A versatile platform for Multidisciplinary MArine Computing APplications

Lead Research Organisation: Scottish Association For Marine Science
Department Name: Scottish Association For Marine Science

Abstract

The Scottish Association for Marine Science (SAMS, http://www.sams.ac.uk/) is Scotland's foremost independent marine research institute. Our aim is monitor, model and predict the marine environment in order to improve its sustainable use. Thus, we deliver cutting edge multidisciplinary research & education in marine processes and climate, marine biotechnology, biodiversity, extreme environments and marine renewable energy. To meet our need for bespoke integration of large interdisciplinary marine environmental datasets, we request high performance processing, storage resources and an improved internet connection. This local repository will facilitate efficient data management and increase our modelling and analysis capability by alleviating the complexity associated with using multiple remote High Performance Computing (HPC) facilities.

Planned Impact

Impact from our science beyond academia is an institutional strength, with uptake of SAMS research outputs & data into policy, legislation and business. Our growing subsidiary company SAMS Research Services Ltd (http://www.samsrsl.co.uk, £2M annual turnover) provides a pathway for our science to reach end-users for economic impact, both in the UK & internationally. Previous NERC grants & capital funding have provided the skills, knowledge and capability to underpin the delivery of work for business and government agencies in the mining (e.g. Papua New Guinea Mineral Resource Authority), energy (e.g. Scottish Power Renewables) and biotechnology sectors (e.g. Mars Group).
The capital will facilitate innovation in biotechnology through increased bioinformatics capacity. In particular, it will further our vision to establish an Algal Genome Centre complementing the Culture Collection of Algae & Protozoa (CCAP, a NERC National Capability). This centre will fill a known gap towards the establishment of algal aquaculture, and the development of algae as a sustainable feedstock for biofuels & high value products such as nutraceuticals and pharmaceuticals1.
The equipment will also complement our MAREMAP activities by enabling us to assemble maps (GIS), satellite and other remote sensing imagery on a single server. It will provide a more efficient platform from which to produce a 'data portal' for the marine renewable energy industry (proposal to be submitted to the NERC/TSB Environmental Data call in September, the design parameters of which are currently being scoped under the NERC Environmental Data Scoping Study). The proposed capital will facilitate advances in developing real time and long term models with integrated biological and geochemical parameters. Such multidisciplinary modelling capability is essential to fully understand the potential impact of marine industry developments such as renewable energy and inform effective marine governance such as the designation of Marine Protected Areas and fisheries.

1 Research needs in ecosystem services to support algal biofuels, bioenergy & commodity chemical production in the UK. 2012, Algal Bioenergy Special Interest Group Publication.

Publications

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Adams T (2015) Connected networks of sea lice populations: dynamics and implications for control in Aquaculture Environment Interactions

 
Description To meet our need for bespoke integration of large interdisciplinary marine environmental datasets, we were awarded funds to purchase high performance processing &
storage resources. This local repository facilitates efficient data management and increases our modelling and analysis capability, by alleviating the complexity associated with
using multiple remote High Performance Computing (HPC) facilities.
Exploitation Route This equipment is the backbone of our high-power computing facility and we expect to be in use for years to come. We are now exploring options to make it available to external users as well.
Sectors Aerospace, Defence and Marine,Digital/Communication/Information Technologies (including Software),Education,Environment

