Upcoming courses organized or co-organized by FoSW.
This course will provide a basic understanding of potential and limitations of different high throughput omics methods, and enable students to use this knowledge for building a proper multi-omics perspective fitting their biological question. We will have a specific focus on gene annotation since genes are the key for allowing us to integrate and connect different omics approaches.
Contact & registration: Maliheh Mehrshad (Maliheh.mehrshad@slu.se). Please include the following details: your name, affiliation.
Synchrotron X-ray methods are of increasing importance in environmental science and nowadays they are part of many researchers’ toolbox. There are many different X-ray methods; on this course we will focus mainly on microfocus imaging techniques (μ-XRF, STXM) and on X-ray absorption spectroscopy (EXAFS, XANES).
Potential participants should send an e-mail to jon-petter.gustafsson@slu.se no later than 2025-03-01. Please include the following details: your name, affiliation, and the title of your PhD project!
The aim of this course is to:
Focussing on ecosystem functioning in inland waters (lakes and streams) and terrestrial ecosystems (soils, riparian habitats, agricultural and forest landscapes), this course covered basic definitions, the relationship between ecosystem functioning and ecosystem services, and several currently topical themes in ecosystem functioning research. These include the roles of functional traits and calculation of functional diversity (including practical exercises in R), multifunctionality, and an overview of biodiversity-ecosystem functioning research.
Contact & registration: Brendan Mckie (Brendan.Mckie@slu.se)
Aim: To illustrate the application of number of multivariate methods on ecological data. Ordination and classification procedures will be demonstrated in lectures and exercises. The course is given in two parts. Part 1 consists of lectures and calculation exercises, and part 2 is a supervised project on your own data. You can take either only part 1, or the full course.
See this link for more information on the course and how to apply: Multivariate methods for ecologists
Would you like to know more about how to communicate your science to the general public? To communicate science teaches how to plan and perform communication work and what measures and channels that can be used to reach different target groups.
This course is organised jointly by the NJ Research Schools (Ecology - basics and applications, Focus on Food and Biomaterials, Focus on Soils and Water, Organism biology, People, Society and Sustainability, Sustainable systems for food, energy and biomaterials) and the divisions of Planning and Communication.
The course will be in hybrid format, with two physical meetings in Ultuna and some Zoom lectures in between the physical meetings. For more information about the course, and to apply, follow the link below.
Understanding & Programming in R is a week-long course designed to help researchers new to the R programming language or those who haven’t mastered R’s programming environment to become confident in using R and to design & implement analyses specific to their own research questions. It also include some pre-course preparation.
Contact Jon-Petter Gustafsson
Contact Josefin Sundin
P000102: GIS and Spatial Analysis in R
Contact Matt Low
Providing basic knowledge on N&P cycling in terrestrial and aquatic ecosystems, state‐of‐the-art techniques, including isotopes, farming, management, sustainable use, mitigation options minimizing eutrophication.
The aim of this course is to (i) provide background knowledge and their research application in the main disciplines of soil science, (ii) to discuss the current soil threats and their possible mitigation (iii) to identify synergies between different disciplines to describe and understand phenomena occurring in soils.
Aim: To illustrate the application of number of multivariate methods on ecological data. Ordination and classification procedures will be demonstrated in lectures and exercises. The course is given in two parts. Part 1 consists of lectures and calculation exercises, and part 2 is a supervised project on your own data. You can take either only part 1, or the full course.
See this link for more information on the course and how to apply: Multivariate methods for ecologists
Would you like to know more about how to communicate your science to the general public? To communicate science teaches how to plan and perform communication work and what measures and channels that can be used to reach different target groups.
This course is organised jointly by the NJ Research Schools (Ecology - basics and applications, Focus on Food and Biomaterials, Focus on Soils and Water, Organism biology, People, Society and Sustainability, Sustainable systems for food, energy and biomaterials) and the divisions of Planning and Communication.
The course will be in hybrid format, with two physical meetings in Ultuna and some Zoom lectures in between the physical meetings. For more information about the course, and to apply, follow the link below.
Understanding & Programming in R is a week-long course designed to help researchers new to the R programming language or those who haven’t mastered R’s programming environment to become confident in using R and to design & implement analyses specific to their own research questions. It also include some pre-course preparation.
