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Essential components of Script of Scripts (SoS)

Project description

Computationally intensive disciplines such as computational biology often requires one to exploit a variety of tools implemented in different programming languages, and to analyze large datasets on high performance computing systems. Although scientific workflow systems are powerful in organizing and executing large-scale data analysis processes, there are usually non-trivial learning curve and engineering overhead in creating and maintaining such workflows, making them unsuitable for data exploration and prototyping. To bridge the gap between interactive analysis and workflow systems, we developed Script of Scripts (SoS), a system with strong emphases on readability, practicality, and reproducibility for daily computational research. For exploratory analysis SoS provides a multi-language file format and scripting engine that centralizes all computations, and creates dynamic report documents for publishing and sharing. As a workflow engine, SoS provides an intuitive syntax to create workflows in process-oriented, outcome-oriented and mixed styles, as well as a unified interface to executing and managing tasks on a variety of computing platforms with automatic synchronization of files between isolated systems. In this paper we illustrate with real-world examples the use of SoS as both interactive analysis tool and pipeline platform for all stages of methods development and data analysis projects. In particular we demonstrate how SoS can easily be adopted based on existing scripts and pipelines, yet resulting in substantial improvement in terms of organization, readability and cross-platform computation management.

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