2013 - University College Cork

UNIVERSITY COLLEGE CORK 

MARINE RESEARCH 

PROJECTS DIRECTORY 

2012 2013 

2008 2009 2010 2011 

2014 2015

CONTENTS 

1. FOREWORD 2 

2. INTRODUCTION 4 

3. MARINE RESEARCH CENTRES 6 

AND INITIATIVES AT UCC 

– Aquaculture and Fisheries Development Centre 

– Coastal and Marine Research Centre 

– Hydraulics and Maritime Research Centre 

– Irish Maritime and Energy Resource Cluster 

4. MARINE RESEARCH PROJECTS 10 

See next page for full list

0 

24 

36 

4.1 AQUACULTURE AND FISHERIES 

– Atlantic Aquatic Resource Conservation (AARC) 

44 

– Bio-engineered micro Encapsulation of Active 

agents Delivered to Shellfish (BEADS) 

– Beaufort Marine Research Award: Fish Population 

Genetics 

– Management of infectious diseases in oysters and 

mussels in Europe (BIVALIFE) 

– Celtic Sea Trout Project: Genetic Stock 

Identification of Sea Trout in the Irish Sea 

– Cod Broodstock and Breeding Programme for 

Ireland (EIRCOD) 

– Do Nanoparticles induce neurodegenerative 

disesases? (NEURONANO) 

– OYSTERECOVER 

– Shellfish Productivity in the Irish Sea (SUSFISH) 

– Rebuilding depleted fish stocks in the waters 

around Ireland 

– The life history, ecology and dynamics of the black 

scabbard (Aphanopus Carbo) 

4.2 GEOMATICS AND REMOTE SENSING 

– Coastal Web Atlas (CWA) Development 

– eSurge: Satellite Data for the Storm Surge 

Community 

– Geo-Seas 

– JUTfJUD: Joined-Up Thinking from Joined-Up Data 

– Satellite Based Maritime Surveillance 

– MESMA: Monitoring and Evaluation of Spatially 

Managed Areas 

– NETMAR: Open Service Network for Marine 

Environmental Data 

– ODINAFRICA Technical Coordination and 

Support 

– OSS2015: Ocean Strategic Services Beyond 2015 

4.3 GOVERNANCE AND LAW 

– COEXIST (A Roadmap to Sustainable Integration 

of Aquaculture and Fisheries) 

– KnowSeas - Knowledge-based Sustainable 

Management for Europe’s Seas 

– MARLISCO: MARine Litter in Europe Seas: Social 

AwarenesS and CO-Responsibility 

– PISCES: Partnerships Involving Stakeholders in the 

Celtic Sea Ecosystem 

– SUSTAIN: Assessing Sustainability and 

Strengthening Operational Policy 

56 

64 

74 

4.4 MARINE RENEWABLE ENERGY 

– Components for Ocean Renewable Energy Systems 

(CORES) 

– GeoWAVE – Geotechnical Design Solutions for 

Offshore Renewable Wave Energy 

– Marine Renewable Integrated Application Platform 

(MARINA Platform) 

– Marine Renewables Infrastructure Network 

(MARINET) 

– NAVITAS Commercialisation Project 

– Offshore Renewable Energy Conversion – 

Coordinated Action (ORECCA) 

– Charles Parsons Energy Research 

– SEAGRID: A Dynamic Modelling Tool for Analysis 

of Ocean Energy Devices 

– SOWFIA – Streamlining of Ocean Wave Farms 

Impact Assessment 

– Wavetrain2 

4.5 GEOSCIENCES AND COASTAL 

PROCESSES 

– CeSQuORE 

– Sedimentary Processes & Quaternary Stratigraphy 

of the Celtic and Irish Sea 

– Hotspot Ecosystem Research and Man’s Impact on 

European Seas (HERMIONE) 

– Appraisal of Irish Sea Seabed Imaging for Tidal 

Energy Generation (ISSITEG) 

– Irish Sea Marine Assessment (ISMA) 

– Griffith: Geomatics for Geoscience 

4.6 BIODIVERSITY AND RESOURCE 

MANAGEMENT 

– Beaufort - Ecosystems Approach to Fisheries 

Management 

– BioTomm: Biotelemetry of top marine mammals 

– Marine Mammal Monitoring in Broadhaven Bay 

– The ecology of an avian predator at the top of the 

marine food chain 

– NOISE - Marine Strategy Framework Directive 

– Seal Salmon Interactions Study 

– Marine Biotoxins, the effects on Bivalves and 

Human Cells 

4.7 SUSTAINABLE BIORESOURCES 

AND GREEN TECHNOLOGIES 

– Beaufort Marine Biodiscovery Award 

Marine Research Projects 

– PharmaSea: Increasing Value and Flow in the 

Marine Biodiscovery Pipeline 

– MaCuMBA: Marine Microorganisms: their 

Biotechnological applications 

– Micro B3: Biodiversity, Bioinformatics, 

Biotechnology)

2 

Foreword 

FOREWORD 

Professor Alan Dobson 

Director, Environmental Research Institute 

The Environmental Research Institute (ERI) is one of Ireland’s leading research centres in the areas of 

Marine, Environmental and Energy research. The goals of the Institute are (a) to provide knowledgebased 

solutions addressing major societal challenges and opportunities (b) to train post-graduate 

research students for careers in environmental sciences and engineering and (c) to contribute to 

strengthening Ireland’s leadership in eco-innovation and the green economy. The Institute brings 

together over 200 researchers from the science, engineering and social science disciplines to work 

together in large, multi-skilled teams drawing on each discipline’s core competences. The ERI currently 

has over 200 researchers, publishes approximately 130 peer-reviewed publications annually 

and has secured €37 M in recurrent income between 2006-2010. 

Marine research is one of the ERI flagship research pillars. UCC has a long tradition of marine 

research, and is at the forefront of marine, maritime and marine energy based research both nationally 

and internationally; with particular expertise in areas such as marine energy, renewables, 

fisheries & aquaculture, marine biology/biotechnology, coastal management, environmental protection 

and in maritime law and policy teaching. Marine research at UCC is centred in a number of 

internationally recognised centres and research clusters including the Coastal & Marine Research 

Centre, Aquaculture & Fisheries Development Centre, Hydraulics & Maritime Research Centre, 

Marine Biotechnology Centre and Aquatic Services Unit. The University was recently awarded 

€14m to build the Beaufort Laboratory on the IMERC campus at Ringaskiddy, Cork which will provide 

space for an additional 135 researchers to become the world’s largest marine renewable energy 

facility upon completion in 2014. UCC marine based researchers continue to be very successful 

in obtaining research funding to support their research activities, some of which will be described 

in this catalogue. The EU Framework Programme for Research (FP7: 2007-2013) continues to be 

a major source of competitive R & D funding for Irish marine researchers; with UCC consistently 

being one of the top performers in attracting EU funding in the area of marine research.

The Aquaculture & Fisheries Development (AFDC), together with the School of Biological Earth 

and Environmental Sciences (BEES), undertakes marine fisheries and aquaculture, marine biology 

and ecology and aquaculture commercialisation research and development. The Marine Biotechnology 

Centre (MBC) focuses on exploiting marine microorganisms for biotechnology applications in 

the Food, Biopharmaceutical and Industrial biotechnology areas. The Aquatic Services Unit (ASU) 

undertakes in laboratory analysis, environmental monitoring and environmental impact assessment 

in marine and transition waters. The Coastal and Marine Research Centre (CMRC) performs both 

applied and basic research and also works on commercial contracts with government agencies and 

industry in the areas of coastal processes and seabed mapping, marine geomatics, marine ecology, 

coastal governance and applied remote sensing and GIS. 

The Hydraulics and Maritime Research Centre (HMRC) is a centre of excellence in Ireland for 

marine renewables and coastal engineering that provides support to maritime industries as well 

as carrying out fundamental R&D. These two centres, along with the Sustainable Energy Research 

Group (SERG) form the UCC component of the Irish Maritime and Energy Resource Cluster 

(IMERC), through the recent establishment of the Beaufort Laboratory at Ringskiddy. IMERC is 

a critical inter-institutional organisation linking UCC, the National Maritime College of Ireland 

(NMCI) and the Irish Naval Service (INS) with the overall aim of facilitating the development of 

maritime and energy research in Cork. 

The aim of this directory is to bring together and showcase ongoing marine based projects currently 

being undertaken by University College Cork marine researchers. The directory has one-page 

features of over 50 research projects along with profiles of marine research centres and clusters at 

ERI and UCC. We hope that it will be of value to all involved in the promotion and development 

of a marine economy in Ireland. 

Foreword 

3

4 

Introduction 

INTRODUCTION 

Dr Andy Wheeler 

Lead Principal Investigator, ERI Marine Pillar 

Head of Geology & Vice Head of School of Biological, 

Earth & Environmental Sciences 

The Environmental Research Institute is particularly proud of the contribution that marine researchers 

in UCC make to the national and international marine research agenda. This directory 

showcases that achievement. At the time of publication major national and international marine 

research strategies are being developed and implemented: Harvesting our Ocean Wealth: an integrated 

Marine Plan for Ireland, and the EU Atlantic Strategy. At this time of increasing marine 

research prioritisation, the ERI has placed a renewed focus on marine research reflecting both the 

University’s research strengths and its commitment to the wider agenda. 

The newly realigned Marine Pillar is one of three priority areas within the ERI that are framed in 

the context of current EU and national policy objectives and that address the challenges facing 

the marine environment and opportunities presented by the sector. The Institute has 3 thematic 

areas that are core to the marine pillar: Governance and Law, Geomatics & Remote Sensing and 

Aquaculture & Fisheries. In addition, there are further 6 thematic areas cross-cutting the Energy 

and Environment Pillars: Marine Renewable Energy, Geosciences & Coastal Processes, Biodiversity 

& Resource Management, Sustainable Bioresources & Green Technologies, Energy Policy and 

Climate Change, and Environmental Health & Protection. 

The Marine Pillar draws researchers from Schools and Research Centres across the University. The 

Coastal & Marine Research Centre (as part of the Beaufort Laboratory) and the Aquaculture & 

Fisheries Development Centre (as part of the School of Biological, Earth & Environmental Sciences) 

strongly contribute to the Marine Pillar thematic areas and are both internationally recognised 

centres of excellence in their areas of research. 

ERI and its research centres have published over 200 publications in marine research from 2008- 

2011 and has over 100 researchers and 40 Principal Investigators working in the marine area. 

OUR CONTEXT 

Ireland’s marine area is ten times that of the land area of the country; the country’s location and 

extensive marine resources represent a unique asset. The Irish marine sector has a turnover of €3 

billion annually and supports over 44,000 jobs. The Marine Institute’s Sea Change Strategy has 

identified future economic opportunities for Ireland in seafood products, marine environmental 

technologies and marine biotechnology. The Forfás Research Prioritisation highlights the opportunities 

for economic growth through research in the areas of aquaculture and wild fisheries, marine 

renewable energy and marine food for health. Nationally, marine research funding will be focused 

on a number of ‘priority areas’ that are likely to include marine bio-resources, marine functional

foods, marine materials for medical applications and renewable ocean energy as key. Marine research 

will also be strongly represented under the Horizon 2020 programme. Almost €4.7 billion 

has been proposed for the Challenge “Food security, sustainable agriculture, marine and maritime 

research, and the bioeconomy.” The Europe 2020 Strategy’s call for a bioeconomy as a key element 

for smart and green growth in Europe will support further research investments in marine food 

and bio-based products. It is within this context, that marine research in UCC positions itself to 

prosper and provide a fundamental benefit to the nation and Europe. 

WHO WE ARE 

UCC is at the forefront of maritime research through research, teaching and practice across several 

internationally recognised Institutes, Centres and Research Clusters including the Environmental 

Research Institute (ERI), one of three flagship research Institutes at the University, established as 

an inter-disciplinary research institute in 2000 to facilitate and support environmental, marine and 

energy based research at UCC. It brings together expertise in the biological, chemical and environmental 

sciences as well as environmental engineering, energy and environmental law. Contributors 

to the Marine Pillar include the: 

– Aquaculture & Fisheries Development (AFDC) 

– Aquatic Services Unit (ASU) 

– Coastal and Marine Research Centre (CMRC) 

– Department of Law 

– Hydraulics and Maritime Research Centre (HMRC) 

– Marine Biotechnology Centre (MBC) 

– School of Biological Earth & Environmental Sciences (BEES) 

– School of Geography & Archaeology: the Human Environment 

– Sustainable Energy Research Group (SERG) 

WHAT WE ACHIEVE 

UCC has a strong track record in knowledge and technology transfer and involvement with industry. 

In the area of Marine Biotechnology UCC has received significant funding and has developed 

technology which led to the establishment of the UCC aquaculture start-up, Gourmet Marine, and 

also the discovery and patenting of anti-infective bioactive compounds resulting from the Beaufort 

Marine Biodiscovery programme funded by the Marine Institute. We also have several industrially 

funded projects especially in the Marine Offshore Renewables sector. 

International cooperation is essential in a rapidly changing world where challenges extend beyond 

a particular research field, region or country. Preserving existing partnerships and developing new 

ones, particularly in areas related to the great societal challenges, like climate change, energy or food 

security is extremely important in strengthening national capacity and enabling Irish researchers 

to remain at the forefront of the knowledge based economy. It can also open up new markets for a 

range of Irish developed knowledge-based products and services. 

The EU Framework Programme for Research (FP7: 2007-2013), continues to be a major source 

of competitive R&D funding for Irish marine researchers. From 2007 to 2010, 43 Irish marine 

research groups, including knowledge-based SMEs, were involved in 64 FP7 collaborative projects 

and drawing down funds in excess of €23.7 million. In 2011, a further 21 marine projects with Irish 

participation were approved subject to successful contract negotiation. 

Introduction 

5

6 

MARINE RESEARCH CENTRES AT UCC 

AQUACULTURE & FISHERIES 

DEVELOPMENT CENTRE 

STRATEGIC VISION 

“To support, stimulate and promote the development of aquaculture 

and fisheries, thereby enabling these sectors to achieve their full 

socio-economic potential by utilising sustainable natural resources” 

The Aquaculture and Fisheries Development Centre (AFDC; est.d 1987) is a centre of excellence 

for aquaculture and fisheries research embedded within the School of Biological, Earth & Environmental 

Sciences and affiliated to the Environmental Research Institute. Although the breadth 

of research conducted at the AFDC is broad, the main aim of this research is to work towards sustainability 

in aquaculture and fisheries with a view to securing Ireland’s future in marine economic 

sectors, whilst working closely with industry and research groups nationally and internationally. 

To achieve this aim, research which addresses the national and EU priorities for sustainability 

within the sector are major drivers of the AFDC work programme. Often this includes research 

into new and emerging aquaculture species and target fisheries of commercial potential. In addition 

to the academic value of AFDC research, other end-users include commercial fishing communities, 

fisheries managers, aquaculturists, national environment agencies, leisure groups (e.g 

anglers), policy makers and regulators. 

Research activities at the centre cover four broadly-descript thematic areas, each led by a Principal 

Investigator from the School of Biological, Earth & Environmental Sciences: 

– Marine Mammals and Fisheries (Dr Emer Rogan) 

– Molecular Genetics (Prof. Tom Cross) 

– Aquaculture (Prof. Gavin Burnell) 

– Shellfish Health (Dr Sarah Culloty) 

The research capability at the centre includes expertise in both inshore and deep-sea fisheries, 

disease research, focussing on the impact of fishing practices on the environment, bycatch and 

discards, on Genetic Stock Identification of exploited fish species and on conservation genetics 

of endangered species and basic fish biology. Research expertise and influences from numerous 

academic departments ensure a multidisciplinary approach to research projects. The AFDC actively 

co-ordinates and participates in collaborative R&D projects (national and European) and 

provides consultancy and training services for both public and private sector clients, nationally 

and internationally. Research is conducted at the leading edge of aquaculture in collaboration with 

industry and academic partners, and activities are continually expanding to include developing 

areas. The AFDC also supports research by undergraduate and post-graduate students, from UCC 

and further afield. 

Over the years, the AFDC has built up a significant public profile and has made a valuable contribution 

to the development of aquaculture and the sustainability of fisheries, both nationally and 

internationally, through successful participation in research programmes, regional development 

and training initiatives. In these activities the AFDC maintains active links with universities and 

companies in all EU countries.

THE COASTAL AND MARINE 

RESEARCH CENTRE 


The Coastal and Marine Research Centre (CMRC) is located on the Naval Base, Haulbowline 

Island in Cork Harbour and is a key research centre within the Environmental Research Institute. 

The CMRC conducts multidisciplinary fundamental and applied research on nationally and internationally 

funded programmes and undertakes commercial contracts with government agencies 

and industry. Centre staff teach undergraduate and postgraduate degree courses in UCC and provide 

tailored short training courses for industry professionals. The CMRC currently has 40 staff 

working in five specific key thematic areas in order to enhance the knowledge and understanding 

of marine and coastal issues in Ireland and abroad: 

Applied Remote Sensing and GIS. Works with spatial data from various data sources to provide 

information which can assist in enhanced resource management. Applications include storm 

surge forecasting, improving ocean biogeochemical products, subsidence mapping in raised bogs, 

vegetation seasonality monitoring, soil moisture estimation and ship detection. 

Coastal Governance. Currently engaged in innovative research in a range of fields including 

the application of the ecosystem approach to fisheries and marine management and the use of scenario 

science and visualisation technology to plan for coastal change. Active in the areas of marine 

tourism, coastal and maritime spatial planning and adaptation to climate change. 

Marine Geomatics. At the forefront of geospatial information management research and development 

within Europe and beyond. Leader in the development of web-GIS systems and standards-based 

data management and exchange. Harmonised data formats, content management and 

3D visualisation of large geospatial databases are emerging areas of interest for the Group. 

Marine Ecology. Research focuses on assessing the abundance, distribution, and foraging ecology 

of key species and their interactions with human activities through a combination of surveys, 

long term monitoring, diet studies and biotelemetry. Research outcomes are used to inform conservation 

policy and provide guidance on appropriate mitigation measures to ensure an ecosystems 

approach to the management of marine resources. 

Coastal Processes and Seabed mapping. Focuses on mapping various marine habitats 

including deep-water corals, scallop grounds, sand and gravel resources. Mapping is undertaken 

through the use of remotely sensed and ground based methods. Coastal research includes monitoring 

coastal processes (e.g. beach erosion) using a range of instrumentation and advising on 

contemporary coastal management issues. 

These groups work collaboratively under the interdisciplinary environment fostered by the Centre 

and have been involved in successful research collaborations with over 250 institutions from 25 

countries. The Centre maintains strong links with UCC notably with the schools of Biology, Ecology 

and Earth Science and the Human Environment and with research Centres including the Hydraulics 

and Maritime Research Centre (HMRC). 

HMRC, CMRC and Sustainable Energy Research Group (SERG) secured significant funding from 

the HEA under PRTLI5, the DECNR and Bord Gais to construct a new start the state-of-the-art 

Beaufort Laboratory, adjacent to the National Maritime College of Ireland. It will represent UCC’s 

physical presence on the IMERC campus – a joint initiative between UCC, Cork Institute of Technology 

and the Irish Naval Service to promote Ireland’s maritime and energy potential. 

