Past courses

  • Face to Face Training Course: Introductory Bioinformatic Course to Sequencing Data Processing

    Course overview

    Bioinformatics is a must-have skill required in every modern research lab. This coursLeaflete will explore the fundamentals of bioinformatics analysis. The participants will be provided with end-to-end hands-on training, along with an introduction to basic concepts, in using popular tools. Participants will gain an understanding of bioinformatics analysis in the context of aquaculture research. The key learning objectives are for participants to understand the utility of NGS for a range of aquaculture-related objectives and bioinformatics pipelines for NGS data, and to gain knowledge of specific pipelines for RADseq and RNAseq protocols.

    Course content

    Training will be provided through blended learning elements such as lectures, practical exercises and a mini industry seminar. 

    Lectures topics will include;

    • Unix/Linux command system and basic scripting
    • Sequence alignment (genomic and transcriptomic)
    • Variation calling (SNP)
    • RNA-Seq expression measurement
    • 16S metagenomics
    • Genome assembly with short and long reads
    • Marker development (GBS/RAD-Seq)

    Date & Time

    This course will take place from Monday the 26th of August until Friday the 30th of August, at the Institute of Aquaculture, University of Stirling (UoS), Scotland, UK. 

    Target Audience

    The target audience is primarily students and lab researchers who want to be introduced to bioinformatics concepts and analysis. This course is not an advanced course for bioinformatists, but rather a starter course for researchers that want to have a better understanding of their data, gain more insights or to plan experiments better and maximise the analytics output.
    Required competence level: basic knowledge of molecular biological methods.

    Course Tutors:

    • Dr Michaël Bekaert - UoS, UK

    Dr Michaël Bekaert, senior lecturer in bioinformatics and genomics, is working extensively on the genomics of fish (cyprinids, salmonids, cichlids), mussels, sea lice, pathogenic bacteria and viruses, and SNP-based genetic mapping in aquaculture. Dr Bekaert has been involved in cloud-based software solutions for next generation diagnostics in infectious diseases. More recently, Dr Bekaert has addressed questions of genetic diversity, genome assembly, and marker discovery in farmed fish.

    • Christophe Klopp - INRA, France

    Christophe Klopp currently works at the Department of Applied Mathematics and Informatics, French National Institute for Agricultural Research. Christophe leads a group of bioinformaticians providing services to INRA, biologists working in animal genomics and co-leads the local bio-informatic Genotoul platform. These teams develop software packages, train biologists and take part in research projects.

     

    General Data Protection Regulation

    The AQUAEXCEL2020 project partners are subject to the EU General Data Protection Regulation (GDPR) which came into force on 25th May 2018. Data that is collected and processed for the purposes of facilitating and administering AQUAEXCEL2020 training courses is therefore subject to GDPR. Please review our Data Management Policy here.

    It is a requirement of GDPR that all data subjects (i.e. training course applicants) give explicit consent to the storage and processing of their personal data. A separate GDPR Consent Form is therefore provided, and this must be completed by an individual applying for an AQUAEXCEL2020 training course. This should be attached to the training course application.

    Registration

    To apply, please send the following documents to aquaexcel@aquatt.ie,  with the subject line:  AQUAEXCEL2020 /TrainingCourse_Bioinformatics_UoS

    • Completed Registration Form - NOW CLOSED
    • CV / Résumé
    • A Letter of Motivation
    • Completed GDPR Consent Form - Here

     

    The application deadline is 21st June 2019: NOW CLOSED

     

    Further information

    Course attendance is free, thanks to EC H2020 funding. Participants are expected to pay for their own travel, subsistence and accommodation. Places will be confirmed, at the latest, one month before the start of the training course. Admittance to the course will be confirmed officially through e-mail.

    Please do not make travel arrangements unless you have received official confirmation of your place on the course.

    For further information about the course content, fees and other information of interest, please click here.

    Participants are expected to have a laptop.

  • Face-to-Face Training Course: Laboratory Animal Science for Aquatic Research Facilities

    Course descriptionLeaflet

    This course will give participants an insight into the current European legislation around animal science in research and the ethical requirements to be considered when working with animals in aquatic research facilities. This course will also train researchers in effective experimental design, experimental modelling, application of sampling regimes and maintenance of aquaculture systems by focusing on topics including; ways of Reducing, Refining and Replacing fish in experiments, transfer protocols for optimal welfare and performance, water quality and welfare in aquaculture, correct fish handling and scaling, and tank size and fish management.

