The immune response involves the coordinated action of millions of cells of different types. Their collective behavior is regulated by multiple factors acting on the molecular to the organism level. Despite tremendous progress in identifying the many components of the immune system, an integrated predictive theory or quantitative dynamic model is still lacking. Such models will be crucial for leveraging advances in basic research towards practical applications in disease treatment and prevention. Moreover, modern experimental techniques provide growing amounts of quantitative data requiring mathematical analysis. These modern techniques include high throughput methods such as multi-channel flow cytometry deep sequencing, gene expression arrays and genome wide association; and very precise quantitative methods such as single cell imaging and single genome amplification.

Further progress in quantitative and predictive understanding of the immune system faces several challenges. An overarching theme is the development of quantitative models and tools that are mathematically rigorous and predictive on one hand, and capture the relevant experimental complexity on the other. Several specific subthemes of high importance are:

1. development of novel methods to extract relevant information from large amounts of data, such as generated by whole genome sequencing or single cell tracking experiments;
2. vertical integration of multiple scales – from intracellular signaling on the timescale of seconds to the behavior of interacting cell populations on the time scale of hours and days, and all the way up towards long term effects, such as immune memory, on the time scale of months and years;
3. development of closer ties between immunologists, virologists and the modeling community, thus bridging the ‘culture gap’ in the modeling and experiment design approaches.
4. critical examination of the significance of the many stochastic features of cell behavior when monitored at single cell level.

The purpose of the workshop is to bring together researchers from different disciplines (immunology, cell biology, virology, mathematical biology, physics, structural biology, bioinformatics) for an in depth exchange of ideas and development of new concepts and approaches to tackle the outstanding challenges, identifying the areas where modeling is expected to be important. The program will be roughly divided into several specific themes:

1. within-host dynamics of infection and inter- cellular regulation of the immune response;
2. intra-cellular signaling and activation of the immune system;
3. diversity and within-host co-evolution of the microorganism and of the immune systems and
4. imaging and measurement in the immune system.