The course will cover the basic concepts necessary to understand what minerals are and how they are classified according to their crystal structures and compositions. It will explain how these features affect mineral properties, and in turn how such properties may influence the properties of soils and sediments. Emphasis will be placed on mineral groups that are of the most common occurrence in soils and sediments. The structure and properties of different clay minerals will be covered in detail along with the classification of clay minerals. The origins of minerals in soils and sediments will be explained in terms of the concepts of neoformation, transformation and inheritance. X-ray methods and identification of minerals, particularly clay minerals, will be covered in some detail including practical exercises. Students will also learn the basics of how to quantify minerals in soils and sediments by the application of X-ray powder diffraction methods.
The aim of this course is to (i) introduce working with the database system PostgreSQL, (ii) apply two database-driven process-oriented models using an example dataset and visualize the outcomes using the R software, (iii) develop different agricultural management scenarios for simulations and (iv) evaluate simulation results from a process and soil systems perspective. The course consists of two parts: 1) A preparatory online meeting on 20th May 2024, 9:30-12:00, and 2) A workshop, which will be held at campus Ultuna (Uppsala, Sweden) from 27th to 31st May 2024
This course gives a theoretical foundation to navigate the maze of methods available to study communities of bacteria, archaea, fungi and other microbial eukaryotes. You will get well-acquainted with best practices for sampling, extracting, and preparing DNA and RNA for sequencing and quantification of taxonomic and functional markers from different environments. You will also gain insights into approaches to analyzing sequencing data.
The course consists of a once-per-week journal club and discussions starting 13th October (in-person or remote) and a 1-week on-campus workshop from 13th-17th November consisting of lectures, discussions, study visits, and practical laboratory and data analysis exercises. There is opportunity to develop and discuss a personal research plan after the workshop. The course is split in two parts: discussions and workshop (P000050/F0045) and a post-workshop assignment (P000051/F0043)
This course aims at improving the effectiveness of the scientific code you write by tapping into generally less utilized capabilities of R and its software ecosystem. The course will teach you how to write more ordered code and to deal with the automation of data and code handling tasks. This will allow you to save time and handle bigger data-sets.
Understanding & Programming in R is a week-long course designed to help researchers new to the R programming language or those who haven’t mastered R’s programming environment to become confident in using R and to design & implement analyses specific to their own research questions. It also include some pre-course preparation.
Would you like to know more about how to communicate your science to the general public? To communicate science teaches how to plan and perform communication work and what measures and channels that can be used to reach different target groups.
This course is organised jointly by the NJ Research Schools (Ecology - basics and applications, Focus on Food and Biomaterials, Focus on Soils and Water, Organism biology, People, Society and Sustainability, Sustainable systems for food, energy and biomaterials) and the divisions of Planning and Communication.
The course will be in hybrid format, with two physical meetings in Ultuna and some Zoom lectures in between the physical meetings. For more information about the course, and to apply, follow the link below. Registration deadline 2023-08-21.
Focus is on methods for evaluating human impacts. Connecting a broader understanding of watersheds and their interconnectedness to environmental monitoring and assessment, using existing databases. Overview about threats to water, and introduction to environmental monitoring and assessment to manage and mitigate the threats. Overview on national and international goals and legislation. Introduction into design and planning of monitoring programs, and large-scale assessment. Introduction to established monitoring methods, and to new and possible future ones, such as remote sensing and barcoding/molecular methods. Introduction into data management, environmental databases, and related error sources.
A course with focus on organic chemical pollutants in the aquatic environment, including their measurement and transport from source to tap.
Short introduction to soil system sciences with focus on micro-analytical techniques and their application to environmental samples. Literature review combined with a 1-week seminar with invited international scientists.
Aim: To illustrate the application of number of multivariate methods on ecological data. Ordination and classification procedures will be demonstrated in lectures and exercises.
Almost every field researcher uses maps but not everyone has been formally trained. This course is a short and basic introduction into GIS (geographic information system). The course will introduce GIS, GIS-software (ArcGIS), how to download and import geodata, using SLU’s GIS resources. Students will work on own geodata/questions. Course topics will cover
A PhD course in the Krycklan catchment September 15-21, 2022
How to plan and perform efficient communication using different methods and channels that can be used to reach different target groups.