    Course content

    The course will consist of four days of lectures, exercises, mini seminars and site visits designed and provided by a range of experts from around Europe. Each day will focus on a specific aspect of animal science for aquatic research facilities, these include;

    • Legislation, ethics and the 3Rs and welfare
    • Experimental models and model animals
    • Experimental fish handling
    • Scaling and experimental design

    During the course there will be a visit to IMR Matre Research station (https://bit.ly/2WGca3A) and the Austevoll research station (https://bit.ly/2TxUHZ3) which will include a mini seminar entitled ‘From Laboratory to Industry’.

    There will also be opportunities for participants to take part in modelling exercises, putting into practice skills learned from the lectures and talks provided.

    Date & Time

    This course will take place from Monday the 17th until Friday the 21st of June, at the Institute of Marine Research, Bergen, Norway.

    Target Audience

    Primarily aquaculture researchers and students and aquaculture industry stakeholders working directly with animals.

    Course Tutors

    • Tom Hansen - IMR, Norway
    • Ragnar Nortvedt - IMR, Norway
    • Åsa Espmark - NOFIMA, Norway
    • Dr Elin Kjørsvik – NTNU, Norway
    • Dr Sylvain Milla – UL, France
    • Dr Martine Føre -  NTNU, Norway
    • Rolf Erik Olsen - NTNU, Norway
    • Dr Lars Helge Stien - IMR, Norway
    • Dr Liv Søfteland - IMR, Norway
    • Dr Anna Wargelius - IMR, Norway
    • Dr Nina Sandlund - IMR, Norway
    • Dr Per Gunnar Fjelldal - IMR, Norway
    • Dr Birgitta Norberg - IMR, Norway
    • Joachim Nordbø - IMR, Norway
    • Dr Tore.Kristiansen - IMR, Norway
    • Dr Jonatan Nilsson - IMR, Norway
    • Dr Frode Oppedal - IMR, Norway
    • Dag Atle Tuft - NFSA, Norway
    • Ep Eding - WU, the Netherlands

     

    For more information on course tuition, please email Tom Hansen at tomh@hi.no, or Ragnar Nortvedt at ragnar.nortvedt@hi.no.

    General Data Protection Regulation

    The AQUAEXCEL2020 project partners are subject to the EU General Data Protection Regulation (GDPR) which came into force on 25th May 2018. Data that is collected and processed for the purposes of facilitating and administering AQUAEXCEL2020 training courses is therefore subject to GDPR. Please review our Data Management Policy here.

    It is a requirement of GDPR that all data subjects (i.e. training course applicants) give explicit consent to the storage and processing of their personal data. A separate GDPR Consent Form is therefore provided, and this must be completed by an individual applying for an AQUAEXCEL2020 training course. This should be attached to the training course application.

    Registration

    To apply, please send the following documents to aquaexcel@aquatt.ie, with the subject line: AQUAEXCEL2020 /TrainingCourse_Lab_IMR

    • Completed Registration Form - CLOSED
    • CV / Résumé
    • A Letter of Motivation
    • Completed GDPR Consent From - Download here

     

    The application deadline has been extended to 17th April 2019

    Further information

    Course attendance is free, thanks to EC H2020 funding. Participants are expected to pay for their own travel, subsistence and accommodation. Places will be confirmed, at the latest, two months before the start of the training course. Admittance to the course will be confirmed officially via email.

    Please do not make travel arrangements unless you have received official confirmation.

    For further information about the course content, fees and other information of interest, please click here.

  • Face to Face Training Course: Recirculating Aquaculture Systems (RAS) Technology (2)

    Course overviewLeaflet

    Recirculating Aquaculture Systems (RAS) were originally developed to grow freshwater species and produce marine juveniles. However, RAS technology has increasingly been used for the on-growing of a wide variety of fish (including marine species) and shellfish. RAS can be operated irrespective of the target temperature and salinity, and the annual production capacity of some industrial systems can now amount to thousands of tons.

    As part of this course, leading experts in RAS technology will present the principles and concepts in RAS and discuss the operation of conventional and ‘ecosystem approach’-based RAS. Participants will gain an understanding of the principles of recirculation technology, the types of RAS and their specificities, capabilities and limitations, the advantages and necessary conditions for the optimal use / operation of RAS, and the ongoing research which can increase its efficiency and nutrient use.

