NTRE FOR BIOENGINEERING

2011-2012

TRINITY CENTRE FOR BIOENGINEERING

2011-2012

MSc in Bioengineering

Course Handbook

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MSc in Bioengineering

Course Handbook

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0BTABLE OF CONTENTS

Welcome from course directors 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 Bioinstrumentation 9 Rehabilitation Engineering (optional module) 10 Biomaterials 11 Neural Engineering (optional module) 13 Cell & Tissue Engineering (optional module) 14 Research Methods 15

Thesis 17 All Ireland Faculty Members 31 Course Regulations 36

Recommended reading material 39

Careers in Bioengineering 40

Course Administrators 42 Campus Maps

TCD Campus Map 43 UL Campus Map 44 UCD Campus Map 45 NCAD Campus Map 46

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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.

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3BANNUAL SCHEDULE & 2BCOURSE STRUCTURE

MODULE

MODULES

ECTS

TERM

LECTURE DATES

EXAM DATES

MODULE COORDINATORS

Biomechanics

10

Michaelmas

5 - 9 September 2011

12 Dec 2011

Dr Conor Buckley

Basic Medical Sciences

5

Michaelmas

7 October – 2 December 2011

Dr Aoife Gowran

Bioinstrumentation

10

Michaelmas

7 – 11 November 2011

14 Dec 2011

Dr Hussain Mahdi

Rehabilitation Engineering*

10

Michaelmas

21 – 25 November 2011

16 Dec 2011

Prof David Fitzpatrick

Biomaterials

10

Hilary

11 - 18 January 2012

7 May 2012

Dr Ken Stanton

Dr Eamon De Barra

Research Methods

15

Hilary

6 – 17 February 2012

Dr Ciaran Simms

Neural Engineering*

5

Hilary

22 – 24 February 2012

9 May 2012

Prof Richard Reilly

Cell and Tissue Engineering*

5

Hilary

5 – 8 March 2012

11 May 2012

Dr Conor Buckley

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

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25BM.Sc. COURSE MODULES BIOMECHANICS

60BCourse Coordinator: Dr. Conor Buckley, School of Engineering, TCD

61BModule Dates: Monday 5 t h to Friday 9 t h September 2011

62BModule Object ives

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.

63BSyllabus

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.

64BAssessment

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:

• Cardiovascular Devices (Dr B. Murphy) Submission date: Friday 23rd September

• Musculoskeletal Biomechanics (Mr. G. Lyons & Dr C. Simms) Submission date: Friday 7th October

• Laboratory Reports Submission date: Friday 28th October

1. Damage and histology of compact bone 2. Poroelastic mechanical properties of cartilage tissue

Submission of assignments and labs via WebCT

Final Examination: 12 December 2011

The exam will consist of two parts: all 12 questions in the first part must be answered, and any 3 of the 11 questions

in part two must be answered. Exam duration is 3 hours.

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M.Sc. COURSE MODULES BIOMECHANICS All lectures will be held in the Arts Block, Trinity College, Dublin, September 5th - 9th 2011

Module Coordinator: Dr. Conor Buckley (conor.buckley@tcd.ie)

Monday 5th Sept Location: Room 2041B (Teatar Mhairtin Ui Chadhain), Lecturer

(9.00-9.30) Opening remarks and introductions Dr. K. O'Kelly/Dr. C. Buckley

(9.30-10.00) Welcome Coffee Reception

Lect. 1 (10.00-10.30) Introduction to WebCT Ms. Catherine Kane

Lect. 2 (10.30-11.00) Pre-laboratory talks Dr. C. Buckley

Lect. 3 (11.00-12.00) Soft Tissue Microstructures Prof. D. Taylor

BREAK

Lect. 4 (13.00-14.00) Tissue growth and adaptation Prof. D. Taylor

Lect. 5 (14.00-15.00) Ligament tendon and muscle viscoelasticity Dr. C. Simms

Lect. 6 (15.00-16.00) Cartilage mechanics Dr. D. Kelly

Lect. 7 (16.00-17.00) Biomechanics of the spine and intervertebral disc Dr. C. Buckley

