A versatile platform for Multidisciplinary MArine Computing APplications
Lead Research Organisation:
Scottish Association For Marine Science
Department Name: Dunstaffnage Marine Laboratory
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.
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.
Organisations
- Scottish Association For Marine Science (Lead Research Organisation)
- National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) (Collaboration)
- Chinese Academy of Sciences (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- Fisheries Development Institute (Collaboration)
- University of Innsbruck (Collaboration)
- Carnegie Institution for Science (CIS) (Collaboration)
- Macquarie University (Collaboration)
- French Research Institute for the Exploitation of the Sea (Collaboration)
People |
ORCID iD |
| Claire Gachon (Principal Investigator) |
Publications
Adams T
(2016)
Temporal variability in sea lice population connectivity and implications for regional management protocols
in Aquaculture Environment Interactions
Adams T
(2015)
Connected networks of sea lice populations: dynamics and implications for control
in Aquaculture Environment Interactions
Adams T
(2014)
Offshore marine renewable energy devices as stepping stones across biogeographical boundaries
in Journal of Applied Ecology
Adams T
(2014)
Larval dispersal of intertidal organisms and the influence of coastline geography
in Ecography
Aleynik D
(2017)
Impact of remotely generated eddies on plume dispersion at abyssal mining sites in the Pacific
in Scientific Reports
Allewaert C
(2018)
Life history determinants of the susceptibility of the blood alga Haematococcus to infection by Paraphysoderma sedebokerense (Blastocladiomycota)
in Algal Research
Atamanchuk D
(2015)
Detection of CO 2 leakage from a simulated sub-seabed storage site using three different types of p CO 2 sensors
in International Journal of Greenhouse Gas Control
Badis Y
(2019)
Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide
in European Journal of Phycology
| 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 |