Due for completion in early 2014 this facility will house some 135 researchers, provide international 

quality test facilities and workshops and act as a focal point for Maritime activity in UCC. 

7


HYDRAULICS AND MARITIME 

RESEARCH CENTRE (HMRC) 

The Hydraulics and Maritime Research Centre (HMRC) is a centre of excellence for Ocean Renewable 

Energy and Coastal Engineering providing support to the maritime industry as well as 

fundamental research and development. Since its establishment in 1979 the HMRC has undertaken 

a variety of fundamental and applied research projects alongside industrial design contracts. The 

centre is a semi-autonomous unit within the Department of Civil and Environmental Engineering 

in University College Cork. It provides infrastructure and research facilities to developers of ocean 

energy devices. In order to achieve results the HMRC has adopted a hands on approach; device 

prototypes, based on thorough research, calculations and modelling, are built and tested to verify 

and advance the field. 

HMRC currently has a staff of 42 and comprises postdoctoral researchers, engineers and PhD 

students across a range of engineering and other disciplines, from hydrodynamics, civil, electrical 

and mechanical engineering to marine law and economics. This provides a diverse assortment of 

experience and skills to explore the multi disciplinary technology. 

HMRC, which is principally a dedicated research facility, also offers a teaching and education 

function. It houses the only facilities for wave simulation in Ireland with a Wave Flume and an 

Ocean Wave Basin and was designated as the National Ocean Test Facility in 2009. There are 

also several electrical and mechanical test rigs for linear actuation, turbine test and pneumatic 

emulation. These facilities have recently undergone a €2.5m upgrade, giving them state-of-the-art 

capabilities. The Centre also has its own supercomputing facilities as well as a suite of numerical 

modelling packages, both industry standard and bespoke. Electrical grid research involves the 

production of commercial, dynamic, grid-connect models for ocean wave and tidal systems. 

The HMRC offers independent advice and support to developers through model testing, concept 

design, computer modelling, design performance validation, resource assessments and offshore 

data recording. Many prominent international projects have used the facilities and knowledge of 

the HMRC at some stage in their development. The HMRC have also outlined a protocol for how 

wave energy devices should be developed, providing a useful guideline for developers and investors. 

The Centre aims to become an international centre of excellence for Ocean Energy research, 

training, consultation and support, growing from an existing strong national integrated base. 

The HMRC will relocate to a new €14m state-of-the-art facility in Ringskiddy called the Beaufort 

Laboratory in 2014. Three groups will be merged; the Hydraulics and Maritime Research Centre 

(HMRC), the Coastal and Marine Research Centre (CMRC), and the Sustainable Energy Research 

Group (SERG). The three groups under the Irish Maritime & Energy Research Cluster (IMERC) aim 

to promote Ireland as a world-renowned research and development location that unlocks Ireland’s 

maritime and energy potential.

THE IRISH MARITIME AND 

ENERGY RESOURCE CLUSTER 

MARINE RESEARCH INITIATIVES AT UCC 

The Irish Maritime and Energy Resource Cluster (IMERC) initiative comes about at the dawn of a 

new era for maritime Ireland, stimulated by the growing realisation of the economic opportunities 

around maritime and energy resources. This awakening is evidenced by a number of complementary, 

strategic national initiatives. These include Harnessing Our Ocean Wealth, Smart Ocean and 

the work of inter-governmental Marine Co-ordination Group, as well as Ireland’s submissions to 

the EU Integrated Maritime Policy and associated Atlantic Strategy. 

The IMERC core partners of University College Cork (UCC), Cork Institute of Technology (CIT) 

and the Irish Naval Service (INS) are combining resources to respond to this maritime and energy 

economic opportunity. The IMERC vision is to become a research and commercial cluster 

of world standing, by realising Ireland’s potential in the global, maritime and energy markets of 

tomorrow. IMERC will be an engine for new ideas through research and many of these ideas will 

translate into sustainable innovative enterprises of the future. 

Together, this tripartite alliance will deliver a new research campus in Ringaskiddy, Cork located 

alongside the National Maritime College of Ireland and the INS headquarters in Haulbowline. It 

will feature UCC’s new Beaufort Building, which will house the largest marine renewable energy 

research group in the world (funded by the Higher Education Authority, the Department of Communications, 

Energy and Natural Resources, Bord Gáis Éireann and the Glucksman Foundation). 

The Beaufort Laboratory will be a new home for three well-established UCC research groups; the 

Coastal & Marine Research Centre (CMRC), the Hydraulics & Maritime Research Centre (HMRC) 

and the Sustainable Energy Research Group (SERG). These groups will work together in the new 

€14 million custom-built Beaufort Laboratory, currently under development in Ringaskiddy and 

due for completion in 2014. It will include the national ocean energy test-tank facility, which will 

support device development from national and international industry and research groups. 

The UCC Beaufort Laboratory, as integral part of the greater IMERC campus, will contribute to 

the critical mass of expertise on site. The knowledge within the cluster provides a unique mix of 

academic, defence, industrial and professional elements focused on transforming traditional institutional 

approaches to problem solving. 

This expertise will be brought to bear on job creation in IMERC’s four strategic pillars of Marine Energy; 

Maritime Security and Safety; Shipping, Logistics and Transport; and Marine Recreation. 

The IMERC campus will cater for industry partners through the provision of co-located industry 

suites, incubation units, networking and brokering programmes, innovation partnerships and 

joint ventures. An industry-centred approach will be used to develop an ecosystem of innovation 

that will yield intellectual property, high potential start-up companies and jobs in Ireland’s Smart 

Economy. 

IMERC has already gained recognition at many levels through the signature of memoranda of 

understanding with international institutions as well as becoming the first ever Maritime Project 

to win An Taoiseach’s Public Service Excellence Award.

MARINE RESEARCH PROJECTS 

0 

4.1 AQUACULTURE 

AND FISHERIES

Current research in this theme is undertaken at the Aquaculture 

and Fisheries Development Centre (AFDC) and the Coastal and 

Marine Research Centre (CMRC). The majority of this research is 

applied, underpinning the ethos of sustainable development, management 

and conservation of the marine environment, and involves 

collaborations with a range of UCC disciplines, including Geography, 

Geology, Food and Nutritional Sciences, Civil Engineering, 

Law and associate researchers within. The AFDC and CMRC have 

extensive research and industry collaborations both nationally and 

internationally and have been able to exploit funding schemes that 

require industry/RTD collaborations which are pivotal to the applied 

research focus of the theme. Strategic partnerships within 

this theme are funded by MI, BIM, EU FP7 and INTERREG funding 

programmes and include projects such as the Beaufort Marine 

Research Awards for Ecosystem Approach to Fisheries Management 

and Fish Population Genetics, OYSTERECOVER, COEXIST, 

BEADS, BIVALIFE, SALSEA-MERGE, AARC. The breadth of research 

themes at the AFDC and CMRC ensures a multidisciplinary 

approach to research under the Aquaculture & Fisheries theme. 

PRINCIPAL INVESTIGATORS 

Dr Sarah Culloty (Lead PI) 

Professor Gavin Burnell 

Professor Tom Cross 

Dr Emer Rogan 

Professor Peter Jones 

Dr Joe Kerry 

Professor John Benzie 

Dr Phil McGinnity 

Mr Jeremy Gault 

Dr Michelle Cronin 

Mr Ger Morgan 

Dr Ray Alcorn 

Aquaculture and Fisheries

RESEARCH PROJECTS 

Aquaculture and Fisheries 

2 

ATLANTIC AQUATIC RESOURCE 

CONSERVATION (AARC) 

Research Centre/Department/School: 

AFDC, School of Biological, Earth & Environmental Sciences 

Contact PI: Dr Phil McGinnity (p.mcginnity@ucc.ie); 

Prof. Tom Cross (t.cross@ucc.ie) 

Researchers: Dr Jamie Coughlan, Dr Jens Carlsson, Dr Eileen Dillane 

Start Year: 2010 – End Year: 2012 

Funding Body: ERDF INTERREG 4 Atlantic Area Programme 

Funding: €255,429 

Collaborating Partners: Ireland, UK, France, Spain and Portugal 

Web: http://afdc.ucc.ie 

Some of the most potentially productive Atlantic salmon rivers in Europe have been harnessed 

for hydro-electric power generation e.g. Shannon (Ireland), Conan (Scotland), Linares (Spain). In 

Ireland alone some 35% of the potential salmon producing habitat is impounded above hydroelectric 

dams. In compensation, hatchery mitigation programmes were established in most of these 

rivers, in order to compensate for the loss of productivity, to maintain natural runs and to preserve 

biodiversity. Despite the best efforts of these hatchery programmes, many of the salmon populations 

above these facilities are effectively extinct. The large hatchery programmes continue to exist 

but are increasingly coming under the spotlight from cost benefit analyses and their success in 

maintaining fisheries and protecting biodiversity. 

Most of these mitigation schemes were developed many decades ago before much of the contemporary 

information about sub-specific population genetics was developed. Thus, it would seem 

timely to reassess and redirect mitigation programmes with respect to the large body of evolutionary, 

population and quantitative genetic knowledge that now exists, particularly in terms of 

meta-population theory, landscape genetics and new knowledge about the biology of the salmon 

(effective population size etc). It might also be possible to simulate natural re-colonisation processes, 

by combining ecological and evolutionary biological principles to resolve these most difficult 

fisheries management problems. Specifically for the Shannon this project addresses a number of key 

questions: What is the status of the hatchery strain used currently for mitigation and restoration? 

Are there other more suitable genetic resources available in neighbouring wild populations? How 

do the contemporary wild (feral) and hatchery maintained populations compare genetically to the 

historical Shannon population(s): What is the provenance of the fish that are currently spawning 

naturally in the system? Did genetically distinct populations of salmon exist prior to the establishment 

of hydro-plant, and if so, is there semblance of original material still in existence?

Research Projects Listing 

BIO-ENGINEERED MICRO ENCAPSULATION OF 

ACTIVE AGENTS DELIVERED TO SHELLFISH (BEADS) 



Contact PI: Dr Sarah Culloty (s.culloty@ucc.ie) 

Researchers: Grainne Darmody, Dr Aaron Maloy, Dr Sharon Lynch 

Start Year: 2010 – End Year: 2013 

Funding Body: EU FP7 Funding Programme 

Funding: €303,899 

Collaborating Partners: Ireland, UK and Spain 

Web: www.projectbeads.eu; http://afdc.ucc.ie 

Within the marine food sector, aquaculture is rapidly growing in importance and is currently contributing 

approximately 25% of fish/shellfish consumption. In particular, shellfish aquaculture is a 

low environmental impact industry which has expanded considerably across Europe over the past 

years, providing employment in many remote coastal locations. The development of shellfish (e.g., 

oysters, mussels, clams, cockles, scallops) aquaculture has been hampered by episodic contamination 

of the product with naturally occurring potent algal toxins (e.g., paralytic shellfish poisoning 

(PSP), amnesic shellfish poisoning (ASP) and diarrhetic shellfish poisoning (DSP) toxins) derived 

from phytoplankton that are harmful to human health and by microbiological (bacteria and viral) 

contamination with faecal material, derived from human or animal sources. The development of 

shellfish-based industries and the concomitant increase in demand for the introduction and transfer 

of different shellfish species and stocks has also increased the risks of spreading their parasites 

and diseases (e.g., bonamiasis) across Europe and the world. 

The BEADS project is continuing research on the development in delivering active agents (immunostimulant 

and probiotics) to bivalve molluscs through micro-encapsulation, in particular 

research at UCC will concentrate on boosting the immune response of O. edulis to B. ostreae. The 

application of probiotics in food is accepted by consumers and it is most likely that the ability of 

probiotic bacteria to degrade toxins, outcompete pathogens or aid host virulence will be advantageous 

for applications in shellfish safety and shellfish productionIt is a two year collaborative 

project involving partners from Ireland, UK and Spain. 


3



4 

BEAUFORT MARINE RESEARCH AWARD: 

FISH POPULATION GENETICS 



Contact PI: Dr Phil McGinnity (Principal Investigator), (p.mcginnity@ucc.ie) 

Prof. Tom Cross (Grantee), (t.cross@ucc.ie) 

Researchers: Dr Jamie Coughlan, Dr Jens Carlsson, 

Dr Eileen Dillane, Ms Ciar O’Toole (PhD student) 


Funding Body: The Beaufort Marine Research Award is carried 

out under the Sea Change Strategy and the Strategy for Science 

Technology and Innovation (2006-2013), with the support of 

the Marine Institute, funded under the Marine Research Sub- 

Programme of the National Development Plan 2007–2013. 

Funding: €2,710,236 

Collaborating Partners: UCC, QUB 


Five strategic areas were selected for funding through the Beaufort Award Programme. One of 

these was in the area of fish population genetics. The project has sought to build research capacity; 

to establish an all-island research centre of excellence (a key objective for the Sea Change 

programme); to conduct high quality research in the area of fish population genetics; to advise the 

industry on genetic aspects of the management of fisheries and aquaculture resources to ensure 

sustainability and conservation; to establish national and international networks; to publish high 

quality relevant papers. The most notable achievements in the first three years of the project are a 

fully integrated North South fish population genetics research team, working in partnership with 

the state agencies responsible for fisheries management and conservation; A successful programme 

of grant acquisition with €1.85m in leveraged grants in addition to the €1.6m received to date via the 

award; This group has produced 60 scientific manuscripts for publication (55 of which are now in 

the peer-reviewed literature with the remaining 5 in review), 20 non peer publications and reports, 

71 oral presentations and supporting 18 postgraduate projects (ten PhDs and nine MSc’s). Several 

of these achievements received widespread media coverage: parthenogenesis in sharks; genetic 

tagging of lobsters; predictions of impact of climate change on salmon; genetic based forensic 

identification of mislabelled smoked salmon. 

KEY PUBLICATIONS AND OUTPUTS 

Details of publications can be provided on request.

MANAGEMENT OF INFECTIOUS DISEASES IN 

OYSTERS AND MUSSELS IN EUROPE (BIVALIFE) 



Contact PI: Dr Sarah Culloty (s.culloty@ucc.ie) 

Researchers: Dr Aaron Maloy, Dr Sharon Lynch 



Funding: €256,410 

Collaborating Partners: France, Italy, Ireland, Israel, 

Spain, The Netherlands, United Kingdom 

Web: http://afdc.ucc.ie; http://www.bivalife.eu/ 


BIVALIFE aims to provide innovative knowledge related to pathogens infecting oysters and mussels 

and to develop practical approaches for the control of infectious diseases and associated mortalities. 

The project will focus on three mollusc species, the Pacific oyster Crassostrea gigas and two 

mussel species Mytilus edulis and M. galloprovincialis, the most important species in terms of 

European production. Pathogens investigated include the virus OsHV-1, Vibrio species including 

V. splendidus and V. aestuarianus, as well as the parasite Marteilia refringens and the bacterium 

Nocardia crassostreae. 

The project will address the major issues identified by the European commission (i.e. detection 

and management of infectious diseases in oysters and mussels) since the increase in international 

and intra EU trade and exchanges of animals increases the risk of pathogen transfer and infectious 

disease outbreak occurrence. The validation of existing diagnostic methods for oyster and 

mussel pathogens and the development of innovative complementary diagnostic approaches will 

be carried out. Characterisation of culture sites in Europe regarding presence of pathogens and 

associated mortalities will be undertaken. Pathogen life cycle, mechanisms allowing pathogens to 

survive outside the host and their original source will be investigated. Pathogen intrinsic virulence 

factors and effects on host defence mechanisms will be identified. An assessment will be carried 

out on the relationship between the presence of pathogens and their role in observed mortality. 

Methods will be developed and recommendations given for pathogen control and eradication in 

Europe. Bivalife involves partners from seven countries-France, Italy, Ireland, Israel, Spain, The 

Netherlands and UK. 


5



6 

CELTIC SEA TROUT PROJECT: GENETIC STOCK 

IDENTIFICATION OF SEA TROUT IN THE IRISH SEA 



Contact PI: Dr Phil McGinnity (p.mcginnity@ucc.ie); Prof. Tom Cross, (t.cross@ucc.ie) 



Funding Body: ERDF INTERREG Funding Programme 

Funding: €359,830 

Collaborating Partners: Inland Fisheries Ireland, 

Bangor University, Environment Agency 

Web: http://afdc.ucc.ie. www.celticseatrout.com 

Sea trout and particularly their behaviour at sea, are not well understood. There are several issues of 

interest; the distribution and ecology of sea trout at sea, their fate in marine and estuarine mixedstock 

fisheries and their response with respect of biodiversity and life history to environmental 

pressures, particularly climate change. Genetic stock identification offers a very elegant solution 

for acquiring information on the composition of mixed ocean and estuarine samples; enabling the 

contribution of individual river systems to be evaluated and the potential to address the questions 

posed above. There is no other way of acquiring such information since tagging of large numbers 

of wild juveniles is impractical and greatly increases mortality. Preliminary results from the genetic 

analysis suggest remarkably strong population structuring among rivers and regions, with patterns 

that appear to reflect the post-glacial history of the Irish Sea associated with the retreat of the icesheet. 

In addition, the assignment of trout captured at sea to their rivers of origin, further suggest 

complex patterns of behaviour and the Irish Sea as single, integrated and complicated ecosystem.


COD BROODSTOCK AND BREEDING PROGRAMME FOR 

IRELAND (EIRCOD) 



Contact PI: Prof. Tom Cross, (t.cross@ucc.ie); Dr Phil McGinnity, (p.mcginnity@ucc.ie) 



Funding Body: Marine Institute and the Marine Research 

Sub-programme of the National Development Plan 2007-2013 

Funding: €213,088 

Collaborating Partners: UCC, NUIG, BIM, Irish Seafood 

Producers Group, Trosc Teoranta, Dr Ashie Norris 

Web: http://afdc.ucc.ie. www.celticseatrout.com 

With declining catches of wild fisheries and caution over exploitation and depletion of stocks, 

there has been an ever-growing pressure on aquaculture to service and supply the market needs 

and this is reflected in diverse initiatives to expand production volumes and to increase the variety 

of farmed species, including cod. An intrinsic part of this process is the establishment of Broodstock 

programmes to exploit the inherent genetic ‘Biodiversity’ embodied in wild populations 

and allowing continued selected breeding and possible improved performance in farmed stocks. 

Initiatives in this regard have been in operation in Ireland since 2001/2 and this has now led to the 

completion of the life cycle in Ireland from larval production to on-growing at sea and finally the 

harvesting of cod for market from a commercial production unit. 

The overall objective of the EIRCOD project is to design, establish and operate a Cod Broodstock 

and Breeding programme, customized for the Irish environment and underpinning the native fish 

farming industry, which will draw on the potential genetic reservoir of local cod populations and 

utilize the best available technologies, with necessary and appropriate International links, such 

that the emerging Industry can gain maximum competitive advantage from using a customized 

cod farming stock that has enhanced performance capacity, including, higher growth rates to increase 

production & yield, shorter life span at sea/to market reducing production costs, improved 

conversion efficiencies giving more efficient use of feeds, lowered stress, fewer health issues and 

less mortalities and improved flesh quality. The overall work programme over the 7 year period 

involves a number of integrated work packages. 


