guidelines on Marking for Project/Dissertation Assessment
Mark Range Criteria

85-100 Exceptional project report showing broad understanding of the project area and excellent
knowledge of the relevant literature. Exemplary presentation and analysis of results, logical
organisation and ability to critically evaluate and discuss results coupled with insight and
originality.
70-84 A very good project report showing evidence of wide reading, with clear presentation and
thorough analysis or results and an ability to critically evaluate and discuss research
findings. Clear indication of some insight and originality. A very competent and well
presented report overall but falling short of excellence in each and every aspect.
60-69 A good project report which shows a reasonably good understanding of the problem and
some knowledge of the relevant literature. Mostly sound presentation and analysis of
results but with occasional lapses. Some relevant interpretation and critical evaluation of
results, though somewhat limited in scope. General standard of presentation and
organisation adequate to good.
50-59 A moderately good project report which shows some understanding of the problem but
limited knowledge and appreciation of the relevant literature. Presentation, analysis and
interpretation of the results at a basic level and showing little or no originality or critical
evaluation. Insufficient attention to organisation and presentation of the report.
40-49 A weak project report showing only limited understanding of the problem and superficial
knowledge of the relevant literature. Results presented in a confused or inappropriate
manner and incomplete or erroneous analysis. Discussion and interpretation of result
severely limited, including some basic misapprehensions, and lacking any originality or
critical evaluation. General standard of presentation poor.
20-39 An unsatisfactory project containing substantial errors and omissions. Very limited
understanding, or in some cases misunderstanding of the problem and very restricted and
superficial appreciation of the relevant literature. Very poor, confused and, in some cases,
incomplete presentation of the results and limited analysis of the results including some
serious errors. Severely limited discussion and interpretation of the results revealing little or
no ability to relate experimental results to the existing literature. Very poor overall standard
of presentation.
0-19 A very poor project report containing every conceivable error and fault. Showing virtually
no understanding or appreciation of the problem and of the literature pertaining to it.
Chaotic presentation of results, and in some cases incompletely presented and virtually
non-existent or inappropriate or plainly wrong analysis. Discussion and interpretation
seriously confused or wholly erroneous revealing basic misapprehensions.
Note: The pass mark for the course is 50%

42
RECOMMENDED READING MATERIAL
Developments in bioengineering and medical technology have led to spectacular progress in clinical medicine. As a
result, increased numbers of courses are available in the area of bioengineering and clinical technology. These often
include modules dealing with basic biological and medical sciences, aimed at those taking up these studies, who have a
background in engineering.
To date, relatively few participants from medicine have taken up courses in biomedical engineering, to the detriment
of scientific exchange between engineers and medics. The European Society for Engineering and Medicine (ESEM)
aims to bridge the gap between engineering and medicine and biology. It promotes cultural and scientific exchanges
between the engineering and the medical/biological fields.
This primer consists of a series of First Step chapters in engineering and is principally presented for those with a
medical or biology background who intend to start a MSc programme in biomedical engineering, and for medics or
biologists who wish to better understand a particular technology. It will also serve as a reference for biomedical
engineers.
Written by engineers and medics who are leaders in their field, it covers the basic engineering principles
underpinning: biomechanics, bioelectronics, medical informatics, biomaterials, tissue engineering, bioimaging and
rehabilitation engineering. It also includes clinically relevant examples. Available in Trinity College library, the
Primer can also be purchased online at www.iospress.nl or To purchase click here
H H H
43
CAREERS IN BIOENGINEERING
Where are the jobs?
The medical device and diagnostic industry continues to be a vibrant growth sector and a cornerstone of the Irish
economy. Circa 160 companies are involved in developing, manufacturing and marketing a diverse range of products
and services from disposable plastic and wound care products to precision metal implants including pacemakers to
microelectronic devices, orthopaedic implants, diagnostics, contact lenses and stents.
Some key facts/ figures:
There are currently over 160 medical technology companies in Ireland, exporting 6.8b worth of product
annually and employing 24,000 people - the highest number of people working in the industry in any
country in Europe, per head of population.
Exports of medical devices and diagnostics products now represent 8% of Irelands total merchandise
exports; and growth prospects for the industry globally remain good.
Many of the worlds top medical technology companies have invested significantly in Ireland and a number
of exciting, research-based, indigenous companies are emerging and competing internationally.
Over 90 of the companies in the sector are indigenous (ref Enterprise Ireland)
The Irish government has identified the medical technology sector as one of the key drivers of industrial
growth for the future and provides a wide range of supports to encourage and foster this growth.
The medical technology industry in Ireland is changing from being prominently manufacturing to being
more complex and driven by R&D. It now involves intensive collaboration between a broad range of
partners, including research institutions, clinicians, manufacturing companies and government agencies.
Ireland is well placed to capitalise on the growing global market for medical technology products and services. The
challenge is to continue to develop and integrate the broad range of strategic competencies and support systems that
will enable this island to compete as a mature, high value added economy, with innovation at its core.
Employment in the bioengineering industry in Ireland has grown to the level where the industry now directly
employs over 12,000 people in Ireland, of which up to 20% are graduate engineers and scientists (see www.ida-
H
ireland.ie ). The engineer working in this industry needs to be both technically competent and capable of integrating
H
those aspects of biology and medicine related to the medical device. Many bioengineers are involved in applying
science and engineering knowledge to the manufacture of medical products.
44
CAREERS IN BIOENGINEERING
Finding Opportunities: recommended resources

www.tcd.ie/Careers
www.gradireland.com
www.prospects.ac.uk
Jobs websites such as www.meddevicejobs.ie/www.biotechnologyireland.com/www.irishjobs.ie/
www.monster.ie/
Professional Bodies IMDA, IEI
www.ibec.ie/Sectors/IMDA
www.iei.ie
Graduate Employer Careers Fairs: RDS in June and October
http://www.gradireland.com/Jobs
CAS surveys on pharmaceutical, chemical & bio industry, medical devices,
http://www.tcd.ie/Careers/resources/occupations/
FAME Directory
Scientific and Professional Journals
But.. Not all j obs are advertised so you need to use c reative approaches
Using your networks for information/ advice and opportunities
Information and advisory interviews
Taking the stepping stone approach
Scanning media
Letting people know you are looking
Professional networks organisations, journals
Work shadowing
Training in area related to your target
Speculative applications to employers
And make use of your network

