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diff --git a/peer-review/1-review.txt b/peer-review/1-review.txt new file mode 100644 index 0000000..16e227b --- /dev/null +++ b/peer-review/1-review.txt @@ -0,0 +1,788 @@ +From: cise computer org +To: mohammad akhlaghi org, + infantesainz gmail com, + boud astro uni torun pl, + david valls-gabaud observatoiredeparis psl eu, + rbaena iac es +Received: Tue, 22 Sep 2020 15:28:21 -0400 +Subject: Computing in Science and Engineering, CiSESI-2020-06-0048 + major revision required + +-------------------------------------------------- + +Computing in Science and Engineering,CiSESI-2020-06-0048 +"Towards Long-term and Archivable Reproducibility" +manuscript type: Reproducible Research + +Dear Dr. Mohammad Akhlaghi, + +The manuscript that you submitted to Computing in Science and Engineering +has completed the review process. After carefully examining the manuscript +and reviews, we have decided that the manuscript needs major revisions +before it can be considered for a second review. + +Your revision is due before 22-Oct-2020. Please note that if your paper was +submitted to a special issue, this due date may be different. Contact the +peer review administrator, Ms. Jessica Ingle, at cise computer.org if you +have questions. + +The reviewer and editor comments are attached below for your +reference. Please maintain our 6,250–word limit as you make your revisions. + +To upload your revision and summary of changes, log on to +https://mc.manuscriptcentral.com/cise-cs, click on your Author Center, then +"Manuscripts with Decisions." Under "Actions," choose "Create a Revision" +next to the manuscript number. + +Highlight the changes to your manuscript by using the track changes mode in +MS Word, the latexdiff package if using LaTex, or by using bold or colored +text. + +When submitting your revised manuscript, you will need to respond to the +reviewer comments in the space provided. + +If you have questions regarding our policies or procedures, please refer to +the magazines' Author Information page linked from the Instructions and +Forms (top right corner of the ScholarOne Manuscripts screen) or you can +contact me. + +We look forward to receiving your revised manuscript. + +Sincerely, +Dr. Lorena A. Barba +George Washington University +Mechanical and Aerospace Engineering +Editor-in-Chief, Computing in Science and Engineering + +-------------------------------------------------- + + + + + +EiC comments: +Some reviewers request additions, and overview of other tools, etc. In +doing your revision, please remember space limitations: 6,250 words +maximum, including all main body, abstract, keyword, bibliography (12 +references or less), and biography text. See "Write For Us" section of the +website: https://www.computer.org/csdl/magazine/cs + +Comments of the Associate Editor: Associate Editor +Comments to the Author: Thank to the authors for your submission to the +Reproducible Research department. + +Thanks to the reviewers for your careful and thoughtful reviews. We would +appreciate it if you can make your reports available and share the DOI as +soon as possible, per our original invitation e-mail. We will follow up our +original invitation to obtain your review DOI, if you have not already +included it in your review comments. + +Based on the review feedback, there are a number of major issues that +require attention and many minor ones as well. Please take these into +account as you prepare your major revision for another round of +review. (See the actual review reports for details.) + +1. In general, there are a number of presentation issues needing +attention. There are general concerns about the paper lacking focus. Some +terminology is not well-defined (e.g. longevity). In addition, the +discussion of tools could benefit from some categorization to characterize +their longevity. Background and related efforts need significant +improvement. (See below.) + +2. There is consistency among the reviews that related work is particularly +lacking and not taking into account major works that have been written on +this topic. See the reviews for details about work that could potentially +be included in the discussion and how the current work is positioned with +respect to this work. + +3. The current work needs to do a better job of explaining how it deals +with the nagging problem of running on CPU vs. different architectures. At +least one review commented on the need to include a discussion of +continuous integration (CI) and its potential to help identify problems +running on different architectures. Is CI employed in any way in the work +presented in this article? + +4. The presentation of the Maneage tool is both lacking in clarity and +consistency with the public information/documentation about the tool. While +our review focus is on the article, it is important that readers not be +confused when they visit your site to use your tools. + +5. A significant question raised by one review is how this work compares to +"executable" papers and Jupyter notebooks. Does this work embody +similar/same design principles or expand upon the