CALL FOR APPLICATIONS
REFOLANA SUMMER SCHOOL
Use of open source tools for spatial ecological modelling
–
based on GRASS, Qgis, AWK, GNUPLOT, GDAL/OGR, under Linux
Environment
UNIVERSITY OF COPENHAGEN, JUNE 28 – JULY 9, 2010
Forest & Landscape Denmark
Deadline for applications: May 1st, 2010
FEES: 300 €
CREDITS: 10 ECTS
PROGRAMME
This 2-weeks REFOLANA course aims at demonstrating different free and open sources
tools to carry out spatial ecological modelling and spatial analysis in ecology.
The course comprises a set of short lectures that present modelling concepts and
procedures, as well as practical sessions for participants where participants can use the
software and scripting routines to achieve large-scale data analysis and stand-alone.
The first week is dedicated to lectures and exercises of the open source software. During
the hands-on software practical sessions, participants will actively interact with different
tools and carry out spatial data analysis by manipulating data from different case studies.
Different exercises will be proposed and participants will have the opportunity to
improve their computational skills in both testing ecological theory and solving practical
questions while producing maps and summary statistics. Particular emphasis will be
placed on forest ecosystems applications.
During the second week participants will practice their acquired knowledge on a short
personal project. The participants will be supervised in their work and will have the
opportunity to analyse their own dataset and solve their own project. This short project
will allow them to briefly go through the different phases of spatial ecological
applications: conceptualization, data preparation, model fitting, model evaluation, spatial
prediction, assessment of model applicability, application of the model results and
summary statistics.
All lectures are in English
Coordination
Dr. Annemarie Bastrup-Birk,
University of Copenhagen,
Forest & Landscape Denmark,
Hørsholm Kongevej 11 DK-2970 Hørsholm
Tlf. +45 3533 1897 ab@life.ku.dk
Lecturers
Dr. Giuseppe Amatulli (giuseppe.amatulli@gmail.com)
Dr. Stefano Casalegno (stefano@casalegno.net)
Dr. Annemarie Bastrup-Birk (ab@life.ku.dk)
Dr. Patrik Nyed Karlsson (pnka@life.ku.dk)
Lucia Seebach (lucia.seebach@jrc.ec.europa.eu)
OBJECTIVES
At the end of the course participants should acquire a basic knowledge of a selection of
open source tools that are available in the context of spatial ecological modelling and
GIS/spatial analysis. After this training the students should be able to progress
independently and learn how to process data using open source software. The course
gives a useful background for data analysis in the context of forest, biodiversity,
conservation, landscape planning and other related topics such as precision farming,
geo-statistic, socio-economic issues, remote sensing and non-spatial modelling.
Tools
Linux shell scripting, GRASS and Qgis geographic information systems, R language and
environment for statistical computing and graphics, AWK programming language for
processing text- based data, gnuplot program for two- and three-dimensional plots of
functions and data, geo-tools library for the manipulation of geospatial data (Gdal and
OGR translator library for raster and vector geospatial data).
TARGET GROUP
This training is addressed to a diverse population of students at master's or doctoral level
with a common interest on spatial data analysis and ecological modelling.
Students should have a basic knowledge of GIS to be able to follow the training and
better improve their computational skills.
Students are expected to provide an idea for a one week project as well as needed data
to be processed in order to fulfil the project task. If needed a project proposal with its
related data
can be provided in agreement with students and with the responsible of the Department of
Forest & Landscape.
A maximum of 30 students can be enrolled in the course.
CREDITS: 10 ECTS
In order to obtain the 10 ECTS (European Credit Transfer System) the participants
should present the project and the results at the end of the course - or submit a paper
(min. 10 pages) on the results at the latest 1 month after the end of the course.
Training exercises
Appropriate exercises will be provided allowing students to practice the use of tools and
methods in spatial data handling. The exercises and examples are applied within a large
variety of topics: forestry, landscape planning, predictive modelling, mapping, nature
conservation and spatially related fields of study. In agreement we can adjust key
examples and focus exercises on other special needs.