Tuesday 6th Sept Location: Room 2043 (Thomas Davis Theatre) Lecturer

Lect. 8 (9.00-10.00) Bone as a composite material Dr. D. Hoey *

Lect. 9 (10.00-11.00) Physiological blood flow and function of the heart Prof. T.C.Lee*

Lect. 10 (11.00-12.00) Non-linear elasticity of blood vessels 1 Mr. T. Nagel

Lect. 11 (12.00-13.00) Non-linear elasticity of blood vessels 2 Mr. T. Nagel

BREAK

Lect. 12 (14.00-15.00) Cardiovascular stents & Angioplasty catheters 1 Dr .B. Murphy

Lect. 13 (15.00-16.00) Cardiovascular stents & Angioplasty catheters 2 Dr. B. Murphy

Lect. 14 (16.00-17.00) Disease and degeneration of tissues Prof. T.C. Lee*

Wednesday 7th Sept Location: Room 2041B (Teatar Mhairtin Ui Chadhain) Lecturer

Lect. 15 (9.00-10.00) Medical devices: directives, regulations and standards Mr. W.Higgins**

Lect. 16 (10.00-11.00) Risk analysis and risk management in medical devices Mr. W.Higgins**

Lect. 17 (11.00-12.00) Transcatheter Heart Valves Dr. B. Murphy

Lect. 18 (12.00-13.00) Introduction to injury biomechanics Mr. G. Lyons

BREAK

Lab. (Group 1) Damage and histology of compact bone Mr. P. Mauer*

Lab. (Group 2) Poroelastic mechanical properties of cartilage tissue Mr. T. Mesallati

Thursday 8th Sept Location: Room 2041B (Teatar Mhairtin Ui Chadhain) Lecturer

Lect. 19 (9.00-10.00) Musculoskeletal biomechanics Dr.C.Simms

Lect. 20 (10.00-11.00) Optimization and calculation of muscle forces Dr.C.Simms

Lect. 21 (11.00-12.00) Bioacoustics Prof. H.Rice

Lect. 22 (12.00-13.00) Impact injuries to long bones, chest and abdomen Mr. G.Lyons BREAK

Lect. 23 (14.00-15.00) Impact injuries to the long bones and abdomen Mr. G.Lyons

Lect. 24 (15.00-16.00) Bone mechanics 1 Dr. C. Buckley

Lect. 25 (16.00-17.00) Bone mechanics 2 Dr. C. Buckley

Friday 9th Sept Location: Room 2041A (Jonathan Swift Theatre) Lecturer

Lect. 26 (9.00-10.00) Pedestrian kinematics and injuries in collisions with vehicles Dr. C.Simms

Lect. 27 (10.00-11.00) Bone and joint replacements - design and materials selection Prof. D. Taylor

Lect. 28 (11.00-12.00) Medical device innovation- From concept to patent to product Dr. B.Murphy

Lect. 29 (12.00-13.00) Hands on innovation in the medical devices sector Mr. R. Dalton BREAK

Lab. (Group 1) Damage and histology of compact bone Mr. P. Mauer*

Lab. (Group 2) Poroelastic mechanical properties of cartilage tissue Mr. T. Mesallati

* RCSI *CEN

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M.Sc. COURSE MODULES MEDICAL SCIENCES

65BCourse Coordinator: Dr Aoife Gowran, School of Medic ine, TCD

66BModule Dates: Fr iday 7th October to Friday 2nd December 2011

67BModule Object ives

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.

68BAssessment

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 Presentations will take place from 2pm on Friday, December 2nd 2011 (please assemble in lecture hall beforehand to

upload presentations).

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 on Nov. 26th. 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.