    Course content

    Training will be provided through traditional lectures, practical exercises and field visits to experimental facilities. 

    Lectures topics will include;

    • Aspects of recirculation technology relevant to research
    • Design, management, operation and evaluation of RAS
    • Fish consumption and production: system mass balance and model
    • Closing systems
    • Minimising water and nutrient use
    • Different use of Recirculating Aquaculture Systems (RAS)

     

    The course will include a RAS Industry Mini Seminar organised with NGvA (the Dutch association for aquaculture) and Aquarius (aquaculture student organisation). This seminar will include discussions on the state of RAS in the world, the requirements of Atlantic salmon smolts and post smolts in RAS, Yellowtail Kingfish and off flavour and RAS in practice. It will also present an opportunity to network and discuss RAS developments with other course participants and experts from research and industry.

    As part of the course, participants will take part in a technical visit to experimental facilities; the Aquaculture and Fisheries Group - Aquatic Research Facility (AFI-ARF) and the Recirculating eel farm (200 MT production capacity).

    Date & Time

    This course will take place from Monday the 6th of May until Thursday the 9th of May, at Wageningen University, Wageningen, The Netherlands.

    Target Audience

    This course is designed for aquaculture professionals (e.g. engineers, researchers, etc.) interested in the potential applications of RAS. Participants should have (basic) knowledge of aspects of recirculation technology. This knowledge can be on the design or operational use.

    The industry mini-seminar is designed (1) for the participants to network with professionals and (2) for professionals who would like to hear the latest discussions and scientific developments in the RAS sector and to better understand the needs for RAS development in other countries.

    Course Tutors:

    • Geert Wiegertjes - WU, the Netherlands
    • Johann Verreth – WU, the Netherlands
    • Johan Schrama – WU, the Netherlands
    • Ep Eding - WU, the Netherlands
      • "Fish, consumptions and productions: system mass balance and model"
      • "Biofiltration principles"
    • Vasco Mota - Nofima
      • "Water Quality Requirments in RAS"
      • "Design, dimensioning and operational of RAS research facilities"
      • "Requirements of Atlantic salmon smots and postsmolts in RAS"
    • Raoul Piedrahita – California, USA
      • "Tank hydraulics and solids removal processes"
      • "Suspended Solids characterisation and control/removal"
      • "Gas control (oxygen, carbon dioxide and nitrogen gas)"
    • Olaf Valdstein – NTNU
      • "Biofiltration and bacterial environment"
      • "Bacterial control and bio-security"
    • Per Bovbjerg Pedersen - DTU
      • "Low energy RAS"
      • "Energy control in RAS design"
    • Edward Schram - ASG, the Netherlands
      • "Off flavour"
    • TBC - Kingfish Zeeland, the Netherlands

    General Data Protection Regulation

    The AQUAEXCEL2020 project partners are subject to the EU General Data Protection Regulation (GDPR) which came into force on 25th May 2018. Data that is collected and processed for the purposes of facilitating and administering AQUAEXCEL2020 training courses is therefore subject to GDPR. Please review our Data Management Policy here.

    It is a requirement of GDPR that all data subjects (i.e. training course applicants) give explicit consent to the storage and processing of their personal data. A separate GDPR Consent Form is therefore provided, and this must be completed by an individual applying for an AQUAEXCEL2020 training course. This should be attached to the training course application.

    Registration

    To apply, please send the following documents to aquaexcel@aquatt.ie,  with the subject line: AQUAEXCEL2020 /TrainingCourse_ RAS2_WU 

    • Completed Registration Form - Here
    • CV / Résumé
    • A Letter of Motivation
    • Completed GDPR Consent From - Here

     

    The application deadline is 19th March 2019

    Further information

    Course attendance is free, thanks to EC H2020 funding. Participants are expected to pay for their own travel, subsistence and accommodation. Places will be confirmed, at the latest, one month before the start of the training course. Admittance to the course will be confirmed officially through e-mail.

    Please do not make travel arrangements unless you have received official confirmation.

    For further information about the course content, fees and other information of interest, please click here.