Aim: To illustrate the application of number of multivariate methods on ecological data. Ordination and classification procedures will be demonstrated in lectures and exercises.
The course gives an overview of the research frontiers in the area of organic matter dynamics in terrestrial and aquatic ecosystems. From molecular chemistry, via the interplay between organisms and organic matter, to biogeochemical cycling of carbon at the global scale. Literature reviews combined with a 1‐week seminar with invited scientists (see attached schedule).
Aim: to help each student overcome the initial steep learning curve that is associated with learning R, and how to think in a structured and logical way to make programming easier.
Aquatic systems are governed by complex and scale-dependent interactions between abiotic and biotic components. As organic matter links many biogeochemical cycles e.g., carbon, nitrogen, and phosphorus, it is a robust proxy to understand the complex processes in aquatic systems and constitutes an indicator of overall health of aquatic ecosystems. In this course, we will explore the controls of organic matter stability and fate in a range of aquatic systems.
The course consists of lectures and exercises by Stephen Hillier from The James Hutton Institute in Aberdeen, Scotland. Steve Hillier is a highly qualified scientist in mineralogy in sediments and has held a guest professorship at our department at SLU. With his team at James Hutton he has won first (2008, 2018) and second (2006, 2012, 2014) place in The Reynolds Cup competition in quantitative mineralogy.
The aim of this course is to (i) provide an introduction to soil system sciences, (ii) give an overview of emerging micro-analytical techniques and their application to environmental samples; (iii) present examples of soil system sciences to study ecosystem services and (iv) to discuss challenges and the future of this research discipline.
The aim of the course is to illustrate the application of number of multivariate methods on ecological data. Ordination and classification procedures will be demonstrated in lectures and exercises.
A course with focus on organic chemical pollutants in the aquatic environment, including their measurement and transport from source to tap.
Focussing on ecosystem functioning in inland waters (lakes and streams) and terrestrial ecosystems (soils, riparian habitats, agricultural and forest landscapes), this course covered basic definitions, the relationship between ecosystem functioning and ecosystem services, and several currently topical themes in ecosystem functioning research. These include the roles of functional traits and calculation of functional diversity (including practical exercises in R), multifunctionality, and an overview of biodiversity-ecosystem functioning research.
This course focused on preparing students to analyze, interpret and report their data using the most up-to-date methods in R. Special attention was given to discuss questions springing from the students own work and the biological interpretation of data.
This course was run together with the 4th International Workshop on High Temporal Resolution Water Quality Monitoring and Analysis held at SLU 31 May - 2 June 2021. The general focus of the course was on exploring recent technological and scientific advances in water quality measurements allowing for high-resolution determination of chemicals in water with a range of instruments. The objectives of the course were to discuss how these new technologies and data can further advance catchment science and contribute to water resources management.
A PhD course and an opportunity to learn more about programming in R! Basic knowledge in the R programming language and tools for programming, processing data and analyses. Planned for May and autumn 2021. For more information, please please see the website of RS Ecology.
The course aims to illustrate the application of a number of multivariate methods on ecological data. Following the course, participants should be familiar with different multivariate techniques, and how they can be applied on various types of data. The course will focus on developing an understanding of the application of multivariate techniques, with only a minimum amount of effort placed on comprehending the underlying mathematical detail.
More details at the Department of Aquatic Sciences and Assessment.
This course recognises the importance of agricultural catchments and their sensitivity to global change and provides a comprehensive synthesis of dominant processes shaping agricultural
landscapes: hydrological, biogeochemical, ecological, economic and societal. The course comprises theoretical lectures and practical assignments focused on environmental assessment and management, all adapted to maximise the potential of distant based learning.
The course aims at improving the effectiveness of the scientific code you write and will teach you how to write more ordered code and to deal with the automation of data handling tasks. This will allow you to save time and handle bigger data-sets. The course includes three main themes and learning targets, those are to: 1) write reproducible code, 2) confidently manipulate data and R-objects and 3) check for and fix errors in data and code.
A PhD course and an opportunity to learn more about programming in R! Basic knowledge in the R programming language and tools for programming, processing data and analyses.
How to plan and perform an effective communication using different methods and channels. Research school cooperation. Please contact course coordinator Elisabeth Müllner for more information.
Overall the objectives of the course is to help the students to navigate scientific publications, and to understand the process of scientific communication.
