Constraint-based modeling: Introduction and Advanced topics

This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods, omics data integration, multi-scale modeling and microbial community modeling. The course will combine theoretical lectures with tutorial exercises and computational… Continue reading

Integrated Modeling and Optimization (2024) – Fundamental course

In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques… Continue reading

Multi-Omics and Data Sciences in Complex Diseases

Many diseases are complex, their polygenic nature combined with gene-environment interactions leads to a situation where single omics are insufficient to both understand the biology and to make reliable diagnostic or prognostic predictions. This course will cover advanced multi-omics screening technologies and look at how we use cutting edge data science to make sense of our measurements and bring explainability… Continue reading

RNA-seq data analysis

The 9th edition of the RNA-seq Data Analysis course will be held on 8-12 April – 2024 in Breda, The Netherlands. This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux… Continue reading

Knowledge graphs in the life sciences

Course coordinator  Jasper Koehorst, Wageningen University (location WUR-campus)  Lecturers  Onder Babur (Wageningen University & Research)  Anna Fensel (Wageningen University & Research)  Jasper Koehorst (Wageningen University & Research)  Course credits  1.5 ECTS for following the course, 3 ECTS when successfully completing a final assignment  Course overview  The term “FAIR Linked Data” refers to a set of best practices for publishing, interlinking… Continue reading

Integrated Modeling and Optimization (Fundamental)

Course date 12-16 December 2022, Wageningen Location: The course will be held at: Forum Building (building nr 102), with number B0508. Course coordinator Natal van Riel, Eindhoven University of Technology Dr. Dragan Bosnacki, Eindhoven University of Technology Lecturers Jaap Molenaar, Wageningen University & Research, jaap.molenaar@wur.nl Robert Smith, Wageningen University & Research, robert1.smith@wur.nl Aalt-Jan van Dijk, Wageningen University & Research, aaltjan.vandijk@wur.nl… Continue reading

Life Sciences Data Integration Challenge

Data science is revolutionizing our understanding of biology in biotechnology and systems health… What can you do in one week? Current and future scientific problems require multi-disciplinary solutions and research teams composed of members from broad domain backgrounds. The Life Sciences Data Integration Challenge 2022 is targeted at PhD candidates and MSc students from life science, biotechnology, and bioinformatics fields.… Continue reading

Computational Metagenomics (Advanced)

Course coordinators Marnix Medema, Wageningen University Jingyuan Fu, University Medical Centre Groningen Lecturers Marnix Medema, Wageningen University Jingyuan Fu, University Medical Centre Groningen Walter Pirovano, Baseclear Vittorio Tracanna, University of Cologne Mattias den Hollander, Netherlands Institute of Ecology Saskia Hiltemann, Erasmus Medical Center Tatiana Gurbich, European Bioinformatics Institute Anne Kupczok, Wageningen University Chrats Melkonian, Wageningen University / Utrecht University Daniel… Continue reading

Single-Cell Analysis

This week-long course will cover the practicalities of single-cell sample prep and analysis with a particular focus on single-cell RNA-seq libraries.  Course coordinators: Dr. Susan Kloet (LUMC) Dr. Miao-Ping Chien (Erasmus MC) Dr. Ahmed Mahfouz (LUMC) Course Credits: The study load of this course is 2 ECTS credits. Participants will get a certificate after successfully completing this course. Course overview:… Continue reading

Constraint-based modeling: Introduction and advanced topics

This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods, omics data integration, multi-scale modeling and microbial community modeling. The course will combine theoretical lectures with tutorial exercises and computational… Continue reading