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Advanced Courses in Life Sciences

3rd Edition

Introduction to Agent Based Models in Ecology Using NetLogo

October 3rd-7th, 2016, Barcelona (Spain)

Introduction to Agent Based Models in Ecology Using NetLogo

In Ecology many patterns at the population or community level emerge from processes, variability and interactions at the individual scale. Therefore it is increasingly acknowledged that the basic entities in many ecological models should be individuals. This is the aim of individual based modelling (or agent based models).

In this course, we present the principles of individual based modelling. We will introduce participants to NetLogo**, a development environment and a domain specific computer language for individual based modelling. In lectures, we explain techniques to develop, analyse, test and document individual based simulation models. Hands on session will familiarise participants with the concepts: In small groups they will develop, implement and analyse an individual based model to answer an ecological question. Questions will be suggested by the instructors and will comprise applied (e.g. sustainable forestry) and theoretical topics. Every group will present their project and their experiences at the end of the course in a short presentation. Our intention is that after the course the participants are able to implement and analyse simple models in NetLogo.

** Wilensky, U. 1999. NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modelling, Northwestern University. Evanston, IL.

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, nº 1
08781 Els Hostalets de Pierola, Barcelona.

Spain – CRIP

LANGUAGE

English

COURSE LENGHT & ECTS

36 hours on-site.

This course is equivalent to 4 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Instructors

Jürgen Groeneveld instructor for Transmitting Science

Dr. Jürgen Groeneveld
Helmholtz Centre for Environmental Research – UFZ
Germany

Alexander Singer instructor for Transmitting Science

Dr. Alexander Singer
Swedish University of Agricultural Sciences
Sweden

Nina Schwar instructor for Transmitting Science

Dr. Nina Schwarz
Helmholtz Centre for Environmental Research – UFZ
Germany

Coordinators

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Jesús Marugán-Lobón instructor for Transmitting Science

Dr. Jesús Marugán-Lobón
Universidad Autónoma de Madrid
Spain

Judit Marigó coordinator at Transmitting Science

Dr. Judit Marigó
Muséum national d’Histoire naturelle / Institut Català de Paleontologia Miquel Crusafont
France / Spain

Requirements

All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Recent version (5.0.2 or later) of the free software NetLogo has to be installed on the participant’s laptop (http://ccl.northwestern.edu/netlogo/).

Program

Monday, October 3rd, 2016.

  • Morning. Lecture: Introduction into process-based ecological models.

In the first lecture we will give a general overview on model applications in ecology. We will present a range of modelling approaches and discuss their abilities. We will then focus on our main course topic: Process-based spatially explicit individual based models. This model type is suitable in the context of many ecological problems, as it allows incorporation of many sources of natural variability and heterogeneity (e.g. spatial, temporal or individual variability).

  • Afternoon. Lecture: First Steps in NetLogo.

In the afternoon session we will introduce the participants to a development environment and a domain specific computer language for individual based modelling, NetLogo. We will present basic functionality and example models during the first NetLogo session.


Tuesday, October 4th, 2016.

  • Morning. Lecture: Example Model in NetLogo.

Our main intention is that after the course the participants are able to implement and analyse simple models in NetLogo. Therefore a substantial amount of time is dedicated to hands on exercises and project work. Thus, in the morning, we will demonstrate the development and implementation of an ecological model in NetLogo.

  • Afternoon. Project work: Presentation of instructive ecological research questions that will be solved by participants in groups of two during the week applying ecological modelling.

In the afternoon we will introduce participants to the instructive modelling projects they will develop during the course. In essence, we will suggest a selection of ecological research questions. Participants will select and investigate one of them by developing, implementing and analysing their own individual-based model in NetLogo. The suggested modelling problems will cover fields of population ecology, behavioural ecology and resource management. The modelling projects are chosen specifically to familiarise participants with strategies to develop solutions to typical practical problems in the field of ecological modelling.

Wednesday, October 5th, 2016.

  • Morning. Project work: Development and implementation of models to solve the instructive ecological research question.

In the morning participants will work on their projects assisted by the course instructors.

  • Afternoon. Lecture: Analysing and testing models.

In the afternoon lecture, we will discuss the issues of model analysis and testing. In particular we will address the analysis of complex and stochastic model outcomes. We present techniques of pattern oriented modelling (sensu Grimm et al. 2004, Science) as a means for multi-dimensional model calibration. Sensitivity analysis will be introduced to identify how simulation results depend on the chosen parameters and their values. Therefore we will introduce the NetLogo tool BehaviorSpace and present examples from case studies.


Thursday, October 6th, 2016.

  • Morning. Project work: Analysis of self-developed models.

In the morning participants will finish their model projects assisted by the course instructors.

  • Afternoon. Lecture: Model documentation.

In the afternoon lecture we will discuss documentation and communication of models. We will introduce the ODD-protocol (Grimm et al. 2006, Ecol. Model.). The ODD-protocol provides a hierarchical framework for model description by first given a general Overview then presenting specific modelling Design decisions and finally providing Details of the model implementation. ODD is becoming a standard for the description of complex individual-based models; it facilitates model comparison and communication. To practice model description and communication, participants will be given time to write an ODD description for their own model project. In this process, they will make use of the Info tab of NetLogo.