COURSE OUTLINE
1 . Course Presentation
1. Knowing each other: trainers and student's background
2. Identifying student's needs
3. Course objectives and schedule
2 . The Open Source tools
1. Linux environment
2. Why and what to use
3. Introducing the Ubuntu virtual machine
3 . Lectures
1. The basic modelling concepts and procedures in ecology
2. Introduction to Spatial ecological modelling
3. Models examples: non-parametric algorithms, ensemble classifiers, machine
4. learning techniques
5. Forest habitat suitability modelling
6. Forest fire danger forecast model
4. UNIX/LINUX Bash programming
1. Why to use Unix/Linux command line
2. The basic commands
3. Command syntax
4. File management
5. Read and explore a text file
6. Meta-characters and their use
7. Concatenate process
8. The use of variable
9. The ‘for’ loop
10. Case study and exercise
5. AWK Programming language
1. Why to use AWK command line
2. The basic commands Command syntax
3. Built in variables
4. Import variables
5. String functions
6. Numerical functions
7. Query function
8. Manipulate large files before importing in R
9. Case study and exercise
6. GNUPLOT
1. Why to use GNUPLOT command line
2. Commands syntax
3. Plotting data
4. Use AWK language inside GNUPLOT
5. Case study and exercise
7. GEO-TOOLS
1. Introduction to GDAL/OGR
2. Command syntax
3. Raster data manipulation
4. Built up specific geo-tools
5. Case study and exercise
8. R environment for statistical analysis and graphics
1. Introduction to R environment
2. R structure, libraries, scripting and getting help
3. Command syntax, R objects
4. Basic commands (input, output, data creation)
5. Data manipulation
6. Plotting data and graphical parameters
7. Programming (functions, if and if else condition, for loop, while, system variable)
8. Spatial and ecological modelling libraries Basic statistic
9. A linear model and step-wise regression
10. More complex algorithms (Classification and Regression Tree / Random Forest)
11. Importing geo-data
12. Model prediction
13. Exporting the data
14. Case study and exercise
9. Quantum GIS
1. Introduction to Quantum gis
2. Import and export data
3. Data visualization and map creation
4. Qgis as Gui to GRASS and as a learning tool
10. GRASS Geographical Resources Analysis Support System
1. Introduction to GRASS
2. Data structure in GRASS
3. Command syntax and general commands of data handling
4. Raster and vector data import, export, display and conversion
5. Raster map calculator
6. Vector manipulation and processing
7. GRASS / Qgis interface
8. Scripting in GRASS: combine BASH commands with GRASS commands
9. Environment variables and their importance for shell scripting
10. Case study and exercise
11 . Case studies, processing procedure - stand alone process
e.g. depending on requests of the student’s
1. Projecting future burnt area in the EU countries under IPCC SRES A2/B2
2. Modelling the Distribution of the Natural Forest Formations in Europe under
present and future climates
12 . Student's project
1. Students presenting their case study dataset and related questions:
generating and testing hypothesis
2. Open discussion on students' interests and new tools to approach case study
3. Identification and statement of students' needs, method of data processing and
expected objectives
4. Data preparation, statistical data analysis, modelling and mapping, synthesis and
presentation of results
5. Students presenting their project and results
NB: Each subject or software tool can be presented in its basic function or in a more
advanced way considering the level of students and their needs.
LOGISTIC and GUEST INSTITUTE REQUIREMENTS
The training is a hands-on oriented approach. Classes will be carried at The University of
Copenhagen, Forest & Landscape, Frederiksberg in rooms with a video projector and
access to computers connected to the internet for each student.
Before the course starts the instructors will install a Linux Ubuntu operating system virtual machine (http://www.gisvm.com/) and all required software on every computer.
A wiki web-site infrastructure will serve as a tool for data exchange, download scripting
procedures, download case study and exercises, uploading exercise results and
group-work.
Each student will receive an account on the wiki and will be able to use it as working
tool.
The web hosting is provided by the instructors.
SCHEDULE AND ORGANISATION (small changes may occur)
Type of class work: Lectures and presentations Student exercises / practical training
Instructors: G. Amatulli, S. Casalegno, A. Bastrup-Birk, L. Seebach (P: students' project)
COURSE TEAM
Dr. Giuseppe Amatulli, Post-Doc position at the Institute for Environment and
Sustainability of the Joint Research Centre since February 2006. Professional Research
experience: His research activity is mainly dedicated to wildland fire with special
emphasis on wildfire occurrence and pattern recognition, wildfire risk assessment based
on human and bio-physical parameters.In the framework of European Forest Fire
Information System he provides scientific and technical support for development,
implementation and improvement of the Fire Weather Index applied to the European
territory. Past and future forest fire trends under potential climate change scenarios,
handling ECMWF and PRUDENCE
climate data. Modeling forest species distribution, current, potential and future trends
using WorldClim dataset. He is dealing with high resolution data in the context of
complex andmodern modeling techniques by stand-alone implementation process.
