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

Machine Learning for bioinformatics and systems biology

In this one-week course, the foundations of machine learning will be laid out and commonly used methods for unsupervised (clustering, dimensionality reduction, visualization) and supervised (mainly classification) learning will be explained in detail. Methods will be illustrated using recent examples from the fields of systems biology and bioinformatics. Methods discussed in the morning lectures will be put into practice during… Continue reading

Algorithms for Genomics (2nd edition)

In this course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. Course coordinators dr. Thomas Abeel (TU Delft) dr. Sandra Smit (Wageningen… Continue reading

RNA-seq data analysis

The 2022 edition of the RNA-seq data analysis course will be held on 9-13 May, 2022 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. Location Address: Hogeschoollaan1, 4818 CR Breda, The Netherlands Course coordinators Andrew Stubbs,… Continue reading

MGC/BioSB Single Cell Analysis Course

Date: 18-22 October, 2021 Location: on-line Organizer: The course will be organised by the MGC – Susan Kloet, Miao-Ping Chien, and Ahmed Mahfouz Course overview This week-long course will cover the practicalities of single-cell sample prep and analysis with a particular focus on single-cell RNA-seq (scRNA-seq) libraries. The course features a mix of lectures and practicals, and you will have the opportunity to perform hands-on… Continue reading

Machine Learning for bioinformatics and systems biology

Date: 11-15 October 2021, Amsterdam (if COVID-19 restrictions are lifted, otherwise online) Course overview Modern biology is a data-rich science, driven by our ability to measure the detailed molecular characteristics of cells, organs, and individuals at many different levels. Interpretation of these large-scale biological data requires the detection of statistical dependencies and patterns in order to establish useful models of… Continue reading

Integrated modeling and optimization

Course date 13-17 December 2021, Wageningen Location: The course will be held at: Forum Building (building nr 102), with number B0409. A Biocafe (on Thursday) will be held in “The Spot” in Building Orion (gebouw nummer 103) in the Wageningen University campus Course coordinator Natal van Riel, Eindhoven University of Technology Lecturers Prof. Natal van Riel, Eindhoven University of Technology… Continue reading

BioSB course: Integrated modeling and optimization

Living organisms are characterized by an amazing degree of hierarchical complexity. Although our ability to collect measurements at different spatial levels and time-scales has grown dramatically, it has become clear that only measurements cannot provide the answer to unravelling biological complexity. This is because the dynamical behavior of complex systems cannot be reduced to the linear sum of the functions of their… Continue reading

BioSB course: Algorithms for biological networks

Molecular biology is concerned with the study of the presence of and interactions between molecules, at the cellular and sub-cellular level. In bioinformatics and systems biology, algorithms and tools are developed to model these interactions, with various goals: predicting yet unobserved interactions, assigning functions to yet unknown molecules through their relations with known molecules; predicting certain phenotypes such as diseases;… Continue reading

Machine Learning for bioinformatics and systems biology

From October 5-9, 2020 the next BioSB course on Machine Learning for bioinformatics and systems biology will be organised as an online course. Course overview Modern biology is a data-rich science, driven by our ability to measure the detailed molecular characteristics of cells, organs, and individuals at many different levels. Interpretation of these large-scale biological data requires the detection of… Continue reading