 
Description This award has supported a major upgrade of our high-power computing facility, including safe storage, improved Internet connectivity to support data transfer. Thanks to match-funding, a data manager position has been created, which guarantees the application of strict data policies and standard in all our work. Since the award was made, the equipment has been used to support our institutional research in oceanography, environmental modelling and bioinformatics. Applications are as diverse as SAMS research portfolio but as of March 2019, the cluster is predominantly used for research and commercial activities supporting aquaculture: e.g. sea-lice modelling (project Off-aqua) and harmful algal bloom reporting services for Shellfish farmers & finfish farmers utilising the FVCom\WestCOMs models (Projects: SS-HAB, PRIMROSE, Shelleye, Aquasens). The workstations are mostly used for ecosystem modelling and bioinformatics purposes. Occasionally, the equipment is being made available to external users on request. The numbers of users, publications and other outputs generated thanks to this news hardware has been steadily growing, and the reinforcement of our IT staff with a data manager position has had a strong impact on streamlining the publication of research outputs, as well as data management procedures across the institution. The data manager position that we've created thanks to the award is now sustained thanks to additional funding. In order to respond to the increasing usage and demand for this infrastructure, we are now in the process of upgrading the equipment using external funds: the cluster is being equipped with an upgraded storage system by addition of SSD storage nodes (~20TB, ca. £11K). the cluster is also supplemented by a separate THREDDS\ERDDAP server to provide data distribution services (principally, but not exclusively) for model data (ca. £14K). Finally, one of the workstations is being upgraded through the addition of 24 cores (2.6Ghz), a SSD NAND hard drive, a 6Tb SSD drive with SATA interface, and a 10Gb Ethernet connection (ca. £11k).
Sector Education,Environment
Impact Types Economic

 
Description Meeting with Marine Scotland Aquaculture planning and Fish Health Inspectorate
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Aquaspace: Ecosystem Approach to making Space for Aquaculture
Amount € 2,990,111 (EUR)
Funding ID 633476 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 03/2015 
End 02/2018
 
Description COST Action FA1406 - Piloting lipid-mediated delivery of Cas9/sgRNA complexes in Ectocarpus gametes
Amount € 1,250 (EUR)
Funding ID COST-STSM-FA1406-30857 
Organisation European Cooperation in Science and Technology (COST) 
Department COST Action
Sector Public
Country Belgium
Start 11/2015 
End 02/2016
 
Description European Social Fund
Amount £103,000 (GBP)
Organisation University of the Highlands and Islands 
Sector Academic/University
Country United Kingdom
Start 10/2017 
End 03/2021
 
Description GCRF GlobalSeaweed* - Safeguarding the future of seaweed aquaculture in developing countries
Amount £5,419,059 (GBP)
Funding ID BB/P027806/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 12/2021
 
Description Genomia Fund Pilot project
Amount £60,000 (GBP)
Organisation Genomia fund 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2014 
 
Description Genomia Fund Pilot project
Amount £50,000 (GBP)
Organisation Genomia fund 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2014 
 
Description H2020-MSCA-ITN-2014
Amount € 3,796,000 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2015 
End 12/2018
 
Description IOF pump-priming plus networking call
Amount £414,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2014 
End 12/2017
 
Description International Exchanges 2014 NSFC
Amount £5,200 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2015 
End 03/2017
 
Description MASTS small grant scheme - TRAFALGAR-Transgene-Free Algal Genome Remodeling
Amount £2,240 (GBP)
Funding ID ABS6-PSFRSA- SASG1 
Organisation Marine Alliance for Science and Technology for Scotland 
Sector Academic/University
Country United Kingdom
Start 10/2015 
End 12/2015
 
Description MIDAS: Managing Impacts of Deep-seA reSourc exploitation
Amount € 9,000,000 (EUR)
Funding ID 603418 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2013 
End 12/2016
 
Description PEER funding
Amount £800 (GBP)
Organisation Marine Alliance for Science and Technology for Scotland 
Sector Academic/University
Country United Kingdom
Start 06/2014 
End 07/2014
 
Description Summer studentship
Amount £700 (GBP)
Organisation British Phycological Society 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2016 
End 08/2016
 
Description Windy HABs: Minimising the risk of harm to aquaculture and human health from advective harmful algal blooms (HABs) through early warning
Amount £312,296 (GBP)
Funding ID BB/M025934/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2015
 
Title ERDDAP: Easier access to scientific data 
Description ERDDAP is a data server that gives a simple, consistent way to download subsets of gridded and tabular scientific datasets in common file formats and make graphs and maps. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact This tool will allow SAMS to serve tabular and gridded data in different formats and also with rich metadata. This tool also allows query the data and make plots, making easy to the scientists have a quick look through the content without having to download the entire dataset. SAMS will be much benefited with this tool, making output research accessible in an easier way. 
URL https://erddap.sams.ac.uk
 
