PARAFAC course

“Parallel Factor Analysis for DOM fluorescence” is an online course run by Kathleen Murphy (Chalmers University of Technology), Urban Wünsch (Technical University of Denmark), and Colin Stedmon (Technical University of Denmark).

In our course, you will learn how to analyze the fluorescence composition of dissolved organic matter using PARAFAC.

The course

Overview

This online course will provide instruction on best-practice application of PARAFAC to fluorescence datasets, demonstrated using the drEEM toolbox for MATLAB.

The course will be mainly delivered online using written documents, recorded lectures and videos. In person Question & Answer sessions will be held via Zoom on Mondays during each week of the course. To accommodate participants in different time zones, Zoom meetings will take place on Monday morning 0800-1000 CEST* then will be repeated at 1600-1800 CEST*. Recordings of these meetings will be available to participants who are unable to attend on either occasion.

Participants are expected to upload an assignment during each week of the course. You can bring your own data or use the datasets provided. The expected workload is 10-30 hours per week depending on prior experience. All participants need to have access to MATLAB (2018 or later) and the ability to install the drEEM toolbox for MATLAB (admin rights not required).

The course is part of a long-term collaboration between researchers at Chalmers University of Technology and the Technical University of Denmark.

If you are a student, you can obtain a certificate recommending the award of 5.0 ECTS credits after completing the course. Its an important distinction as we can only award points to students enrolled in our PhD program.

*Timezone: Central European Summer Time (CEST) +0200 UTC

Learning outcome

After completing the course, the student should be able to independently produce a validated PARAFAC model from fluorescence and absorbance measurements using the drEEM toolbox in MATLAB.

Students demonstrate their progress in the course by uploading assignments. A certificate recommending the award of 5 ECTS (Higher Education Credits) will be sent to participants that complete all three assignments.

Specific learning goals

  1. Describe the theory of PARAFAC for fluorescence and its underlying assumptions
  2. Describe why inner filter effects occur and how to deal with them
  3. Clean a fluorescence dataset (identify and eliminate bad data)
  4. Model a fluorescence EEM dataset
  5. Validate the model using internal and external methods
  6. Interpret a PARAFAC model of FDOM

What will be covered? What will we discuss?

  1. Content covered in videos/lectures
  2. Content covered in papers where instructors were co-authors
  3. Using the drEEM toolbox
  4. Cleaning and modelling EEM datasets.
  5. Validating and exporting PARAFAC models
  6. Interpreting PARAFAC models of DOM fluorescence.

What will not be covered

The list of topics that users want to discuss is very long. Unforntunately we cannot cover everything. From previous experiences, we have to refrain from the following topics in the interest of time:

  • Using and calibrating your fluorometer
  • Measuring and applying spectral correction factors
  • EEM calibration, i.e. conversion to RU or QSE units
  • Implementing PARAFAC using different software platforms: e.g. PLS_Toolbox, staRdom, DOMFluor.

The course schedule

The main part of the course will span over three weeks. Each week covers several topics that are introduced and discussed in a Zoom session. This session is supplemented with video material that participants can view on their own schedule. The topics are then also discussed in weekly assignments that are meant to deepen the understanding of each topic and show which software tools can be used for specific tasks. Here’s a list of the topics per week:

Course schedule

The teachers

The team

Kathleen (Kate) Murphy

Kathleen Murphy

Kate’s research focuses on the interpretation of fluorescence from dissolved organic matter in natural waters and the application of fluorescence for distinguishing between water sources and detecting changes in water quality. Recent research projects relate to detecting changes in organic matter character during recycled and drinking water treatment, and tracing the geographical origin of ships’ ballast water. She has instigated several open-source projects aimed at improving the modelling and interpretation of natural organic matter fluorescence, including the MATLAB toolbox drEEM and the online database of fluorescence spectra OpenFluor.

Kate is a Associate Professor at Chalmers University of Technology (Gothenburg, Sweden)

Urban Wünsch

Urban Wünsch

Urban’s research focusses on the analytical chemistry, ultraviolet-visible spectroscopy, chemometrics, and software development. Urban is an active contributor to the drEEM toolbox and is currently developing the the Environmental Data Fusion toolbox (EDF toolbox). He continues to design new approaches to deconvolute dissolved organic matter (DOM) fluorescence by combining analytical methods with the latest chemometric tools. His current project focusses on the cycling of DOM in the Arctic ocean, especially the role of photodegradation.

Urban is a postdoctoral researcher at the Technical University of Denmark.

Colin Stedmon

Colin Stedmon

Colin’s current research is centred around chemical oceanography and environmental spectroscopy. Chemical oceanography is the study of the chemical composition of seawater and understanding how both physical and biological processes influence the biogeochemical cycling of elements in the sea. Spectroscopy is the study of the interaction of light with matter. In his research he use it as an approach to study the distribution and turnover (biogeochemistry) of matter in the ocean. This he does in both in the laboratory but also in the field as optical oceanography, which is in essence environmental spectroscopy.

Colin’s research builds on and now revives an earlier world leading position that Denmark had within the field optical oceanography (Jerlov, Copenhagen University) and takes it further by integrating it with modern chemical oceanography and new instrumental and computational capabilities. The organic matter spectroscopy techniques he has developed for oceanography has now spread to a wide range of other fields such as drinking and waste water treatment, recirculated aquaculture and ballast water assessment.

Colin is a Professor at the Technical University of Denmark.

Prices

Basic registration:

  • Early-bird registration: 4900 DKK (approx. $760 or 660€)
  • Standard registration: 5500 DKK (approx. $850 or 740€)

Depending on how close you register to the event, one of these options will be available to you.

In certain cases, we offer reduced rates. These are not available on the website and we kindly ask you to contact us at dreem@openfluor.net for information how to register with these rates. We’re applying the World Bank’s statistics for income (low and lower middle income) to offer discounted rates for developing countries (link to the map).

Special rates:

  • Developing country: 2900 DKK (approx. $445 or 390€)
  • Multiple lab-member registration: 4300 DKK (approx. $665 or 590€) for each member
When?

The next course will run in from January 31st to Feburary 25th 2022.