7

RESEARCH PROJECTS Aquaculture and Fisheries 

DO NANOPARTICLES INDUCE NEURODEGENERATIVE 

DISESASES? UNDERSTANDING THE ORIGIN OF 

REACTIVE OXIDATIVE SPECIES AND PROTEIN 

AGGREGATION AND MIS-FOLDING PHENOMENA IN 

THE PRESENCE OF NANOPARTICLES (NEURONANO) 



Contact PI: Dr Sarah Culloty, (s.culloty@ucc.ie) 

Researchers: Ms Grainne Darmody, Dr Sharon Lynch 



Funding: €167,000 

Collaborating Partners: Department of Biochemistry & School 

of Biological, Earth & Environmental Sciences, UCC. Also project 

partners in Brazil, Germany, Italy, Japan, Mexico, UK and US 


Nanotechnology is the science of engineering nanoparticles (eNPs) to have structural features and 

specific physiochemical compositions to exploit properties and functions associated with their 

dimension. While nanomaterials and nanotechnologies are expected to yield numerous health 

and health care advances, it is recognised that they also may have unwanted effects. Domestic and 

industrial wastes and byproducts tend to end up in aquatic systems and there is concern about the 

effects industrial-scale eNPs may have on aquatic biota. 

Filter feeding organisms represent a sensitive target group for nanoparticle toxicology. Bivalves 

process large volumes of water per unit time (3-9 I h-1 g dry mass t-1). Self-aggregation of nanoparticles 

into larger particle masses will increase the bioavailability (increased uptake and internal 

exposure) of engineered nanoparticles to suspension-feeding bivalves. Nanoparticle aggregates 

will sink increasing the flux of nanoparticles to the benthos. Suspension and deposit feeders will 

be exposed to large concentrations of these materials which will have implications for nanoparticle 

bioaccumulation in bivalves and the transfer to higher trophic levels including humans. 

In NeuroNano, Mussels, Mytilus spp., and the ragworm, Nereis diversicolor, will be studied. The 

hemocyte function parameter lysozyme retention test (LRT) will be carried out and tissues will be 

screened for eNPs using transmission electron microscopy (TEM). Histology will be carried out 

to investigate host response. Neuronano is a collaborative project between the Department of Biochemistry 

(Prof. Dave Sheehan) and the School of Biological, Earth and Environmental Sciences, 

UCC with partners from Brazil, Germany, Italy, Japan, Mexico, the UK and the US.

ESTABLISHING THE SCIENTIFIC BASES AND 

TECHNICAL PROCEDURES AND STANDARDS TO 

RECOVER EUROPEAN FLAT OYSTER PRODUCTION 

THROUGH STRATEGIES TO TACKLE THE MAIN 

CONSTRAINT BONAMIOSIS (OYSTERECOVER) 



Contact PI: Dr Sarah Culloty, s.culloty@ucc.ie 

Researchers: Grace Flannery, Jeanette Carlsson, 

Dr Sharon Lynch, Dr Jens Carlsson, Prof. Tom Cross 



Funding: €730,894 

Collaborating Partners: Ireland, UK, Denmark, the Netherlands, France, Spain 



The European flat oyster, Ostrea edulis, has been part of the human diet for many centuries and is 

farmed in many European countries including Ireland, France, Spain and Holland. In the first half 

of the 20th century stocks were greatly reduced due to overfishing and mismanagement of oyster 

beds but populations were completely devastated in the 1970’s and 80’s with the introduction of 

two invasive parasites, Marteilia refrigens and Bonamia ostreae. B. ostreae has no implications 

for human health but it is a serious disease of flat oysters with up to 80% mortality occurring 

in populations and is listed as a notifiable disease. Production numbers in Ireland have significantly 

reduced despite much research, several breeding programmes and the establishment of 

new management practices to tackle the parasite. Many aspects of the biology of B. ostreae remain 

unknown; for example, uncertainties exist about its life cycle, and the possibility that species other 

than oysters could act as vectors. The recovery of flat oyster production, achieved through the 

control of B. ostreae, would be an important boast to the shellfish industry in Europe. 

OYSTERECOVER is an industry led project funded under the EU FP7 Capacities programme. It 

is a three year collaborative project involving seven research centres and seven European shellfish 

producers and representative assocaitions from six countries – Ireland, UK, Denmark, the Netherlands, 

France, Spain. The main objective of the project is to aid conservation of the native flat 

oyster O. edulis ultimately resulting in more production of this oyster throughout Europe. 

KEY PUBLICATIONS & OUTPUTS 

Flannery, G., Lynch, S. & Culloty S. DATE. An update on the prevalence 

of Bonamia ostreae at two Irish sites. 5th Microcell Working 

Group, Lelystad, the Netherlands. Oral Presentation. 

Flannery, G., Lynch, S., Carlsson, J., Cross, T., Culloty, S.C. 2012. An 

assessment of the ongoing impact of the pathogen Bonamia ostreae 

in the European flat oyster Ostrea edulis at two sites with different 

histories of exposure. National Shellfisheries Association, 2012 

Seattle, America. Oral Presentation. 

Flannery, G., Lynch, S., Carlsson, J., Cross, T., Culloty, S.C. 2011. 

The current status in Ireland of the pathogen Bonamia ostreae in 

the European flat oyster Ostrea edulis. Shellfish Restoration 2011, 

Stirling, Scotland. Poster Presentation. 

RESEARCH PROJECTS


20 


SHELLFISH PRODUCTIVITY IN THE IRISH SEA: 

WORKING TOWARDS A SUSTAINABLE FUTURE 

(SUSFISH) 



Contact PI: Dr Sarah Culloty, s.culloty@ucc.ie 

Researchers: Dr Sharon Lynch, Maud Cross, Emer Morgan 


Funding Body: ERDF INTERREG 4A Funding Programme 

Funding: €618,399 

Collaborating Partners: Ireland, Wales 


SUSFISH, a project between University College Cork, Ireland and Bangor University, Swansea 

University and Aberystwyth University, Wales, UK, will identify the effects that climate change 

will have on shellfish stocks in the Irish Sea and from these findings will produce guidelines for future 

fisheries management. Climate change is a global threat and numerous studies have linked the 

increased incidence of disease and mortality in marine organisms to climatic alterations and anthropogenic 

inputs. The Irish Sea is a rich source of shellfish species, both in terms of abundance 

and species diversity. The shellfish industry have concerns about the biological, environmental 

and economic impacts of climate change on aquaculture in this region. SUSFISH will identify 

strategies for exploiting potential opportunities from the changing climate as well as identifying 

how best to mitigate economic losses. An interdisciplinary approach is being taken which will 

investigate the biological (bivalve physiology, bivalve and pathogen population genetics, bivalve 

disease and development) and environmental impacts (temperature, salinity, acidification) of climate 

change in numerous shellfish species (the Pacific oyster, Crassostreagigas, the European flat 

oyster, Ostreaedulis, the soft shell clam, Myaarenaria, the razor clam, Ensissiliqua/E. arcuatus, the 

edible cockle, Cerastodermaedule, and the blue mussel, Mytilusedulis (wild and cultured stocks)) 

in the Irish Sea. Mathematical modelling of host parasite interactions is being undertaken on the 

collated data. The research carried out at University College Cork will focus on field and laboratory 

based trials over the three year duration of the project. 


Cross, M.E., Lynch, S.A., Whitaker, A., O’Riordan, R.M., Culloty, 

S.C. 2012.“The reproductive biology of the softshell clam, Myaarenaria, 

in Ireland, and the possible impacts of climate variability. 

Journal of Marine Biology (Open Access). 

Lynch, S.A., Carlsson, J., O’Reilly, A., Cotter, E., Culloty, S.C. 

2012.“A previously undescribedostreid herpes virus (OsHV-1) 

genotype detected in the Pacific oyster, Crassostreagigas, in Ireland.” 

Parasitology doi:10.1017/S0031182012000881. 

Morgan, E., O’Riordan, R.M., Kelly, T.C. &Culloty, S.C. 2012.The 

influence of disseminated neoplasia, trematode infections and 

gametogenesis on surfacing and mortality in the cockle, Cerastodermaedule. 

Diseases of Aquatic Organisms, 98: 73-84.

REBUILDING DEPLETED FISH STOCKS IN THE 

WATERS AROUND IRELAND 


AFDC, School of Biological, Earth & Environmental Science 

Contact PI: Dr Emer Rogan (e.rogan@ucc.ie) 

Researchers: Dr Sarah B. M. Kraak (sarah.kraak@marine.ie) 

Start Year: 2008 – End Year: ongoing 

Funding Body: National Development Plan 2007—2013 

Science, Technology & Innovation Programme (SeaChange) 

Funding: €627,633 

Collaborating Partners: Marine Institute, 

University of Essex (U.K.) 



The current challenges in fisheries management are (i) achieving MSY for all stocks by 2015 (as 

agreed in the Johannesburg declaration), (ii) mixed fisheries, where several species are caught by 

the same fishery in different mixtures, and (iii) the Ecosystem Approach to Fisheries Management 

(EAFM). This project aims to look at these challenges in the context of the demersal fisheries 

in waters around Ireland. The project will do this through proposals for fisheries management 

systems, and evaluating them through simulations. The work started with a critical evaluation of 

automated Management Strategy Evaluations (MSE), especially those MSEs that had overlooked 

the human factor: Harvest Control Rules (HCR) may lead to stock recovery if implemented perfectly, 

but it is impossible for them to be implemented perfectly under the reality of rational fisher 

behaviour. The second study looked at fisher behaviour in the context of the Tragedy of the Comments, 

and analysed under which conditions fishers might be expected to behave more for the 

common good. The third study proceeded with the actual proposal of a new management system, 

which not only takes into account mixed fisheries and ecosystem considerations, but also allows 

flexibility to the fishers and incentivises fishing behaviour that will lead to keeping their activities 

within agreed limits. The fourth study critically evaluated the current EU plan for four cod stocks, 

especially noting that the human factor had been one of the causes for the plan’s failure to meet its 

objectives. The collaboration in the fifth study explores spatial management of fisheries, which is 

now facilitated by the new technologies of the VMS, e-logbooks, and Fully Documented Fisheries 

concepts. The project is steadily working towards unravelling the causes for a failure of fisheries 

management and improving the approach to fisheries management based on these new insights. 


KRAAK, S. B. M., Kelly, C. J., Codling, E. A., and Rogan, E. 2010. On scientists’ discomfort in fisheries advisory science: the 

example of simulation-based fisheries management-strategy evaluations. Fish and Fisheries, 11, 119-132. 

KRAAK, S. B. M. 2011. Exploring the ‘Public Goods Game’ model to overcome the Tragedy of the Commons in fisheries 

management. Fish and Fisheries, 12, 18-33. 

KRAAK, S. B. M., Reid, D. G., Gerritsen, H. D., Kelly, C. J., Fitzpatrick, M., Codling, E. A., and Rogan, E. 2012. 21st century fisheries 

management: a spatio-temporally explicit tariff-based approach combining multiple drivers and incentivising responsible 

fishing. ICES Journal of Marine Science, 69(4): 590–601, doi:10.1093/icesjms/fss033. 

KRAAK, S. B. M., Bailey, N., Cardinale, M., Darby, C., De Oliveira, J. A. A., Eero, M., Graham, N., Holmes, S., Jakobsen, T., 

Kempf, A., Kirkegaard, E., Powell, J., Scott, R. D., Simmonds, E. J., Ulrich, C., Vanhee, W., and Vinther, M. 2012. Lessons for 

fisheries management from the EU cod recovery plan. Marine Policy. http://dx.doi.org/10.1016/j.marpol.2012.05.002 

Gerritsen, H. D., Lordan, C., Minto, C., KRAAK, S. B. M. 2012. Spatial patterns in the retained catch composition of Irish 

demersal otter trawlers: high-resolution fisheries data as a management tool. Fisheries Research, 129–130: 127–136. 10.1016/ 

j.fishres.2012.06.019. 


2


22 


THE LIFE HISTORY, ECOLOGY AND DYNAMICS OF 

THE BLACK SCABBARD (APHANOPUS CARBO) 

IN THE DEEP WATER ECOSYSTEM OF THE NORTH 

EAST ATLANTIC 


AFDC, School of Biological, Earth & Environmental Science 

Contact PI: Dr Emer Rogan (e.rogan@ucc.ie) 

Researchers: MS Ana Santos 

Start Year: 2008 

End Year: 2012 

Funding Body: Marine Institute 

Funding: €115,000 

Collaborating Partners: Marine Institute 


In the deep waters to the west of Ireland, landings from commercial fishing operations increased 

over the period 1973 to the late 1990’s. This was driven by the decline of traditional shelf fisheries 

and the greatly improved technology of vessels that allowed fishing in depths of up to 1,200 meters. 

Black scabbard (Aphanopus carbo) form an important part of both the mixed and directed 

fisheries of the north east Atlantic. Landings reached 9,100 tonnes in 2002, but declined to 3,500 

tonnes in 2005. Black scabbard is poorly understood in terms of its life history, ecology and dynamics. 

It has a wide distribution in the north east Atlantic between 200 and 1,600 m, but there is 

very little objective information available on the stock structure of the species. Distribution of the 

species has led to the hypothesis of a single stock but this remains uncertain (Anon. 2006b). There 

is still controversy on the ageing of black scabbard fish. Published ageing estimates used whole 

otoliths, and indicate maximum ages of 8 years (Moralis-Nin and Sena-Carvahlo; 1996). However, 

unpublished work carried out at the Marine Institute in the late 1990’s, suggest that they are much 

longer lived (up to 22 years). This has major implication for understanding the dynamics of the 

species (Anon. 2006a; 2006b). This project will increase our understanding of one of the most 

common and widely dispersed species. This new knowledge will inform the establishment of an 

ecosystem approach to deep water fisheries management. 


Ribeiro Santos, A., Connolly, P. & Rogan, E. Biological aspects of Black Scabbardfish (Aphanopus carbo) in North East Atlantic 

– preliminary results for a management plan. The Fisheries Resource – Linking Advice, Research and the Fishing Industry, 

Marine Institute, Galway, Ireland, 23rd-24th June 2010. Oral Presentation. 

Ribeiro Santos, A., Rogan, E. & Connolly, P. Feeding Ecology of Black Scabbardfish, Aphanopus carbo Lowe 1839, in the deep 

water of NE Atlantic. 8th Marine Biological Association Postgraduate Conference, Queen’s University Belfast, Northern Ireland, 

16-19th May 2011. Oral Presentation. 

Ribeiro Santos, A., Trueman, C., Shephard, S., Connolly, P & Rogan, E. Migration and stock structure of black scabbardfish 

Aphanopus carbo in the NE Atlantic: evidence from feeding and reproductive ecology and otolith stable isotopes. 6th World 

Fisheries Congress, Edinburgh, Scotland, 7 – 11th May 2012. Oral Presentation. 

Ribeiro Santos, A., Trueman, C., Shephard, S., Connolly, P & Rogan, E. Migration and stock structure of black scabbardfish 

Aphanopus carbo in the NE Atlantic: evidence from reproductive ecology and otolith stable isotopes. 9th Marine Biological 

Association Postgraduate Conference, University College Cork, 21-25th May 2012. Oral Presentation.

OTHER AQUACULTURE AND FISHERIES RESEARCH PROJECTS 

Bridging the gap between 

science and producers to 

support the European marine 

mollusc production sector 

(EUROSHELL) 

Research Centre/Department/ 

School: AFDC, School of Biological, 


Contact PI: Dr Sarah Culloty, 

s.culloty@ucc.ie 

Researchers: Dr Maria O’Mahoney 


Funding Body: EU FP7 Funding 

Programme 

Funding: €18,168 

Collaborating Partners: France, 

Belgium, Spain, Italy, Ireland, The 

Netherlands, UK 

IFI Strategic Partnership 

Project - Setting 

Conservation Limits. National 

Salmon Conservation Stamp 


School: AFDC , School of 

Biological, Earth & Environmental 

Sciences 

Contact PI: Dr Phil McGinnity, 

p.mcginnity@ucc.ie; Prof. Tom 

Cross, t.cross@ucc.ie 

Researchers: Dr Jamie Coughlan 


End Year: ongoing 

Funding Body: IFI Research 

Partnership Project. Inland Fisheries 

Ireland. 


A pilot project to undertake 

genetic stock of origin 

identification of European 

Atlantic salmon captured at 

west Greenland 2002-2010 









Funding Body: Atlantic Salmon 

Trust 


Ministerial request for mixed 

stock fisheries analyses for 

the Cromane & Waterford 

Estuary experimental salmon 

fisheries 









Funding Body: Inland Fisheries 

Ireland 

Funding: €100,000 


The genetic structure, 

foraging ecology, movement 

patterns and habitat choices 

of bottlenose dolphins 

(Tursiops truncatus) along 

the west coast of Ireland 




Contact PI: Dr Emer Rogan, 

e.rogan@ucc.ie 


Funding Body: School of BEES 

Crawford Hayes Scholarship/ 

National Parks and Wildlife Service 

Funding: NPWS funding: €45,000 


The application of signal 

detection methods to the 

fisheries management system 




Contact PI: Dr Emer Rogan 

Researchers: Deepak George 

Pazhayamadom 



Funding: €115,000 

Collaborating Partners: Dr Edward 

Codling, University of Essex, UK 



Advancing understanding 

of Atlantic Salmon at Sea: 

Merging Genetics and 

Ecology to Resolve Stockspecific 

Migration and 

Distribution patterns 







Researchers: Dr Jamie Coughlan, 

Dr Jens Carlsson, Dr Eileen Dillane 



and the Marine Research 

Sub-programme of the National 

Development Plan 2007-2013 

Funding: €891,000 


www.celticseatrout.com 

Genomics as a tool for 

detecting selection in 

farm Atlantic salmon and 

interactions between escaped 

farm and wild salmon 




Contact PI: Dr Phil McGinnity 

(Principal Investigator), 

p.mcginnity@ucc.ie. Prof. Tom Cross 

(Grantee), t.cross@ucc.ie 

Researchers: Dr Jamie Coughlan, 

Dr Jens Carlsson, Dr Eileen Dillane 

Funding Body: Norwegian 

Research Council ES375319 




23

24 


4.2 GEOMATICS AND 

REMOTE SENSING

The Geomatics and Remote Sensing thematic area includes expertise 

available in the Coastal and Marine Research Centre and in 

Geography and Archaeology: School of the Human Environment. 

Expertise covers applications of optical and radar remote sensing in 

the terrestrial, marine and coastal domain, image processing, end 

user requirements analysis, standards-based spatial data management 

and exchange, database design, data visualisation, web-GIS 

implementation and metadata management. The thematic area has 

been successful in developing a number of spatial data management, 

analysis and visualisation systems (e.g. Marine Irish Digital Atlas) as 

well as thematic maps demonstrating the potential of remote sensing. 

The group fosters national and international collaboration with 

bodies such as the EPA, Teagasc, OSI, National Space Centre, the 

Technical University of Vienna, the National Oceanographic Centre 

UK, the Nansen Centre, Norway and with IFREMER in France. The 

groups also play a key role in developing teaching activities e.g. MSc 

in Geographical Information Systems and Remote Sensing (RS). At 

present the Remote Sensing strand represents the largest concentration 

of RS researchers within Ireland, and the Geomatics strand 

is recognised internationally as a leader in providing solutions for 

marine geospatial data management. 


