Set Operations in Python for Translational Medicine

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

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Published in:International journal of translational medicine Vol. 2; no. 2; pp. 174 - 185
Main Author: Takefuji, Yoshiyasu
Format: Journal Article
Language:English
Published: Jackson MDPI AG 29.04.2022
Subjects:
Age groups
Code Ocean
Coronaviruses
COVID-19 vaccines
dataset
Datasets
Gender
Keywords
Linux
Medicine
Open source software
Packaging
Patients
PyPI package
Python program
Reproducibility
Software upgrading
translational medicine
VAERS
Windows operating system
ISSN:2673-8937, 2673-8937
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Abstract This is the world’s first tutorial article on Python programing on set operations for beginners and practitioners in translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Via the PyPI packaging, a Python application with a single source code can run on Windows, MacOS, and Linux operating systems. In addition to the PyPI packaging, the reproducibility and quality of the source code must be guaranteed. This paper shows how to publish the Python application in Code Ocean after the PyPI packaging. Code Ocean is used in IEEE, Springer, and Elsevier for software reproducibility validation. First, programmers must understand how to scrape a dataset over the Internet. Second, the dataset files must be read in Python. Third, a program must be built to compute the target values using set operations. Fourth, the Python program must be converted to the PyPI package. Finally, the PyPI package is uploaded. Code Ocean plays a key role in publishing validation for software reproducibility. This paper depicts a vaers executable package as an example for calculating the number of deaths due to COVID-19 vaccines. Calculations were based on gender (male and female), age group, and vaccine group (Moderna, Pfizer, and Novartis), respectively.
AbstractList This is the world’s first tutorial article on Python programing on set operations for beginners and practitioners in translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Via the PyPI packaging, a Python application with a single source code can run on Windows, MacOS, and Linux operating systems. In addition to the PyPI packaging, the reproducibility and quality of the source code must be guaranteed. This paper shows how to publish the Python application in Code Ocean after the PyPI packaging. Code Ocean is used in IEEE, Springer, and Elsevier for software reproducibility validation. First, programmers must understand how to scrape a dataset over the Internet. Second, the dataset files must be read in Python. Third, a program must be built to compute the target values using set operations. Fourth, the Python program must be converted to the PyPI package. Finally, the PyPI package is uploaded. Code Ocean plays a key role in publishing validation for software reproducibility. This paper depicts a vaers executable package as an example for calculating the number of deaths due to COVID-19 vaccines. Calculations were based on gender (male and female), age group, and vaccine group (Moderna, Pfizer, and Novartis), respectively.
Author Takefuji, Yoshiyasu
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Cites_doi 10.1038/d41586-021-01222-5
10.1002/9781119487142
10.3390/ijerph110100271
10.1038/s41467-021-22648-5
10.1038/s41587-021-00912-9
10.1038/d41586-021-00727-3
10.1038/d41586-021-00263-0
10.1038/srep17230
10.1038/s41598-021-02528-0
10.3390/ijerph17061939
ContentType Journal Article
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References Irwin (ref_10) 2021; 592
Jacquez (ref_1) 2014; 11
Manzini (ref_6) 2021; 11
Callaway (ref_8) 2021; 593
Pintacuda (ref_13) 2021; 12
ref_3
ref_2
Gaviria (ref_9) 2021; 39
Takefuji (ref_4) 2021; 1
Perkel (ref_11) 2021; 590
ref_5
Reimann (ref_12) 2016; 6
ref_7
References_xml – ident: ref_7
– volume: 593
  start-page: 325
  year: 2021
  ident: ref_8
  article-title: Pfizer COVID Vaccine Protects against Worrying Coronavirus Variants
  publication-title: Nature
  doi: 10.1038/d41586-021-01222-5
– ident: ref_5
– volume: 1
  start-page: 323
  year: 2021
  ident: ref_4
  article-title: Python Programming in PyPI for Translational Medicine
  publication-title: Int. J. Transl. Med.
– ident: ref_3
  doi: 10.1002/9781119487142
– volume: 11
  start-page: 271
  year: 2014
  ident: ref_1
  article-title: Residential Mobility and Breast Cancer in Marin County, California, USA
  publication-title: Int. J. Environ. Res. Public Health
  doi: 10.3390/ijerph110100271
– volume: 12
  start-page: 2580
  year: 2021
  ident: ref_13
  article-title: Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-22648-5
– volume: 39
  start-page: 546
  year: 2021
  ident: ref_9
  article-title: A network analysis of COVID-19 mRNA vaccine patents
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-021-00912-9
– volume: 592
  start-page: 176
  year: 2021
  ident: ref_10
  article-title: What It Will Take to Vaccinate the World against COVID-19
  publication-title: Nature
  doi: 10.1038/d41586-021-00727-3
– volume: 590
  start-page: 173
  year: 2021
  ident: ref_11
  article-title: Five Reasons Why Researchers Should Learn to Love the Command Line
  publication-title: Nature
  doi: 10.1038/d41586-021-00263-0
– volume: 6
  start-page: 17230
  year: 2016
  ident: ref_12
  article-title: Normothermic Mouse Functional MRI of Acute Focal Thermostimulation for Probing Nociception
  publication-title: Sci. Rep.
  doi: 10.1038/srep17230
– volume: 11
  start-page: 23458
  year: 2021
  ident: ref_6
  article-title: reString: An open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-021-02528-0
– ident: ref_2
  doi: 10.3390/ijerph17061939
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SubjectTerms Age groups
Code Ocean
Coronaviruses
COVID-19 vaccines
dataset
Datasets
Gender
Keywords
Linux
Medicine
Open source software
Packaging
Patients
PyPI package
Python program
Reproducibility
Software upgrading
translational medicine
VAERS
Windows operating system
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