First steps into the cloud: Using Amazon data storage and computing with Python notebooks

Daniel J. Pollak; Gautam Chawla; Andrey Andreev; David A. Prober

doi:10.1371/journal.pone.0278316

Peer Review History

Original SubmissionDecember 15, 2021
8 Feb 2022 Decision Letter - Chee Kong Chui, Editor PONE-D-21-39110First Steps into the Cloud Using Amazon Data Storage and Computing with Python NotebooksPLOS ONE Dear Dr. Andreev, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Mar 25 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Chee Kong Chui, PhD Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 4. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. Additional Editor Comments: The manuscript too brief to be qualified as a journal paper but I like the topic. Cloud computing has practical importance. The author should do a major revision of the paper. The paper should present sufficient information so that a reader can reproduce the work, and also provide sufficient insights so that a reader can appreciate the problems and contributions. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature? Reviewer #1: Yes ******** 2. Has the protocol been described in sufficient detail? Descriptions of methods and reagents contained in the step-by-step protocol should be reported in sufficient detail for another researcher to reproduce all experiments and analyses. The protocol should describe the appropriate controls, sample sizes and replication needed to ensure that the data are robust and reproducible. Reviewer #1: Partly ****** 3. Does the protocol describe a validated method? The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data. Reviewer #1: Yes ****** 4. If the manuscript contains new data, have the authors made this data fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: N/A ****** 5. Is the article presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please highlight any specific errors that need correcting in the box below. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The article presents a protocol on using Amazon Web Services and computing with Python notebooks. It also comes with a step-by-step guide attached as a supporting file. The guide is comprehensive and suitable for users with limited programming experience. Programming languages covered include Python and Julia. Overall, the article is fine but requires some revision as per my comments below: The author did a brief walkthrough using data from their work regarding zebrafish brain calcium activity. Although it is understood that such articles are meant to be brief, the current article is too brief. It is good that the supporting file provides step-by-step guide with screenshots to guide users. But the main article should have substantial amount of information and description to allow users to follow through and understand each main step of analysis with reference to the validated case (of zebrafish data). In the article’s current state, a person into his/her “first steps” will not understand well. Please improve on this. In this article and/or the supporting file, it will be good to also include some potential issues that the user might face while following through the steps, as well as troubleshooting methods. As this is a protocol for “First steps into the cloud” as described by the title, the author should address the concerns that a beginner might have regarding cloud computing. For example, although the protocol is focused on Amazon, you should also compare AWS to other IaaS providers. What are the advantages and disadvantages? Is it easier to use? Is it more cost effective? Can the described methods in this article be applied directly to other IaaS in the same manner? 3rd paragraph of Introduction: “Replicability challenges faced by academics are formidable”. The word “formidable” is unclear and confusing. Is it in a good way, or bad way? 3rd paragraph of sub-heading Introduction: “As the biological sciences become more computationally- and data-driven,collaborators and information consumers increasingly try to replicate both hardware and software”. The word “replicate” is not a good choice of word here. Replicate suggests the need to make exact copies of hardware and software, which may not be necessary. Please rephrase. 1st paragraph of sub-heading Materials and methods: “AWS uses a framework called Organizations to control who can use AWS resources outside of the Organization administrator”. Please use academic writing. It sounds very much like the author is casually speaking. Similarly, in the same paragraph, the author wrote “Which AWS services will we be using?” before answering the question. Having ideas/points written in the form of questions is not appropriate for a proper article. Please change it. In fact, there are other instances where the English expressions used are too casual. Please check through the entire article and change to academic writing style. Last bullet-point of sub-heading Costs and use cases: “For a primer on best practices for data storage, see [1].” Please include the authors’ names every time you include a reference. This is not only for better academic writing, but also allows readers to know the work immediately without going around to find that reference. For sub-heading Costs and use cases: Costs and use cases seem to be very different topics. Unless the author is trying to relate costs to use cases (which I do not observe), it should be kept as separate sub-headings. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0278316.r001
Revision 1
6 Oct 2022 Author Response Dear PLOS One editor, We are thankful for the opportunity to present our work and communicate with larger research community about practical applications and challenges of cloud computing on commercial platforms such as Amazon Web Services. As suggested by the editor and the reviewer, we have performed major revision of the paper to provide more details and insights for the readers even not familiar with cloud computing. Specifically, we expanded discussion of every section: from concerns about budgeting and billing, to description of process to start virtual machines. Below we provide details response to reviewer’s comments. Additional Editor Comments: The manuscript too brief to be qualified as a journal paper but I like the topic. Cloud computing has practical importance. The author should do a major revision of the paper. The paper should present sufficient information so that a reader can reproduce the work, and also provide sufficient insights so that a reader can appreciate the problems and contributions. We have expanded text to include more details in every section. Cloud infrastructure is discussed in more details to help those new to the concept of distributed computing, and specifically to Amazon’s cloud architecture. We have expanded section about organization of cloud computing for the whole lab, discussing how users can have separate budgets and access rights. We focused on how researchers can avoid accidentally wasting money. We have also included a step-by-step guide on setting up computing environment, so that just reading the paper (even before opening the protocol.io document) users can get valuable insights and reference material. We have also included more screenshots. We have discussed how python language and Jupyter notebooks can be leveraged to increase reproducibility of the research. 