Dr Ned Dwyer (Lead PI) 

Dr Fiona Cawkwell (Lead PI) 

Mr Anthony Patterson 

Mr Declan Dunne 

Dr Yassine Lassoued 

Ms Vicki O’Donnell 

Geomatics and Remote Sensing 

25


26 


COASTAL WEB ATLAS (CWA) DEVELOPMENT: THE 

MARINE IRISH DIGITAL ATLAS (MIDA) AND THE 

INTERNATIONAL COASTAL ATLAS NETWORK (ICAN) 

Research Centre/Department/School: CMRC 



Funding Body: HEA, Northern Ireland 

Environment Agency, CMRC 

Researchers: Kathrin Kopke, Rory Scarrott, 

David Roig Cervera, Miguel Castillo, Ned Dwyer, 

Declan Dunne, Yassine Lassoued, Ali Al-Othman 

Contact PI: Ned Dwyer (n.dwyer@ucc.ie) 

Website: http://mida.ucc.ie and http://ican.science.oregonstate.edu/home 

The Marine Irish Digital Atlas (MIDA) is a coastal web atlas (CWA), which provides a unique 

resource where people interested in coastal and marine information can visualise and identify pertinent 

geospatial datasets and determine where to acquire them. The atlas offers digital geospatial 

data, incorporates text and uses multimedia elements. Integrating the latest advances in web-based 

mapping techniques, MIDA allows the display of data layers from numerous coastal and marine 

organisations, thus providing the best single resource for finding and viewing existing coastal and 

marine data related to the Island of Ireland. MIDA is a node in the Irish Spatial Data Infrastructure 

(ISDE) and in 2011 alone; MIDA had an average of 800 unique visits per month. CMRC attained a 

key role in advancing CWA development through the MIDA project and is one of the founders of 

the International Coastal Atlas Network (ICAN). 

The ICAN, a pilot project of UNESCO’s International Oceanographic Data and Information Exchange 

(IODE) programme since 2011, aims to be a global reference for the development of coastal 

web atlases. The Network has currently over 50 member organisations from more than 14 different 

countries. A key aim of ICAN is to share experiences and to find common solutions to CWA development, 

while ensuring maximum relevance and added value for the end users. Recent achievements of 

ICAN include the publication of a handbook on how to develop a coastal web atlas and the ongoing 

development of an interoperability demonstrator showing how CWAs can be linked together. 


Report of International Coastal Atlas Network Workshop 5: Coastal Atlases 

as Engines for Coastal & Marine Spatial Planning, Dwyer, N., Kopke 

K., Berman M., Belpaeme K., O’Dea L., Haddad T., and Wright D. , Cork, 

Ireland, (2012). 

O’Dea, E. K., Dwyer E., Cummins V. and Wright, D. J., 2011, Potentials and 

limitations of coastal web atlases, Journal of Coastal Conservation: Planning 

and Management, Volume 15, Issue 1, p.1-21, (2011) 

Coastal Informatics: Web Atlas Design and Implementation, Wright, 

Dawn(ed.) J., Dwyer Edward(ed.), and Cummins(ed.) V. , 344 pages (2010), 

Published by: Information Science Reference, IGI Global, Hershey, PA. 

Dwyer, N., Kopke, K., Cummins, V., O’Dea, E. and Dunne, D., 2010 Ireland. 

In: D. Wright, E. Dwyer and V. Cummins (ed.) Coastal Informatics: Web 

MIDA Screenshot of interactive map 

Atlas Design and Implementation, between pages 105-130, 344 pages, Published 

by: Information Science Reference, IGI Global, Hershey, PA. 

O’Dea, L, Dwyer, E, Cummins, V, Dunne, D., 2010 Harmonising Marine Data Exchange in Ireland. In: Green, D. (ed.) Coastal 

and Marine Geospatial Technologies. In series: Coastal Systems and Continental Margins, Vol. 13. Springer. 451pp, ISBN: 

978-1-4020-9719-5. 

ICAN Interoperability prototype: http://netmar.ucc.ie/discovery/

eSURGE: SATELLITE DATA FOR THE 

STORM SURGE COMMUNITY 



End Year: 2013 

Funding Body: European Space Agency 

Researchers: Rory Scarrott, Declan Dunne, Ned Dwyer 


Website: http://www.storm-surge.info 


The eSurge project, funded by the European Space Agency, aims to increase the usage of satellite 

Earth Observation data in storm surge modelling and forecasting, by making it easier for the community 

to access and use this data. 

Currently in its development phase, the project outputs will allow users easy and effective access to 

a wide range of satellite and in-situ datasets for a number of historical storm surge events, whilst 

also providing data for new surge events in near-real-time. A series of outreach and training events 

will demonstrate and inform users on how to use the project data and tools, enhancing the opportunities 

for research into and improved forecasting of storm surges. 

CMRC is part of a consortium and is responsible for development of the eSurge web portal, production 

of validation datasets through data collation and satellite image analysis, and organisation 

of the outreach and training activities. 

Effects of a storm surge which hit Wexford town in 2004 


27


2 


GEO-SEAS: PAN-EUROPEAN INFRASTRUCTURE FOR 

MANAGEMENT OF MARINE AND OCEAN GEOLOGICAL 

AND GEOPHYSICAL DATA 




Funding Body: EU FP7 

Researchers: Declan Dunne, Gerry Sutton 

Contact PI: Gerry Sutton (Gerry.sutton@ucc.ie) 

Website: http://www.geo-seas.eu/ 

Geo-Seas is implementing an e-Infrastructure of 26 marine geological and geophysical data centres, 

located in 17 European maritime countries. Geo-Seas will contribute to e-Infrastructure development 

in the areas of Scientific Data (coherent management and access to data) and Standards 

(data management, metadata, formats, delivery). Users will be able to identify, locate and access 

pan-European, harmonised and federated marine geological and geophysical datasets, and derived 

data products held by the data centres through a single common data portal. 

It will expand the existing SeaDataNet marine and ocean data management infrastructure to 

handle marine geological and geophysical data, data products and services, creating a joint infrastructure 

covering both oceanographic and marine geoscientific data. The Geo-Seas partnership 

is assuring the archival and long-term stewardship of data for re-use by new applications in 

many fields, thus preserving the availability of unique observational data, which can be difficult 

or impossible to re-create. The aims of Geo-Seas are aligned with European directives and recent 

large-scale framework programmes on global and European scales, such as GEOSS and GMES, 

EMODNET and INSPIRE. 

Geo-Seas 3D Digital Terrain 

Model viewer illustrating a 

merged bathymetry product. 

Viewer developed by IFREMER. 

Original bathymetry datasets 

supplied by INFOMAR and 

SHOM. Merged bathymetry 

data product developed by 

SHOM. Merged bathymetry 

data integration in 3D viewer 

developed by CMRC.

JUTFJUD: JOINED-UP THINKING FROM 

JOINED-UP DATA 




Funding Body: Marine Institute/Sea Change 

Researchers: Liam Caffrey (MI/CMRC) 

Contact PI: Jeremy Gault (j.gault@ucc.ie) 


The primary objective of the project is to develop and implement a strategy which will integrate 

and enable data interrogation across all data sources used by the MI’s Fisheries Science Services 

(FSS) Group. 

The project has the following objectives: 

• Recommendations based on review of best practice and rigorous testing, for all FSS data models 

and internal MI data collection/sampling methods. 

• Capacity building in geospatial representation and analysis techniques for fisheries datasets. 

• Identification and implementation of best practice in data management for an EAFM on a level 

that competes with international leaders in the field. 

• Tools to enable flexible, simultaneous interrogation of all FSS data sources for maximum data 

optimisation. 

• Enhanced interoperability from the development of ontologies and controlled vocabularies. 

• An FSS data strategy for 2010 to 2015. 

Additional achievements: 

• Improved efficiency and effectiveness from data interoperability resulting in enhanced performance 

across a number of MI research areas. 

• National capacity building in EAFM by linking computer scientists with fisheries biologists and 

other domain experts. 

• Synergy with the Beaufort Award initiative, other relevant SeaChange research and FP7/FP8 

funded European projects. 

• Direct benefits for fisheries management including rebuilding of fish stocks by improving capacity 

for sophisticated data interrogation. 

This Beaufort Marine Research Award is carried out under the Sea Change Strategy and the Strategy 

for Science Technology and Innovation (2006-2013), with the support of the Marine Institute, funded 

under the Marine Research Sub-Programme of the National Development Plan 2007–2013. 


P. L. Connolly and L. Caffrey, 2011, Supply chaining fishery advice. 

ICES J. Mar. Sci., 68(8): 1706-1711 doi:10.1093/icesjms/fsr119 


2


30 


SATELLITE BASED MARITIME SURVEILLANCE 





Researchers: Ying Wu, Anthony Patterson, 

Cathal O’Mahony, Chiara Pratola 

Contact PI: Anthony Patterson (a.patterson@ucc.ie); 

Cathal O’Mahony (c.omahony@ucc.ie) 

Website: http://www.anistiamo.org/ 

Two recently started projects, funded by the European Space Agency, are building on previous 

research that focused on how information could be derived from satellite observations to improve 

maritime security. Maritime agencies (e.g. naval organisations, coast guards) are the users of such 

satellite-based products and services. A focus of the first project called ANISTIAMO, and led by 

Kongsberg Satellite Services in Norway, is to develop the capacity in Ireland to implement and 

operate software to detect ships in radar (synthetic aperture radar) satellite imagery. In addition to 

ship location, research will also be carried out to determine ship course and speed and the ability 

to track vessels over time. 

The second project called Next Generation Recognised Maritime Picture (RMP), and led by Skytek, 

a Dublin based company, aims to greatly enhance the quality and accuracy of the recognised 

maritime picture for the Irish Naval Service (INS) through integration of data sources not currently 

used to generate an RMP. One of the key data sources will be satellite AIS (Automatic Identification 

System). In these projects the CMRC is focussing on radar data processing and analysis, data mining 

and pattern recognition activities as well as working closely with the end users which include the 

Irish Naval Service and the Irish Coast Guard. The other Irish partner in these projects in addition 

to the CMRC and Skytek is the National Space Centre, based near Midleton in Co. Cork. 


CMRC will produce software components encapsulating the algorithms tested and validated within these 

projects. These components will be capable of being reused within other systems, particularly within the 

maritime security domain. It is hoped that the overall system will be used not only by the INS and Irish Coast 

Guard, but by other small navies and coastguard services throughout the world. 

Irish Naval Service 

Vessels in action. Image 

Copyright to the Irish 

Naval Service

MESMA: MONITORING AND EVALUATION OF 

SPATIALLY MANAGED AREAS 





Researchers: Yassine Lassoued, Ali Al-Othman, Ying Wu 


Website: http://www.mesma.org/ 


The MESMA project focuses on marine spatial planning and aims to produce integrated management 

tools (concepts, models and guidelines) for monitoring, evaluation and implementation of 

Spatially Managed Areas (SMAs). The project results will support integrated management plans 

for designated or proposed sites with assessment methods based on European collaboration. The 

main tasks in the project are information analysis, the development of a generic framework (Fig 

1), the testing and evaluation of this framework through case-studies and the development of a 

toolbox. A significant proportion of the effort will be centered on the case studies within five geographical 

regions: the North Sea, Baltic, Mediterranean, Atlantic, and Black Sea. This approach 

makes it possible to compare pressures on an inter-regional level (e.g. Offshore wind farms in the 

North Sea, Black Sea and Baltic), or a multi-pressure level for a specific region (e.g. SMA in Fishing, 

Wind-energy, Geo-hazards and Tourism in the Black Sea). 


The project is now in year 3 of 4 and a number of peer reviewed publications and key reports 

are have been published. To access these and other up-to-date developments refer to the project 

main website http://www.mesma.org/. CMRC is leading a work package (WP5) that is developing 

and demonstrating the deployment of Web-based GIS infrastructures and standards for discovering, 

accessing, managing, and manipulating multiple types of marine spatio-temporal data that 

are required for monitoring and evaluation of SMAs. In accordance with current best practice 

used by the existing infrastructures e.g. EMODNET, the MESMA infrastructure adapts, uses and 

promotes specific international standards such as EU Inspire, and ISO) that govern the way the 

datasets are structured described and documented through thematic classification schemes and 

metadata inventories. One of the main outputs of the project will be a web portal that integrates 

the MESMA Work package and case-study elements. 

MESMA web portal Architecture 


3


32 


NETMAR: OPEN SERVICE NETWORK FOR MARINE 

ENVIRONMENTAL DATA 




Funding Body: FP7 

Researchers: Declan Dunne 

Contact PI: Declan Dunne (d.dunne@ucc.ie) 

Website: http://netmar.nersc.no 

The NETMAR project will develop a pilot European Marine Information System (EUMIS) that 

will enable users to search, download and integrate satellite, in situ and model data from ocean 

and coastal areas. EUMIS will be a user-configurable system offering flexible discovery of data and 

geo-processing services. Access to these services and also workflow chaining facilities for these 

services will be based on open web GIS standards. EUMIS will be a distributed system where a 

number of services and subsystems will be integrated and made interoperable by means of semantic 

technologies. EUMIS will use a semantic framework coupled with ontologies for identifying 

and accessing distributed data. 

The implementation of EUMIS will be done through a set of case studies from different marine 

application domains, ranging from near real-time monitoring and forecasting of marine pollution 

to the exploration of long-term historical time series variables for climate change assessment. The 

EUMIS subsystems will be based on open source software, and will be offered as contributions to 

the SISE (Single Information Space in Europe for the Environment) and SEIS (Shared Environmental 

Information System). The subsystems will support the implementation of the INSPIRE 

Directive and be of benefit to the implementation of GMES (Global Monitoring for Environment 

and Security) and GEOSS (Global Earth Observation System of Systems). 

CMRC is leading work packages concerning the specification of the NETMAR System Architecture 

and Semantic Framework. CMRC is also leading the coastal web atlas interoperability pilot 

which is targeted towards the International Coastal Atlas Network (ICAN) user community. 


D2.1: Review of projects, initiatives and technologies addressing system 

architectures for distributed Environmental Information Systems 

D2.4.2: Authoritative specification of NETMAR system architecture 

D3.2: Review of available ontology tooling 

D3.3: Review of available ontologies and their interfaces 

D3.8: Prototype interlinked ontology resource fully populated to 

NETMAR requirements 

D4.1: Review semantic frameworks 

D4.4.2: Implementation of semantic framework 

D4.5: Authoritative specification of semantic framework 

D5.1.1: Data delivery services – Basic data services 

D5.1.2: Data delivery services – Semantically enabled data services 

D5.2.1: Data processing services – Basic processing services 

D5.2.2: Data processing services – Semantically enabled processing services 

D5.3.1: WPS server – Basic WPS package 

D5.3.2: WPS server – Fully semantically enabled processing services 

D6.5: Final version of NETMAR portal (http://eumis.nersc.no) 

D7.7: NETMAR cookbooks for data delivery and processing services 

D7.8: NETMAR cookbooks for semantic data delivery and processing services 

D7.9.2: ICAN semantic interoperability pilot cookbooks 

NETMAR semantic discovery client which 

uses ontologies for identifying and accessing 

distributed data and geo-processing services.

ODINAFRICA 

TECHNICAL COORDINATION AND SUPPORT 




Funding Body: UNESCO – International Oceanographic Data 

and Information Exchange 

Researchers: Yassine Lassoued, Ali Al-Othman 

Contact PI: Yassine Lassoued (y.lassoued@ucc.ie) 


Through its work in the International Coastal Atlas Network (ICAN) the CMRC has supported 

and coordinated the technical development of the African Marine Atlas (AMA) as part of the 

IODE sponsored ODINAFRICA project. The AMA is now in the phase of developing national 

coastal atlases for Africa, therefore a common technology is required to facilitate this task. 

The focus of the SmartAtlas sub-project is to provide such a common atlas technology. SmartAtlas 

builds on the opensource-based technology and solution developed for the Marine Irish Digital 

Atlas (MIDA). This is being achieved through the development of new web client mapping applications 

which feature expanded functionality, plug-in-free animation and a new Model-View- 

Control (MVC) architecture with a rich user experience for every browser. These mapping clients 

are developed using open source software technology with greater performance such as web technologies 

like AJAX, much more simplified, flexible and customisable interface based on the latest 

JavaScript frameworks like ExtJS and GeoExt and new mapping tools for adding features, zooming, 

drawing, measuring, and customised printing. 

SmartAtlas also introduces integration of Catalogue Services for Web (CSW). The atlas can be 

configured to connect to metadata catalogue servers (e.g. Geonetwork, ESRI ArcServer, etc.) so 

that users can search for data layers within the atlas or other metadata stores included in the 

search through the distributed CSWs. 


The SmartAtlas web atlas engine, demo available at http://smartatlas.ucc.ie, download page: 

http://smartatlas.ucc.ie/downloads 

Screenshot of the 

smartatlas interface 


33


34 


OSS2015: OCEAN STRATEGIC SERVICES BEYOND 2015 





Researchers: Ned Dwyer, Sarah Twomey, Declan Dunne 


Website: http://www.oss2015.eu/ 

OSS2015 is aimed at developing a range of nowcast, forecast and climatological mixed layer biogeochemical 

products. These products are based on the fusion of satellite ocean colour data 

(multispectral sea surface radiance) and in-situ measurements of ocean-going platforms (e.g. buoys, 

drifters, gliders). Project activities complement the ongoing European Commission funded 

Marine Core Service, known as MyOcean2. The project aims to: (i) derive 3-Dimensional spatial 

and temporal representations of biogeochemical variables; (ii) generate & validate satellite derived 

global time series of advanced biogeochemical products such as Particulate Organic Carbon, Net 

Primary Production, Phytoplankton Functional Types, Particle Size Distribution for carbon cycle 

science; (iii) Develop a prototype web platform to deliver these biogeochemical products. CMRC 

is responsible for coordinating the in-situ data gathering in the North Atlantic. The Centre is also 

contributing to the gathering of user needs and the set up of a standards compliant in-situ data 

management system. 

Coccolith bloom 

along the coastline 

of the Northeast 

Atlantic, acquired by 

the European Space 

Agency’s MERIS sensor

Climate Observation System 

Development and Analysis 




Funding Body: Environmental Protection 

Agency 

Researchers: Ned Dwyer 


CoralFISH 




Funding Body: European Commission 

Researchers: Paula Harrison, Anthony 

Patterson, Gerry Sutton 


Web: http://www.eu-fp7-coralfish.net/ 

Development of a Decision 

Support Environmental Tool 

for the Irish Coast Guard 




Funding Body: Irish Coast Guard, Department 

of Transport 

Researchers: Max Kozachenko 

Contact PI: Vicki O’Donnell (v.odonnell@ucc.ie) 


OTHER GEOMATICS AND REMOTE SENSING RESEARCH PROJECTS 

ESA Climate Change 

Initiative Phase 1 – Soil 

Moisture 





Researchers: Rory Scarrott 


Website: http://www.esa-cci.org/ 

SECAD Community Trails 

Development Initiative 




Funding Body: South & East Cork Area 

Development Ltd. 