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27BM.Sc. COURSE MODULES MEDICAL SCIENCES

69B

7th Oct

2.00pm

2.15pm

3.15pm

Introduction

Cells, Tissues, Organs Pathology

Dr Aoife Gowran

Dr Aoife Gowran

Prof O. Sheils

L

L

L

15min

1hr

2hr

Crossland Lecture

Theatre, Dept

Mechanical

Engineering, TCD

14th Oct

2.00pm

4.00pm

The Human Brain

Muscle

Dr Sarah Harney

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L

2hr

1hr

Crossland

Lecture Theatre

21st Oct

2.00pm

4.00pm

The Respiratory System

Circulatory System

Dr Áine Kelly

L

L

2hr

2hr

Crossland

Lecture Theatre

28th Oct

2.00pm

3.00pm

4.00pm

Blood

Immune System

The Renal System

Dr Aoife Gowran

L

L

L

1hr

1hr

1hr

Crossland

Lecture Theatre

4th Nov

2.00pm

4.30pm

Bone and cartilage

Patient Investigation: St. James‘s Hospital

Diagnostic Imaging & Histopathology

Dr Aoife Gowran

L

Visit

1hr

2h

Crosslands

Diagnostic Imaging

Reception,

St. James‘s Hospital

11th Nov

2.00pm

3.00pm

4.30pm

The Endocrine System

Case Study of endocrine disorder: Diabetes

Gastrointestinal system

Dr Aoife Gowran

Dr Mensud Hatunic

Dr Aoife Gowran

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L

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1hr

1hr TBC

1hr

Crossland

Lecture Theatre

18th Nov

2.00pm

3.00pm

Case Study: Paediatrics

Case Study: Surgical Patient

Dr E. Roche

Prof Kevin Mulhall

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L

1hr TBC

1hr TBC

Crossland

Lecture Theatre

25th Nov

2.00pm

Revision & preparations of presentations

2nd Dec

1.45pm

Presentations and hand-in of individual

assignments

BMS class 2011/12

L

4hr

Crossland

Lecture Theatre

Lectures will take place in Crossland Lecture Theatre, Parsons Building, Trinity College Dublin

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8BM.Sc. COURSE MODULES BIOINSTRUMENTATION

70BCourse Coordinator: Dr. Hussain Mahdi , University of L imerick

71BModule Dates: Monday 7 t h to Friday 11 t h November 2011

72BModule Object ives

To provide students with a substantial knowledge of the theory, principles and applications of signal processing 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: 1. An understanding of the concepts involved in instrumentation design. 2. An ability to perform signal processing procedures including synthesis, analysis and design and to understand the role of advanced signal processing in biomedical engineering. 3. An ability to design and implement signal processing algorithms and system using DSP and to critically evaluate existing systems. 4. An understanding of the role of medical device regulations and how they affect the design of medical devices.

73BSyllabus

This course is taught at UL over one intensive week of 30 contact hours followed by four weeks of self-study using self-learning assignments. The self-study 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.

74BAssessment

Assessment will be by way of assignments and a final examination. Course assignments Cumulative assignments will account for 40% of the total marks. Final reports on all course assignments should be submitted to WebCT and by email to Ms Christine Roche (christine.roche@ul.ie) and cc Dr Hussain Mahdi (hussain.mahdi@ul.ie) by 5th March 2012 Final Examination: 14 December 2011 The final (written) exam will account for 60% of the total marks.

The Syllabus will cover the following:

1. Basic concepts of Medical Instrumentation. 2. Medical Devices Regulations. 3. Action Potential. 4. ECG, EEG, ENG, EMG, MEG. 5. Chemical Sensors, Glucose and pH sensors. 6. Heart Sound and Blood pressure measurement. 7. Advanced tissue optics. 8. Doppler Flowmetry, Spirometry, Pulse Oximetry. 9. Biomedical Electrodes. 10. Wireless endoscopy. 11. Medical Imaging: MRI, X-ray CT, PET. 12. Medical devices safety: isolation

13. Sensors – Physical and Chemical 14. Analog processing – Op Amps, Filters,

Conditioning 15. Digital Processing – ADC, DSP, Micro-

controller Architecture 16. Lab work: Matlab – Introduction;

Biomedical Applications in ECG 17. Lab work: Design & testing of an ECG

front end

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32BM.Sc. COURSE MODULES REHABILITATION ENGINEERING

33B*optional module

82B

Course Coordinator: Dr. David FitzPatrick, Universi ty Col lege Dublin

83BModule Dates: Monday 21 November to Friday 25 November 2011

84BSyllabus

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.