established alternatives? +In any event, a discussion of this should be included in +background/motivation and related work to help readers understand the clear +need for a new approach, if this is being presented as new/novel. + +Reviews: + +Please note that some reviewers may have included additional comments in a +separate file. If a review contains the note "see the attached file" under +Section III A - Public Comments, you will need to log on to ScholarOne +Manuscripts to view the file. After logging in, select the Author Center, +click on the "Manuscripts with Decisions" queue and then click on the "view +decision letter" link for this manuscript. You must scroll down to the very +bottom of the letter to see the file(s), if any. This will open the file +that the reviewer(s) or the Associate Editor included for you along with +their review. + +-------------------------------------------------- + + + + + +Reviewer: 1 +Recommendation: Author Should Prepare A Major Revision For A Second Review + +Comments: + + * Adding an explicit list of contributions would make it easier to the + reader to appreciate these. + + * These are not mentioned/cited and are highly relevant to this paper (in + no particular order): + + * Git flows, both in general and in particular for research. + * Provenance work, in general and with git in particular + * Reprozip: https://www.reprozip.org/ + * OCCAM: https://occam.cs.pitt.edu/ + * Popper: http://getpopper.io/ + * Whole Tale: https://wholetale.org/ + * Snakemake: https://github.com/snakemake/snakemake + * CWL https://www.commonwl.org/ and WDL https://openwdl.org/ + * Nextflow: https://www.nextflow.io/ + * Sumatra: https://pythonhosted.org/Sumatra/ + * Podman: https://podman.io + * AppImage (https://appimage.org/), Flatpack + (https://flatpak.org/), Snap (https://snapcraft.io/) + * nbdev https://github.com/fastai/nbdev and jupytext + * Bazel: https://bazel.build/ + * Debian reproducible builds: https://wiki.debian.org/ReproducibleBuilds + + * Existing guidelines similar to the proposed "Criteria for + longevity". Many articles of these in the form "10 simple rules for + X", for example (not exhaustive list): + * https://doi.org/10.1371/journal.pcbi.1003285 + * https://arxiv.org/abs/1810.08055 + * https://osf.io/fsd7t/ + + * A model project for reproducible papers: https://arxiv.org/abs/1401.2000 + + * Executable/reproducible paper articles and original concepts + + * Several claims in the manuscript are not properly justified, neither in + the text nor via citation. Examples (not exhaustive list): + + * "it is possible to precisely identify the Docker “images” that are + imported with their checksums, but that is rarely practiced in most + solutions that we have surveyed [which ones?]" + + * "Other OSes [which ones?] have similar issues because pre-built + binary files are large and expensive to maintain and archive." + + * "Researchers using free software tools have also already had some + exposure to it" + + * "A popular framework typically falls out of fashion and requires + significant resources to translate or rewrite every few years." + + * As mentioned in the discussion by the authors, not even Bash, Git or + Make is reproducible, thus not even Maneage can address the longevity + requirements. One possible alternative is the use of CI to ensure that + papers are re-executable (several papers have been written on this + topic). Note that CI is well-established technology (e.g. Jenkins is + almost 10 years old). + +Additional Questions: + +1. How relevant is this manuscript to the readers of this periodical? + Please explain your rating in the Detailed Comments section.: Very + Relevant + +2. To what extent is this manuscript relevant to readers around the world?: + The manuscript is of interest to readers throughout the world + +1. Please summarize what you view as the key point(s) of the manuscript and + the importance of the content to the readers of this periodical.: This + article introduces desiderata for long-term archivable reproduciblity + and presents Maneage, a system whose goal is to achieve these outlined + properties. + +2. Is the manuscript technically sound? Please explain your answer in the + Detailed Comments section.: Partially + +3. What do you see as this manuscript's contribution to the literature in + this field?: Presentation of Maneage + +4. What do you see as the strongest aspect of this manuscript?: A great + summary of Maneage, as well as its implementaiton. + +5. What do you see as the weakest aspect of this manuscript?: Criterion has + been proposed previously. Maneage itself provides little novelty (see + comments below). + +1. Does the manuscript contain title, abstract, and/or keywords?: Yes + +2. Are the title, abstract, and keywords appropriate? Please elaborate in + the Detailed Comments section.: Yes + +3. Does the manuscript contain sufficient and appropriate references + (maximum 12-unless the article is a survey or tutorial in scope)? Please + elaborate in the Detailed Comments section.: Important references are + missing; more references are needed + +4. Does the introduction clearly state a valid