Researcher: Rory Scarrott 

Contact PI: Vicki O’Donnell (v.odonnell@ucc.ie) 

Project Website: http://secad.ie/trails 


35

36 


4.3 GOVERNANCE 

AND LAW

The Governance & Law thematic area spans the Coastal and Marine 

Research Centre, the Hydraulics and Maritime Research Centre, the 

Faculty of Law, the School of the Human Environment and the School 

of Biological, Earth and Environmental Sciences. It has links with the 

National Maritime College of Ireland and Cork Institute of Technology 

as well as the Irish Naval Service (INS) through IMERC. The thematic 

area conducts leading-edge research at the national, European 

and international levels on a range of issues including Environmental 

Law, Regulation and Policy, Maritime Spatial Planning, Integrated 

Coastal Zone Management, Climate Change Adaptation and Public 

Participation. Researchers in this area have been at the forefront of 

coastal management research for nearly twenty years and the CMRC 

is an internationally recognised centre of excellence gained through 

participation in key national and EU funding initiatives. The group 

has numerous national and international collaborations. European 

links have been established with EU agencies, research centres and 

NGOs such as CEFAS, DELTARESEEA, GKSS, IFREMER, NERC, 

SAMS and WWF. Internationally links have been forged with the 

Brazilian Space Agency, Memorial University, Virginia Institute of 

Marine Science and the University of Rhode Island. 


Jeremy Gault/Dr Val 

Cummins (Joint Lead PI) 

Darius Bartlett 


Professor Robert Devoy 

Dr Margaret Desmond 

Dr Maria Falaleeva 

Kathrin Kopke 

Jimmy Murphy 

Dr Owen McIntyre 

Dr Barry O’Dwyer 

Dr Anne Marie O’Hagan 

Cathal O’Mahony 

Dr Aine Ryall 

Dr Benedicte Sage 

Dr Colin Sage 

Mark Mellett (INS) 

Governance and Law 

37


3 


COEXIST (INTERACTION IN COASTAL WATERS: 

A ROADMAP TO SUSTAINABLE INTEGRATION OF 

AQUACULTURE AND FISHERIES) 





Researchers: Jeremy Gault, Vicki O’Donnell, 

Anne Marie O’Hagan (HMRC), Mike Fitzpatrick (MI), 

Gavin Burnell (AFDC), Kathrin Kopke 


Website: http://www.coexistproject.eu/ 

Coastal areas are subject to ever increasing competition for space as a result of commercial and 

leisure activities and the desire to protect environmentally sensitive locations (for example, under 

Natura 2000). Small scale fisheries and aquaculture operations rely on access to appropriate sites 

but the extent of coastal waters available may be restricted due to the creation of Marine Protected 

Areas (MPA) or may also be of interest to other sectors such as tourism and offshore energy. This 

can lead to issues with spatial management of the coastal resource and can potentially lead to 

conflict between competing interests. 

COEXIST is a broad, multidisciplinary approach to evaluate these interactions with the ultimate 

goal to provide a roadmap to better integration, sustainability and synergies among different activities 

in the coastal zone. The project brings together 13 partner institutions from 11 countries 

with expertise in both aquaculture, fisheries and governance. They will work together to assess the 

interactions between capture fisheries and aquaculture and other coastal users and evaluate the 

mutual benefits and potential sources of conflict. 


As part of the proposed research, Partners will look at operations at five case study areas, in the 

Atlantic, Adriatic and North Sea, and use the experience of local stakeholders, combined with 

the outcomes of existing international case studies, to evaluate the performance of current spatial 

management tools. This information will then be synthesised to produce guidelines for best practice 

in spatial planning for the fisheries and aquaculture industries with respect to other coastal 

interests for use by the European Commission and its policy makers as well as national decision 

makers with a view to assisting in the implementation of the EU’s Integrated Maritime Policy. 

Aquaculture in Ireland

KNOWSEAS - KNOWLEDGE-BASED SUSTAINABLE 

MANAGEMENT FOR EUROPE’S SEAS 





Researchers: Cathal O’Mahony, Mark Jessopp, Jeremy Gault 


Website: http://www.knowseas.com/ 


Europe’s four regional seas (Baltic, Black, Mediterranean and NE Atlantic) have suffered severe 

environmental degradation due to human pressure. Existing measures to manage pressures have 

proven inadequate and the EU Member States have recently responded by adopting a new policy 

(Maritime Strategy Blue Book) and environmental legislation (Framework Marine Strategy Directive). 

These instruments rely on the Ecosystem Approach, a management paradigm that encompasses 

humans and the supporting ecosystem. But the science base for this approach needs 

strengthening and practical tools must be developed and tested for policy implementation. 

The overall objective of the project is: a comprehensive scientific knowledge base and practical 

guidance for the application of the Ecosystem Approach to the sustainable development of Europe’s 

regional seas. CMRC is actively involved in four work packages of KnowSeas, which are 

distributed within four thematic areas of the overall project. 


Mark J. Jessopp, Michelle Cronin, Thomas K. Doyle, Mark Wilson, Abigail McQuatters-Gollop, 

Stephen Newton & Richard A. Phillips (in prep) Transatlantic migration by post-breeding puffins 

enables exploitation of a temporarily abundant food resource. 

Malte Busch, Andreas Kannen, Stefan Garthe, Mark Jessopp (in review) Consequences of a cumulative 

perspective on marine environmental impacts: offshore wind farming and seabirds at North Sea 

scale in context of the EU Marine Strategy Framework Directive. Ocean & Coastal Management. 

The Arklow Bank 

Wind Park is the 

first offshore wind 

farm in Ireland. 


3


40 


MARLISCO: MARINE LITTER IN EUROPE SEAS: 

SOCIAL AWARENESS AND CO-RESPONSIBILITY 





Researchers: Jeremy Gault 


Marine environments are central to human well-being, but they are also extensively threatened by 

our activities. The MARLISCO project seeks to raise societal awareness of both the problems and 

the potential solutions relating to marine litter, which has been identified as a key issue threatening 

marine habitats worldwide. A major objective of MARLISCO is to understand and facilitate 

societal engagement in order to inspire changes in attitudes and behaviour. In order to achieve 

this the project will include industrial sectors, users of coastal and marine waters, waste management 

sectors, Regional Sea Commissions and EU representatives, local municipalities, citizen 

groups, school children and the general public. MARLISCO recognises the need for a concerted 

approach to encourage co-responsibility through a joint dialogue between the many players. This 

will be achieved by organising activities across 15 European countries, including national debates 

in 12 of them, involving industry sectors, scientists and the public, a European video contest for 

school students, educational activities targeting the younger generation together with exhibitions 

to raise awareness among the wider public. MARLISCO will make use of innovative multimedia 

approaches to reach the widest possible audience, in the most effective manner. 

The project will develop and evaluate an approach that can be used to address the problems associated 

with marine litter and which can also be applied more widely to other societal challenges 

where there are substantial benefits to be achieved through better integration among researchers, 

stakeholders and society. 

Litter in intertidal zone 

at Cork Harbour beach


PISCES: PARTNERSHIPS INVOLVING STAKEHOLDERS 

IN THE CELTIC SEA ECOSYSTEM 

Research Centre/Department/School: Coastal and Marine Research Centre 



Funding Body: Life+ 

Researchers: Sarah Twomey, Cathal O’Mahony 

Contact PI: Gerry Sutton (gerry.sutton@ucc.ie) 

Website: http://projectpisces.eu 

Large marine areas and regional seas present management challenges. They are often bordered by 

numerous maritime jurisdictions and host multi-sector activity under varying governance arrangements. 

Regional marine management involves a range of mechanisms and approaches to ensure 

stakeholders have an opportunity to engage in the process; and these approaches can differ in their 

legal and regulatory conditions. At present, no such comparable structures exist at the transnational 

level for the ecosystem-based management of the Celtic Sea. Against this backdrop, a pioneering 

project using a participative process, involving representatives from differing sectors of activity in 

the Celtic Sea spanning four Member States, was established to identify realistic and meaningful 

management principles in line with the goals of the EU’s Marine Strategy Framework Directive. This 

international partnership is working with a common objective – to support sustainability by creating 

practical guidelines to deliver an ecosystem approach to marine management in the Celtic Sea. 


Towards Sustainability in the Celtic Sea: A guide to implementing the ecosystem approach through the Marine 

Strategy Framework Directive. 

11 short videos produced showcasing case studies of marine management and the stakeholders’ experiences of 

the PISCES project: http://www.youtube.com/playlist?list=UU_hebvHe1SGnPJKdgydIMug&feature=plcp 

Sarah Twomey presented PISCES at the Marine Strategy 2012 Conference: Research and Ecosystem Based 

Management Strategies in Support of the Marine Strategy Framework Directive in Copenhagen, Denmark, 

14-16 May 2012. 

Sarah Twomey will be presenting PISCES at the Life+ MARMONI project Stakeholders’ workshop in Latvia, 

15-16 November 2012. 

Stakeholder engagement 

at PISCES workshop 


4


42 


SUSTAIN: ASSESSING SUSTAINABILITY AND 

STRENGTHENING OPERATIONAL POLICY 




Funding Body: INTERREG IVC 

Researchers: Cathal O’Mahony, Sarah Twomey 

Contact PI: Cathal O’Mahony (c.omahony@ucc.ie) 

Website: http://www.sustain-eu.net 

The increasing intensity of human activities along our coastline (e.g. the development of ports and 

harbours, coastal protection, land reclamation, tourism and sand/gravel extraction) will impact on 

coastal communities and natural habitats. 

The key objective of SUSTAIN is to have in place, at the end of three years, a fully implementable 

policy tool, applicable for all 22 coastal states of the EU, which will ensure that the integrated management 

of coastal issues will be sustainable. This entails the agreement within the project, of a set 

of criteria which are readily measurable (using indicators) and which cover both the threats of an 

unsustainable development and the opportunities provided by a sustainable future which faces all 

coastal authorities and communities throughout Europe. 

The SUSTAIN project partnership comprises 13 partners (including authorities [regional and local], 

universities and NGOs); and the project is pan-European in scope with partners representing 

the N. Atlantic and S. Atlantic seaboards, the Mediterranean, Baltic and Black Seas 


To date, SUSTAIN has organised six international workshops with a focus on aspects of sustainability, 

and methodologies for measurement of sustainability. Key to the success of SUSTAIN is the 

exchange of good practices in terms of implementing sustainability and positively influencing policy 

to support sustainability. The results of the project’s activities will be used to develop two guides: 

– A Guide for Sustainability Improvement 

– An Implementation Guide for Authorities (local and regional). 

In addition two reports will be produced, so that the results can be accessed throughout the EU: 

– A report on the exchange of experience 

– A report on the sustainability criteria and their assessment. 

The project activities and outputs will be presented at the SUSTAIN International Conference 

– “Delivering Sustainable Coasts”, taking place in Southport, UK, September 18th-19th 2012. 

Sustain partners at workshop 

in Samothraki, Greece, 2011.

OTHER GOVERNANCE AND LAW RESEARCH PROJECTS 

CLAD - Coastal Climate 

Adaptation and Development 

Tool 




Funding Body: Environmental Protection Agency 

Researchers: Maria Falaleeva, Stefan Grey 

Contact PI: Maria Falaleeva (m.falaleeva@ucc.ie) 

CoastAdapt 




Funding Body: INTERREG 

Researchers: Cathal O’Mahony 


Website: http://www.coastadapt.org 

GEOSPECS: Geographic 

Specificities and Development 

Potentials in Europe 




Funding Body: ESPON 

Researchers: Kathrin Kopke, Aidan O’Donoghue, 

David Roig Cervera 

Contact PI: Kathrin Kopke (k.kopke@ucc.ie) 

Website: http://www.geospecs.eu 

ICIP - Ireland’s Climate 

Information Platform 





Funding Body: EPA 

Researchers: Barry O’Dwyer, Anthony Patterson 


Irish Coastal Network 

(ICoNet) 


Project Status: ongoing active 


Website: http://iconet.ucc.ie/ 

TEMPUS: Improvement of 

Education on Environmental 

Management 




Funding Body: EU Tempus Programme 

Researchers: Maria Falaleeva 

Contact PI: Maria Falaleeva (m.falaleeva@ucc.ie) 

Website: http://ecotempus.com 


43

44 


4.4 MARINE RENEWABLE 

ENERGY

Expertise for the Marine Renewable Energy thematic area resides in the 

Hydraulics and Maritime Research Centre (HMRC). The HMRC is centre 

of excellence within Ireland for Ocean Renewables and Coastal Engineering 

providing support to the maritime industry as well as fundamental R&D. 

It currently has a staff of 35 and comprises postdoctoral researchers, engineers 

and PhDs across a range engineering and other disciplines, from 

hydrodynamics, civil, electrical and mechanical engineering to marine law 

and economics. The HMRC houses the only facilities for wave simulation in 

Ireland with a Wave Flume and an Ocean Wave Basin and was designated 

as the National Ocean Test Facility in 2009. There are also several electrical 

and mechanical test rigs for linear actuation, turbine test and pneumatic 

emulation. These facilities have recently undergone a €2.5m upgrade, giving 

them state-of-the-art capabilities. The Centre also has its own supercomputing 

facilities as well as a suite of numerical modelling packages, both 

industry standard and bespoke. Electrical grid research involves the production 

of commercial, dynamic, grid-connect models for ocean wave and tidal 

systems. The Centre has provided research services to device developers 

in this area from all over the world. Over 25 different concepts have been 

tested with developers from Ireland, U.K., Denmark, Portugal, Netherlands, 

U.S.A., Japan and Australia. Device testing at prototype scale (connection of 

1MW prototypes at sea) is also underway, investigating the electrical issues, 

environmental impact and economics. The HMRC / National Ocean Test 

Facility will transfer to the new UCC Beaufort Research Laboratory within 

the IMERC campus at Ringaskiddy in 2014. 


Professor Tony Lewis (Lead PI) 

Dr Ray Alcorn (Lead PI) 

Professor Alistair Borthwick (Lead PI) 

Dr Jimmy Murphy 

Mr Brian Holmes 

Dr Gordon Dalton 

Dr Dara O’Sullivan 

Dr Wanan Sheng 

Dr Anne Marie O’Hagan 

Marine Renewable Energy 

45


46 


COMPONENTS FOR OCEAN RENEWABLE ENERGY 

SYSTEMS (CORES) 


Hydraulics and Maritime Research Centre (HMRC) 

Contact PI: Prof. Tony Lewis (t.lewis@ucc.ie) 

Researchers: Prof. Tony Lewis, Dr. Ray Alcorn, 

Dr. Dara O’ Sullivan, Mark Healy, Florent Thiebaut, 

Judy Rea, Dr. Wanan Sheng, John O’ Callaghan. 


Funding Body: European Community 

Seventh Framework Programme (FP7) 

Funding: €3.6 million 

Collaborating Partners: Ocean Energy Ltd, Queens University Belfast, University 

of Exeter, Wave Energy Centre (Portugal), Universita di Bologna, Aalborg University, 

Robotiker Tecnalia, Instituto Superior Tecnico (Lisbon), MCS Kenny, Kymaner 

(Portugal), University of Limerick, Fraunhofer IWES 

Web: http://www.fp7-cores.eu/ 

CORES is a European collaborative research project with 7 partners. It is the first EU project to be 

co-ordinated by an Irish research centre. 

Wave Energy Converters are at an early stage of development. First generation devices have been 

deployed at the shoreline and normally consist of Oscillating Water Column systems. In order for 

these systems to progress towards full commercial realisation they must develop into units suited 

to mass production. 

This project follows the successful FP6 funding round in which several fixed oscillating water column 

wave energy convertors were funded at demonstration level. These systems are now evolving 

from fixed to floating devices in deeper water, further offshore. This brings new challenges which 

this project aims to address. The end goal is to develop a low-risk way of addressing existing 

problems in order to consolidate all of the essential components of wave energy systems into one 

system model. 

This project concentrates on the development of new concepts and components for power-takeoff, 

control, moorings, risers, data acquisition and instrumentation based on floating OWC system 

with the intention however of them having relevance to other floating device types. 

KEY PUBLICATIONS 

& OUTPUTS 

Thiebaut et al., (2011), Testing of a 

floating OWC device with movable 

guide vane impulse turbine power 

take off, EWTEC 2011. 

Kelly et al., (2012), Challenges and 

lessons learned in the deployment of 

an offshore oscillating water column, 

EVER 2012. 

The OE Buoy being towed to the 

Galway Bay Wave Energy Test Site

GEOWAVE – GEOTECHNICAL DESIGN SOLUTIONS 

FOR THE OFFSHORE RENEWABLE WAVE ENERGY 

INDUSTRY 




Contact PI: Dr. Ray Alcorn (r.alcorn@ucc.ie) and Dr. Wanan Sheng (w.sheng@ucc.ie) 

Researchers: a Postdoctoral Researcher and a Research Assistant (to be confirmed) 



Funding Body: European Community Seventh Framework Programme (FP7) 

Funding: €1,130,000 

Collaborating Partners: University of Dundee, University of Western Australia, 

WaveBob, Seaflex and Deep Sea Anchors, Lloyds Register and Cathie Association. 

GeoWAVE is an EC FP7 funded project for the benefit of small and medium-sized enterprises 

(SMEs), which brings 3 Research and Technology Development (RTD) performers and 3 SMEs 

together for developing an economic mooring/anchoring system for wave energy converter deployments 

in sea. The main target of the project is to seek a mooring configuration by implementing 

the Seaflex mooring component to the mooring system so that the mooring system will have 

a reduced footprint, a minimised impedance to wave energy production and a minimised load on 

the anchor, and hence bring down the cost of the station-keeping system for wave energy device 

deployment (and the results will be also input to the industry standards). 

Three RTD performers and three SMEs (the developers of device, mooring and anchor design, 

respectively) will be working together in the development of an entire and practical deployment 

system for wave energy converters. To achieve the overall goal, different approaches will be applied 

and checked, including: (i) numerical simulations of wave energy converter, mooring and anchor 

systems; (ii) small scale physical model tests: a wave energy converter and mooring system in wave 

tank and an anchor model in the geotechnical centrifuges; (iii) field test of an prototype anchor in 

a specific location. 

UCC is the lead of Work Package 2 and will perform the numerical simulations of the wave energy 

converter and mooring system in this package as well as also leading the small scale model test in 

a wave tank in Work Package 3. 


This project only began in September 2012 but it is expected that GeoWAVE will deliver key Intellectual 

Property to the SMEs involved. 


47


4 


MARINE RENEWABLE INTEGRATED APPLICATION 

PLATFORM (MARINA PLATFORM) 



Contact PI: Dr. Jimmy Murphy (jm.hmrc@ucc.ie) 

Researchers: Dr. Jimmy Murphy, Dr. Dara O’Sullivan, 

Katie Lynch, Pedro Oliveira, Fiona Devoy McAuliffe, 

Keith O’ Sullivan (PhD Student). 


End Year: Ongoing 

Funding Body: European Community Seventh 

Framework Programme (FP7) 


Collaborating Partners: 17 partners spread across 12 EU countries. 

