Summer School 2017 | Lisbon

Date: 12th-14th July 2017

Venue: Laboratório Nacional de Engenharia Civil (LNEC), Lisbon, Portugal.



The summer school took place from July 12th to 14th in  LNEC, Lisbon, Portugal. Scholars were trained to use the Co-ReSyF platform as a key resource for their proposed research project, with continuous technical support on the platform functionality. Eight successful applicants attended the Co-ReSyF Summer School, where they were given access to:

(a) the Co-ReSyF platform,

(b) training material and

(c) technical support to develop their proposed ideas into new coastal applications.

The summer school training focused on practical hands-on use of the platform along with lectures, exercises and opportunities to give feedback. Adding to current Co-ReSyF Research Applications, the development of new ideas allows these early platform users to demonstrate the capabilities and broader scope of Co-ReSyF to the wider scientific community.


Summer School Participants:

Name Affiliation
Dr. Ailbhe Kavanagh University College Cork (UCC), Ireland
Dr. Ana Nobre Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Portugal
Dr. Cristina Lira Portuguese Meteorological and Geophysical Observatory (Institute Dom Luiz, IDL), Portugal
Mr. Damien Haberlin University College Cork (UCC), Ireland
Mr. Francisco Campuzano University of Lisbon, Portugal
Mr. Ricardo Martins National Laboratory of Civil Engineering (LNEC), Portugal
Mr. Tiago Ferradosa Faculty of Engineering, University of Porto, Portugal
Mr. Diogo Silva Mendes University of Lisbon, Portugal

Summer School Materials can be downloaded here:

1-1_Intro to Co-ReSyF

1-1_Intro to EO

1-2 Platform Overview

1-3_Co-ReSyF_RA Lecture_HypertemporalTimeSeries

1-3_Co-ReSyF_RA Lecture_Vessel&Oil

1-4_Co-ReSyF_RA Lecture_BathymetrySAR

1-4_Co-ReSyF_RA Lecture_WaterQuality_Benthos_BathymetryOPTICAL

2-1_Co-ReSyF_RA Lecture_Coastal Altimetry

2-2 & 2-3_Learn to use Co-ReSyF

2-2_Learn to use Co-ReSyF_da-training

2-3_Learn to use Co-ReSyF_dcs-training

3-1_Resources at your disposal

3-1_The way forward as a researcher

Other useful information includes:



Summer School_Programme.

Summer School Participant Projects:

Proposal 1 – Dr Ailbhe Kavanagh

Irish waters are geologically diverse and highly productive in terms of natural resources, such as fisheries and fossil fuel production. The region also supports over 20 species of cetaceans (whales and dolphins), many of which are protected under both national and international law. Despite this, our understanding of the distribution of many species remains poor, compromising our ability to effectively manage populations, and to understand potential impacts of human activities. This study aims to predict habitat availability for protected cetacean species in Irish waters and map potential overlap with anthropogenic development. This is particularly important for areas such as the Porcupine Basin, which are generally under-surveyed, and where Oil and Gas exploration has increased markedly over the last ten years.

This study will employ statistical modelling techniques to examine cetacean occurrence in conjunction with earth observation data. I aim to identify the environmental predictors of cetacean distribution, and to use these data to predict key habitats for cetacean species across Irish waters. I will examine the influence of both physiographic variables (water depth, slope, distance to coast, distance to shelf edge, distance to 200m contour) and remote sensing variables (for example: SST, SSH, Chl-a) on cetacean occurrence. In addition, I would like to include information on ocean currents. However, I have not been able to identify a suitable data source, and therefore, I propose to use SST data to map ocean circulation features.

Ireland’s marine jurisdiction is nearly 10 times its land area resulting in key challenges for cost-effective monitoring of coastal and offshore waters. The project will use new statistical methodologies to model in situ cetacean data and remotely sensed data to understand the key environmental drivers of cetacean distribution. Thus, this research will enable these significant existing data sources to be combined to determine critical cetacean habitat. In an Irish context, such information will supply environmental impact assessments with real data vital for effective management of human activities such as Oil and Gas exploration. In a broader context, the wider implications of this work includes applying the methods developed here in other coastal and offshore marine systems with poor survey coverage, such as the waters off West Africa, so that existing data sources can be used to fill critical gaps in knowledge of cetacean distribution at a global scale.

