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Federico Marini - iSEEing is believing: exploration of sequencing data, made easy and efficient
Recent technological advancements in the life and medical sciences have allowed these fields to evolve into quantitative disciplines.
Gene expression profiling with RNA-sequencing, protein quantification via mass spectrometry, high throughput imaging are complex assays that often require advanced methods for processing and generating actionable results. Notably, large and heterogeneous datasets need specific techniques also for the exploration, and I found that an effective combination of interactivity and reproducibility is essential for doing this properly.
Interactive visualization can be a key player in this regard: for quality assessment of often noisy multivariate data, for hypothesis generation and exploration, for the visualization of results, as well as for the efficient communication of findings. Another essential aspect is that often the scientists generating the primary data might not be well versed in programming, notably increasing the iterations required to extract insight out of it.
Many of these aspects are common in other fields than bioinformatics, and I will present in detail the functionality of a Bioconductor software I co-developed, iSEE (http://bioconductor.org/packages/iSEE/) as an application. Leveraging point-and-click user interfaces with guided tours, I will show how users can efficiently explore high-dimensional datasets, automatically retrieve the code for the generated output, and learn (by doing) how to generate compelling scientific figures.
About Federico (https://federicomarini.github.io/, @FedeBioinfo):
I am a Postdoctoral Virchow Fellow at the Center for Thrombosis and Hemostasis (CTH) and at the Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) in Mainz, Germany, where I can sit at the interface with many other disciplines and focus on translational bioinformatics. My research interests involve the development of methods and software for interactive and reproducible research, bringing together the fields of bioinformatics, statistics, genomics, and biology.
I love working in the R programming language, and with software from the Bioconductor project, where I also contributed some packages over the years (pcaExplorer, ideal, iSEE).
Pizzas and drinks will be provided.