Title Oceanographic Data Product Viewer 
Description This application is based on OpenLayers and Javascript. It allows to display different raster and vector layers online. It will obtain layers from a WMS server (Geoserver). 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact This tool is important for scientific purposes because model outputs can be easily shared via this web applications. 
URL http://mapping.sams.ac.uk
 
Title ProkComp: PROKaryotic COMParative Genome Analysis 
Description "ProkComp" is a bioinformatic pipeline being developed by Frederik De Boever, as part of his PhD research. It is designed to discover phylogenetic and functional relationships amongst 100s of prokaryotic genomes. It implements a series of bioinformatic routines that critically require parallel processing by multiprocessor linux systems. The pipeline is based on a customised work-flow using open-source software such as CheckM, CompareM, BUSCO, JSpecies, Prokka, Anvi'o, GraftM, Phylophlan, Pfamscan, RAxML and visualisation in R. This is a research infrastructure that significantly improves our ability to derive biologically meaning from big data sets - in this instance, prokaryotes. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact Analysis of 72 Marinobacter (a cosmopolitan oil-degrading bacterial group) whole genomes has identified that the genotypic similarities (functional attributes) among the organisms are predictable from their evolutionary relatedness. This means that single marker genes such as 16S rRNA can be used to infer a number of key functional attributes of the phylogroups found within the genus. This analysis has identified specific gene enrichment in the different functional groups that can be linked to the biogeographic niche from where they were originally isolated. In particular, it has identified the unique genome adaptations associated with Marinobacter found in polar regions. 
 
Title RNA-seq analysis pipeline 
Description RNA-seq pipeline is a bioinformatic tool developed in Python that allows analysing samples to assemble them into a transcriptome to ultimately use it for differential expression analysis. The pipeline involves the following steps: Samples quality control (FastQC), trimming (Trimmomatic), Contamination analysis (Blast databases and RSEM), assembly (Trinity, samtools and bamToFastq), Assembly Statistics (bowtie2), Gene Expression analysis (RSEM), Differential expression analysis (edgeRa and DESeq2). This tool is documented using Sphinx and under the version control system Git. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? No  
Impact This pipeline has helped us to automate the RNA-seq pipeline for the Rare and Overlooked Microbial Eukaryotes (ROME) project. This analysis leads us to find a new Chytrid species where the corresponding article is in preparation. Also, it will help us to determine the genes involved in the pathogen-host interation between Asterionella and the Chytrid. 
 
Title Drift model for surface objects 
Description Unstructured or structured grid model for surface floating objects with variable buoyancy, including current, wind, and wave effects. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Tide turbine stranding predictions Chile mass mortality work (paper Hausserman) 
 
Title MOULINETTE 
Description A new Bioinformatic pipeline for denovo OTU targetting approach and automatic retrieval of GPS coordinates. Applications for biodiversity studies, biogeography and molecular diagnostic of pathogens using public nucleotide database. 
Type Of Material Data analysis technique 
Year Produced 2016 
Provided To Others? No  
Impact Paper in Prep - Hidden Diversity in the Olpidiopsis genus is a global threat to red algal cultivation - Highlights the worldwide occurence of destructive asian pathogens 
 
Title My Seaweed Looks Weird 
Description Our aim is to accelerate the description of algal diseases worldwide, by screening samples submitted by scientists, seaweed professionals or members of the public. We will use the data to identify and map diseases, as well as describe novel or emerging issues. With time, we will make the results of this work available for free, through Open Access publications and a (yet-to-be-built) online disease atlas. This portal, and the underpinning database will be populated through several geographically-focused grants (GCRF GlobalSEaweed* for developing countries, H2020 GENIALG for European waters). We also welcome any sample submission from seaweed professionals, or members of the public anywhere in the world who wish to support our effort. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact We hope that this portal will substantially accelerate the description and discovery of novel algal diseases. 
URL https://www.globalseaweed.org/?page_id=889
 
Title SHUFFLINETTE 
Description Read-mapper output processing pipeline designed for the identification of next generation sequencing reads involved in specific genomic rearrangments. 
Type Of Material Data analysis technique 
Year Produced 2018 
Provided To Others? No  
Impact No impact yet, as Pipeline just entered Beta testing. 
 
