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NGS: RNA-seq data analysis

  The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis from September 26-28, 2016. This is an advanced course for people with experience in NGS. The course will consist of seminars and hands-on command line, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples… Continue reading →

Kick start R (4th edition)

This is a one-day introduction to the possibilities of the statistical calculation environment R for those who would like to use it, or have already started using R for statistical data analysis but would like to obtain a bit more background. We will start with a lecture in which the philosophy behind the R-language will be explained. This will allow… Continue reading →

In silico life: constraint-based modelling at genome scale

Constraint-based modelling is a powerful modelling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modelling is the use of a genome-scale reconstructions (GSR’s) that maps out the metabolism of a cell as a biochemical reaction network. In this course… Continue reading →

Algorithms for Biological Networks (4th edition)

Date: May 23-27, 2016, Delft,  The Netherlands Target audience: The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The BioSB course “Pattern recognition” and the ASCI course “Advanced pattern recognition” (a1) discuss many of the tools used in this course, but it is… Continue reading →

Matlab

This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on… Continue reading →

Quantitative and Predictive Modelling

The main theme of the Quantitative and Predictive Modelling course is how to describe the dynamic behaviour of biological systems and integrate experimental data. Concepts of modelling are introduced via a great variety of examples taken from diverse practices. The emphasis is on providing an overview of modelling approaches rather than an in-depth treatment of a few techniques. A short… Continue reading →

Kick start R (3rd edition)

As the title says, the main goal is to provide the participant with a kick-start in R. Clearly, good and practically applicable knowledge of R will only be gained by subsequent self-study. A kick start is achieved through the following sub-goals: The participant will become acquainted with the structure and philosophy behind the R-language. The participant will thereby be able… Continue reading →

Comparative Genomics: from evolution to function

Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to… Continue reading →

NGS: RNA-seq Data Analysis

The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis from September 7-9, 2015. This is an advanced course for people with experience in NGS. The course will consist of seminars and hands-on command line, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will… Continue reading →

Protein structures: production, prowess, power, promises, and problems

In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have… Continue reading →