Web: http://www.marina-platform.info 

Marina Platform is a European collaborative research project with 17 partners. Research in the 

MARINA Platform project will establish a set of equitable and transparent criteria for the evaluation 

of multi-purpose platforms for marine renewable energy (MRE). 

Using these criteria, the project will produce a novel, whole-system set of design and optimisation 

tools addressing, inter alia, new platform design, component engineering, risk assessment, spatial 

planning, platform-related grid connection concepts, all focused on system integration and reducing 

costs. These tools will be used, incorporating into the evaluation all presently known proposed 

designs including (but not limited to) concepts originated by the project partners, to produce 

two or three realisations of multi-purpose renewable energy platforms. These will be brought to 

the level of preliminary engineering designs with estimates for energy output, material sizes and 

weights, platform dimensions, component specifications and other relevant factors. This will allow 

the resultant new multi-purpose MRE platform designs, validated by advanced modelling and 

tank-testing at reduced scale, to be taken to the next stage of development, which is the construction 

of pilot scale platforms for testing at sea. 

HMRC are involved in each of the key technical work packages 

of the project. HMRC are leading the critical component assessment 

work package for combined wind and ocean energy 

concepts and have developed an economics assessment tool for 

these combined concepts as part of the project and are testing 

physical models of the various concepts in the wave basin. 


There have been a number of papers presented at conferences and 

in journals as well as a number of public deliverables all available 

on the project website. 

Physical model testing of a tension 

leg floating wind platform

MARINE RENEWABLES INFRASTRUCTURE 

NETWORK (MARINET) 




Researchers: Prof. Tony Lewis, Dr. Ray Alcorn, Mark Healy, Brian Holmes. 



Framework Programme (FP7), Grant Agreement No 262552 

Funding: €9 million 

Collaborating Partners: HMRC is the Coordinator of this 

network initiative of 29 partners with 42 specialist test facilities 

spread across 11 EU countries and 1 FP7-partner country (Brazil). 

The two Irish partners are UCC-HMRC and the Sustainable 

Energy Authority of Ireland (SEAI). 

Web: www.fp7-marinet.eu 


Marine renewable energy systems – wave energy and tidal stream converters as well as offshorewind 

turbines – are mostly at the pre-commercial stage of development. These systems require 

research and testing to be undertaken at a series of scales along the path to commercialisation. 

MARINET is an infrastructure initiative comprising a network of research centres and organisations 

that are working together to accelerate the development and commercial deployment of 

these technologies. The initiative aims to streamline and facilitate testing by offering periods of 

free-of-charge access to world-class test facilities and by developing joint approaches to testing 

standards, research and industry networking & training. 

Companies and research groups can avail of periods of free-of-charge access to cross-border facilities 

to test devices or sub-systems at any scale or to access environmental data. In total, over 700 

weeks of access is available to an estimated 300 projects and 800 external users, with at least four 

calls for access applications over the 4-year initiative. 

MARINET partners are working together in parallel to implement common testing standards in 

order to streamline the development process, conduct coordinated research to improve testing 

capabilities and facilitate industry networking & training in the form of user workshops, staff 

exchange and free-of-charge training courses in order to provide opportunities for collaboration, 

joint ventures and expertise development. 


A new marine renewable energy test infrastructure network to coordinate current and future research 

direction, free-of-charge public access to test facilities, publications of test systems and 

instrumentation best practices, research to improve test infrastructures and techniques, industry 

networking & training events. 


4


50 


NAVITAS COMMERCIALISATION PROJECT 



Contact PI: Dr. Gordon Dalton (g.dalton@ucc.ie) 

Researchers: Michael O’Connor, Chris O’Donoghue, Slawomir Krupa, 



Funding Body: Enterprise Ireland Commercialisation Fund 

Funding: €350,000 

Web: http://www.ucc.ie/en/hmrc/projects 

NAVITAS is a techno-financial marine renewable energy tool that can be used to assess the feasibility 

of wave, tidal and offshore wind projects. The program contains a database of marine renewable 

locations together with technical information on leading devices. The user can add to these 

databases by uploading their own location or device information. Using this information Navitas 

calculates the amount of energy a particular device will produce at a particular location. 

The financial section of Navitas allows the user to input all the costs associated with planning, 

installing, commissioning, operating and decommissioning a marine renewable project. Navitas 

combines the financial information with the energy output data to produce a cash flow sheet for 

the entire duration of a project. It returns financial indicators such as Net Present Value, Internal 

Rate of Return and Payback Period. With this information users can explore which devices and 

locations are the most promising in terms of future marine renewable deployments. 

Navitas has been developed over the last three years under the Charles Parsons Initiative and has 

contributed to the findings of over ten peer reviewed research papers. It has been also been used 

by device developers, utilities, government agencies, industry and on EU FP7 research projects. 

The current project will transform Navitas from its existing user intensive excel based format into 

a commercially available product on a new platform that can be sold to wave energy device and 

project developers, research centres, utilities, government agencies, supply chain operators and 

financiers. 


Dalton GJ, Lewis T. (2011) “Metrics for measuring job creation by renewable energy technologies, using Ireland 

as a case study”. Renewable and Sustainable Energy Reviews: 15:4: 2123-2133. 

Dalton GJ, Alcorn R, Lewis T. (2011) “A 10 year installation program for wave energy in Ireland, a sensitivity 

analysis on financial returns”. Renewable Energy; , 40:1: 80-89. 

O’Connor M, Lewis T., Dalton GJ. “Techno-economic performance of the Pelamis P1 and Wavestar at different 

ratings and various locations in Europe”, Renewable Energy; in Press. , 50 (1) (2012), pp. 889-900

OFFSHORE RENEWABLE ENERGY CONVERSION 

– COORDINATED ACTION (ORECCA) 



Contact PI: Dr. Jimmy Murphy (jm.hmrc@ucc.ie) 

Researchers: Dr. Jimmy Murphy, Katie Lynch. 




Framework Programme (FP7) 


Collaborating Partners: 28 partners spread across 

12 EU countries, USA and Canada. 

Web: http://www.orecca.eu 


The ORECCA (Offshore Renewable Energy Conversion Platform Coordination Action) Project 

was an EC FP7 funded collaborative project in the offshore renewable energy sector. The project’s 

principal aim was to overcome the fragmentation of know how available in Europe and its transfer 

amongst research organisations, industry stakeholders and policy makers stimulating these communities 

to take the necessary steps to foster the development of the offshore renewable energy 

sector in an environmentally sustainable way. 

The project brought together a combination of world class experts from a wide variety of multinational 

companies, research institutions, consultancies, utilities and project developers. The project’s 

focus was pan-European and pan-technology, with a specific focus on the opportunities that exist 

across Europe when the three offshore renewable energy sectors within the project’s scope are considered 

together. Within the ORECCA Project, the scope of the offshore renewable energy sector 

(”offshore renewables”) was confined to offshore wind, wave energy and tidal stream energy. 

These energy sectors have been identified as those that are currently expected to make significant 

contributions to the energy system in the medium to long term. As a result, other sectors, such 

as tidal barrage and ocean thermal energy conversion (OTEC) were not covered in the scope of 

the project. 


HMRC led the resource work package which produced a publically available webGIS tool combining 

wind and ocean energy resource across Europe together with some site selection parameters 

such as ports and water depths; available at: http://map.rseweb.it:8082/orecca/map.phtml 

A site selection methodology was subsequently developed to assess viable combined renewable 

energy sites in Europe; results are available in the deliverable (report on the website): “Site Selection 

Analysis for Offshore Combined Resource Projects in Europe” and will be presented at the 

ICOE 2012 conference in Dublin this year. 


5


52 


CHARLES PARSONS ENERGY RESEARCH 




Researchers: Dr. Dara O’Sullivan, Dr. Gordon Dalton, Dr. Wanan Sheng, Dr. Anne 

Marie O’Hagan, Brendan Cahill (PhD Student), Brian Flannery (PhD Student), Anne 

Blavette (PhD Student) 



Funding Body: SFI 

Funding: €3.5million 

Web: http://www.sfi.ie/investments-achievements/ 

investments/charles-parsons-energy-research-awards/ 

The Charles Parsons Energy Research Awards were established in 2007 by the Minister for Communications, 

Marine, and Natural Resources. Seven research centres/groups were successful in 

their bid for these prestigious awards following evaluation by international experts. The awards 

allows for the employment of senior research staff, with funding available for a period of 7 years, 

providing for a solid and sustainable stream of research. 

This award is focused on ocean energy research and extremely significant in that it allows the 

building of a sustained critical mass of research staff in the HMRC centre. The aims and outputs 

of the project are summarised as follows: 

– Support for indigenous wave device developers—Ocean Energy Ltd., ESBI. 

– Test Rig - 20kW, quarter-scale electrical system for control and power testing. 

– Support for European projects—Waveplam, Cores, Marina, Marinet, Sofia and GeoWAVE. 

– Public awareness and promotion activities—school talks on wave energy. 

The research and those conducting the research are as follows: 

SENIOR RESEARCHERS 

– Device Development and Hydrodynamics 

– Electrical Issues for Devices and Farms 

– Environmental Issues 

– Economic Issues related to Ocean Energy Development 

PhDs 

– Device Modelling in the Time Domain 

– Device Array Modelling 

– Electrical Generators/Power Conditioning 


Navitas – http://www.ucc.ie/en/hmrc/projects/ Seagrid – http://www.ucc.ie/en/hmrc/projects/ 

Sheng, W., Lewis, T. “Assessment of wave energy extraction from seas: numerical validation”, Journal of 

Energy Resources Technology (in press). 

Consultation on the Strategic Environmental Assessment for Ocean Renewable Energy in Ireland. 

Hosting of Public Stakeholder Engagement at the Belmullet Test Site.

SEAGRID: A NEW DYNAMIC MODELLING TOOL FOR 

POWER SYSTEM ANALYSIS OF OCEAN ENERGY 

DEVICES 



Contact PI: Dr. Dara O’ Sullivan (d.osullivan@ucc.ie) 

Researchers: Dr. Dara O’ Sullivan, Dr. Sara Armstrong, Darren Mollaghan, Anne 

Blavette (PhD Student). 



Funding Body: Enterprise Ireland Commercialisation Fund 

Funding: €317,128 

Collaborating Partners: RE Vision, USA; Powertech Labs, Canada; Tecnalia, Spain 


As the ocean energy industry approaches commercial readiness, there will be a greater focus on 

integration of ocean energy devices (OEDs) into the electrical power system network. Device developers 

will be required to provide dynamic models of their device for grid connection, and ensure 

their device operates within the limits laid out in the grid code. Project developers will need to 

assess the impact of different wavefarm configurations, ratings for the electrical equipment, power 

losses, and performance during a fault. Grid operators will require dynamic models to investigate 

the impact an OED will have on the grid and also for future grid planning studies. 

The SEAGRID dynamic modelling tool address each of these issues using its generic modelling 

approach. The SEAGRID model is capable of producing a scalable time domain power system 

dynamic model using empirical test data and component specifications, bypassing the need for a 

full hydrodynamic study of the device. 

The current SEAGRID model has undergone an initial proof-of-concept phase. Current and future 

research focus is on the further refinement of the SEAGRID model, making it more robust to allow 

for more device types and configurations. The next phase of the project will have a particular 

emphasis on modelling device aggregation, and also on model validation which will be a crucial 

task in SEAGRID’s development progression. 


D. Mollaghan, D. O. Sullivan, A. Blavette et al, “Generic Dynamic 

Modelling for Grid Integration of Ocean Energy Devices,” 

in 3rd International Conference on Ocean Energy, 2010. 

D. O’ Sullivan, D. Mollaghan, A. Blavette and R. Alcorn (2010). 

“Dynamic characteristics of wave and tidal energy converters & 

a recommended structure for development of a generic model 

for grid connection”, a report prepared by HMRC-UCC for the 

OES-IA Annex III. [Online], Available: www.iea-oceans.org. 

S. Armstrong, D. Mollaghan, Anne Blavette, Dara O’Sullivan 

“An Initialisation Methodology for Ocean Energy Converter 

Dynamic Models in Power System Simulation Tools”; 47th International 

Universities’ Power Engineering Conference, London, 

UK, September 2012. 


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54 


SOWFIA – STREAMLINING OF OCEAN WAVE FARMS 

IMPACT ASSESSMENT 



Contact PI: Dr. Anne Marie O’Hagan (a.ohagan@ucc.ie) and 

Brian Holmes (b.holmes@ucc.ie) 

Researchers: Dr. Anne Marie O’Hagan, Brian Holmes, John O’Callaghan 



Funding Body: Intelligent Energy Europe 

Funding: €1.923m 

Collaborating Partners: University of Plymouth, University 

of Exeter, Wave Energy Centre (Portugal), Inabensa (Spain), 

Ente Vasco de la Energia (Spain), European Ocean Energy 

Association, Ecole Centrale de Nantes, Uppsala University 

(Sweden), Hidromod (Portugal). 

Web: http://www.sowfia.eu 

SOWFIA is a three year Intelligent Energy Europe (IEE) funded project which brings together 

ten project partners from across Europe who share an interest in planning for wave farm developments. 

Wave energy is an innovative and developing technology which aims to contribute to 

meeting EU renewable energy targets. As part of the consenting process for wave energy sites, 

developers must comply with Environmental Impact Assessment (EIA) legislation. Consequently 

they must supply large amounts of environmental information so that permitting agents can make 

informed decisions on whether the proposed development will have an environmental impact. The 

EIA legislation was not designed with the wave energy industry in mind and associated national 

requirements can vary across Europe. As a nascent industry environmental effects of wave energy 

projects are largely unknown at this time. Similarly, the socio-economic impacts of wave energy 

developments are scarcely addressed in existing consenting processes and are also unknown. 

The aim of SOWFIA is to investigate the current situation and then provide recommendations 

for the streamlining of approval processes and impact assessment requirements for wave energy 

developments in Europe. This should ensure the protection of marine ecosystems while simultaneously 

encouraging the development of renewable energy. Through regional coordination via 

the SOWFIA project collaboration, the exchange, sharing and transfer of impact assessment and 

policy experience and associated knowledge and good practices will be enabled. There is no better 

way to improve the understanding for the future commercial phase than to learn from existing 

smaller-scale developments. 


For journal and conference papers see: http://www.sowfia.eu/index.php?id=23 

For project deliverables see: http://www.sowfia.eu/index.php?id=22

WAVETRAIN2 




Researchers: Prof. Tony Lewis, Dr. Gareth Thomas, Julien Cretel (PhD student) 




Framework People Programme 

Funding: €3,580,000 

Collaborating Partners: 13 partner institutions and 

17 associated partners spread across 7 EU countries. 

Web: http://www.wavetrain2.eu 


The WaveTrain2 project was a multinational Initial Training Network which aimed to face the wide 

range of challenges that industrial-scale wave energy implementation faces, focusing on technical 

issues, from hydrodynamic and Power Take-Off design, to instrumentation issues and energy 

storage and cost reduction shown to be critical for successful deployment. Non-technical barriers, 

typically less tangible difficulties related to legal issues (licensing, conflicts of use, EIA procedures, 

grid connection and regional differences) and the non-sufficient representation of socio-economic 

benefits of the sector, were also dealt with, as they are seen as a major obstacle for fast implementation 

on a European scale. As there was a shortage of trained engineers and researchers in the wave 

energy field, especially those with industrial experience, another aim of the project was to create 

the next generation of wave energy experts. 

The Wavetrain2 Initial Training Network involved a very significant number of researchers and 

institutions. As these early stage researchers had none or very limited knowledge on wave energy 

a large effort was made to quickly introduce them to the many complex issues that these technologies 

face. This was attained through the organization of short courses and stimulating the fellows 

to attend a number of other scientific events and conferences in this area. 

This project linked together 13 academic institutes with 17 commercial entities. In each instance 

an early stage researcher (e.g. a PhD) worked or studied in an academic institute on a project 

linked to a company. 

KEY OUTPUTS 

The Wavetrain2 short courses, lectured by a large share of the most important 

senior wave energy researchers in the world, were very successful and 

have become very recognized by the wave energy scientific community. 

Seven short courses were organized throughout the project. 

During the project, an impressive number of 22 early stage researchers 

were contracted by the 13 partner institutions, totalling 606.5 researcher 

months. This corresponds to more than 50 researcher-years of technological 

development with a very impressive impact in this emerging sector. 


55

56 


4.5 GEOSCIENCES AND 

COASTAL PROCESSES

This thematic area encompasses expertise available in the School of 

Biological, Earth & Environmental Sciences, the Coastal and Marine 

Research Centre and Geography and Archaeology: School of 

the Human Environment. Expertise covers bedrock mapping and 

stratigraphy, seabed mapping, marine geology, petroleum geology, 

mineral resources, economic geology, sedimentology, coastal processes, 

sea-level studies, Quaternary geology, igneous and metamorphic 

geology, structural geology and geohazards, micro- and macro 

palaeontology, environmental geology, geotechnics, geophysics. 

Researchers are involved in a diversity of research programmes 

involving laboratory and field based study, on land, underground 

and offshore. They comprise renowned experts with peer-review 

publications in leading journals, such as Science, and books including 

some landmark papers. They also have strong collaborative links 

throughout the world, a track record in grant capture and close ties 

with industry. They have facilities with technical support for rock 

preparation (cutting, thin-section and powders), sediment analysis, 

palynology and microfossil sample preparation and extensive field 

equipment e.g. boats, and coring and levelling equipment as well as 

access to national marine research vessels. 


Dr Andy Wheeler (Lead PI) 

Professor Robert Devoy 

Professor John Gamble 

Professor Ken Higgs 

Professor Brian Williams 

Dr Alistair Allen 

Dr Bettie Higgs 

Dr Ed Jarvis 

Dr Max Kozachenko 

Dr Pat Meere 

Dr John Reavy 

Mr Gerry Sutton 


Geosciences and Coastal Processes 

57


5 


CELTIC SEA SEDIMENTARY PROCESSES, 

QUATERNARY STRATIGRAPHY AND OFFSHORE 

RENEWABLE ENERGY DEVELOPMENT (CeSQuORE) 


School of Biological, Earth & Environmental Sciences 

Contact PI: Andy Wheeler (a.wheeler@ucc.ie) 

Researchers: Marian McGrath 

Start Year: January 2012 

End Year: December 2012 

Funding Body: Geological Survey of Ireland 

Funding: €30k 

The CeSQuORE project aims to develop an understanding the geological development of Quaternary 

offshore sedimentary sequences up to the present-day seabed conditions. This insight reveals 

details of sedimentary sequences development and responses to environmental change culminating 

ion the present hydrodynamic regime. By links the present to the past, we hope to gain a better 

understanding on the past environmental conditions from the retreat of the Irish Ice Stream and 

through the present marine transgression. The project reconstructs the late Quaternary history of 

the northern Celtic Sea through the interpretation of seismic and core data. In addition, an optimisation 

of INFOMAR data outputs within an image analysis GIS-based framework to aid better 

interpretation seabed data thereby quantify recent sedimentary processes in the northern Celtic 

Sea. These outputs are to be integrated into a hydrodynamic model for the area. In the first six 

months of this project we have collected offshore seismic data, multibeam data, vibro-cores and 

grab samples with data interpretation ongoing.