Proposal 2 – Dr Ana Nobre

Seaweed aquaculture (~30 million metric tons in 2014, with a farmgate value of ~US $7 billion in FAO, 2016) makes up between a quarter to a third of all aquaculture production. Seaweed production increased at 8% per year in the past decade, following a 6.2% increase in the previous decade (FAO, 2016). This ever increasing amount of seaweed production comes from aquaculture, principally in Asia and South America, with very small quantities produced in Europe. As world population expands, culture of seaweeds is also expected to expand. Seaweeds are bioextractive organisms, providing important ecosystem and bioextraction services by releasing oxygen and by taking up excess nutrients generated by other species.

Due to the implementation of small scale macroalgae production systems in the western countries, the economics and ecological interactions of large farms remain obscured. Simulation of large macroalgae cultivation systems could remove at least part of the unknowns, and also help the planning, design and operation of such farms.

To be useful for farmers models will require among other automatic daily inputs with the most recent farm and environmental data (hindcast and forecast) for variables such as PAR, water temperature and salinity. In particular PAR is a good candidate to be provided from global EO systems, while the other two parameters might depend on the cultivation location (if in ponds, tanks or in estuaries field measurements or local modelling solutions are required). PAR will be (or is already) available as an ESA Sentinel 3 OLCI product with a frequency of less than 2 days. In the past up to 2005 PAR was also available from JRC (SeaWIFS and MODIS). Since 2004 and with a periodicity of up to 15 minutes global irradiation is available from the Copernicus Atmosphere monitoring service but needs further conversion into PAR.

The objective of this project is to use and make available at the Co-ReSyF platform an algorithm to correlate global irradiation and PAR in order to fill the gaps of PAR data availability (regarding time period and frequency) and thus to allow calculation of the photosynthetic limitation coefficient for any given species of macroalgae.

Proposal 3 – Dr Cristina Lira

Estuaries mouths are coastal areas with particularly complex morphodynamic characteristics, which results from the complex interactions between various hydrodynamic and morphological processes taking place at a wide range of time scales, from hours/days (short term), to months/decades (medium term) and hundreds of years (long term). A notable element of this dynamic is the development of ebb-tidal deltas on the seaward side of the inlet, which are formed by inlet sediment bypassing which accumulates and forms these structures.

Although, ebb-tidal deltas play an important role in the exchange of water and sediment between the back-barrier basin and the coastal zone, most research has focused on the dynamics of the tidal inlet itself. Thus, there is an incomplete understanding of how the components within these systems interact, specifically how the ebb-tidal delta may affect the adjacent coastline. This topographic obstacle exerts an influence on the propagation of incoming waves, resulting in wave significant transformation around this feature. The ebb- tidal delta morphology, and its cyclical changes, greatly controls the sediment that is supplied to the adjacent beach. Ultimately, the beaches adjacent are controlled by the processes acting upon the ebb-tidal delta, with different responses in beach sediment volume and cycles of accretion and erosion over the long and medium terms.

The main objective is to evaluate and characterize the morphological changes of the Tagus ebb-tidal delta, focusing on the Bugio sand body geometry. During recent decades, the Tagus estuary entrance region has undergone significant morphological changes. The most striking change was the migration and late disappearance of the emerged portion of Bugio sand bank (island), which has exhibited a pattern where long (pluri-annual) stabilization periods alternate with sudden changes in its configuration, in a clear link to the adjacent coastal area. This new configuration has also been linked with other important morphodynamic changes, such as the shortage of sand on the Costa da Caparica beaches and the accumulation of sand on the left bank of the Tagus river, between Cova do Vapor and Trafaria, a coastal stretch of extreme socio-economic value.

This proposal aims to perform reconstructions of Tagus ebb-tidal delta in the last 40 years, making use of high and very high resolution optical satellite imagery to derive the bathymetric information and the emerged sand bank contours. Nautical charts and available single and multibeam bathymetric surveys of the area will be used to validate the satellite derived bathymetry results. The goal is to develop a simple but robust methodology, using existing satellite-derived bathymetry methodologies (e.g. use Co-ReSyF Research Application 2) that can support the generation of multitemporal bathymetric data in such complex systems. Results will be useful to understand system dynamics and to support the use (and validation) of morphodynamics numerical models (e.g. Delft 3D) and therefore will contribute to the prediction of future changes (e.g. climate change, sea-level change) in the adjacent coast.