85BAssessment

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: 16 December 2012 The exam will account for 60% of the total result.

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30BM.Sc. COURSE MODULES BIOMATERIALS I & II

76BCourse Coordinator: Dr. Kenneth Stanton, Universi ty Col lege Dublin

77BModule Dates: Wed 11 t h January to Fr iday 13 t h January 2012 (UCD) 78B

76BCourse Coordinator: Dr. Eamonn De Barra, University of L imerick

77BModule Dates: Monday 16 t h January to Wednesday 18 t h January (UL)

79BModule Object ives

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.

80BSyllabus

This course is taught at UL and UCD over two intensive half weeks totaling 27 contact hours followed by four weeks of self-study using self-learning assignments. The self-study will include 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.

1: Introduction to Biomaterials Definition and general classification of biomaterials (natural and synthetic) 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 and their usage Biopolymers/bioplastics, bioceramics metals and metal alloys, shape memory alloys composites woven and non-woven fabrics hydrogels bio-adhesives controlled drug delivery systems. 4: Key Materials Issues in Biomaterials Polymer science and technology for the fabrication of medical devices. Chemical, physical and mechanical properties of ceramic materials for hard tissue implants. The development of medical grade metals and metal alloys: shape memory alloys. Composite materials (polymer/polymer, polymer/metal, polymer/ceramic): fibre/particulate reinforced. 5: Sterilisation and packaging considerations 6: Regulation and standards for quality and safety FDA, EU - Medical Device Directives, GMP, ISO, CE marking. 7: Risk assessment (COSHH) and the handling of clinical waste 8: Biomaterials in Medical and Dental Devices and Prostheses: Material choice implications based on device design. General biomaterial evaluation procedures. Replacement of skeletal hard tissues. Cardiovascular implants. Artificial vascular grafts. Biomaterials for ophthalmology. Biomaterials

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31BM.Sc. COURSE MODULES BIOMATERIALS

in audiology. Facial implants. Dental implants. Skin repair/replacement materials. Cosmetic implants, controlled drug delivery systems. Hydrogels and artificial organs. 9: Clinical Aspects of the Use of Biomaterials: Biocompatibility and biomimicery. Surfaces and surface interactions:- tissue and blood interactions. mineralisation and encrustation microbial biofilm formation bacterial adhesion toxicology 10: Surface Modification of Biomaterials for Improved Functionality: Enhancement of biocompatibility by the use of:- Corona discharge and plasma processes. Surface coatings silver/silver oxide silicone hydrogels UV curable systems PC coatings Heparin loaded systems

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.

81BAssessment

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. Eamonn De Barra at eamonn.debarra@ul.ie and WebCT Final Examination: 7 May 2012 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.

34B

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M.Sc. COURSE MODULES NEURAL ENGINEERING

35B*optional module

86B

Course Coordinator: Prof. Richard Rei l ly , Tr inity College Dublin

87BModule Dates: Wednesday 22n d to Friday 24 t h February 2012

88BSyllabus

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

89B

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 WebCT Final Examination: 9 May 2012 The final examination will account for 60% of the total result.

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36BM.Sc. COURSE MODULES CELL & TISSUE ENGINEERING

37B*optional module

90B

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

91BModule Dates: Monday 5 t h March to Thursday 8 t h March 2012

79B

Module Object ives

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

92B

Syllabus

This course is taught partly by self-study and partly by 2½ 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

93B

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 WebCT

Final Examination: 11 May 2012 The final examination will be two hours long. The exam will account for 60% of the total result.