Friday, October 7th, 2016.

  • Morning. Project presentation, wrap up and feedback.

The last (half) day is reserved for the presentation of the participants’ self-developed projects. Each group will present its project and discuss their experience using NetLogo and the IBM approach. Finally there will be time for synthesising comments by the instructors and feedback by the participants.

Books

No reading is required prior to the course. However, if participants are keen on preparing themselves we recommend for a general introduction into individual based modelling in ecology:

  • Grimm V, Railsback SF (2005) Individual-based Modeling and Ecology, Princeton University Press, Princeton N.J., 428 pp.


Furthermore a good introduction to using NetLogo for individual-based Modelling in Ecology is:

  • Railsback SF, Grimm V (2012) Agent-Based and Individual-Based Modeling: A Practical Introduction, Princeton University Press, Princeton, N.J., 329 pp.


And there is lots of information on the NetLogo homepage on additional resources: http://ccl.northwestern.edu/netlogo/.

Testimonials

You will find below some testimonials from former participants to previous editions of this course:

Dr. David Alonso

“I had previous experience in individual based modelling in ecology, but, before attending the course, I had no idea about NetLogo. This programming environment is great to draft a model and perform initial model analysis through simple visual simulations. The nice thing is that, at the third day of the course, you already felt familiar with NetLogo to develop and run your own simulation models. That was as great as unexpected. For instance, according to my experience, I would say that NetLogo is easier to learn than R. Rewards from work come simply sooner. Gorgeous venue, nice working atmosphere, and excellent, experienced teachers made the whole learning process really enjoyable!” (1st Edition)

Dr. David AlonsoCentro de Estudios Avanzados de Blanes - CSIC, Spain
Damien Herfurt

“Courses were very interesting and well organized. The content was part theoretical and part practical with few students and two teachers. This was optimal to learn Individual Based Modelling. General atmosphere was really good with other student from around the world, teachers and organizers. And by the way Spanish food was a pleasure. So get there …” (1st Edition)

Damien Herfurt Institut National de la Recherche Agronomique (INRA), Centre Clermont-Theix-Lyon, France

Previous editions of this course

2nd Edition, June 15th-19th, 2015

Course Introduction to Agent Based Models in Ecology Using NetLogo - 2nd Edition, June 15th-19th, 2015Eight people belonging to the following countries and institutions participated in this edition:

  • France: French Research Institute for Exploitation of the Sea, Université de Reims-Champagne-Ardenne.
  • Sweden: Lund University.
  • Brazil: São Paulo State University.
  • Switzerland: Swiss Ornithological Institute.
  • United Kingdom: University of Exeter, University of Liverpool, University of York.

1st Edition, May 26th-30th, 2014

Course Introduction to Agent Based Models in Ecology Using NetLogo - 1st Edition, May 26th-30th, 2014Eleven people belonging to the following countries and institutions participated in this edition:

  • Spain: Autonomous University of Madrid, Centre de Recerca Ecològica i Aplicacions Forestals, Centro de Estudios Avanzados de Blanes – Consejo Superior de Investigaciones Científicas, University of Cadiz.
  • United Kingdom: Centre for Ecology & Hydrology – Natural Environment Research Council, University of Hull.
  • France: Institut National de la Recherche Agronomique.
  • Norway: Norwegian University of Life Sciences.
  • Denmark: Technical University of Denmark.
  • Switzerland: University of Zurich.

Fees

  • Course Fee
  • Early bird (until April 30th, 2016)
  • 530
  • Regular (after April 30th, 2016)
  • 740
  • This includes course material, coffee breaks and lunches.
  • Accommodation Package
  • Early bird (until April 30th, 2016)
  • 300
  • Regular (after April 30th, 2016)
  • 300
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
  • Course Fee + Accommodation Package
  • Early bird (until April 30th, 2016)
  • 830
  • Regular (after April 30th, 2016)
  • 1,040
  • This includes course material, coffee breaks and lunches.

We offer the possibility of paying in two instalments (contact the course coordinators). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinators.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

Funding

Former participants will have a 5 % discount on the Course Fee.

Scholarship: Thanks to the donations of former participants, this year there is a place for free at the course for PhD students. If you want to apply please send an e-mail to grants@transmittingscience.org including: 1- Full name and country, 2- Short project (maximum 300 words), 3- Letter of your advisor stating if you have any grant to develop your PhD. Deadline: March 31st. Please include the name of the course in the subject line.

Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Spanish unemployed scientists, as well as Spanish PhD students without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, October 2nd, 201619:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, October 3rd through Thursday, October 6th, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:00 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Friday, October 7th, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.

There will be a coffee break during the morning lesson session.

8:00 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
16:00 Arrival at the wine cellar.
17:30 Bus to Barcelona city.
19:00 Arrival at Plaza Catalunya (Barcelona).

There will be a coffee break during the morning lesson session.

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Organizers

Transmitting Science Logo
Universidad Autónoma de Madrid (UAM) Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration

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