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PhD course: Dynamic Ecological Modeling, 1.5 Credits (one full week of study)

Start period: Autumn 2015, for one week, 7-11 September, 2015. Location:

Sweden, Stockholm University, The Department of Ecology, Environment and Plant Sciences (DEEP) www.su.se/emb - four days (7-10 Sept.),

Askö laboratory - one day in (11 Sept., Friday), city Trosa, 80 km South from Stockholm; travel from Stockholm to Askö and back covered by the course.

Registration: Those interested in the course, please send me an e-mail lena.konovalenko@su.se with information about your research interest and place of study. The course is free of charge for PhD students from European Union, but the number of participants is limited. However, participants are expected to cover their own costs for travel, board and lodging. Registration is mandatory and should be done as early as possible.

Course description The course is organized for PhD students within Biology, Ecology and Radioecology. The students should bring their own computers for the practical exercises. The maximum number of students who can be admitted to the course is 20. All lectures will be given in English. Compartment modeling is a tool used for describing the transport of material in biological and ecological systems, where the material could be for example food. For example, the compartments can represent different species of animals and plants, and the flow between compartments can account for uptake and loss of food (or energy). Compartment models are often used to describe the outcome of chemical reactions and modelling population dynamics. The aim of the course is to learn the basics of compartment modelling, how to derive ordinary differential equations for a given problem and the principles for analysis and solution of differential equations. Another goal of the course is to become familiar with the modern techniques for dynamic modeling and their application to aquatic and terrestrial ecosystem modeling, and in particular to the problem of nutrients circulation and food web dynamics in the Baltic Sea. The course consists of a half day lecture and half day seminar for practical modeling exercises. Lectures: Introduction to compartment modeling. Systems of Differential equations. The predator–prey equations used to describe the dynamics of biological systems. The Baltic Sea models. Application in the innovative European project “The Future of Fully integrated human exposure assessment of chemicals 4FUN”. The box models of contaminants transport in aquatic and terrestrial ecosystems.

BALTSIM

BALTSIM

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Practical exercises: Application of modeling in Ecology, showing approaches and discussion existing software for effective analysis of ecological problems and assessment of impact on the environment. The Ecolego software tool will be used in the exercises. Ecolego is a tool for creating dynamic models and performing deterministic or probabilistic model simulations. Ecolego will be made available to the students by Facila AB, on a free of charge basis for academic purposes. Several practical Ecolego tutorials will be given during the course. Students who are familiar with the Matlab software, may also use it for the exercises. The application of free software Ecopath/Ecosim as a tool for analysis of exploited aquatic ecosystems will be discuss on the course.

Web link to the course https://sites.google.com/a/facilia.se/ecological-modeling/

Plan of PhD course “Dynamic Ecological Modeling” (1.5 hp)

7-11 September, 2015 Day Time Name Lecture title

Mon. 7 Sept.

9:00-10:00 Lena

Konovalenko,

Compartment models in Biology and Ecology.

10:00-11:00 Eric Johansson, “Ecolego” software as a modelling tool – overview. 11:00-12:00 Boris Shapiro Concepts of differential equations.

12:00-13:00 Lunch 13:00-16:00

Lena

Konovalenko

Practical Exercises and construction of simple model,

Running a model deterministically,

Working with outputs.

Tuesday 8 Sept.

9:00-10:00

Emma Undeman

Modelling fate and bioaccumulation of organic

chemicals.

10:00-12:00 Boris Shapiro Systems of differential equations.

The predator-prey model (Lotka-Volterra model).

12:00-13:00 Lunch

13.00-15:45 Lena

Konovalenko

Construction and implementation the Lotka-Volterra

model and solving numerically using Ecolego or

Matlab.

Wed. 9 Sept.

9:00-12:00 Oleg Savchuk Basics of marine ecosystem modelling.

Modeling of the Baltic Sea eutrophication. 12:00-13:00 Lunch

13:00-15:00 Oleg Savchuk Practical exercises with SANBALTS and

BALTSEM.

Thur. 10 Sept.

9:00-11:00

Susa Niiranen

The application of free software Ecopath/Ecosim as a

tool for analysis of exploited aquatic ecosystems.

11:00-12:00 Boris Alfonso Application in the innovative European project “The

Future of Fully integrated human exposure

assessment of chemicals 4FUN”.

12:00-13:00 Lunch

13:00-15:30 Lena

Konovalenko

Running model probabilistically.

Fri. 11 Sept.