SEDIMENTARY PROCESSES & QUATERNARY 

STRATIGRAPHY OF THE CELTIC SEA, (OFFSHORE 

SOUTH COAST) IRELAND AND THE IRISH SEA 

(OFFSHORE NORTH COAST) IRELAND: IMPLICATIONS 

FOR OFFSHORE RENEWABLE ENERGY 

DEVELOPMENT 




Researchers: Marian McGrath, Alistair Ruffell 

Start Year: October 2011 

End Year: October 2012 

Funding Body: ESB-North South Universities Grant 


Collaborating Partners: Queen’s University of Belfast 

This project aims to quantify recent sedimentary processes and to integrate these into a hydrodynamical 

model for offshore Kilkeel and offshore Dungarvan/Rosslare to better understand the 

engineering significance of geological variability and apply that in the context of windfarm site 

suitability. A GIS based backscatter facies analysis of multibeam data from two areas of interest: 

south coast off Hook Head and northern Irish Sea off Kilkeel was completed. This involved 

defining seabed sediment facies based on visual backscatter density variations and using Quester 

Tangent Classification (QTC) facies interpretation. A rigorous appraisal of the two independent 

interpretations is to be developed to produce a robust seabed facies classification map. 

Additional sparker seismic data, vibrocores as well as multibeam data have collected in the study 

area. Multibeam includes repeat surveys of existing blocks to assess seabed mobility in areas for 

potential offshore renewable wind energy development. Vibrocore samples have been analysed for 

geotechnical properties as well as particle size XRD. This data will be integrated with seismic and 

multibeam interpretations to build up a model of seafloor development to the present data within 

a geotechnical framework. 


5


60 


HOTSPOT ECOSYSTEM RESEARCH AND MAN’S 

IMPACT ON EUROPEAN SEAS (HERMIONE) 




Researchers: Boris Dorschel 





Collaborating Partners: 38 partners including National 

University of Ireland, Galway & GeoZentrum Nordbayern 

Web: www.eu-hermione.net/ 

Cold-water coral mounds of Lophelia pertusa are widespread across the Scandinavian shelf, which 

was completely ice-covered during the Last Glacial Maximum between 22 to 18 ka BP. Rapid 

deglacial meltdown of the Fennoscandian inland ice and the retreat of its ice-streams freed most 

of the shelf of ice by ˜15 ka BP. However, cold-water coral growth commenced only after the 

Pleistocene-Holocene transition at 11.65 ka BP, when modern-like climatic patterns and oceanographic 

conditions were established. A tight climatic coupling has been constrained with U-series 

ages. Coupled 14 C ages provide local reservoir ages from various gravity cores in a fjord-setting in 

Stjernsund at 70°N and on the open shelf in Trænadjupet at 66°N. Reinvestigation of earlier 14 C 

coral chronologies suggests that coral ecosystems widely established themselves across the entire 

3000 km long Scandinavian shelf prior to ˜10 ka BP. The earliest occurrence of Madrepora oculata 

at ˜2.4 ka BP suggests a late Holocene colonization of the Norwegian shelf, which is linked to a 

prominent mound growth hiatus in Trænadjupet (64°N). Mound growth rates near the northern 

biogeographic boundary of L. pertusa with up to ˜614 cm ka -1 during certain growth periods are 

much higher than the previously reported fastest rates of ˜220 cm ka -1 from the Irish margin. Contemporaneous 

rapid fjordbasin sedimentation is slower with ˜63 cm ka -1 . Matrix 14 C ages overlap 

with coral 14 C ages from the same horizon. This indicates rapid framework construction and efficient 

trapping of background sediment. Hiatuses are frequent in on-mound sediments and only 

short periods of coral growth are recorded. Coupled Δ 14 C and εNd values indicate a persistent 

Holocene inflow of the North Atlantic Current in Stjernsund, but also deglacial meltwater mixing 

during the early Holocene prior to ˜9.5 ka BP. Reservoir ages are overall close to the surface marine 

reservoir age, but ΔR is highly localized (Lopez Correa et al., 2012). 


Lopez Correa, M., Montagna, P., Joseph, N., Ruggesberg, A., Fietzke, J., Flogel, S., Dorschel, B., Goldstein, S.L., 

Wheeler, A., Freiwald, A. (2012). Preboreal onset of cold-water coral growth beyond the Arctic Circle revealed by 

coupled radiocarbon and U-series dating and neodymium isotopes. Quaternary Science Reviews, 34, 24-43.

APPRAISAL OF IRISH SEA SEABED IMAGING FOR 

TIDAL ENERGY GENERATION (ISSITEG) 




Researchers: Boris Dorschel 

Start Year: January 2012 

End Year: December 2012 

Funding Body: Geological Survey of Ireland 



The most reliable and predictable renewable energy source is tidal energy. This predictability makes 

tidal energy an ideal source to supply the base load for a secure renewable energy mix. The technology 

of tidal energy generation is however still at its infancy with only a few test sites worldwide including 

Strangford Lough. The Irish government has included tidal energy in the Strategic Environmental 

Assessment (SEA) of the Offshore Renewable Energy Development Plan (OREDP). 

In the ORDEP the tidal energy potential was only assessed from a coarse 2-dimensional tidal model 

with a 500 m cell resolution. The existing 2D model only indicates areas of enhanced tidal energy on 

a country-wide base. It is insufficient to accurately assess local tidal resources of potential sites for 

offshore energy extraction thus underestimating Ireland’s tidal energy potential. Furthermore, it does 

not consider seabed topography, an important parameter for the distribution of tidal energy, and 

only incorporates 2 directly measured tidal current data sets for the entire Irish foreshore area. 

Based on the results from the Codling Deep test site, ISSITEG will developed a methodology to 

identify and characterise sites of high tidal energy potential based on seabed topography, backscatter 

data, sedimentary bedforms and particle size (a tidal energy potential fingerprint). In the 

second phase of ISSITEG, this fingerprint will be used to assess the multibeam covered study area 

for its tidal energy potential. 


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62 


IRISH SEA MARINE ASSESSMENT (ISMA) 




Researchers: Mark Coughlan, Boris Dorschel 



Funding Body: Gaelectric Developments Ltd 


The Irish Sea Marine Assessment (ISMA) is a collaborative research survey undertaken by University 

College Cork, the INFOMAR programme (Geological Survey of Ireland & Marine Institute), 

and Gaelectric Developments Ltd. Its purpose is to produce integrated seabed and sub-seabed 

mapping products to assist in a fundamental understanding of the seabed and how it changes 

through time, thereby deriving information pertinent to the development of offshore renewable 

energy resources. 

Four study areas where surveyed. The Codling Deep is a long north-south deep (or channel) in 

which tidal currents flow strong. The seabed it typified by mobile sands and gravels, and areas 

covered by cobbles (stoney ground) rich in seabed life. The sub-seabed geology is complicated 

with localised drift bodies and numerous erosional surfaces. The next three areas are relatively flat 

and experience decreasing current intensity resulting in a decrease in seabed sediment-type particle 

size from sand (Lambay area) to fine sands (Rockabill area) to muds (Northern Mudbelt). All 

three areas show sub-horizontal layers of deposits below the seafloor consisting of sands to muds 

underlain by glacial diamict tills (muds with bolders) and rock. The Northern Mudbelt sub-seabed 

shows shallow accumulation of (biogenic) gas (although not enough to form a geohazard). 

In total 352.65 km2 (35,265 hectares) of seabed 

was mapped, 534 km of sparker seimic 

lines were shot imaging into the sub-seabed by 

50 m, 2179 km of pinger seismic lines (down 

to 30 m penetration) were also recorded. 269 

sediment samples were taken, 171 biological 

samples were taken with an additional 7 faunal 

samples frozen for DNA studies. 20 cores 

where sunk into the seabed up to a depth of 3 

m from as well as 5 Reineck box-cores which 

preserve the upper 30 cm for palaeoenevironmental 

and geotechnical studies. 975 good 

quality digital still photographs of the seabed 

were taken in 15 areas and a 1 month long 

measurements of variation in current speeds 

throughout the water column was also taken 

for one key location.

GRIFFITH: GEOMATICS FOR GEOSCIENCE 


Contact PI: Gerry Sutton (g.sutton@ucc.ie) 

Researchers: Declan Dunne, Ying Wu, Trung Pham 



Funding Body: NDP 

Funding: €850 000 

Web: http://griffith.ucc.ie/ 


The Griffith Geomatics for Geoscience initiative involves a high level of collaboration between the 

CMRC and the GSI. The objectives of the project are: 

1. To facilitate open access to GSI data via web enabled services 

2. To achieve innovations in geoscience data management and delivery 

3. To build experience within and collaboration between the GSI and CMRC 

4. To engage the interest of the Irish geoscience community by providing examples of the benefits 

of data sharing. 

Three Postdoctoral researchers are working on the Geomatics for GeoScience project in CMRC, 

and are focused on developing: 

1. An integrated database for geological data 

2. An interoperability platform enabling web-enabled delivery of metadata and data 

3. Web-enabled 4D visualisation of geological datasets. 

The Griffith Geomatics for GeoScience project has been funded under the Griffith Geoscience 

Research Awards scheme. The funding for the award is part of the National Geoscience Programme 

2007 – 2013 coinciding with the timeframe of the NDP (National Development Plan). In total 8 

GeoScience related projects are active under the Griffith programme. The award is administered 

by the Geological Survey of Ireland. 


Best practice recommendations for: 

• Geological data models, geological data formats, and metadata profiles 

• Interoperability of geographic information and services 

• Conforming to ISO, OGC and INSPIRE standards 

• Ontologies, controlled vocabularies, and associated semantic resource tooling 

• Web-delivery of geological data and metadata 

• Web-enabled visualisation of geological data 

Development of: 

• Integrated database system 

• Data loading tools for integrated database system 

- ETL (Extract, Transform and Load) using Natural 

Language Processing for schema matching 

• Semantic interoperability framework using 

ontologies and controlled vocabularies 

• Geological data and metadata web delivery system 

• Web-enabled visualisation tools for geological data 

• Demonstrator geoportal 

Multibeam Bathymetry 


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64 


4.6 BIODIVERSITY AND 

RESOURCE MANAGEMENT

There is an urgent need, and legal obligation, to ensure that our valuable 

but limited natural resources are managed sustainably. Resource 

depletion, loss of biodiversity, climate change and the control of invasive 

species are just some of the factors that make environmental 

management a major challenge, and one that can only be met with 

the aid of targeted and applied research. Current research in this area 

includes a range of general topics in Environmental Science, Ecology 

and Evolution, and spans all major taxa from algae, plants and shellfish, 

to invertebrates, birds and mammals. Research encompasses all major 

habitats, including estuarine, coastal and oceanic marine environment. 

There is expertise in a range of modern analytical, molecular and experimental 

techniques. Strategic partnerships have been developed 

with international centres of excellence in biodiversity and resource 

management, and with government and industry partners. 


Professor John O’Halloran (Lead PI) 

Professor Pete Jones 


Professor Tom Cross 

Professor Paul Giller 

Dr Marcel Jansen 

Dr Paddy Sleeman 

Dr Pádraig Whelan 

Dr John Quinn 

Dr Debbie Chapman 

Dr Sarah Culloty 

Dr Emer Rogan 

Dr Rob McAllen 

Dr Simon Harrison 

Dr Ruth Ramsay O’Riordan 

Professor John Gamble 

Dr Andy Wheeler 

Dr Barbara Doyle 

Dr Tom Kelly 

Mr Ger Morgan 

Dr Michelle Cronin 

Dr Tom Doyle 


Mr Gerry Sutton 

Professor John Benzie 

Biodiversity and Resource Management 

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BEAUFORT - ECOSYSTEMS APPROACH TO 

FISHERIES MANAGEMENT 

Research Centre/Department/School: CMRC and AFDC 



Researchers: Dr Michelle Cronin, 

Mike Fitzpatrick, Dr Mark Jessopp, 

Martha Gosch, Cian Luck, Dr Susie Brown, 

Dr Emer Rogan, Gemma Hernandez-Milian 

Contact PI: Prof Gavin Burnell (g.burnell@ucc.ie) 

Jeremy Gault (j.gault@ucc.ie) 

Website: http://www.beaufort-eafm.eu/ 

Funded under the Irish Beaufort Marine Research Awards, the EAFM is a 7 year €3.9m project involving 

a consortium comprising research groups from University College Cork, Queens University 

Belfast, and the Marine Institute. The EAFM is a move away from traditional single stock fisheries 

management and includes links between fish species and wider fisheries-ecosystem interactions 

e.g. if sand-eel stocks are depleted what impacts does this have on both commercial species like 

cod and other animals such as dolphins and seabirds. Critically the EAFM also recognises that a 

management system which ignores social aspects of fisheries is bound to fail and in UCC the project 

is jointly delivered by the CMRC and BEES (AFDC). 

CMRC: The Centre is involved in two core elements of the EAFM project, marine governance and 

interactions between top predators and Irish fisheries. The research builds on previous and ongoing 

research at CMRC, addressing fundamental aspects of the ecology of pinnipeds and seabirds, 

such as estimating population sizes, habitat use and foraging ecology of key marine mammal and 

seabird species in Irish waters.. This is complemented by governance research which is focussed 

on key issues surrounding the legal and policy frameworks, effective stakeholder mapping and 

engagement and capacity building for collaborative management approaches. 

BEES (AFDC): The school is conducting Ecological Risk Assessments for the Effects of Fishing 

(ERAEF) under the EAFM project. These assessments identify the activities within fisheries with the 

potential to impact aspects of the ecosystem, including target and non-target species, habitats and 

communities. In addition to examining the impact of fishing activities on the ecosystem as a whole, 

the school is looking in detail at the interactions between fisheries and cetacean species. Dietary 

information is being collected from stranded and bycatch animals and is being used to identify dietary 

preferences, estimate annual food consumption, assess their role top predators and the impacts of 

overfishing/stock collapse on these species. The outputs from these elements of the EAFM project 

can be used to contribute to management plans for fisheries and the species they impact. 


Cronin, M. A., Gerritsen, H & D. Reid. 2012. Evidence of low 

spatial overlap between grey seals and a specific fishery off the 

west coast of Ireland. Biological Conservation 150, 136-142. 

Cronin, M. A. 2011. The conservation of seals in Irish waters: 

how research informs management. Marine Policy 35, 748-755 

Cronin, M. A. 2011. The status of the harbour seal (Phoca 

vitulina vitulina) in the Republic of Ireland. NAMMCO Sci 

Publ. 8: 129-142. 

Fitzpatrick, M., Graham, N., Rihan, D. J., and Reid, D. G. 2011. 

The burden of proof in co-management and results-based 

management: the elephant on the deck! – ICES Journal of 

Marine Science, 68: 1656–1662.

BIOTOMM: BIOTELEMETRY OF TOP MARINE 

MAMMALS 




Funding Body: HEA 

Researchers: Michelle Cronin, Mark Jessopp, Diego DelVillar 

Contact PI: Michelle Cronin (michelle.cronin@ucc.ie) 

Website: http://sealtrack.ucc.ie 


BioTomm is a study using a top marine predator as a means to collect data on oceanographic 

parameters in coastal waters in Ireland. It contributes to a larger project on environment and climate 

change under the PRTLI4 funding mechanism. Sophisticated tagging devices are deployed 

on seals in SW Ireland. The tags incorporate temperature sensors and collect oceanographic data 

(e.g. water temperature data) and test the hypothesis that instrumentation deployed on seals can 

distinguish between the characteristics of different water masses. These data are used to validate 

ocean/climate models developed by PRTLI4 project partners at NUIG and contribute to our understanding 

of climate change. 

The tags also collect information on the seals movements and behaviour and provide an understanding 

of habitat use of these key species. Understanding the processes driving the foraging 

ecology and dynamics of these top marine predators is necessary to enable us to use them as indicators 

of environment and climate change. Hotspots of space use by seals in Irish waters are also 

being identified in order to quantify the overlap/competition between top marine predators and 

human resource utilisation/extraction e.g. fisheries, oil and gas exploration. 


Cronin, M., Pomeroy, P & M. Jessopp. 2012. Size and seasonal influences on the foraging range of female grey 

seals in the northeast Atlantic. Marine Biology (in review) 

Del Villar, D., Cronin, M. T. Dabrowkski and D. 

Bartlett. 2012. Seals as collectors of oceanographic 

data in the coastal zone. Estuarine Coastal and 

Shelf Science. (in review) 

Jessopp, M., Hart, T. & Cronin, M. 2012.Fine-scale 

habitat use and midwater foraging in free-ranging 

grey seals. MEPS (in review) 

Cronin, M.A., Zuur, A.F., Ingram, S. & Rogan. E. 

2011. A modeling framework to optimize timing 

of haul-out counts for estimating harbour seal 

abundance, NAMMCO Sci. Publ. 8, 213-226. 

Del Villar, D. (2010) Using Telemetry derived 

temperature data from instrumented seals 

(harbour and grey seals) to examine fine scale 

changes in the water temperature of the Irish 

west coast and to assess the feasibility of using 

seals as oceanographers. MSc thesis, University 

College Cork. 

Tagged grey seal (Halichoerus grypus) – Image copyright CMRC 


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MARINE MAMMAL MONITORING IN 

BROADHAVEN BAY 




Funding Body: Enterprise Energy Ireland Ltd. 

Researchers: Damian Haberlin, Anja Brandecker, Clodagh Collins 


As part of the planning for the development of the CORRIB gas field off western Ireland, Enterprise 

Energy Ireland Ltd (subsequently taken over by Shell) commissioned the Coastal & Marine 

Research Centre to develop an independent marine mammal baseline monitoring programme 

for the Broadhaven Bay area 2001-02. As Broadhaven Bay and its neighbouring coastal waters 

were found to represent an important area for marine mammals and many other species, many 

of which are protected under national and international conservation legislation, Shell committed 

to continue the programme of marine mammal monitoring, at a minimum during the CORRIB 

development’s marine construction activities which had the potential to impact on these protected 

species. In addition to a short period during 2005, the monitoring programme has been running 

continuously since the summer of 2008 building up a highly valuable dataset on abundance and 

population trends of marine mammals. 


Anderwald, P., Brandecker, A., Haberlin, D., Coleman, M., Collins, C., O’Donovan, M., Pinfield, R. and Cronin, 

M. (2012). Marine mammal monitoring in Broadhaven Bay 2011. Progress Report to RSK Environment Limited 

Group. Coastal and Marine Research Centre, University College Cork, Ireland. 

Anderwald, P. , Coleman, M., O’Donovan, M., Pinfield, R., Walshe, L., Haberlin D., Jessopp, M. & M. Cronin 

(2010). Marine Mammal Monitoring in Broadhaven Bay 2010. Report to RSK Environment Limited Group, 

Coastal and Marine Research Centre, University College Cork, Ireland. 

F. Visser, M. Coleman, H. Denniston, M. O’Donovan, L. Walshe, A. Ponzo & M. Cronin (2009) 

Marine mammal monitoring in Broadhaven Bay 2009. Report to RSK Environment Limited Group. Coastal 

and Marine Research Centre, University College Cork, Ireland. 

M. Coleman, E. Philpott, M. O’Donovan, H. Denniston, 

L. Walshe, M. Haberlin, A. Englund (2008) 

Marine Mammal Monitoring in Broadhaven Bay 

SAC, 2008 Report to RSK Environment Limited 

Group. Coastal and Marine Research Centre., University 

College Cork, Ireland. 