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38BM.Sc. COURSE MODULES RESEARCH METHODS

94BCourse Coordinator: Dr. Ciaran Simms, TCD

95BModule Dates: Monday 9 t h to Friday 13 t h Apri l 2011

97BSyllabus

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

98BLearning 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

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38BM.Sc. COURSE MODULES RESEARCH METHODS

Component

Marks (%)

Details

Assessment by

Estimated Student hours

Research Proposal

10

5 page report on proposed project work;

(template provided)

Thesis supervisor

40

Industrial Design

20

Industrial Design module at NCAD

NCAD

30

Ethical Issues

10

Students attend lectures in Ethical Issues in Clinical Research, students answer questionnaire on application to project work (template provided); submitted as Appendix of thesis

Thesis supervisor

20

Statistics

20

Short course on Statistics

Lab and case study

60

Innovation and Entrepreneurship

10

Evening seminar: talks from Business & Industry; students answer questionnaire on application to project work (template provided); submitted as Appendix of thesis.

Thesis supervisor

20

Oral Presentation

20

Midterm presentation with external examiner: 10 minutes presentation, 5 minutes questions

Course Director & External Examiner

20

Referencing Methods Training

Training Session in Endote (organised by TCD library)

5

Short Paper

10

Short Paper based on thesis work (template provided); submitted as Appendix of thesis

Thesis supervisor

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39B

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THESIS

109BObjectives

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.

110BProject T it les

144BHere 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 Parkinson‘s 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

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Guidelines for Thesis Report and Presentations

This section emphasises the Trinity Centre for Bioengineering‘s 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.

113BPreparing 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.

114BReport Outl ine

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.

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115BSchedul ing

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.

121BTitle Page

This page should include:

- Concise title (not more than 15 words) Should be informative. Abbreviations should be avoided

- Author‘s name

- Supervisors name

- Affiliation

- Date

- Degree for which thesis is being submitted

122BAbstract

- 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.

123BContents page

- This should include chapter headings and details of sections within chapters, with page numbers.

124BList of Tables

- This should include details of all tables with page numbers.

125BList of Figures

- This should include details of all figures with page numbers.

126BAcknowledgements

- 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.

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- 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.

- 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).

127BIntroduction

- 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.

128BLiterature 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.

129BMethods

- 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.

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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.

130BResults

- 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.

131BDiscussion

- 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.

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This list is by no means exhaustive and the categories will often overlap, but it should be helpful at the planning stage.

56BReferences

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…‘.

132BStyle 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.

145BJournal 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.

146BBook

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.

147BChapter in a book

Cited in text as: (Lalor, 2009)

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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.

57BAppendices

- 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.

133BFigures 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).

134BGrades 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]

135B

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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.

136BSpelling, 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.

- Student‘s t test should have a capital and apostrophe); the t should be italicised.

- ―It‘s‖ 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'.

137BHeaders 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.

138BPagination

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.

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139BFont 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.

140B

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.

141BSpecial 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.

142BPreparing 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.

143BPlagiarism:

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 one‘s 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 student‘s work b) enlisting another person or persons to complete an assignment on the student‘s 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

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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 one‘s 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 student‘s 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

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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 industry‘s 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 isn‘t 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.

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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.

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THESIS SUBMISSION

112BDissertation submission date is 30 August 2012

Submit two hard bound copies to the Course Administrator in Tr ini ty Centre for

Bioengineering off ice. A copy must a lso be emai led to tcbe@tcd.ie.

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 Hthesis submission guidelines H, these regulations are on the Graduate Studies website. 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.

8B

Sample Thesis Cover Sample Page 1 Title Sample Page 2 Declaration

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47BThe 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.

148BAdditional 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.

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9BALL IRELAND FACULTY MEMBERS

, BE, MEngSc, PhD, MIEI, MIEE, SMIEEE, FTCD Course Director

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. Since July 2008 he has been the Director of the Trinity Centre for BioEngineering. 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 has 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: richard.reilly@tcd.ie]

, BE (NUI), MEngSc (NUI), PhD (Dub) Course Director of the M.Sc. in Bio-medical Engineering in University of Limerick. He is an Associate Professor in Biomedical Engineering at Department of Mechanical and Aerospace Engineering at the University of Limerick. He is the Director of the Centre for Applied Biomedical Engineering Research at UL. He has research interests in bioengineering with a particular interest in vascular and cardiovascular hemodynamics, orthopaedic implants for joint replacement and medical devices in general.