Proposal 4 – Damien Haberlin

Jellyfish can have a substantial negative impact on the sustainable operation of aquaculture in many regions. Periodic jellyfish blooms have occasionally caused 100% mortalities on farms with little or no warning for aquaculture managers. In addition, several harmful species reach high densities annually and contribute to substantial levels of mortality (ca. 50% during 2014) every year, either through injury from stings or from secondary infection. Under these circumstances fish are not eligible for human consumption. Currently there is no mitigation strategy other than harvesting fish early to avoid harmful species, nor is there a method by which blooms and population increases can be predicted at present.

One particular species, Muggiaea atlantica, is responsible for much of the impact on farms annually, but there are large knowledge gaps with regard to its life history and ecology. M atlantica is a neritic species restricted to shelf waters and is likely driven by the hydrography of the Celtic Sea. The study of harmful phytoplankton blooms in the southwest has revealed the Celtic Sea hydrography to be a key driver of blooms, with seasonal currents transporting phytoplankton from the Celtic Sea to the southwest of Ireland. M atlantica has co-occurred with plankton blooms in the past and it is likely that the same process influences both phytoplankton and small jellyfish like M atlantica. The conditions or changing conditions that cause mass water transport along the southern Irish coastline, advecting harmful species into a region of aquaculture, represents a large knowledge gap which EO data can potentially address.

This proposal aims to use EO data to find correlations between oceanographic changes in the Celtic Sea, i.e. altimetry, surface currents and temperature, and high mortality events on farms. The ultimate goal being to use EO real time surveillance as a predictive tool for aquaculture, giving managers a warning period in which to act and protect stock. We are involved in an on-going project with Marine Harvest Ireland, which aims to provide mitigation strategies to protect against jellyfish. Our existing dataset includes zooplankton counts from the southwest over several years and accurate estimates of mortalities over the same period. Combing this data with EO data would add enormous value to the existing work.

Proposal 5 – Francisco Campuzano

The proposed research intends to complete, support and integrate in the MyCoast project proposal submitted to the Atlantic Area Interreg programme for the period 2017-2019. MARETEC-IST contribution focuses in the Greater Lisbon (GreLis) coastal area, defined as the coastal stretch that includes the Tagus and Sado estuaries and their Regions of Fresh water Influence. The obtained capacities in Co-ReSyF will enhance our group potential to explore EO data at global scale.

In MyCoast project, MARETEC-IST will promote the development of a Coastal Observatory covering Greater Lisbon area and will collect the available operational information including the Instituto Hidrográfico HF Radar observations and the circulation and wave forecast models already available. The project´s main goal is tackling coastal risks such as eutrophication, coastal flooding, marine litter, oil spills. The Co-ReSyF Earth Observation (EO) course and capacities would be applied for exploring: inundation areas, river flow estimation from altimetry, bathymetry evolution due to storm surges and flooding events. Moreover, these remote sensing observations will be collected and displayed in the GreLis Coastal Observatory and thus, becoming accessible by other potential stakeholders. EO data will enhance the project to evaluate the bathymetry and benthic habitats evolution and to validate long-term modelling series of (10 years) of meteorological forcing, hydrodynamics (temperature, waves and currents) and water quality (Chlorophyll) modelling results. The candidate will use altimetry data to estimate river flow and to analyse tidal propagation and amplification within the above-mentioned estuaries, i.e. tidal gauges located at their mouths.

Finally, the candidate’s PhD field of research relates to the extension and variability of estuarine plumes and their associated space and time scales (Campuzano et al., 2016; Brito et al., 2015). For that reason, he would be interested to analyse the influence of river/estuarine inputs in the formation of coastal fronts of temperature and salinity and the impact in primary production in the continental coast of Portugal. The candidate is willing to compare the obtained modelling results with EO data and in situ data.

Proposal 6 – Ricardo Martins

Coastal zones are vulnerable to the effects of climate changes. The sea level rise and the increase of extreme weather conditions can cause beach erosion, inland flooding and damages in infrastructures with high social, economic and environmental impacts. An example of a high-risk coastal sector is the Costa da Caparica, located in Portugal. This area has been subject of coastal management measures, such as artificial sand nourishment, reinforcement of structural coastal defences, and monitoring programs. The proposed research project aims to contribute to answer several questions: 1) How can we determine the coastline transformations (e.g. erosions) in a less expensive and effective way? 2) How can we contribute to public awareness of the coastal risks in a near future?

This project is focused on developing an application to monitor the coastline, with storage and processing. The coastline is obtained by processing fetched or uploaded input data such as EO datasets and other data sources. The workflow is described as follows:

  1. Process the Sentinel images for that coastal zone by using algorithms to generate the waterline.
  2. The waterline is corrected with data from tidal, topographic or aerial sources in order to obtain a most accurate representation of the coastline.
  3. After the correction, map the coastline and calculate the rate-of-change relative to a user pre-defined baseline. Statistics for the whole region are computed thereafter.