Title SWAN West Coast of Scotland 
Description A setup of the non-stationary SWAN coastal wave model on an unstructured grid for the west coast of Scotland 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Necessary for drift model to allow accurate Stokes drift prediction to be made. It may in future be used by different groups in conjunction with the other west coast models in SAMS to provide full oceanographic conditions 
 
Description Description of the Anisolpidiales as a novel order of oomycetes & discovery of a novel family of cadherins in oomycetes 
Organisation University of Aberdeen
Country United Kingdom 
Sector Academic/University 
PI Contribution We provided the biological material and expertise required to characterise a little-known pathogen of brown algae, Anisolpidium ecotcarpii. Additionally, we provided the necessay data and expertise to describe a novel family of giant cadherins, in oomycetes. This is signifant, because these genes were mostly described in animals, and might play an important role in cell-cell signalling.
Collaborator Contribution Kyle Fletcher, a PhD student registered in the University was hosted in our laboratory to acquire the necessary skills and perform this work.
Impact Gachon CMM, Strittmatter M, Badis Y, Fletcher KI, van West P, Müller DG. Pathogens of brown algae: culture studies of Anisolpidium ectocarpii and A. rosenvingei reveal that the Anisolpidiales are uniflagellated oomycetes. European Journal of Phycology doi: 10.1080/09670262.2016.1252857
Start Year 2015
 
Description In silico investigation of Japanese kelp (Saccharina japonica) defence genes 
Organisation Chinese Academy of Sciences
Department Institute of Oceanology
Country China 
Sector Learned Society 
PI Contribution As a result of a presentation of our GlobalSeaweed activities (Sydney, 2014), a joint proposal was developped with Prof Feng Liu (IOCAS, Qiongdao, China). Funded by the Royal Society Cost share visiting scheme, this enabled Prof Liu to visit SAMS for two months, in May-June 2015. During he stay, we trained him in the functional annotation of defence genes, particularly a family of candidate defence genes of Saccharina japonica.
Collaborator Contribution Prof Feng is very active in seaweed aquaculture, and has been instrumental in introducing us to the cultivation practices employed in his country. A stay in his laboratory facilities by Drs Gachon and Badis was organised in April 2016.
Impact Prof Feng is a co-author on the policy brief that we developed in partnership with the United Nations University, to which he contributed a case study on the Chinese kelp industry.
Start Year 2015
 
Description Marine connectivity of salmon farms 
Organisation Fisheries Development Institute
Country Chile 
Sector Charity/Non Profit 
PI Contribution Working with Pablo Reche Garcia and colleagues to develop new approaches to analysing salmon farm connectivity
Collaborator Contribution Hosted visit to Chile, visited UK, working on paper
Impact Report to MASTS following visit to Chile, writing in progress
Start Year 2017
 
Description Martin Ostrowski - Oomycete parasite diversity in Australian Seawater Metabarcoding 
Organisation Macquarie University
Country Australia 
Sector Academic/University 
PI Contribution Identification and curation of Olpidiopsis/oomycetes metabarcodes
Collaborator Contribution Gave Access to unpublished database of the Australian Marine Dataset
Impact Paper at submission stage "Hidden diversity in the Olpidiopsis genus is a global threat to red algal cultivation and preservation"
Start Year 2017
 
Description Molecular phylogeny and biogeography of oomycete parasites of diatoms 
Organisation French Research Institute for the Exploitation of the Sea
Country French Polynesia 
Sector Academic/University 
PI Contribution Saccharina was used to run computationally demanding phylogenetic analysis and in silico investigations on the worldwide distribution of novel described microeukaryotes parasitising diatoms.
Collaborator Contribution 5/9 molecular markers used to investigate the distribution and phylogeny of the novel organisms came from IFREMER.
Impact A publication is currently submitted in Environmental Microbiology: "Novel widespread oomycetes parasitising diatoms, including the toxic genus Pseudo-nitzschia: genetic, morphological and ecological characterisation" Authors: Andrea Garvetto, Elisabeth Nézan, Yacine Badis, Gwenael Bilien, Paola Arce, Eileen Bresnan, Claire M.M. Gachon, Raffaele Siano. The results have been object of presentations at the Phycotox Meeting (France - 03.2017), International Congress Of Protistology (Prague, 07.2017), International Phycological Congress (Poland 08.2017)
Start Year 2017
 
