2014 PICES
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    PICES 2014 Summer School
    on End-to-End Models for Marine Resources Management and Research

    August 26–29, 2014
    Gangneung-Wonju National University (GWNU), Korea

    Please download electronic versions of lecture notes (http://www.webhard.net, in preparation) with lecturers’ names ahead for yourself to be better prepared for summer school courses. Dr. Chung Il Lee will update the above site as soon as he receives additional materials from lecturers, so check the above site until you leave your country. If you have any problem with downloading these files, please contact Dr. Lee directly. Local organizers will provide you with a printed version of lecture notes at the registration desk. As color printing would be limited during the summer school period, please bring your own printed color version if you think it is of help to you.


    Day 1: Tuesday (August 26)
    Introduction to End-to-End Modeling
    Topics: Why do we build models (e.g., hypothesis testing, understanding, diagnosing, forecasting); What is an end-to-end model; continuous and discrete differential eq. with example of NPZD (continous); IBM (discrete, difference equation); time-stepping schemes (Euler Forward/Backward the stability, Runge-Kutta and numerical integration for non-linear equations)

      08:30-09:20 Opening addresses
      09:20-10:30 Instructor: Isaac Kaplan
    Introduction to End-to-End models [Why do we build models? Definitions and examples of end-to-end models].
      10:45-12:30 Instructors: Emanuele Di Lorenzo and Kenneth A. Rose
    Continuous and discrete equations and dynamics [NPZD equations, discretization and numerical schemes, example for IBM].
      13:30-15:45 Instructor: Emanuele Di Lorenzo
    Modeling Lab. [MATLAB Tutorial with a point model NPZD, sensitivity to quadratic mortality, closing with simple IBM].
      16:00-17:00 Instructor: Isaac Kaplan
    Building the puzzle: how to assemble data needed for ecosystem models.
      17:10-18:30 Instructor: Rubao Ji
    Zooplankton and their role in marine food-web: ecology and modelling.


    Day 2: Wednesday (August 27)
    Food-Web Models: Ecopath and Ecosim
    Topics: Theory, structure and application of Ecopath, Ecopath with Ecosim (EwE); Adding climate forcing and fishing pressur; Ecopath is a balanced time independent model, Ecosim has time.

      08:30-09:30 Instructor: Chris Harvey
    Representing growth mortality and reproduction [how to account for these dynamics in models that include fish].
      09:30-10:00 Instructors: Chris Harvey and Chung Il Lee (contribution)
    Introduction of Ecopath food-web Model.
      10:10-10:30 Instructors: Chris Harvey and Chung Il Lee (contribution)
    Parameters for Ecopath food-web Model.
      10:45-12:30 Instructors: Chris Harvey and Chung Il Lee (contribution)
    Modeling Lab [Ecopath tutorial, use model to test impacts of fishing on other species].
      13:30-14:00 Instructor: Chris Harvey
    Introduction of Ecosim dynamic model and parameterization.
      14:00-14:30 Instructor: Chris Harvey
    Ecosim: Including the effects of time-varying fishing in ecosystem models.
      14:30-15:00 Instructor: Chris Harvey
    Ecosim: Including the effects of time-varying climate in ecosystem models.
      15:00-17:00 Instructor: Chris Harvey
    Modeling Lab [Tutorial to use a simple Ecosim and add fishing/climate].


    Day 3: Thursday (August 28)
    Atlantis Ecosystem Model
    Topics: Adding time dependent forcing in the ecosystem model (e.g. climate forcing and fishing pressure). Making key decisions about spatial representation, biological groups, fisheries, and oceanography.

      08:30-09:30 Instructor: Isaac Kaplan
    Atlantis Overview [Strategic models, Management Strategy Evaluation, Data requirements overview].
      09:30-10:15 Instructor: Isaac Kaplan
    Atlantis case studies Part I [California Current – Key topics: Management applications, uncertainty, and modeling choices].
      10:30-11:15 Instructor: Isaac Kaplan
    Hands-on demonstration: Running Atlantis and viewing Atlantis output.
      11:15-12:30 Instructor: Isaac Kaplan
    Modeling Lab I [Tutorial to analyze Atlantis output and calculate impacts of fishing on abundance, biomass, and size-at-age. Begin new simulations].
      13:30-14:30 Instructor: Isaac Kaplan
    Atlantis case studies Part II [California Current and Gulf of California, Mexico – Key topics: fishery fleet dynamics, global change, cumulative impacts].
      14:30-16:00 Instructor: Isaac Kaplan
    Modeling Lab II [Groups analyze their new model output; evaluate impacts of changes in biological and fishery parameters].
      16:15-17:00 Instructors: All [Discussion of how earlier model do or do not handle space, individual behavior, and dispersal]
    Summary of model types – review of NPZD, Ecopath with Ecosim, Atlantis, and discuss role of IBMs.


    Day 4: Friday (August 29)
    Individual-Based Models
    Topics: Overview of Individual Based models; Lagrangian particle dynamics, using physical models to implement particle tracking algorithm; adding behavior to particle to develop IBMs.

      08:30-10:00 Instructor: Kenneth Rose
    Overview of Individual-based models.
      10:00-11:00 Instructor: Kenneth Rose
    Intro to IBM Models: Growth, mortality, reproduction, and movement.
      11:00-12:30 Instructor: Kenneth Rose
    Book-keeping and super-individuals.
      13:30-14:30 Instructors: Emanuele Di Lorenzo and Kenneth Rose
    IBM Models: particle tracking and physical circulation (overview of the physical model).  Instructors:
      14:30-16:30 Instructor: Emanuele Di Lorenzo
    Modeling Lab. [Example of MATLAB lagrangian/IBM: Case of a gradient/front structure in 2D with temperature as the cue for behavior, with some eddies at the front].
      16:30-17:00 Instructor: Kenneth Rose
    IBM Models: Adding behavior (e.g., theory of movement, implementing behaviors in particle tracking algorithms).
      17:00-17:30 Instructors: All
    School Summary, and question-and-answer period.
      18:00-20:00 Social event
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