45
COURSE ADMINISTRATION M.Sc. BIOENGINEERING
Trinity College Dublin

Course Administra tor: June OReilly
Contact Address: Trinity Centre for Bioengineering
Trinity Biomedical Sciences Institute
152-160 Pearse Street, Dublin 2.
Telephone: +353-1-8964214
Email: [email protected]
University College Dublin

Course Administra tor: Oran ORua
Contact Address: School of Electronic, Electrical and Mechanical
Engineering, UCD, Dublin
Telephone: +353-1-7161787
National College of Art and Design

Course Administra tor: Paul Fortune
Contact Address: Department of Industrial Design,
National College of Art and Design,
100 Thomas Street, Dublin 8
Telephone: +353-1-6364272
46
CAMPUS MAPS
Trinity College Dublin

47
48
CAMPUS MAPS M.Sc. in BIOENGINEERING
National College of Art and Design
The National College of Art and Design is situated at 100 Thomas Street, about 5 minute walk from Christchurch
Cathedral and 15 minutes from Trinity College.
There is limited car parking in the College - use the rear entrance along Oliver Bond Street. If the College car park is
full, there is pay-and-display street parking on Oliver Bond Street. There is also an NCP car park on Oliver Bond
Street, close to the intersection with Bridgefoot Street.
There is a limited canteen service in the College but there are several cafes in the immediate vicinity.
Public Transport Links

The college is well served by public transport. Dublin Bus operate 4 services through Thomas Street: 51B, 51C ,
78A, 123 and 206 . In addition Dublin Bus operates the 90 Railink service from both Connolly and Tara Street rail
stations. This bus stops at the Statoil filling station on Usher's Quay, to the rear of the college.
The new Luas tram system passes close by, the nearest station being Smithfield, at Phoenix Street North. There are
H H
also stops at James's Hospital and Heuston station
The college is also a short, 10 minute walk from Heuston station which operates routes to and from Cork, Tralee,
Limerick, Waterford, Ballina/Wesport, Galway, Kildare and Clonmel.
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What are the main objectives of the MSc in Bioengineering course?

What are the main objectives of the MSc in Bioengineering course?

What institutions are involved in delivering the MSc in Bioengineering course?

What institutions are involved in delivering the MSc in Bioengineering course?

MSc NTRE

Course Handbook 2012-2013

TRINITY CENTRE FOR BIOENGINEERING

Neural Engineering Cardiovascular Biomaterials Regenerative Musculoskeletal

Dear M.Sc. Student, Dear Bioengineer,

The M.Sc. in Bioengineering is a unique venture between Trinity College Dublin,

Professor Richard Reilly

Welcome from course director 1

Course Structure, Annual Schedule & Dates of Examinations 4

M.Sc. Course Modules

Recommended reading material 44

Trinity College Academic Year Structure 51

Specifically the aims are:

By way of case studies and assignments, to give students a familiarity with

To give students a sound understanding of how to apply the scientific method to

To give students a knowledge of how the medical device industry is regulated

MODULE ECTS TERM LECTURE DATES EXAM MODULE

Basic Medical Sciences 5 Michaelmas 5 October 7 Dr Aoife Gowran

Physiological 10 Michaelmas 5 9 November 2012 12 Dec 2012 Prof. Richard Reilly

Rehabilitation 10 Michaelmas 19 23 November 2012 14 Dec 2012 Prof David Fitzpatrick

Research Methods 15 Hilary 18 22 February 2013 Dr Ciaran Simms

Dissertation 30 Trinity 30 August 2012

Course Coordinator: Dr. Conor Buckley, School of Engineering, TCD

Submission of assignments and labs via Blackboard

Final Examination: 10 December 2012 9.00am 12.00pm

Individual Assignment: The assignment topic is self-assigned by an individual student and

Cells, Tissues, Organs

The Human Brain

The Respiratory System

The Renal System

Bone and cartilage

Patient Investigation: St. Jamess Hospital

Diagnostic Imaging & Histopathology

The Endocrine System

Case Study of endocrine disorder: Diabetes

Case Study: Paediatrics

Case Study: Surgical Patient

Revision & preparations of presentations

Presentations and hand-in of individual assignments

Course Coordinator: Prof. Richard Reilly

Monday 5th Nov

Tuesday 6th Nov

Wednesday 7th Nov

Thursday 8th Nov

Lect. 21 Biomedical Signal Analysis Richard Reilly

Friday 9th Nov

*** Royal College of Surgeons in Ireland and Beaumont Hospital

Examination Date: Wednesday 12th December 2012 at 9.00am

The following is an indicative list of lecture topics:

The following is an outline description of each 4-hour lecture/lab topic content:

Assessment will be by way of course assignments and a final examination.

Course Lecturers: Dr. Alun Carr, U niversity College Dublin

2: Applications and Markets for Biomaterials

3: Common Biomaterial Types

4: Key Materials Issues in Biomaterials