6. Review Comments to the Author Although it is understood that such articles are meant to be brief, the current article is too brief. […] But the main article should have substantial amount of information and description to allow users to follow through and understand each main step of analysis with reference to the validated case (of zebrafish data). In the article’s current state, a person into his/her “first steps” will not understand well. Please improve on this. We have expanded the amount of text covering motivation and explanation for each section in the manuscript. We provided more detailed discussion of concepts used in cloud computing and Amazon cloud, specifically. In this article and/or the supporting file, it will be good to also include some potential issues that the user might face while following through the steps, as well as troubleshooting methods. We have highlighted several issues that users can face: inability to connect to new instance (that can be fixed by firewall settings – we provide information) and budget over-runs (which can be alleviated by managing budgets and users – we provide discussion of some tools for that) As this is a protocol for “First steps into the cloud” as described by the title, the author should address the concerns that a beginner might have regarding cloud computing. For example, although the protocol is focused on Amazon, you should also compare AWS to other IaaS providers. […] We have briefly compared Amazon with other cloud providers; however, we note that all providers are different from each other, and translating knowledge between them is not easy. Hence, here we explicitly focus on Amazon provider as they provide the largest suite of tools, and we have the most experience with Amazon. 3rd paragraph of Introduction: “Replicability challenges faced by academics are formidable”. The word “formidable” is unclear and confusing. Is it in a good way, or bad way? 3rd paragraph of sub-heading Introduction: “As the biological sciences become more computationally- and data-driven,collaborators and information consumers increasingly try to replicate both hardware and software”. The word “replicate” is not a good choice of word here. Replicate suggests the need to make exact copies of hardware and software, which may not be necessary. Please rephrase. Edited language 1st paragraph of sub-heading Materials and methods: “AWS uses a framework called Organizations to control who can use AWS resources outside of the Organization administrator”. Please use academic writing. It sounds very much like the author is casually speaking. Similarly, in the same paragraph, the author wrote “Which AWS services will we be using?” before answering the question. Having ideas/points written in the form of questions is not appropriate for a proper article. Please change it. In fact, there are other instances where the English expressions used are too casual. Please check through the entire article and change to academic writing style. Significantly changed language to be more within academic style, and more precise Last bullet-point of sub-heading Costs and use cases: “For a primer on best practices for data storage, see [1].” Please include the authors’ names every time you include a reference. This is not only for better academic writing, but also allows readers to know the work immediately without going around to find that reference. Changed references to PLOS style For sub-heading Costs and use cases: Costs and use cases seem to be very different topics. Unless the author is trying to relate costs to use cases (which I do not observe), it should be kept as separate sub-headings. Edited to split costs and applications in separate sections Attachments Attachment Submitted filename: 220216_andreev_response.docx https://doi.org/10.1371/journal.pone.0278316.r002
25 Oct 2022 Decision Letter - Mudassir Khan, Editor PONE-D-21-39110R1First Steps into the Cloud Using Amazon Data Storage and Computing with Python NotebooksPLOS ONE Dear Dr. Andreev, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Kindly revise your manuscript as per reviewers comments. Please submit your revised manuscript by Dec 09 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Mudassir Khan, Ph.D Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature? Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the protocol been described in sufficient detail? To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files. The step-by-step protocol should contain sufficient detail for another researcher to be able to reproduce all experiments and analyses. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Does the protocol describe a validated method? The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data. Reviewer #1: Yes Reviewer #2: Yes ****** 4. If the manuscript contains new data, have the authors made this data fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: N/A Reviewer #2: N/A ****** 5. Is the article presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please highlight any specific errors that need correcting in the box below. Reviewer #1: Yes Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Authors have amended the article according to the previous comments made. Therefore, the article is better now. Reviewer #2: Dear authors The screenshots you presented in this paper is not clear and create some confusion. Try to avoid use of screenshots. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0278316.r003
Revision 2
4 Nov 2022 Author Response To the editor, We thank the editor and the reviewers for feedback and timely response to our re-submission. We have amended the manuscript by adding DOI links to the data (hosted on CaltechDATA archive) and Protocols.IO. We would like to specifically address comment from the Reviewer #2: The screenshots you presented in this paper is not clear and create some confusion. Try to avoid use of screenshots. We feel that using screenshots in the main article text helps us to “demystify” cloud computing interfaces, which is the main goal of the article. We reviewed the captions to make sure they are as clear as possible and contain enough information to guide the reader. Attachments Attachment Submitted filename: 20221103_rebuttal.docx https://doi.org/10.1371/journal.pone.0278316.r004
15 Nov 2022 Decision Letter - Mudassir Khan, Editor First Steps into the Cloud Using Amazon Data Storage and Computing with Python Notebooks PONE-D-21-39110R2 Dear Andrey Andreev, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Mudassir Khan, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Thanks for submitting your article in PLOS ONE. I hope you understand the journal reviewing policies. Thanks for your cooperation and understanding. Reviewers' comments: https://doi.org/10.1371/journal.pone.0278316.r005
Formally Accepted
22 Nov 2022 Acceptance Letter - Mudassir Khan, Editor PONE-D-21-39110R2 First steps into the Cloud: Using Amazon data storage and computing with Python notebooks Dear Dr. Andreev: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Mudassir Khan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0278316.r006

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