thesis? Please explain your + answer in the Detailed Comments section.: Could be improved + +5. How would you rate the organization of the manuscript? Please elaborate + in the Detailed Comments section.: Satisfactory + +6. Is the manuscript focused? Please elaborate in the Detailed Comments + section.: Satisfactory + +7. Is the length of the manuscript appropriate for the topic? Please + elaborate in the Detailed Comments section.: Satisfactory + +8. Please rate and comment on the readability of this manuscript in the + Detailed Comments section.: Easy to read + +9. Please rate and comment on the timeliness and long term interest of this + manuscript to CiSE readers in the Detailed Comments section. Select all + that apply.: Topic and content are of limited interest to CiSE readers. + +Please rate the manuscript. Explain your choice in the Detailed Comments +section.: Good + +-------------------------------------------------- + + + + + +Reviewer: 2 +Recommendation: Accept If Certain Minor Revisions Are Made + +Comments: https://doi.org/10.22541/au.159724632.29528907 + +Operating System: Authors mention that Docker is usually used with an image +of Ubuntu without precision about the version used. And Even if users take +care about the version, the image is updated monthly thus the image used +will have different OS components based on the generation time. This +difference in OS components will interfere on the reproducibility. I agree +on that, but I would like to add that it is a wrong habit of users. It is +possible to generate reproducible Docker images by generating it from an +ISO image of the OS. These ISO images are archived, at least for Ubuntu +(http://old-releases.ubuntu.com/releases) and for Debian +(https://cdimage.debian.org/mirror/cdimage/archive) thus allow users to +generate an OS with identical components. Combined with the +snapshot.debian.org service, it is even possible to update a Debian release +to a specific time point up to 2005 and with a precision of six hours. With +combination of both ISO image and snapshot.debian.org service it is +possible to obtain an OS for Docker or for a VM with identical components +even if users have to use the PM of the OS. Authors should add indication +that using good practices it is possible to use Docker or VM to obtain +identical OS usable for reproducible research. + +CPU architecture: The CPU architecture of the platform used to run the +workflow is not discussed in the manuscript. During software integration in +Debian, I have seen several software failing their unit tests due to +different behavior from itself or from a library dependency. This not +expected behavior was only present on non-x86 architectures, mainly because +developers use a x86 machine for their developments and tests. Bug or +feature? I don’t know, but nowadays, it is quite frequent to see computers +with a non-x86 CPU. It would be annoying to fail the reproducibility step +because of a different in CPU architecture. Authors should probably take +into account the architecture used in their workflow or at least report it. + +POSIX dependency: I don’t understand the "no dependency beyond +POSIX". Authors should more explained what they mean by this sentence. I +completely agree that the dependency hell must be avoided and dependencies +should be used with parsimony. Unfortunately, sometime we need proprietary +or specialized software to read raw data. For example in genetics, +micro-array raw data are stored in binary proprietary formats. To convert +this data into a plain text format, we need the proprietary software +provided with the measurement tool. + +Maneage: I was not able to properly set up a project with Maneage. The +configuration step failed during the download of tools used in the +workflow. This is probably due to a firewall/antivirus restriction out of +my control. How frequent this failure happen to users? Moreover, the time +to configure a new project is quite long because everything needs to be +compiled. Authors should compare the time required to set up a project +Maneage versus time used by other workflows to give an indication to the +readers. + +Disclaimer: For the sake of transparency, it should be noted that I am +involved in the development of Debian, thus my comments are probably +oriented. + +Additional Questions: + +1. How relevant is this manuscript to the readers of this periodical? + Please explain your rating in the Detailed Comments section.: Relevant + +2. To what extent is this manuscript relevant to readers around the world?: + The manuscript is of interest to readers throughout the world + +1. Please summarize what you view as the key point(s) of the manuscript and + the importance of the content to the readers of this periodical.: The + authors describe briefly the history of solutions proposed by + researchers to generate reproducible workflows. Then, they report the + problems with the current tools used to tackle the reproducible + problem. They propose a set of criteria to develop new reproducible + workflows and finally they describe their proof of concept workflow + called "Maneage". This manuscript could