This workflow can be achieved by using the existing Co-ReSyF framework functionalities, such as cloud, algorithms, processing tools and EO datasets. For this call, the application will be implemented for the Costa da Caparica coastline, from where a significant amount of data is available. Predefined application requisites will enable its future application to other coastal areas.

Proposal 7 – Tiago Ferradosa

Risk analysis and mitigation, e.g. in marine renewable energy structures, ports and coastal protection systems, as well as the activities of coastal management and preservation, require a deep knowledge of climate extremes in those coastal areas. The knowledge of extreme coastal events is also a key step to account for adaptive coastal planning, considering climate change scenarios. An accurate assessment of the extreme events, ultimately leads to uncertainty reduction in risk and safety management of marine infrastructures and coastal dynamics. Frequently, the professionals and researchers struggle to combine the physical/numerical modelling of coastal phenomena with the proper statistical modelling. The Extreme Coastal Data Evaluation (ECODE) is a Research Application (RA), which allows the users to perform online advanced analysis of extreme values based on Earth Observation (EO) data.

The main goal of ECODE is to process EO data (waves, winds and sea level) and to compile several statistical techniques, which may be applicable in research works, engineering projects, infrastructures’ design, risk mitigation plans (e.g., coastal flooding), among others. Moreover, ECODE also incorporates joint probability analysis and reliability analysis tools, which enable the estimation of the probabilities of occurrence of extreme events and the probabilities of failure in coastal systems (e.g., overtopping or collapse of harbour breakwaters, beach erosion) based on the users’ knowledge of their systems’ failure function. With a friendly user environment, ECODE will be able to interact with commonly used software such as MATLAB, R or Excel. This RA not only connects the users with the satellite altimetry data, but it also makes it possible for a non-expert in statistical fields to obtain relevant information in terms of long-term predictions and hazards quantification. ECODE can also work with the user’s own data sets, enabling comparisons with the EO available. By compiling different modelling approaches for long-term variables, and simultaneously using the specialised algorithms and updated corrections from Co-ReSyF data, ecologists, engineers, biologists, modellers and coastal planners will be able to update their estimates concerning extreme events occurrence. The user of ECODE can also request the alert function of the reliability toolbox, which informs whenever the failure probability exceeds a defined threshold for the system analysed. This RA will contribute to generalise the use of EO data in scientific and professional activities, for coastal areas. It will also disseminate the statistical techniques for risk quantification. ECODE provides a suitable set of web-tools to combine EO data in the evaluation of extreme coastal events.

Since the RA can be used with different available data sets, it can also be used to compare the results from the different sources of data (secondary goal). The ECODE already accounts for the graphic interfaces to enable a user-friendly experience both for data analysis and visualisation.

Proposal 8 – Diogo Silva Mendes

Objective: Estimation of the topo-bathymetry of a wave-dominated inlet based on the optical images of SENTINEL 2 and assesses its adjustment to a ground truth survey.

Introduction: Wave-dominated inlets are usually located in meso-tidal and wave dominated environments around the world (i.e. Portugal, Australia, United States). They connect the open sea to a coastal lagoon and control the exchange of sediments, nutrients and water renewable rates. These inlets are very dynamic with drastic morphological evolutions within a few days (Mendes et al., 2016). The capability to estimate their evolution based on remote sensing techniques constitutes a promising avenue of research to better understand and predict their morphodynamics.

Methods: The topo-bathymetric estimate based on the optical satellite images is going to be derived using the methods presented by Pacheco et al. (2015) and Guerreiro and Moura (2015). In 26th July a traditional survey was performed in the Albufeira lagoon using a RTK-GPS. This survey covered the adjacent beaches located nearby in the open sea and the main morphological features of a wave-dominated inlet, such as the ebb-delta, the flood-delta and the transitional channel. The satellite topo-bathymetric estimate will be compared qualitatively and quantitatively against the ground truth survey using difference maps and descriptive statistics.


  1. A tool to estimate the topo-bathymetry of a wave-dominated inlet based on an optical satellite image.
  2. A tool to assess the skill against a ground truth survey.
  3. A tool to obtain the cross-sectional area of the inlet.

All the algorithms developed under this study will be fully available.

Posted on: 20th July 2017, by : admin