The objectives of this course are:
Multivariate methods for ecologists, 4,5 hp. October 2019. More information is available here.
Watershed Ecology and Biogeochemistry. A PhD course in the Krycklan catchment September 19-25, 2019. 'Watershed Ecology and Biogeochemistry' addresses the foundational concepts and modern challenges within the broad field of watershed science. More information here.
PNG0079 Mini-course: UN Sustainable Development goals: relevance, achievements, conflicts and politics. Workshop 8th of February 2019, Uppsala, and optional ‘mini-course’, 1 ECTS.Syllabus. Find detailed information about the workshop 8th of February here
PNS0169 Traditional and molecular methods to assess biodiversity. Focus on DNA (meta)barcoding & Aquatic Organisms, 7hp.Detailed schedule is available here (pdf). Course page with syllabus.
PNS0171. Nitrogen cycling in terrestrial ecosystems, 4hp. 25-29th of March 2019
Understanding and coding the R programming language, 2 hp. April 1-5 (Mon-Fri) 2019. Course flyer. Course plan.
PNG0044 How to write and publish a scientific paper, 4.5 HEC
Ecological stability in times of rapid environmental change (3 credits). 15 – 19 October, 2018
Multivariate Methods for Ecologists (3 + 1.5 ECTS), 12 – 16 Feb 2018, Optional 19 Feb – 2 March
Understanding & Coding the R Programming Language (2 ECTS), April 23 - 27th 2018, Course flyer & Course plan
Organic micropollutants in the aquatic environment – measurements and transport processes (5 ECTS), April 11 - May 16 2018, Course web page & More information about the course
Reviewing and Summarizing Science: A guide on how to navigate through and ocean of paper (2ECTS), 15 to 18 May 2017
Phosphorus cycling in terrestrial and aquatic ecosystems (3 ECTS), 12 to 16 June 2017
Watershed Ecology and Biogeochemistry (7.5 ECTS), September 14 - 20 2017
How to write and publish a scientific paper (4.5 HEC), 18 Aug 2016 - 26 Jan 2017
Soil systems: Analytical methods for integrating the chemical, biophysical interface in soils (3 ECTS), 5 Oct 2016 - 30 Nov 2016
Minerals in soils and sediments and their X-ray identification and quantification, 5.0 credits, 2016-04-11
Multivariate methods for ecologists 3 (+1.5 optional) ECTS, 2016-02-29
Organic micropollutants in the aquatic environment – measurements and transport processes 5 hp, 2015-04-13
Systems Analysis, Model Building and Simulation 6.0 (+1.5) ECTS, 2015-09-14
Carbon cycling: from molecular to global processes, 3 (+1.5 Optional) ECTS, 2015-09-30
Ecological stability vs resilience: straightening up concepts and making them useful for management 3.0 ECTS, 2015-10-26
Linear mixed models and experimental design with applications to agricultural field experiments 3 ECTS, 2014-01-27
X-ray image processing and analyses 3.0 credits, 18 - 21 November 2014.
How to write and publish a scientific paper 3 ECT, 3 September - 12 November, 2013
Statistics in Practice, 2013-09-06
Research communication with the media: training and skills acquisition 2 HEC, 2013-10-01
Biogeochemical cycles at different scales 3 HEC, 2013-10-21
Research communication with the media: training and skills acquisition 1.5 HEC, 2012-03-06
Biogeochemical cycles at different scales 3 ECTS, 2012-03-12
The role of DOC and DON in plant-soil C and N cycling 5.0 HEC, 2012-03-20
Environmental Impact Assessment (EIA) for Natural Scientist 3 HEC, oct-nov 2012
Soil systems: Integrating the chemical & biophysical interface in soils, 2011-03-02
Ecosystem services in soil and water research 3-4 ECTS, May-June 2011
An introduction to R and MS Access (1.5 ECTS), February 2010
Constraints on decomposition, March 2010
PhD-course 'Soil Organic Matter Modeling'
PhD-course "Climate impacts on terrestrial and aquatic ecosystems"
PhD-course "Legumes: Plant - soil interactions and agricultural applications"
Biogeochemical cycles at different scales, april 2009
Soil and Water Chemistry Modelling 5 (+2 optional) ECTS, May 2008
PhD-course ''Modelling of chemical and hydrological processes using PHREEQC''