help researchers to improve + their workflow to obtain reproducible results. + +2. Is the manuscript technically sound? Please explain your answer in the + Detailed Comments section.: Yes + +3. What do you see as this manuscript's contribution to the literature in + this field?: The authors try to propose a simple answer to the + reproducibility problem by defining new criteria. They also propose a + proof of concept workflow which can be directly used by researchers for + their projects. + +4. What do you see as the strongest aspect of this manuscript?: This + manuscript describes a new reproducible workflow which doesn't require + another new trendy high-level software. The proposed workflow is only + based on low-level tools already widely known. Moreover, the workflow + takes into account the version of all software used in the chain of + dependencies. + +5. What do you see as the weakest aspect of this manuscript?: Authors don't + discuss the problem of results reproducibility when analysis are + performed using CPU with different architectures. Some libraries have + different behaviors when they ran on different architectures and it + could influence final results. Authors are probably talking about x86, + but there is no reference at all in the manuscript. + +1. Does the manuscript contain title, abstract, and/or keywords?: Yes + +2. Are the title, abstract, and keywords appropriate? Please elaborate in + the Detailed Comments section.: Yes + +3. Does the manuscript contain sufficient and appropriate references + (maximum 12-unless the article is a survey or tutorial in scope)? Please + elaborate in the Detailed Comments section.: References are sufficient + and appropriate + +4. Does the introduction clearly state a valid thesis? Please explain your + answer in the Detailed Comments section.: Yes + +5. How would you rate the organization of the manuscript? Please elaborate + in the Detailed Comments section.: Satisfactory + +6. Is the manuscript focused? Please elaborate in the Detailed Comments + section.: Satisfactory + +7. Is the length of the manuscript appropriate for the topic? Please + elaborate in the Detailed Comments section.: Satisfactory + +8. Please rate and comment on the readability of this manuscript in the + Detailed Comments section.: Easy to read + +9. Please rate and comment on the timeliness and long term interest of this + manuscript to CiSE readers in the Detailed Comments section. Select all + that apply.: Topic and content are of immediate and continuing interest + to CiSE readers + +Please rate the manuscript. Explain your choice in the Detailed Comments +section.: Good + +-------------------------------------------------- + + + + + +Reviewer: 3 +Recommendation: Accept If Certain Minor Revisions Are Made + +Comments: Longevity of workflows in a project is one of the problems for +reproducibility in different fields of computational research. Therefore, a +proposal that seeks to guarantee this longevity becomes relevant for the +entire community, especially when it is based on free software and is easy +to access and implement. + +GOODMAN et al., 2016, BARBA, 2018 and PLESSER, 2018 observed in their +research that the terms reproducibility and replicability are frequently +found in the scientific literature and their use interchangeably ends up +generating confusion due to the authors' lack of clarity. Thus, authors +should define their use of the term briefly for their readers. + +The introduction is consistent with the proposal of the article, but deals +with the tools separately, many of which can be used together to minimize +some of the problems presented. The use of Ansible, Helm, among others, +also helps in minimizing problems. When the authors use the Python example, +I believe it is interesting to point out that today version 2 has been +discontinued by the maintaining community, which creates another problem +within the perspective of the article. Regarding the use of VM's and +containers, I believe that the discussion presented by THAIN et al., 2015 +is interesting to increase essential points of the current work. About the +Singularity, the description article was missing (Kurtzer GM, Sochat V, +Bauer MW, 2017). I also believe that a reference to FAIR is interesting +(WILKINSON et al., 2016). + +In my opinion, the paragraph on IPOL seems to be out of context with the +previous ones. This issue of end-to-end reproducibility of a publication +could be better explored, which would further enrich the tool presented. + +The presentation of the longevity criteria was adequate in the context of +the article and explored the points that were dealt with later. + +The presentation of the tool was consistent. On the project website, I +suggest that the information contained in README-hacking be presented on +the same page as the Tutorial. A topic breakdown is interesting, as the +markdown reading may be too long to find information. + +Additional Questions: + +1. How relevant is this manuscript to the readers of this periodical? + Please explain your rating in the Detailed Comments section.: Relevant + +2. To what extent is this manuscript