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Stochasticity Tutorials

Tutorials (all are between 14:00 and 15:45)


Monday 19/6


Repertoire Analysis

Jason Vander Heiden

Yale School of Medicine



The field of high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) has experienced significant growth in recent years, but this growth has come with considerable complexity and variety in experimental design. These complexities, combined with the high germline and somatic diversity of immunoglobulin repertoires, present analytical challenges requiring specialized methodologies. This tutorial will cover common investigative approaches and pitfalls in AIRR-seq data analysis. In particular, (1) raw read quality control, (2) dealing with unique molecular identifiers (UMIs), (3) V(D)J gene annotation and novel polymorphism detection, (4) clonal lineage assignment, (5) comparative repertoire diversity analysis, (6) mutational load profiling, (7) building models of somatic hypermutation biases, and (8) quantification of selection pressure. Examples approaches to address these AIRR-seq analysis challenges will be provided using the Immcantation framework (


Required Software


Docker is required to walk through the examples. We will use the "javh/immcantation:release" image available on Docker Hub. The image is rather large (2GB), so it should be pulled before the workshop via the command:


> docker pull javh/immcantation:release


Example Materials


An archive containing example data, scripts and tutorial output can be downloaded from the link below:


Tuesday 20/6


Inferring cellular dynamics from labeling data

Rob de Boer,

Utrecht University



The abstract and general background can be found here


Required Software:




Thursday 22/6


Multiscale modeling in multicellular systems

Haralampos Hatzikirou,

Helmholtz Centre for Infection Research



The dynamics in multicellular systems is crucial for biological development and pathological situations. Multicellular systems are driven by cellular processes as migration, differentiation and proliferation that are tightly regulated by intracellular, cellular and tissue cues. Such multiscale processes in space and time distinguish living from non-living systems. In this lecture, I will attempt to answer how do phenomena at different scales influence each other. We will use lattice-gas cellular automaton (LGCA) models as promising framework to address this question. The models have been inspired by the FHP-LGCA model which formed the basis for lattice-based simulations of complex fluids. The LGCA is a computationally efficient mesoscopic model that allows to analyze the coupling of micro and macro scale phenomena. In particular, I will present the theoretical and computational aspects along with biomedical applications.


Required Software


None. Online Simulation tool:


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