Education: MSc in Forest Science at University of Bari - Italy (2000); MSc in
Geo-Information Science at Wageningen University - The Netherlands (2004); PhD in
'Crop Systems, Forestry, and Environmental Sciences' at Basilicata University - Italy
(2005), carried out manly in The Netherlands and in Spain. The main objective of his
dissertation was the implementation of non-parametric
statistical analysis for fuel model mapping and fire occurrence assessment. Before joining
the JRC he was working at the Universidad de Zaragoza - Spain - Dep. de Geografia as a
Post-Doc researcher scientist.
Dr Stefano Casalegno is a plant ecologist and modeller with a focus on spatial ecological
modelling of forests. He has been involved in various fields of ecological applications:
Plant insect and
plant bird interactions (Univ. Paris Sud and Univ. of Bristol, Kibale Forest Nat. Park
Uganda, 1996); Mountain Forest Ecotones and vegetation belt mapping, (CEFE - CNRS,
France 1997, CIBNOR La Paz - Mexico 1998, INA P-G France 1999-2001); Biofuels,
forestation potential and forest yield estimations (INRA Versailles - MAICh Crete 2002);
Integrated studies for the assessment of forest condition and climate change impact on
European forests (JRC of the European Commission 2004-2008). Recently, he has been
working on suitability modelling of European forests, Urban and peri-urban forests, and
alpine ecosystems. He is involved in the activities of the International Union for Forest
Research Organizations and participating in the European expert panel on forest growth
of the ICP-Forest task force (United Nations Economic Commission for Europe).
Education:
PhD in Applied Forest Ecology (GIS - remote sensing) at INA P-G, France (2001). MSc
Ecology “DEA d’Ecologie” Eco-physiology and Ecosystem functioning at INA P-G
Univ. Paris-Sud XI and Univ. Paris VI (1997). BSc Ecology. “Maitrise d’Ecologie”,
Univ. of Paris-Sud XI (1996). University degree in Natural Sciences “Licence ès
Sciences Naturelles”, University of Paris-Sud XI (1995).
Dr. Annemarie Bastrup-Birk has 20 years research experience. The professional
experience lies within forest biodiversity, forest inventory and monitoring, sampling
design. Recent work have focussed on research within National Forest Inventories and
multiple scale inventories including remote sensing, forest ecosystems, forest
biodiversity, forest resource assessments, geographic information systems.
Education:
B.Sc in Geography and Geoinformatics at the Institute of Physical Geography,
University of Copenhagen. MSc. in Agronomy at the Institute of Agrohydrology and
Bioclimatology, University of Agriculture. PhD. in agronomy at the Institute of
Agrohydrology and Bioclimatology, University of Agriculture, Copenhagen.
Patrik Nyed Karlsson is GIS specialist at the University of Copenhagen
Lucia Seebach is PhD Student at the University of Copenhagen, Forest & Landscape.
REGISTRATION
DEADLINE May 1st, 2010
COURSE FEES 300 €
The registration fees includes course fees, coffee/ tea, conference material
Please send your registration form to bha@life.ku.dk (Mrs. Barbro Haar )
Name:
Affiliation:
Address:
e-mail:
Arrival date and time:
Departure date and time:
Optional: idea for a one week project
Dietary preferences
Participants will be notified for acceptance. Further information on venue and
accommodation will be sent after acceptance
Payment is requested by either
Bank transfer to Danske Bank – mark your name and use of.
Account No: 3306-4490058141
IBAN NR. DK6330004490058141
BIS/SWIFT: DABADKKK
Or
CHECK:
BENIFICIARY:
University of Copenhagen, Forest & Landscape
ADDRESS: Hørsholm Kongevej 11. 2970 Hørsholm. Denmark. Att. Ullla Nielsen
LINKS OF INTEREST
www.spatial-ecology.net