Description Phaeoexplorer: 
Organisation National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS)
Department Biological Station, Roscoff
Country France 
Sector Academic/University 
PI Contribution Our contribution to this project has been to help phrasing the proposal, and will be to support the genome annotation, once the data are available. Specifically, our expected contribution will be to annotate defence-related genes in algal genomes, and also to explore the genomes of two parasitic brown algae.
Collaborator Contribution The Phaeoxplorer project "Exploring the evolution of biological complexity in the brown algae through the establishment of a multi-scale genomic data resource" aims to generate over 50+ genomes for brown algae. Relevant to GlobalSeaweed, this includes commercially-important seaweeds, such as Saccharina latissima, Laminaria digitata, or Undaria pinnatifida. This major initiaitive has already involved over 15 scientists to support the data generation. Over the coming years, over 20 partners have pledged to provide in-kind support with data analysis.
Impact n/a.
Start Year 2016
 
Description Prof. Arthur Grossman - Biogeography of an unknown eukaryote 
Organisation Carnegie Institution for Science (CIS)
Country United States 
Sector Charity/Non Profit 
PI Contribution Automated screening of public metabarcoding datasets, using our custom scripts and workstation, to identify biogeographical patterns of target organisms.
Collaborator Contribution Provided 18S molecular markers of target organisms as input for our custom scripts.
Impact No output yet
Start Year 2017
 
Description Sigrid Neuhauser: Comparative genomics of brown algal pathogens 
Organisation University of Innsbruck
Country Austria 
Sector Academic/University 
PI Contribution We provide the biological and genomic expertise on pathogens of brown algae, including the commercially-valuable kelps and the genome model Ectocarpus siliculosus, mostly oomycetes.
Collaborator Contribution Dr Neuhauser provides similar expertise on another group of pathogens, the phytomixids, which infect plants, brown algae and oomycetes.
Impact Dr Neuhauser had been awarded a grant by the Austrian FWF (ref. Y-801, 01.01.2016 to 30.06.2019) to resource this collaboration.
Start Year 2016
 
Description Ocean Science Meeting: A Drift Model to Predict Where Marine Mammals Struck by Tidal Stream Turbines Might Strand 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference poster: "A Drift Model to Predict Where Marine Mammals Struck by Tidal Stream Turbines Might Strand" Ocean Science Meeting, New Orleans, USA, Feb 2016.
Year(s) Of Engagement Activity 2016
 
Description 4th Norway-Scotland Waves Symposium: Lee waves and hydraulic effects of abyssal bumps 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference talk: "Lee waves and hydraulic effects of abyssal bumps" Dale, Aleynik, Inall. 4th Norway-Scotland Waves Symposium, Edinburgh, UK, Oct 2015.
Year(s) Of Engagement Activity 2015
 
Description A talk or presentation - A talk or presentation - International Seaweed Symposium, The Hague - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of updated results on the diversity of Olpidiopsis pathogens, with a focus on our new Pipeline for exploration of Biogeography and Biodiversity.
Year(s) Of Engagement Activity 2017
URL http://seagriculture.eu/seagriculture-2017-speakers/
 
Description A talk or presentation - A talk or presentation - Wando, Korea - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of updated results on the diversity of Olpidiopsis pathogens, with a focus on our new Pipeline for exploration of Biogeography and Biodiversity.
Year(s) Of Engagement Activity 2017
URL https://www.google.fr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0ahUKEwj1yev-o-LZAhWJCMAKHSLtDtkQ...
 
