Python Programming in PyPI for Translational Medicine
Round 1
Reviewer 1 Report
In this manuscript, the author describes how to use PyPI for translational medicine. The examples presented in the manuscript are very simple and commonly used. I would like to recommend the author to implement his own general tool or script to make the use of PyPI package for translational medicine easier. Such as data collection portal, feature engineering tool, data visualization method, data analysis functions, etc.
Author Response
Comments from reviewer#1:
In this manuscript, the author describes how to use PyPI for translational medicine. The examples presented in the manuscript are very simple and commonly used. I would like to recommend the author to implement his own general tool or script to make the use of PyPI package for translational medicine easier. Such as data collection portal, feature engineering tool, data visualization method, data analysis functions, etc.
Response to comments from reviewer#1:
In order to understand the complete procedure for creating a PyPI package for translational medicine, the tutorial needs to show a simple example rather than a complex one. Besides, there is no CFR (case fatality rate) tool in PyPI packages. As reviewer#1 mentioned, 1) data collection, 2) feature engineering tool, 3) data visualization method, and 4) data analysis functions must be explained respectively.
In order to fulfill the requirement provided by reviewer#1, scorecovid (PyPI package) and deathdaily (PyPI package) were newly added from four viewpoints where scorecovid has been downloaded by 7284 users and deathdaily by 11814 users worldwide respectively.
Scorecovid was peer-reviewed and published in two journals (Healthcare Analytics and Journal of Infection and Public Health):
Author, SCORECOVID: A Python Package Index for scoring the individual policies against COVID-19, Healthcare Analytics, Volume 1, 2021, 100005, ISSN 2772-4425, https://doi.org/10.1016/j.health.2021.100005.
Author, Technological forecasting plays a key role in mitigating the pandemic, Journal of Infection and Public Health, Volume 14, Issue 11, 2021,1666-1667, ISSN 1876-0341, https://doi.org/10.1016/j.jiph.2021.09.010
Deathdaily was also peer-reviewed and published in Dubai Medical Journal:
Author, Artificial Intelligence Suggests that UAE Needs to Mitigate the Small COVID-19 Resurgence, Dubai Med J 2021;4:74–76, https://doi.org/10.1159/000514590
The contexts of two tools were endorsed by peer-reviewed and many practitioners worldwide.
The following sentences were newly added to the revised manuscript.
Four points play a key role in developing a new tool or a PyPI package: 1) data collection, 2) feature engineering tool, 3) data visualization method, and 4) data analysis functions. The following two tools (scorecovid and deathdaily) were explained.
Scorecovid:
1) Scraping the data from the following site on country and population:
https://www.worldometers.info/world-population/population-by-country/
Scraping the data from the following site on total deaths:
https://github.com/owid/covid-19-data/raw/master/public/data/jhu/total_deaths.csv
2) Using pandas library to extract country, population, and total deaths
3) matplotlib library for visualization
4) DataFrame function to compute the number of deaths per population (millions)
Deathdaily:
1) Scraping the data from the following site on daily deaths:
https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/jhu/new_deaths.csv
2) Using pandas library to extract daily deaths
3) matplotlib library for visualization
4) Using numpy.poly1d of numpy library for curve-fitting function to predict the number of daily deaths
Reviewer 2 Report
This manuscript is a practical tutorial on the use of Python Packaging. The author uses covidlag (a PyPI package built to monitor the COVID-19 case fatality rate) as an example of the use of PyPI in medicine and as the opportunity to present it. Data scientists and researchers are already familiar with the Python language, but its value and packages are unknown for medical practitioners. For the majority of the medical practitioners, this is an exclusive and original work that provides introduction and guidance to start understanding and using developed PyPI packages in practice.
Advantages of the work are: correct and precise terminology, step-by-step tutorial, clearly explaining what each file in the PyPI package is necessary for, and the practical and interesting example. covidlag is useful to monitor the case numbers and case fatality rate in a specific time frame and get a quick insight into trends.
However, I would recommend several corrections for the sake of better understanding among general medical practitioners:
1) Maybe author needs to explain that $ sign is the ending of the shell prompt and not the input command (if this paper is aimed at beginners)
2) I would recommend short instructions on how to open the terminal (especially in Windows) and why is using terminal obligatory for this open-source software (also important for beginners).
3) Referencing links for X-Window, VcXserv Windows X Server, and XQuartz are necessary.
4) it should be stated that each PyPI package has other requirements for running. Something about this is mentioned on page 3 line 123. There, I would recommend repeating that the user must use the pip command to install requirements. Therefore all commands listed in the paper should be marked with roman numerals so the author could refer to them precisely and easily (in this case for the command in line 73 on Page 2).
5) It should be noted that researchers and programmers use StackOverflow to find the solutions for the encountered errors.
6) Standard headings (methods, results, and discussion) for the Original research do not apply to this paper. Introduction, installation, and PyPI package structure with conclusion are more logical.
The main issue is that this paper did not describe the results of the validation of the covidlag package neither did compare the results of such study to current tools, so statements on the quality of the package should be avoided because there is no proof of it. The author should keep in mind that this is not an original research paper but a PyPI tutorial in a nutshell.
