Python Programming in PyPI for Translational Medicine

This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, rese...

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Veröffentlicht in:International journal of translational medicine Jg. 1; H. 3; S. 323 - 331
1. Verfasser: Takefuji, Yoshiyasu
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Jackson MDPI AG 24.11.2021
Schlagworte:
Coronaviruses
COVID-19
dataset
Fatalities
Infections
Libraries
Linux
Machine learning
Open source software
Population
PyPI package
Python program
translational medicine
Visualization
Windows operating system
Japan
ISSN:2673-8937, 2673-8937
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Abstract This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users.
AbstractList This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users.
Author Takefuji, Yoshiyasu
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Cites_doi 10.1038/s41598-019-56408-9
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SubjectTerms Coronaviruses
COVID-19
dataset
Fatalities
Infections
Libraries
Linux
Machine learning
Open source software
Population
PyPI package
Python program
translational medicine
Visualization
Windows operating system
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