[Email: tim.mcgloughlin@ul.ie]

, 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.

[email: csimms@tcd.ie]

10B

, 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.

[email: dtaylor@tcd.ie]

, BA, BAI, MSc, PhD Lecturer in Bio-Mechanical Engineering in Trinity College, Dublin. Prior to his current position in TCD he worked as a product development engineer in the medical device industry. For his PhD he worked on two EU fifth framework projects on tissue engineering, which formed part of his thesis on the mechanobiology of osteochondral defect repair. In May 2010, Dr. Kelly was awarded the President of Ireland Young Researcher Award by Science Foundation Ireland. His research interests are in mechanobiology and medical device design and testing.

[email: kellyd9@tcd.ie]

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ALL IRELAND FACULTY MEMBERS

, 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 O‘Connell‘s 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.

[email: brian.oconnell@dental.tcd.ie]

, 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).

[email: fjobrien@rcsi.ie]

, 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.

[Email: hrice@tcd.ie]

, 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.

[email: prinamea@tcd.ie]

, 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

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ALL IRELAND FACULTY MEMBERS of Physiology and is continuing to research the potential of endocannabinoids to provide neuroprotection in Alzheimer‘s disease.

[email: Hgowrana@tcd.ieH]

, PhD, FRCSI, FRCSEd, CEng, FIEI, HRHA

Graduate in science, medicine and engineering of the University of Dublin, a Fellow of the Irish and Edinburgh Royal Colleges of Surgeons and a Chartered Engineer. In 1995-6 he was a Fulbright Scholar at the Orthopaedic Biomechanics Laboratory, Beth Israel Hospital and Harvard Medical School. He 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. His research interests are in bone remodeling, osteoporosis, functional anatomy, mechanobiology and tissue engineering and he is Past-President of the European Society for Engineering and Medicine.

[email: tclee@rcsi.ie]12B

, 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.

[email: clyons@tcd.ie]

, 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: conor.buckley@tcd.ie]

, 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 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: higginw@tcd.ie]

, BSc, MSc, PhD (UL) Lecturer in Materials Science at the University of Limerick. Prior to this, he worked as a Technical/Development Manager at Phoenix Shannon PLC. His current research interests include the development of machinable ceramics for dental and engineering applications, the composition structure property relationships in dental restorative glass ionomer cements and castable glass-ceramic dental restorative systems. [Email: eamonn.debarra@ul.ie]

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ALL IRELAND FACULTY MEMBERS

BSc (Basrah); PhD (Wales); CEng; MIEE; Accredited Teacher of HE (SEDA, UK) Dr Mahdi‘s research interests are Rapid Real-time DSP Tools, Time-frequency Representations of Signals, Efficient Real-time Speech Analysis Tools for Communications and Rehabilitation Applications, Numerical Modelling of Magnetic Materials & Computational Electromagnetics.B.

[Email: Hussain.mahdi@ul.ie]

, 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.

[Email: david.fitzpatrick@ucd.ie]

, 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.

[Email: madeleine.lowery@ucd.ie]

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.

[Email: kenneth.stanton@ucd.ie]

BE MSc PhD

Ed 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

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ALL IRELAND FACULTY MEMBERS

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.

[Email: Hedlalor@tcd.ieH]

BA PhD Dr Bruce Murphy is 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.

[Email: bruce.murphy@tcd.ie]

, 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 O‘Brien, 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. Gleeson‘s 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.

[Email: johngleeson@rcsi.ie]

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22B14BCOURSE REGULATIONS The complete set of regulations is set out in the University Calendar HH. 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.

116B

Attendance, non-sat isfactory 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.

117B

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 student‘s work.

- Enlisting another person or persons to complete an assignment on the student‘s 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

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COURSE REGULATIONS

48BResults

Students are required to pass all modules of the course. Pass mark is 50%. TCD does not award grades to M.Sc. degrees.

118BPostgraduate 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.

119BRegulat ions 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 student‘s 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.