If the author wanted to have a peer review of the covidlag package then a completely different paper is needed where validation study is reported, and discussion is used to compare the results with other similar measures with limitations and advances reported. This tutorial is more suitable for platforms such as preprint servers or as an article on online publishing platforms.
Author Response
Comments from reviewer#2:
This manuscript is a practical tutorial on the use of Python Packaging. The author uses covidlag (a PyPI package built to monitor the COVID-19 case fatality rate) as an example of the use of PyPI in medicine and as the opportunity to present it. Data scientists and researchers are already familiar with the Python language, but its value and packages are unknown for medical practitioners. For the majority of the medical practitioners, this is an exclusive and original work that provides introduction and guidance to start understanding and using developed PyPI packages in practice.
Advantages of the work are: correct and precise terminology, step-by-step tutorial, clearly explaining what each file in the PyPI package is necessary for, and the practical and interesting example. covidlag is useful to monitor the case numbers and case fatality rate in a specific time frame and get a quick insight into trends.
However, I would recommend several corrections for the sake of better understanding among general medical practitioners:
1) Maybe author needs to explain that $ sign is the ending of the shell prompt and not the input command (if this paper is aimed at beginners)
2) I would recommend short instructions on how to open the terminal (especially in Windows) and why is using terminal obligatory for this open-source software (also important for beginners).
3) Referencing links for X-Window, VcXserv Windows X Server, and XQuartz are necessary.
4) it should be stated that each PyPI package has other requirements for running. Something about this is mentioned on page 3 line 123. There, I would recommend repeating that the user must use the pip command to install requirements. Therefore all commands listed in the paper should be marked with roman numerals so the author could refer to them precisely and easily (in this case for the command in line 73 on Page 2).
5) It should be noted that researchers and programmers use StackOverflow to find the solutions for the encountered errors.
6) Standard headings (methods, results, and discussion) for the Original research do not apply to this paper. Introduction, installation, and PyPI package structure with conclusion are more logical.
The main issue is that this paper did not describe the results of the validation of the covidlag package neither did compare the results of such study to current tools, so statements on the quality of the package should be avoided because there is no proof of it. The author should keep in mind that this is not an original research paper but a PyPI tutorial in a nutshell.
If the author wanted to have a peer review of the covidlag package then a completely different paper is needed where validation study is reported, and discussion is used to compare the results with other similar measures with limitations and advances reported. This tutorial is more suitable for platforms such as preprint servers or as an article on online publishing platforms.
Responses to reviewer#2:
1)Maybe author needs to explain that $ sign is the ending of the shell prompt and not the input command (if this paper is aimed at beginners)
The following sentence were newly added.
$ sign is the shell prompt which is not the user’s input command.
2) I would recommend short instructions on how to open the terminal (especially in Windows) and why is using terminal obligatory for this open-source software (also important for beginners).
The following sentences were newly added.
On WSL installed by Microsoft Store (Ubuntu 20.04), run Linux bash command.
Or on Windows 10, install Cygwin and click the Cygwin to open the bash command ter-minal: https://www.cygwin.com/.
On MacOS and Linux OS, click the terminal icon or open the terminal.
The entire open-source is available from the bash-shell or zsh-shell terminal. The open-source visualization is generally based on X Windows.
3) Referencing links for X-Window, VcXserv Windows X Server, and XQuartz are necessary.
The following sentences were newly added.
VcXserv Windows X Server can be downloaded from the following site: https://sourceforge.net/projects/vcxsrv/
XQuartz MacOS X Server can be downloaded from the following site: https://www.xquartz.org/
4) it should be stated that each PyPI package has other requirements for running. Something about this is mentioned on page 3 line 123. There, I would recommend repeating that the user must use the pip command to install requirements. Therefore all commands listed in the paper should be marked with roman numerals so the author could refer to them precisely and easily (in this case for the command in line 73 on Page 2).
I don't agree with Roman numerals. Even without Roman numerals, the reader will naturally command from top to bottom. Commands written in Roman numerals make the user think that the order of commands is critical.
5) It should be noted that researchers and programmers use StackOverflow to find the solutions for the encountered errors.
The following sentences were newly added.
It should be noted that researchers and programmers can often use the following sites to find solutions for the encountered errors:
https://stackoverflow.com/
https://stackexchange.com/
6) Standard headings (methods, results, and discussion) for the Original research do not apply to this paper. Introduction, installation, and PyPI package structure with conclusion are more logical.
The main issue is that this paper did not describe the results of the validation of the covidlag package neither did compare the results of such study to current tools, so statements on the quality of the package should be avoided because there is no proof of it. The author should keep in mind that this is not an original research paper but a PyPI tutorial in a nutshell.
If the author wanted to have a peer review of the covidlag package then a completely different paper is needed where validation study is reported, and discussion is used to compare the results with other similar measures with limitations and advances reported. This tutorial is more suitable for platforms such as preprint servers or as an article on online publishing platforms.
The original headings were revised based on suggested by reviewer#2 to Introduction, installation, and PyPI package.
The new sentences were newly added.
It should be noted that a covidlag tool has not yet been peer-reviewed.
Round 2
Reviewer 2 Report
Author did all suggested changes after the review. Since this is a manuscript published in special issues focused on COVID-19 I find this article acceptable for publication in the present form.