  • Face to Face Training Course: Recirculating Aquaculture System (RAS) Technology

    Course organisers: Ifremer (France), Wageningen University (the Netherlands)
    Location: IFREMER Sète research station, France
    Date: 24-28 October 2016

    Course overview:

    Traditionally, recirculating aquaculture systems were mainly developed in Europe to grow out freshwater species and produce marine fingerlings. However, they have become increasingly used for the on-growing of a wide variety of fish (including marine species) and shellfish. They can be operated irrespective of the target temperature and salinity, and the annual production capacity of some industrial systems can now amount to thousands of tons. Recirculating aquaculture systems (RAS) allow to maintain a constant and adjustable quality of the rearing water (i.e. temperature, oxygen, nitrogen and pathogens) therefore contributing to a more intensive and reliable production and substantial energy savings. 

    The objectives of this course are to review the basics of RAS and examine the different systems, designs, operations and applications. A half day will be dedicated to a RAS industry mini seminar for which we invite industry stakeholders to join. 

    Participants will:

    • Gain solid knowledge about the principles of RAS
    • Become familiar with different types of RAS, their specificities, capabilities and limitations
    • Understand their advantages and the necessary conditions for their optimal use and operation
    • Master the basics for RAS design and sizing
    • Become aware of the ongoing research to increase the efficiency and acceptability of RAS
       

    RAS Industry Mini Seminar (Friday 28 October 2016, 08.30 – 13.00):

    A half day industry mini seminar on RAS evolution and new RAS uses, involving RAS farmers and engineering companies, will give the course participants an opportunity to exchange with industry professionals. 

    Industry stakeholders are also invited to attend the seminar to hear the latest discussions and scientific advances in the RAS sector, and exchange with the course participants to gain information on RAS development and needs for sustainable development in other countries within and outside the EU.

    Registration:

    Participants taking part in the full training course are requested to submit their CV and a brief letter of motivation. Places will be confirmed, at the latest, one month before the start of the training course. 
    E-mail your registration request to aquaexcel@aquatt.ie, using the official registration form (click here). Please indicate the following in the subject: AQUAEXCEL2020 / training course #2 (Ifremer)

    Industry participants attending the industry mini seminar only (Friday 28 October, 08.30 – 13.00) are requested to register by submitting their affiliation and contact details via e-mail to aquaexcel@aquatt.ie. Please indicate the following in the subject: AQUAEXCEL2020 / training course #2 (Ifremer) – industry 

    Deadline: Friday 09 September 2016.

    Further information:

    For further information about the course content, fees and other information of interest, please click here.
    For a full schedule of the course click here, and for practical details see travel and accommodation.

  • Distance Learning Training Course: Experimental data management from generating protocols to sharing data (LIVE)

    Course provider: Institute of Complex Systems, University of South Bohemia in České Budějovice (Czech Republic)
    Location: Online course (live)
    Date: 25 + 27 + 29 April 2016 (3-day course, 90 minutes per day: 10.00 – 11.30hrs CEST)

    Course overview

    The course will deal with best practice experimental data management, including all aspects from preparing experiment protocols to sharing data. It is based on the experimental data repository system developed in FP7-AQUAEXCEL called bioWES. bioWES is a distributed, knowledge-based repository for large datasets, typically applicable in biological and related sciences. The bioWES scientific data management solution provides full control over experiments, from protocol design, through data acquisition and processing to sharing final results.

    Participants will learn how to use the bioWES system for their own experimental work, using their own protocols and real experimental data. The aim is that by the end of the course, each participant will be able to install the bioWES system, create his or her own account, create unique experimental protocols based on their own specific needs, store their own experimental data, create connections between experimental protocols, cooperate with colleagues through sharing and visualize the overview of individual project steps. The participants will also be introduced to the special functionality of the system: data processing modules, plugins for communication with measurement devices and standardization support.

    The course will be organized as an online training with active participation of the users. The organizers will guide the users through every single step of the bioWES system, from installation to sharing of experimental data, during three one and a half hour sessions. The participant will use their own protocols and experimental data to test theoretical knowledge on real examples. The course will be available through standard internet browser for each registered participant. It is believed that the course is particularly useful for researchers involved in AQUAEXCEL2020 TransNational Access (TNA) projects.

    Registration

    E-mail your registration request to aquaexcel@aquatt.ie, using the official registration form (click here)
    Please indicate the following in the subject: AQUAEXCEL2020 / training course # 1 (JU)
    Deadline: Thursday 21 April 2016.

     

    Further information

    For further information about the course content, fees and other information of interest, please click here.