relevant to readers around the world?: + The manuscript is of interest to readers throughout the world + +1. Please summarize what you view as the key point(s) of the manuscript and + the importance of the content to the readers of this periodical.: In + this article, the authors discuss the problem of the longevity of + computational workflows, presenting what they consider to be criteria + for longevity and an implementation based on these criteria, called + Maneage, seeking to ensure a long lifespan for analysis projects. + +2. Is the manuscript technically sound? Please explain your answer in the + Detailed Comments section.: Yes + +3. What do you see as this manuscript's contribution to the literature in + this field?: In this article, the authors discuss the problem of the + longevity of computational workflows, presenting what they consider to + be criteria for longevity and an implementation based on these criteria, + called Maneage, seeking to ensure a long lifespan for analysis projects. + + As a key point, the authors enumerate quite clear criteria that can + guarantee the longevity of projects and present a free software-based + way of achieving this objective. The method presented by the authors is + not easy to implement for many end users, with low computer knowledge, + but it can be easily implemented by users with average knowledge in the + area. + +4. What do you see as the strongest aspect of this manuscript?: One of the + strengths of the manuscript is the implementation of Maneage entirely in + free software and the search for completeness presented in the + manuscript. The use of GNU software adds the guarantee of long + maintenance by one of the largest existing software communities. In + addition, the tool developed has already been tested in different + publications, showing itself consistent in different scenarios. + +5. What do you see as the weakest aspect of this manuscript?: For the + proper functioning of the proposed tool, the user needs prior knowledge + of LaTeX, GIT and the command line, which can keep inexperienced users + away. Likewise, the tool is suitable for Unix users, keeping users away + from Microsoft environments. + + Even though Unix-like environments are the majority in the areas of + scientific computing, many users still perform their analysis in + different areas on Windows computers or servers, with the assistance of + package managers. + +1. Does the manuscript contain title, abstract, and/or keywords?: Yes + +2. Are the title, abstract, and keywords appropriate? Please elaborate in + the Detailed Comments section.: Yes + +3. Does the manuscript contain sufficient and appropriate references + (maximum 12-unless the article is a survey or tutorial in scope)? Please + elaborate in the Detailed Comments section.: Important references are + missing; more references are needed + +4. Does the introduction clearly state a valid thesis? Please explain your + answer in the Detailed Comments section.: Could be improved + +5. How would you rate the organization of the manuscript? Please elaborate + in the Detailed Comments section.: Satisfactory + +6. Is the manuscript focused? Please elaborate in the Detailed Comments + section.: Could be improved + +7. Is the length of the manuscript appropriate for the topic? Please + elaborate in the Detailed Comments section.: Satisfactory + +8. Please rate and comment on the readability of this manuscript in the + Detailed Comments section.: Easy to read + +9. Please rate and comment on the timeliness and long term interest of this + manuscript to CiSE readers in the Detailed Comments section. Select all + that apply.: Topic and content are of immediate and continuing interest + to CiSE readers + +Please rate the manuscript. Explain your choice in the Detailed Comments +section.: Excellent + +-------------------------------------------------- + + + + + +Reviewer: 4 +Recommendation: Author Should Prepare A Major Revision For A Second Review + +Comments: Overall evaluation - Good. + +This paper is in scope, and the topic is of interest to the readers of +CiSE. However in its present form, I have concerns about whether the paper +presents enough new contributions to the area in a way that can then be +understood and reused by others. The main things I believe need addressing +are: 1) Revisit the criteria, show how you have come to decide on them, +give some examples of why they are important, and address potential missing +criteria. 2) Clarify the discussion of challenges to adoption and make it +clearer which tradeoffs are important to practitioners. 