Description A talk or presentation - JGI annual User meeting - Walnut Creek - Poster presentation - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation to expert Next-generation sequencing.
Year(s) Of Engagement Activity 2017
 
Description Annual Conference GdR PHYCOTOX | GIS Cyano 2017 - Poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation of a new taxon of microeukaryotic parasites infecting the toxic bloom forming diatom Pseudo-nitzschia, their biogeography and ecological relevance.
Year(s) Of Engagement Activity 2017
URL https://phycotox2017.sciencesconf.org/resource/page/id/2
 
Description Aquaspace stakeholder workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Talk to industry stakeholders highlighting current state of biophysical models for aquaculture applications. Outlined possibilities for future developments and arranged further meetings/projects to apply and develop models further (industry/local council).
Year(s) Of Engagement Activity 2018
 
Description Biophysical connectivity of sea lice in Scottish waters - talk at MASTS annual science meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Talk at MASTS annual science meeting, initiating closer relationships with a number of key UK organisations involved in regulation of Salmon industry
Year(s) Of Engagement Activity 2017
 
Description C3 Colloquium: Algae-Bacteria Interactions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk to the 2016 C3 Colloquium: Algae-Bacteria Interactions, University Technology Sydney, Dec. 2016. Title: Bacteria, Dinoflagellates, DMSP and a Sprinkling of Sugar.
Year(s) Of Engagement Activity 2016
URL http://www.uts.edu.au/research-and-teaching/our-research/climate-change-cluster/climate-change-clust...
 
Description EMBO | EMBL Symposium "A New Age of Discovery for Aquatic Microeukaryotes - Poster Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of PhD project and exchange of information and routinely used techniques in the field of Eukaryotic Environmental Microbiology.
Year(s) Of Engagement Activity 2016
URL https://www.embo-embl-symposia.org/symposia/2016/EES16-01/index.html?_ga=1.202903889.1950600215.1449...
 
Description Fungal Genetic Conference - Asilomar Conference Grounds - Poster presentation - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presention on our work on Olpidiopsis pathogens and our New bioinformatic pipeline
Year(s) Of Engagement Activity 2017
 
Description GlobalSeaweed media coverage by BBC Alba 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact interview presenting seaweed cultivation, the need to research problems caused by emerging diseases

Contributes increased understanding of seaweed cultivation in the public at regional level.
Year(s) Of Engagement Activity 2015
URL http://www.bbc.co.uk/iplayer/episode/b0605zwl/an-la-01072015
 
Description GlobalSeaweed media coverage by BBC Reporting Scotland 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact seaweed cultivation featured on Scotland news

Increased awareness amongst the general public
Year(s) Of Engagement Activity 2015
URL http://www.bbc.co.uk/iplayer/episode/b060553k/reporting-scotland-01072015
 
Description Invited seminar @ Institute of Oceanology Chinese Academy of Sciences (Qingdao, China) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact GlobalSeaweed activities were introduced, including our research on algal diseases as well as the porfolio of networking, science-into-policy and training activities that we undertake.
Year(s) Of Engagement Activity 2009,2016
 
Description Invited seminar @ Kongju National University (Korea) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact GlobalSeaweed activities were introduced, including our research on algal diseases as well as the porfolio of networking, science-into-policy and training activities that we undertake.
Year(s) Of Engagement Activity 2016
 
Description Invited seminar @ Kongju National University (Korea) - Pythium porphyrae, a plant pathogen seeing red 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Invited seminar for the Biolopgy Department of the Un niversity of Kongju, Korea, Hosted by Prof Gwang Hoon Kim
Year(s) Of Engagement Activity 2016
 
Description Invited seminar @ Ocean University of China (China) - Pythium porphyrae, a plant pathogen seeing red 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited seminar to present our work on Pythium porphyra, Hosted by Dr Liu Feng
Year(s) Of Engagement Activity 2016
 
Description Invited seminar @ Ocean University of China, Qingdao (China) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact GlobalSeaweed activities were introduced, including our research on algal diseases as well as the porfolio of networking, science-into-policy and training activities that we undertake.
Year(s) Of Engagement Activity 2016
 
