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Abstract: Any cutting-edge scientific research project requires a myriad ofcomputational tools for data generation, management, analysis andvisualization. Python is a flexible and extensible scientific programmingplatform that offered the perfect solution in our recent comparative genomicsinvestigation J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. Genomelandscapes and bacteriophage codon usage, PLoS Computational Biology, 4,1000001, 2008. In this paper, we discuss the challenges of this project, andhow the combined power of Biopython, Matplotlib and SWIG were utilized for therequired computational tasks. We finish by discussing how python goes beyondbeing a convenient programming language, and promotes good scientific practiceby enabling clean code, integration with professional programming techniquessuch as unit testing, and strong data provenance.



Author: Julius B. Lucks

Source: https://arxiv.org/







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