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Institute for Computational and Experimental Research in Mathematics (ICERM)

In this workshop, we will consider challenges and best practices in translating theory to software for phylogenetic inference. We will discuss strategies adopted by the tool development community, their relative advantages, and lessons learned through software development. We will discuss a variety of objective functions (parametric and non-parametric) and algorithmic techniques used by inference methods. We will cover parallelization and how it interacts with the choice of objective function and algorithmic technique. Finally, we will discuss best practices for evaluating new and existing software tools, not just to validate the implementation but also to study accuracy and scalability in relation to theory and usage in realistic bioinformatics pipelines. In addition to discussing how theory influences tools, we will examine how tool development can inform the theoretical questions asked.

ICERM;     Email: info@icerm.brown.edu

bioinformatics, phylogenetic inference, software development

Society for Industrial and Applied Mathematics (SIAM)

Society for Industrial and Applied Mathematics (SIAM)

Society for Industrial and Applied Mathematics (SIAM)

USENIX Association

SREcon is a gathering of engineers who care deeply about site reliability, systems engineering, and working with complex distributed systems at scale. Our purpose is to be inclusive as we bring together ideas representative of our diverse community, whether its members are focusing on a global scale, launching new products and ideas for a small business, or pivoting their approach to unite software and systems engineering. SREcon challenges both those new to the profession as well as those who have been involved in it for decades. The conference has a culture of critical thought, deep technical insights, continuous improvement, and innovation.

Software Engineering,    High Performance Computing, Supercomputing, Parallel Computing