Introduction to Network Analysis in Life Sciences
Next edition 2020
Ecology
Course overview
In Ecology and Socio-Ecological systems 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 models should be individuals. This is the aim of individual based modelling (or agent-based modelling).
In this course, we present the principles of agent-based modelling. We will introduce participants to NetLogo**, a development environment and a domain specific computer language for agent-based modelling. In lectures, we explain techniques to develop, analyse, test and document agent-based simulation models. Hands on session will familiarise participants with the concepts: In small groups they will develop, implement and analyse an agent-based model to answer an ecological or socio-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.
DATE
October 21st-25th, 2019
LANGUAGE
English
COURSE LENGTH & ECTS
32 hours on-site.
This course is equivalent to 2 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 14 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
Dr. Jürgen Groeneveld
Institute of Forest Growth and Computer Sciences
Germany
Lukas Egli
Helmholtz Centre for Environmental Research – UFZ
Germany
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 21st, 2019.
- Morning. Lecture: Introduction to agent-based modelling.
In the first lecture, we will give a general overview of model applications in ecology and socio-ecological systems. We will then focus on our main course topic: Process-based, spatially explicit agent-based models. This model type is suitable in the context of many ecological and socio-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 agent-based modelling, NetLogo. We will present basic functionality and example models during the first NetLogo session.
Tuesday, October 22nd, 2019.
- Morning. Classroom exercise: 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 and socio-ecological research questions that will be solved by participants in groups of two during the week applying 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 and socio-ecological research questions. Participants will select and investigate one of them by developing, implementing and analysing their own agent-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 and socio-ecological modelling.
Wednesday, October 23rd, 2019.
- Morning. Project work: Development and implementation of models to solve the instructive ecological and socio-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 24th, 2019.
- 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.). 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 25th, 2019.
- 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 ABM 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/.
Fees
- Course Fee
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- Early bird (until June 30th, 2019):
- 592 € *
(473.60 € for Ambassador Institutions)
- Regular (after June 30th, 2019):
- 810 € *
(648 € for Ambassador Institutions)
- This includes course material, coffee breaks and lunches (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
- Course Fee + Accommodation Package
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- Early bird (until June 30th, 2019):
- 592 € * + 350 € = 942 €
(823.60 € for Ambassador Institutions)
- Regular (after June 30th, 2019):
- 810 € * + 350 € = 1160 €
(998 € for Ambassador Institutions)
- This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
You can check the list of Ambassador Institutions HERE. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.org.
Discounts (see Funding below) are not cumulative and apply only on the fee.
We offer the possibility of paying in two instalments (contact the course coordinators).
Accommodation
Accommodation Package
If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.
A supplemental charge will be added if you prefer to stay in a single room. 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.
Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).
Other accommodation options
If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.
Rural House Can Carol
Rural House Can Carol
Rural House Can Carol
Schedule
Course Schedule
- Monday to Thursday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 18:00 Lessons.
- Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
Accommodation Package Schedule
- Sunday:
- 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information in How to get there.
- 20:00 Registration in the Hotel.
- 20:30 Dinner.
- Monday to Thursday:
- 8:30 to 9:00 Breakfast.
- 20:30 Dinner.
- Friday:
- 8:30 to 9:00 Breakfast.
- 15:00 Meeting point in the Hotel to take the bus to Barcelona city.
- 16:30 Arrival at Plaza Catalunya (Barcelona).
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.
Funding
Discounts
Former participants will have a 5 % discount on the Course Fee.
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).
Unemployed scientists living in Spain, as well as PhD students based in Spain 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 coordinator. 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.
Scholarships
Thanks to the donations of former participants, this year there are scholarships available for PhD students. The scholarships are in the form of tuition fee waivers only, they do not cover travelling and lodging.
If you want to apply please fill up this form. Deadline: June 30th, 2019. You should register for the course before applying.
Introduction to Agent Based-Models Using NetLogo - 5th Edition 2018 (Barcelona, Spain)
Course Introduction to Agent Based-Models Using NetLogo - 4th Edition 2017 (Barcelona, Spain)
Course Introduction to Agent Based-Models Using NetLogo - 3rd Edition 2016 (Barcelona, Spain)
Course Introduction to Agent Based-Models Using NetLogo - 2nd Edition 2015 (Barcelona, Spain)
Course Introduction to Agent Based-Models Using NetLogo - 1st Edition 2014 (Barcelona, Spain)
Testimonials
“I really enjoyed this course. The five days were well organised and the course convenors were friendly. When I arrived at this course, I hadn’t had any experience of Agent-Based Modelling but now I am looking forward to incorporating this method into my research.”
“I had previous experience in individual-based modelling in ecology, but, before attending the course, I had no idea about NetLogo. The nice thing is that, on 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. Gorgeous venue, nice working atmosphere, and excellent, experienced teachers made the whole learning process really enjoyable!”
“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 students from around the world, teachers and organizers. And by the way Spanish food was a pleasure. So get there …”
Organizers
Collaborators
Registration
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Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own Partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.