Description Invited seminar @ Phycomorph Meeting - Cyprus University of Technology - Piloting Genome editing in Brown algae 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presenting the pilot results and scientific strategies to achieve efficient genome editing of brown algae
Year(s) Of Engagement Activity 2016
 
Description Invited seminar at University of York 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited seminar, describing aquaculture based work. Arranged dissertation project for one student over summer 2018 as a result. Possibilities for additional collaboration.
Year(s) Of Engagement Activity 2018
 
Description Invited talk @ Theo Murphy international scientific meeting (Royal Society, Chicheley) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A description of our research work, particularly a transcriptomics analysis of the red algal pathogen Pythium porphyrae was presented. As a result of this workshop, two high-profile reviews have been developed and have been submitted for peer-review.
Year(s) Of Engagement Activity 2016
URL https://royalsociety.org/science-events-and-lectures/2016/06/into-the-genome/
 
Description Knowledge transfer: Overview of baseline data requirements for numerical modelling (plume modeling) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Knowledge transfer: Participation and presentation at workshop convened by Nauru Ocean Resources Inc. considering environmental aspects of their proposed deep-sea mining activities. "Overview of baseline data requirements for numerical modelling (plume modeling)". Dale. London, UK, Dec 2015.
Year(s) Of Engagement Activity 2015
 
Description MIDAS newsletter: Central American Gap winds and abyssal CCZ plumes 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newsletter item on "Central American Gap winds and abyssal CCZ plumes" by Mark Inall, Dmitry Aleynik, Andy Dale and Annemiek Vink
Year(s) Of Engagement Activity 2015
 
Description Oomycete Molecular Genetic Netywork - Asilomar Conference Grounds - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation - 100 Attendees. Spreading awareness of our work on Olpidiopsis genus and the develoment of a new bioinformatic tool.
Year(s) Of Engagement Activity 2017
URL http://omgn.org/program/
 
Description Oomycete Molecular Genetic Netywork - Asilomar Conference Grounds - Poster presentation - Hidden diversity in the Olpidiopsis genus is a Global Threat to red algal cultivation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation - 100 Attendees. Spreading awareness of our work on Olpidiopsis genus and the develoment of a new bioinformatic tool. Sparking questions about the origin of Biotrophy and the extension of our informatic tool to other pathogenic species
Year(s) Of Engagement Activity 2017
URL http://omgn.org/program/
 
Description Oral presentations & poster @ the Oomycete Molecular Genetics Network Annual Meeting (Malmo, Sweden) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral Presentation: Gachon et al. "The Pathogens Of Brown Algae Anisolpidium Ectocarpii And Anisolpidium Rosenvingei Define A New Class Of Marine Anteriorly Uniciliate Oomycetes". This work is now published.
Oral Presentation: Badis et al: "Pythium porphyrae the agent of the red seaweed rot disease: a reformed plant pathogen?".
Poster presentation: Fletcher et al. "A novel family of giant cadherins in the oomycetes". This work is now published.
Year(s) Of Engagement Activity 2011,2016
URL http://omgn.org/wp-content/uploads/OMGN-2016-book-of-abstracts.pdf
 
Description Oral presentations & poster at the International Seaweed Symposium (Copenhagen, Denmark) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation: Gachon et al. "Pythium porphyrae, the agent of the red seaweed rot disease: a reformed plant pathogen?"
Oral presentation: Gachon et al."Introducing nephelometry for non-invasive biomass and growth monitoring macroalgae"
Poster: Strittmatter et al. "Mechanisms and heritability of disease resistance in brown algae"
Year(s) Of Engagement Activity 2016
URL https://www.iss-2016.org/ehome/index.php?eventid=130925&
 
Description Oral presentations @ the Oomycete Molecular Genetics Network Annual Meeting (Malmo, Sweden) - Pythium porphyrae, a plant pathogen seeing red 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Pythium porphyrae, a plant pathogen seeing red.
Year(s) Of Engagement Activity 2016
URL https://www.omgn.org/wp-content/uploads/Programme-OMGN-2016.pdf
 