9:00 Arrival in Askö Visit of Marine laboratory. 9:30-12:00 Birkir Veigarsson Modelling of the authorised releases of radionuclides

to Baltic Sea from nuclear power plants.

12:00-13:00 Lunch 13:00-16:00

Lena

Konovalenko,

Overview of several models for element transport in

biosphere and practical exercises.

16:30 Departure to

Stockholm

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Course coordinator (Participant both in lectures and practical exercises):

Lena Konovalenko,

lena.konvalenko@su.se, tel. +46 8 161744, Department of Ecology, Environment and Plant Sciences Stockholm

University (DEEP), Stockholm University. http://www.su.se/emb/ PhD degree in Marine Ecotoxicology. Research interests focus on Ecology, Radioecology and Modelling of element transport in aquatic ecosystems. The study of carbon circulation and investigation of benthic and pelagic

biochemical cycles and connection between them.

Course leader of lecture sections:

Oleg Savchuk,

oleg.savchuk@su.se, +46 8 674 7581

Baltic Nest Institute,

Stockholm University http://www.balticnest.org/

His main research interest is mathematical modelling as a tool to study marine

ecosystems, with emphasis on biogeochemical cycles. Personal webpage

http://nest.su.se/persons/oleg/

Emma Undeman,

emma.undeman@su.se, +46 8 674 75 17,

Environmental chemistry, Baltic Sea Centre,

Stockholm University

Her research interests are Environmental modeling of organic contaminants;

Modeling persistent organic contaminants in the Baltic Sea.

Personal webpage http://www.aces.su.se/itm/page.php?pid=536&id=207

Susa Niiranen,

susa.niiranen@su.se, +46 8 674 75 63,

Stockholm Resilience Centre, Stockholm University

Her main research interest is modelling Baltic Sea web food web dynamics.

The Ecopath/Ecosim www.ecopath.org as a tool for analysis of exploited

aquatic ecosystems. Personal webpage:

http://www.stockholmresilience.org/21/contact/staff/2-2-2010-niiranen.html

Prof. Boris Shapiro,

shapiro@math.su.se, +468164572

Department of Mathematics http://www.math.su.se/

Stockholm University

His main interests are Applied Mathematics, Algebra and Differential Equations. Personal webpage http://staff.math.su.se/shapiro/

Erik Johansson, erik@facilia.se

Company Facilia, Stockholm

Senior developer.

His main interests are programming, graphical user interface layout and

design. Training and course development in computer programming.

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Boris Alfonso,

boris@facilia.se

Company Facilia, Stockholm

Software engineer and project manager, and in developing and maintaining of

database driven websites (e.g. ERICA Assessment Tool, CONNECT platform,

4FUN project).

Birkir Veigarsson,

birkir.veigarsson@facilia.se

Company Facilia, Stockholm

IT Consultant.

His main interests are Modelling of radionuclide transport, Modelling heat

transfer in goods e.g. fish.

Useful Links:

Tool for management of the Baltic Sea:

The Nest Decision Support System (DSS), with its models and databases, is available online, free of

charge and can be run in both an expert mode and a manager mode. This dual modality is aimed at

both researchers and managers.

http://www.balticnest.org/balticnest/thenestsystem.4.2beb0a011325eb5811a8000127598.html

Practical exercises with SANBALTS and BALTSEM via Nest http://www.balticnest.org/

Ecopath with Ecosim (EwE) is a free ecological/ecosystem modeling software suite. EwE has three

main components: Ecopath- a static, mass-balanced snapshot of the system; Ecosim - a time dynamic

simulation module for policy exploration; and Ecospace - a spatial and temporal dynamic module

primarily designed for exploring impact and placement of protected areas

www.ecopath.org

The commercial Ecolego software tool will be used in the exercises http://ecolego.facilia.se/

Ecolego is a tool for creating dynamic models and performing deterministic or probabilistic model

simulations. Ecolego will be made available to the students by Facila AB, on a free of charge basis for

academic purposes. You can easy register to get demo-version of Ecolego by entering email, click

"Register" in Right Upper Conner of website http://ecolego.facilia.se/ecolego/show/HomePage

Askö Laboratory - a centre for marine research.

http://www.su.se/ostersjocentrum/english/ask%C3%B6-laboratory/about-the-field-station

European project “The Future of Fully integrated human exposure assessment of chemicals 4FUN

MERLIN-Expo tool: general overview of the graphical user interface and simple demonstration of

the software. http://merlin-expo.4funproject.eu/about/