120BCommendation 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 Hhttp://www.tcd.ie/Graduate_StudiesH or Part 2 of the University

Calendar which can be viewed Hhttp://www.tcd.ie/calendar/part2/H. This Calendar contains all information

concerning graduate studies in Trinity College, Dublin.

Commencements

All candidates for conferral in April 2013 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 of €114 is applicable to all making application for conferral. Further information about the application process is available here.

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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

Range Criteria

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.

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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 Hwww.iospress.nlH or HTo purchase click here

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23BCAREERS IN BIOENGINEERING

58BWhere 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 Ireland‘s total merchandise exports; and growth prospects for the industry globally remain good.

Many of the world‘s 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 Hwww.ida-

ireland.ieH). The engineer working in this industry needs to be both technically competent and capable of integrating

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.

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24BCAREERS 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

59BBut…….. Not all jobs 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

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18BCOURSE ADMINISTRATION ALL-IRELAND M.Sc. BIOENGINEERING

41BTrinity College Dublin

42BUniversity of Limerick

43BUniversity College Dublin

44BNational College of Art and Design

Course Administrator : June O‘Reilly Contact Address: Trinity Centre for Bioengineering

Trinity College, Dublin 2.

Telephone: +353-1-8964214 Email: tcbe@tcd.ie

Course Administrator : Christine Roche

Contact Address: Mechanical & Aeronautical Engineering Dept,University of Limerick, Castletroy, Limerick

Telephone: 061-234363

Email : christine.roche@ul.ie

Course Administrator : Oran O‘Rua Contact Address: School of Electronic, Electrical and Mechanical

Engineering, UCD, Dublin

Telephone: +353-1-7161787 Email: oran.orua@tcd.ie

Course Administrator : Paul Fortune Contact Address: Department of Industrial Design,

National College of Art and Design, 100 Thomas Street, Dublin 8

Telephone: +353-1-6364272

Email: fortunep@ncad.ie

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CAMPUS MAPS ALL-IRELAND M.Sc. in BIOENGINEERING 49B

Trinity College Campus

50BSECURITY AT TCD

24 hour Security Centre contact number is 01-8961317 and the emergency number is 01-8961999

51BUseful Websites at TCD:

Trinity Centre for Bioengineering: www.tcd.ie/bioengineering

School of Engineering website: www.tcd.ie/Engineering/

Mechanical Engineering website: www.tcd.ie/mecheng

Graduate Studies website: www.tcd.ie/graduate_studies

Sports: www.tcd.ie/sports

Student Counseling: http://www.tcd.ie/Student_Counselling/

52B

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21BCAMPUS MAPS ALL-IRELAND M.Sc. in BIOENGINEERING

University of Limerick Campus

1. Castletroy Park Hotel & Conference Centre 2. Plassey Student Village 3. Main University Entrance 4. International Science Centre 5. Robert Schuman Building 6. International Business Centre 7. Computer Science Building 8. Silver Apples Creche 9. Glucksman Library & Information Services Building 10. Foundation Building & University Concert Hall 11. Engineering Research Building & Millstream Courtyard 12. Dromroe Student Village 13. Thomond Student Village 14. Health Sciences Building 15. Cappavilla Student Village (opening 2006) 16. Horticultural Unit

17. Kilmurry Student Village 18. University Arena & 50 metre pool 19. The Sports Club 20. East Gate Entrance 21. Salesian RC Church 22. Grounds/Maintenance Compound 23. Schrodinger Building 24. Materials & Surface Science Institute 25. Kathleen Lonsdale Building 26. National Coaching & Training Centre 27. Sports Building 28. Plassey House & University Close 29. Main University Building 30. Student Centre

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19BCAMPUS MAPS ALL-IRELAND M.Sc. in BIOENGINEERING

20B

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21BCAMPUS MAPS ALL-IRELAND M.Sc. in BIOENGINEERING

53BNational College of Art and Design

The National College of Art and Design is situated at 100 Thomas Street, about 5 minutes 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 HLuasH tram system passes close by, the nearest station being Smithfield, at Phoenix Street North. There are 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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