3) Be clearer about +which sorts of research workflow are best suited to this approach. + +B2.Technical soundness: here I am discussing the soundness of the paper, +rather than the soundness of the Maneage tool. There are some fundamental +additional challenges to reproducibility that are not addressed. Although +software library versions are addressed, there is also the challenge of +mathematical reproducibility, particularly of the handling of floating +point number, which might occur because of the way the code is written, and +the hardware architecture (including if code is optimised / +parallelised). This could obviously be addressed through a criterion around +how code is written, but this will also come with a tradeoff against +performance, which is never mentioned. Another tradeoff, which might affect +Criterion 3 is time to result - people use popular frameworks because it is +easier to use them. Regarding the discussion, I would liked to have seen +explanation of how these challenges to adoption were identified: was this +anecdotal, through surveys. participant observation? As a side note around +the technical aspects of Maneage - it is using LaTeX which in turn is built +on TeX which in turn has had many portability problems in the past due to +being written using WEB / Tangle, though with web2c this is largely now +resolved - potentially an interesting sidebar to investigate how LaTeX/TeX +has ensured its longevity! + +C2. The title is not specific enough - it should refer to the +reproducibility of workflows/projects. + +C4. As noted above, whilst the thesis stated is valid, it may not be useful +to practitioners of computation science and engineering as it stands. + +C6. Manuscript focus. I would have liked a more focussed approach to the +presentation of information in II. Longevity is not defined, and whilst +various tools are discussed and discarded, no attempt is made to categorise +the magnitude of longevity for which they are relevant. For instance, +environment isolators are regarded by the software preservation community +as adequate for timescale of the order of years, but may not be suitable +for the timescale of decades where porting and emulation are used. The +title of this section "Commonly used tools and their longevity" is also +confusing - do you mean the longevity of the tools or the longevity of the +workflows that can be produced using these tools? What happens if you use a +combination of all four categories of tools? + +C8. Readability. I found it difficult to follow the description of how +Maneage works. It wasn't clear to me if code was being run to generate the +results and figures in a LaTeX paper that is part of a project in +Maneage. It appears to be suggested this is the case, but Figure 1 doesn't +show how this works - it just has the LaTeX files, the data files and the +Makefiles. Is it being suggested that LaTeX itself is the programming +language, using its macro functionality? I was a bit confused on how +collaboration is handled as well - this appears to be using the Git +branching model, and the suggestion that Maneage is keeping track of all +components from all projects - but what happens if you are working with +collaborators that are using their own Maneage instance? + +I would also liked to have seen a comparison between this approach and +other "executable" paper approaches e.g. Jupyter notebooks, compared on +completeness, time taken to write a "paper", ease of depositing in a +repository, and ease of use by another researcher. + +Additional Questions: + +1. How relevant is this manuscript to the readers of this periodical? + Please explain your rating in the Detailed Comments section.: Relevant + +2. To what extent is this manuscript relevant to readers around the world?: + The manuscript is of interest to readers throughout the world + +1. Please summarize what you view as the key point(s) of the manuscript and + the importance of the content to the readers of this periodical.: This + manuscript discusses the challenges of reproducibility of computational + research workflows, suggests criteria for improving the "longevity" of + workflows, describes the proof-of-concept tool, Maneage, that has been + built to implement these criteria, and discusses the challenges to + adoption. + + Of primary importance is the discussion of the challenges to adoption, + as CiSE is about computational science which does not take place in a + theoretical vacuum. Many of the identified challenges relate to the + practice of computational science and the implementation of systems in + the real world. + +2. Is the manuscript technically sound? Please explain your answer in the + Detailed Comments section.: Partially + +3. What do you see as this manuscript's contribution to the literature in + this field?: The manuscript makes a modest contribution to the + literature through the description of the proof-of-concept, in + particular its approach to integrating asset management, version control + and build and the discussion of challenges to adoption. + + The proposed criteria have mostly been discussed at length in many other + works looking at computational reproducibility and executable papers. + +4. What do you see as the strongest aspect of this manuscript?: The + strongest aspect is the discussion of difficulties for widespread + adoption of this sort of approach. Because the proof-of-concept tool + received support through the RDA, it was possible to get feedback from + researchers who were likely to use it. This has highlighted and + reinforced a number of challenges and caveats. + +5. What do you see as the weakest aspect of this manuscript?: The weakest + aspect is the assumption