Description Porphyra RCN meeting - Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Porphyra, widely used in Asian cyuisine as sushi wrap, is the most valuable seaweed crop worldwide. GlobalSeaweed supported the engagement of the EU (moslty UK) research community in this US-led consortium, by financially enabling the organisation of a genome annotation workshop in Cambridge. The finding of the genome projects are reported in high profile manuscript (submitted). Upon publication, this major international initiative will deliver a high quality genome resource to the research community.
Year(s) Of Engagement Activity 2016
URL http://www.porphyra.org/nsf-rcn
 
Description Presentation and discussion - Global Seaweed Star project - RADseq and population genetics in Sugar Kelp 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A guest lecture on population genetics and the application of RADseq in the sugar kelp Saccharina lattisima given to the Global Seaweed Star project group. The group consisted of a wide range of international postgraduate students from the Philippines, Indonesia and Tanzania. The presentation was followed by a discussion on the application of RADseq and NGS technologies in less developed countries and the benefits of understanding genetic diversity and resilience in seaweed aquaculture.
Year(s) Of Engagement Activity 2018
URL https://www.globalseaweed.org/
 
Description Presentation and discussion - SRUC student visit - Conservation and Ecology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact 12-15 Masters students from the SRUC agricultural college visited SAMS as part of their Conservation and Ecology work module. The talk introduced the aquaculture of seaweed and the application of NGS and RADseq data to the field to the students. The presentation was followed by an engaging discussion on seaweed aquaculture and the use of technology to facilitate its development in Scotland and Europe
Year(s) Of Engagement Activity 2018
 
Description Presentation at Aquaculture Europe 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at Aquaculture Europe conference, Edinburgh.
Year(s) Of Engagement Activity 2016
 
Description Presentation at SeaLice 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation at SeaLice 2016 conference (250 attendees from research and industry). Led to several new contacts and started discussions with new potential collaborators.
Year(s) Of Engagement Activity 2016
 
Description Presentation at iMarCo 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at International Marine Connectivity meeting, St. Andrews, 2016. Led to discussions about future model developments and a collaborative grant application.
Year(s) Of Engagement Activity 2016
 
Description Presentation to MIDAS project annual meeting "Particle-tracking simulations of sediment plumes in the deep sea" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop talk: Presentation to FASTNEt project annual meeting "Modelling alongslope flow interaction with a canyon. The importance of flow direction". Dale. Oban, UK, Nov 2015.
Year(s) Of Engagement Activity 2015
 
Description Presentation to MIDAS project annual meeting "Particle-tracking simulations of sediment plumes in the deep sea" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop talk: Presentation to MIDAS project annual meeting "Particle-tracking simulations of sediment plumes in the deep sea". Dale, Aleynik, Inall. Sintra, Portugal, Nov 2015.
Year(s) Of Engagement Activity 2015
 
Description SMMSS steering committee presentation 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presenting work to the Scottish Marine Mammal Stranding Scheme steering committee. This work is directly relevant to the scheme for their work monitoring turbine deployments and there is scope for applying the work more widely in the scheme. This was to develop engagement with both those responsible for running the scheme day to day but also to get buy in from the higher level policy committee which steers their work. The committee includes policy makers from the Scottish government, SNH, natural england, as well as various academic bodies. As well as positive general interest and discussion there came out of the meeting an intent to develop ways to apply the work in this award to the workings of the stranding scheme.
Year(s) Of Engagement Activity 2016
 
Description Science to policy: Simulating sediment plumes and particle fallout in the deep sea 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Science to policy: Presentation to Science Policy Panel (direct dissemination of EU-funded MIDAS project to European Commission). "Simulating sediment plumes and particle fallout in the deep sea". Dale. Brussels, Belgium, Dec 2015.
Year(s) Of Engagement Activity 2015
 
Description Scientific presentation to the 11th International Phycological Congress, Szczecin, Poland (13-19 Aug. 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Scientific presentation to communicate results of ongoing research relating to marine dinoflagellates. Impact has been development of a new collaboration relating to an enigmatic group of marine dinoflagellates and the potential importance of their microbiome.
Year(s) Of Engagement Activity 2017