A. Englund, M. Coleman, C. Collins (2005) Marine 

mammal monitoring in Broadhaven Bay: June 

– September 2005. Report to RSK/Shell. Coastal 

and Marine Research Centre, University College 

Cork, Ireland. 

O. O’Cadhla, A. Englund, E. Philpott, M. Mackey, S. 

Ingram (2003)Marine mammal monitoring in the 

waters of Broadhaven Bay & northwest Mayo: 2001- 

2002. Report to Enterprise Energy Ireland, Ltd 

SHELL E&P IRELAND Ltd., Dublin 

Bottlenose Dolphin (Tursiops truncates) in 

Broadhaven Bay – Image Copyright CMRC


THE ECOLOGY OF AN AVIAN PREDATOR AT THE TOP 

OF THE MARINE FOOD CHAIN 

Research Centre/Department/School: BEES 

Contact PI: John Quinn (j.quinn@ucc.ie) 

Researchers: Chris Honan (student), Dr. John Quinn (Lecturer in BEES), 

and Dr. Jim Reynolds (Lecturer at the University of Birmingham) 



Funding Body: Private 

Funding: Private 

Collaborating Partners: University of Birmingham 

Great black-backed Gulls are omnivorous, scavengers, kleptoparasites and predators at the top 

of their marine food chain. In common with other marine vertebrates, the ecology of the great 

black-backed gull is likely to be strongly infuenced by human activities. It is widely believed that 

the abundance and distribution of this species has been driven by the availability of discarded fish 

and offal, and by access to human refuse, but this has yet to be tested in this species. This study 

aims to investigate the extent to which changes in fishing industry practices and human refuse 

management have affected great black-backed gull populations in Ireland, and what if any effect 

this has had on their prey species. The PhD student, Chris Honan, has been studying the ecology 

of the great black-backed gull on the island of Ireland’s Eye, off Howth, Co. Dublin since 2009. His 

general approach is to use a range of remote and direct observational techniques for understanding 

how the foraging habits of this top predator are influenced by human activities, how this affects 

individual life histories and in turn what impact this is having on their populations. This single 

population approach is being expanded to examine large scale patterns of variation in population 

characteristics around the Irish coast. The outcome of the research will be an understanding of 

how human activities influence top predator in a marine ecosystem and what effect this is likely to 

have on other species in the food chain. 


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70 


NOISE - MARINE STRATEGY FRAMEWORK DIRECTIVE 




Funding Body: EPA Strive 

Researchers: Mark Jessopp 

Contact PI: Gerry Sutton (gerry.sutton@ucc.ie) 

Website: http://oceansoundmaps.ucc.ie/ 

Noise is considered an acoustic pollutant, and affects many marine animals including marine 

mammals, fish, sea turtles and marine invertebrates. Impacts of acoustic pollution range from 

death due to physical injury and auditory damage to behavioral and habitat use changes. Marine 

mammals rely on sound for navigation, feeding and communication and are known to be particularly 

sensitive to anthropogenic noise. Under the Marine Strategy Framework Directive (MSFD), 

adopted in July 2008, a Good Environmental Status (GES) must be achieved by 2020. This advocates 

the ecosystem approach to the management of human activities that impact on the marine 

environment by integrating the concepts of environmental protection and sustainable use. 

In recent years noise from human activities has increased significantly in the Irish marine environment, 

with sources including shipping, seismic surveys, seabed drilling, sonar, telemetry devices, 

underwater explosions and vibrations. 

Underwater sound modelling will be used to produce a Noise Atlas, representative of seasonal 

and oceanographic situations for Irish waters. This will use data on human activities in the marine 

environment (shipping, seismic surveying, piling, dredging, etc), and be calibrated using in situ 

acoustic measurements. The Noise Atlas will be combined with data on the distribution of marine 

mammals to create ‘Noise Risk Maps’. As well as this, the project aims to design an effective monitoring 

network of noise observation stations for Ireland’s waters. This project will contribute to 

formulating decisions on appropriate use of descriptors for assessing GES in Ireland, and meeting 

our obligations under the MSFD. 


Calibrated Atlas of noise for Irish waters 

Noise Risk maps for marine mammals 

Recommendations for an effective noise monitoring 

network in Irish EEZ waters 

Dissemination workshop (Jan 2013) 

Example risk map towards Harbour Porpoises 

in the British Channel induced by a Pile Driving 

project in summer. 

Above: Tivoli container terminal in Cork Harbour. 

Below: Bottlenose Dolphin (Tursiops truncates)

SEAL SALMON INTERACTIONS STUDY 




Funding Body: Inland Fisheries Ireland 

Researchers: Michelle Cronin, Mark Jessopp, Martha Gosch, Cian Luck 



There is a perceived interaction between seals and salmon returning to rivers in Ireland, but the 

extent of this seal predation on salmon (Salmo salar) is unknown. While salmon remains are rarely 

found in seal diet studies, previous depredation studies indicate that Atlantic salmon are taken 

by both grey (Halichoerus grypus) and harbour (Phoca vitulina vitulina) seals. Inland Fisheries 

Ireland have funded a pilot study to determine the impact of seals on salmonids in two estuaries in 

which seal predation of adult salmon stocks has been problematic in Co. Sligo and Co. Mayo. The 

research will build on existing programmes on-going in Ireland with regard to seal interactions 

with fisheries that CMRC are involved in e.g., Beaufort EAFM project and a BIM study on seal 

depredation in inshore fishery. 

CMRC, in conjunction with partners at UCC BEES and Marine Institute will determine the seasonal 

abundance of local seal species in the river mouth and estuaries of the river Moy and river 

Slaney, study the foraging behavior of seals in the study areas using telemetry and explore the diet 

of seals and seasonal levels of predation by seals on fish stocks, particularly Atlantic salmon in the 

two study areas. Management and mitigation options will also be explored. 

Harbour Seal (Phoca vitulina vitulina) entering water – Image Copyright to CMRC 


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MARINE BIOTOXINS, THE EFFECTS ON BIVALVES 

AND HUMAN CELLS 

Research Centre/Department/School: School of Biological, Earth and Environmental 

Sciences and Department of Pharmacology & Therapeutics 

Contact PIs: Prof. John O’Halloran (j.ohalloran@ucc.ie); 

Dr. Frank van Pelt (f.vanpelt@ucc.ie) 

Researchers: Moira McCarthy, Barbara Doerr, 

Ambrose Furey (CIT), Kevin James (ERI) 



Funding Body: Higher Education Authority (PRTLI4) 

Collaborating Partners: Cork Institute of Technology 

The biological impact of marine biotoxins on both molluscs and humans is only partly understood. 

This project investigates both the morbidity caused by marine biotoxins in economically 

important shellfish as well as the effects of the compounds on endpoints for (sub)chronic toxicity 

in human cell lines to contribute to the risk assessment of these phytotoxins. Acute and sub-acute 

exposure experiments were performed on commercially important bivalve species using the Diarrhetic 

Shellfish Poisoning toxin, okadaic acid. In the blue mussel, pacific oyster and manila clam 

significant pathological effects were observed using histological techniques, particularly in the 

hepatopancreas of the animals. Significant levels of DNA strand breakage was measured in the circulating 

haemolymph and hepatopancreas cells of the blue mussel and pacific oyster. These results 

indicate that this commonly occurring biotoxin has negative effects on these species. The effects of 

okadaic acid and azaspiracid 1,2 and 3 on markers for genotoxicity, cytotoxicity and apoptosis has 

been investigated in three human cell lines representing target tissues for biotoxins (Jurkat T cells, 

CaCo and HepG2). The results show these compounds induce both an increase in DNA breakages 

and apoptosis in a similar dose-related and temporal fashion. These findings indicate that neither 

okadaic acid nor azaspiracid are overtly genotoxic agents. Phytoplankton sampling and adsorptive 

resins were utilised to detect algal species and the toxins they produce at Lough Hyne. In addition 

to toxins previously discovered, the tropical toxins Pinnatoxin G and SPX C were detected using 

LC/MS methods for the first time in Irish waters. 


Skrabakova, Z., O’Halloran, J.,van Pelt, F. N., James, K. J.; (2010) ‘Food contaminant analysis at ultra-high mass 

resolution: application of hybrid linear ion trap - orbitrap mass spectrometry for the determination of the 

polyether toxins, azaspiracids, in shellfish’. Rapid Commun Mass Spectrom, 24: 2966-742966. 

O’Driscoll, D.,Skrabakova, Z.,O’Halloran, J.,van Pelt, F. N.,James, K. J.; (2011) Mussels Increase Xenobiotic 

(Azaspiracid) Toxicity Using a Unique Bioconversion Mechanism. Environ Sci Technol., 45:3102-3108 

James, KJ; Carey, B; O’Halloran, J; Van Pelt, FN; (2010) Shellfish toxicity: Human health implications of marine 

algal toxins. Epidemiology and Infection, 138 (7):927-940

OTHER BIODIVERSITY AND RESOURCE MANAGEMENT 


EcoJel: Managing the Opportunities and Detrimental 

Impacts of Jellyfish in the Irish Sea 




Funding Body: EU Regional Development Fund 

Researchers: Tom Doyle 

Contact PI: Tom Doyle (t.doyle@ucc.ie) 

Website: http://www.jellyfish.ie 

Seal Depredation Study 




Funding Body: Bord Iascaigh Mhara 

Researchers: Michelle Cronin, Mark Jessopp, Martha Gosch 




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4.7 SUSTAINABLE 

BIORESOURCES AND 

GREEN TECHNOLOGIES

Work is focused on developing environmental/green technologies and 

processes to help conserve our natural resources and environment and 

where possible to sustainably exploit these resources for commercial 

purposes. Current research includes work on novel approaches to waste 

management, including the biodegradation of toxic environmental pollutants; 

phytoremediation of chlorinated waste streams; developing 

nano-materials for environmental abatement; and bioconversion of 

waste streams to biodegradable polymers. Research also focuses on 

sensor based technologies to monitor trace atmospheric gases in the 

environment. Genomic/metagenomic based approaches are also being 

employed to exploit the metabolic versatility of terrestrial and marine 

ecosystems; as sources of new antimicrobial bioactive compounds; new 

cytotoxic agents with pharmacological potential and novel biocatalysts 

with industrial applications. Finally work is also focused on the molecular 

epidemiology of different pathogens with a view to developing 

effective methods to combat bacterial infections. 


Professor Alan Dobson (Lead PI) 

Professor Mark Achtman 

Dr Dara Fitzpatrick 

Dr John Hanrahan 

Dr Marcel Jansen 

Professor Peter Jones 

Professor Michael Morris 

Sustainable Bioresources and Green Technologies 

Dr John Morrissey 

Dr Jerry Murphy 

Dr Niall O’Leary 

Professor Fergal O’Gara 

Dr Andy Ruth 

Dr Dean Venables 

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BEAUFORT MARINE BIODISCOVERY AWARD 

Research Centre/Department/School: ERI, Microbiology, Biomerit Research Centre 


End Year: 2015 Funding Body: Marine Institute 

Researchers: Alan Dobson, Fergal O’Gara, Jonathan Kennedy, Marlies Mooij, Burkhardt 

Flemer, Stephen Jackson, Lekha Margassery, John Morrissey, Robert Phelan, 

Teresa Barbosa. 

Contact PIs: Alan Dobson (a.dobson@ucc.ie); Fergal O’Gara (f.ogara@ucc.ie) 

Collaborating Partners: NUIG, QUB 

Web: http://www.biodiscovery.ie 

This project is employing both culture dependent and metagenomicapproaches to study the microbial 

biodiversity of marine sponges. The microbial ecology of these sponges is being studied 

using modern molecular microbial ecology based approaches. Culture dependant approaches arebeingused 

to culture, and subsequently identify and characterise a variety of different bacteria 

and fungi from these sponges. The ability of these isolates to produce bioactive compounds with 

potential antimicrobial, antifungal and anti-biofouling activities is being assessed on an ongoing 

basis. A primary focus is on Actinomycetesas these are known to be a major source of natural 

products, including polyketides and nonribosomal peptides. Twenty candidate microorganisms 

which produce novel bioactivity have been identified to date and their genomes are currently 

being characterised at the molecular level to gain a better understanding of the biochemical pathways 

involved in the production of these compounds. Functional metagenomic based strategies 

are also be employed using novel prokaryotic expression systems, with metagenomic libraries 

being constructed and screened at high-throughput in a number of different microbial expression 

hosts including Gram negative Pseudomonas sp and Gram positive Streptomyces sp. to identify 

bioactive compounds with activity against pathogenic bacteria, fungi and yeast; and which perturb 

signal transduction pathways in these pathogens fromthe different marine associated microbial 

ecosystems. These functional screens are also targeting compounds/molecules which display antibiofilm 

and anti-biofouling activities. 


Selvin J., Kennedy, J., Lejon, D.P.H., Kiran, S. and 

Dobson, A.D.W. (2012). Isolation identification and 

biochemical characterization of a novel halo-tolerant 

lipase from the metagenome of the marine sponge 

Haliclonasimulans. Microbial Cell Factories 11:72. 

Phelan, R.W., O’ Halloran, J.A., Kennedy, J., Morrissey, 

J.P., Dobson, A.D.W., O’Gara, F., and Barbosa, 

T.M. (2012).Diversity and bioactive potential of endospore-forming 

bacteria cultured from the marine 

sponge Haliclonasimulans, isolated from Irish waters 

and their bioactive potential. J ApplMicrobiol. 112(1), 

65-78.Jackson, S.A., Kennedy, J., Morrissey, J.P., O’Gara, 

F. and Dobson, A.D.W.(2012).Pyrosequencing reveals 

diverse and distinct sponge-specific microbial communities 

in sponges from a single geographical location in 

Irish waters. Microbial Ecology64,105-116.


PHARMASEA (INCREASING VALUE AND FLOW IN THE 

MARINE BIODISCOVERY PIPELINE) 


ERI, Department of Microbiology, Biomerit Research Centre 




Researchers: Alan Dobson, Fergal O’Gara, Jonathan Kennedy, 

Marlies Mooij, John Morrissey. 

Contact PIs: Alan Dobson (a.dobson@ucc.ie); Fergal O’Gara (f.ogara@ucc.ie) 

Collaborating Partners: A consortium of 23 European academic and industrial partners. 

The project focuses on obstacles in marine biodiscovery research, development and commercialization 

and brings together a broad interdisciplinary team of academic and industry researchers to 

address and overcome these. The partners aim to demonstrate how to widen the bottlenecks and 

increase the flow of ideas and products derived from the marine microbiome towards a greater 

number of successes in a larger number of application areas. Despite the tremendous potential 

of marine biodiscovery, exploitation, particularly at a commercial scale, has been hampered by 

a number of constraints. These relate to access (physical and legal), genetics of the organisms, 

compound isolation, structure elucidation, early reliable validation of biological activity and best 

mechanisms of flow-through into exploitation. PharmaSea will solve these chronic bottlenecks by 

developing essential actions beyond the state of the art and linking them with best practice and 

appropriate pragmatic approaches. The robust pipeline structure established within PharmaSea 

will process a wide genetic basis including marine microbial strain collections held by partners and 

new strain collections from extreme environments (deep, cold and hot vent habitats) to produce 

new products with desirable characteristics for development by the SME partners in three accessible 

market sectors, health (infection, inflammation, CNS diseases), personal care and nutrition. 


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7 


MaCuMBA (MARINE MICROORGANISMS: 

CULTIVATION METHODS FOR IMPROVING THEIR 

BIOTECHNOLOGICAL APPLICATIONS) 


ERI, Dept of Microbiology and Biomerit Research Centre 




Researchers: Fergal O’Gara, Alan Dobson, Jonathan Kennedy, 


Contact PIs: Fergal O’Gara (f.ogara@ucc.ie); Alan Dobson (a.dobson@ucc.ie) 

Collaborating Partners: A consortium of 20 other European Universities including 

SMEs. 

Web: http://www.nioz.nl/projecten-en.html 

This project aims at developing improved cultivation efficiencies for the isolation of new marine 

microorganisms and involves the development of novel approaches and methodologies, including 

high-throughput procedures; using a widevariety of samples from different marine environments, 

including those with extremeconditions. The project aims to cultivate marine microorganisms 

under conditions that approachtheir natural environment and as such improve the strain isolation 

and cultivation efficiency. The project will also investigate cell-to-cell communication in marine 

microrganismsthereby enhancing isolation, cultivation and expression of silent genes encoding for 

novel bioactive molecules with potential biotechnological applications.

MICRO B3 (BIODIVERSITY, BIOINFORMATICS, 

BIOTECHNOLOGY) 


Research Centre/Department/School: Biomerit Research Centre, ERI, Microbiology, 




Researchers: Fergal O’Gara, Alan Dobson, Jonathan Kennedy, 


Contact PIs: Fergal O’Gara (f.ogara@ucc.ie); Alan Dobson (a.dobson@ucc.ie) 

Collaborating Partners: A consortium of 32 European academic and industrial partners. 

Web: http://www.microb3.eu/ 

The project will develop innovative bioinformatic approaches and a legal framework to make 

large-scale data on marine viral, bacterial, archaeal and protists genomes and metagenomes accessible 

for marine ecosystems biology and to define new targets for biotechnological applications. 

This highly interdisciplinary project involving experts in bioinformatics, computer science, 

biology, ecology, oceanography, bioprospecting and biotechnology. The project will link oceanographic 

and molecular microbial research to integrate global marine data with research on microbial 

biodiversity and functions. The project will also take full advantage of current sequencing 

technologies to efficiently exploit large-scale sequence data in an environmental context. Finally it 

will facilitate the detection of candidate genes to be explored by targeted laboratory experiments 

for biotechnology and for assigning potential functions to unknown genes. 


7

SCHEMATIC REPRESENTATION 

OF ERI RESEARCH PILLARS 

AND THEMATIC AREAS 

SUSTAINABLE ENERGY END USE 

ENERGY POLICY AND 

CLIMATE CHANGE 

SUSTAINABLE ENERGY 

SUPPLY TECHNOLOGIES 

MARINE RENEWABLE ENERGY 

ENVIRONMENTAL HEALTH 

AND PROTECTION 

SUSTAINABLE AGRICULTURE, 

FOOD AND FORESTRY 

ENVIRONMENT PILLAR 

ENERGY PILLAR 

MARINE PILLAR 

ATMOSPHERIC PROCESSES 

AND AIR QUALITY 

GOVERNANCE AND LAW 

SUSTAINABLE BIORESOURCES 

AND GREEN TECHNOLOGIES 

GEOMATICS AND 

REMOTE SENSING 

AQUACULTURE AND FISHERIES 

GEOSCIENCES AND 

COASTAL PROCESSES 

BIODIVERSITY AND 

RESOURCE MANAGEMENT 

PRIMARY THEMATIC AREA 

CROSS-CUTTING THEMATIC AREA

2000 2001 2002 2003 2004 2005 2006 2007 

Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland. 

Phone: +353 (0)21 4901931. Email: eri@ucc.ie Website: http://eri.ucc.ie 

This publication is printed on paper derived from sustainably managed forests

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