that research can be easily compartmentalized + into simple and complete packages. Given that so much of research + involves collaboration and interaction, this is not sufficiently + addressed. In particular, the challenge of interdisciplinary work, where + there may not be common languages to describe concepts and there may be + different common workflow practices will be a barrier to wider adoption + of the primary thesis and criteria. + +1. Does the manuscript contain title, abstract, and/or keywords?: Yes + +2. Are the title, abstract, and keywords appropriate? Please elaborate in + the Detailed Comments section.: No + +3. Does the manuscript contain sufficient and appropriate references + (maximum 12-unless the article is a survey or tutorial in scope)? Please + elaborate in the Detailed Comments section.: References are sufficient + and appropriate + +4. Does the introduction clearly state a valid thesis? Please explain your + answer in the Detailed Comments section.: Could be improved + +5. How would you rate the organization of the manuscript? Please elaborate + in the Detailed Comments section.: Satisfactory + +6. Is the manuscript focused? Please elaborate in the Detailed Comments + section.: Could be improved + +7. Is the length of the manuscript appropriate for the topic? Please + elaborate in the Detailed Comments section.: Satisfactory + +8. Please rate and comment on the readability of this manuscript in the + Detailed Comments section.: Readable - but requires some effort to + understand + +9. Please rate and comment on the timeliness and long term interest of this + manuscript to CiSE readers in the Detailed Comments section. Select all + that apply.: Topic and content are of immediate and continuing interest + to CiSE readers + +Please rate the manuscript. Explain your choice in the Detailed Comments +section.: Good + +-------------------------------------------------- + + + + + +Reviewer: 5 +Recommendation: Author Should Prepare A Major Revision For A Second Review + +Comments: + +Major figures currently working in this exact field do not have their work +acknowledged in this work. In no particular order: Victoria Stodden, +Michael Heroux, Michela Taufer, and Ivo Jimenez. All of these authors have +multiple publications that are highly relevant to this paper. In the case +of Ivo Jimenez, his Popper work [Jimenez I, Sevilla M, Watkins N, Maltzahn +C, Lofstead J, Mohror K, Arpaci-Dusseau A, Arpaci-Dusseau R. The popper +convention: Making reproducible systems evaluation practical. In2017 IEEE +International Parallel and Distributed Processing Symposium Workshops +(IPDPSW) 2017 May 29 (pp. 1561-1570). IEEE.] and the later revision that +uses GitHub Actions, is largely the same as this work. The lack of +attention to virtual machines and containers is highly problematic. While a +reader cannot rely on DockerHub or a generic OS version label for a VM or +container, these are some of the most promising tools for offering true +reproducibility. On the data side, containers have the promise to manage +data sets and workflows completely [Lofstead J, Baker J, Younge A. Data +pallets: containerizing storage for reproducibility and +traceability. InInternational Conference on High Performance Computing 2019 +Jun 16 (pp. 36-45). Springer, Cham.] Taufer has picked up this work and has +graduated a MS student working on this topic with a published thesis. See +also Jimenez's P-RECS workshop at HPDC for additional work highly relevant +to this paper. + +Some other systems that do similar things include: reprozip, occam, whole +tale, snakemake. + +While the work here is a good start, the paper needs to include the context +of the current community development level to be a complete research +paper. A revision that includes evaluation of (using the criteria) and +comparison with the suggested systems and a related work section that +seriously evaluates the work of the recommended authors, among others, +would make this paper worthy for publication. + +Additional Questions: + +1. How relevant is this manuscript to the readers of this periodical? + Please explain your rating in the Detailed Comments section.: Very + Relevant + +2. To what extent is this manuscript relevant to readers around the world?: + The manuscript is of interest to readers throughout the world + +1. Please summarize what you view as the key point(s) of the manuscript and + the importance of the content to the readers of this periodical.: This + paper describes the Maneage system for reproducibile workflows. It lays + out a bit of the need, has very limited related work, and offers + criteria any system that offers reproducibility should have, and finally + describes how Maneage achieves these goals. + +2. Is the manuscript technically sound? Please explain your answer in the + Detailed Comments section.: Partially + +3. What do you see as this manuscript's contribution to the literature in + this field?: Yet another example of a reproducible workflows + project. There are numerous examples, mostly domain specific, and this + one is not the most advanced general solution. + +4. What do you see as the strongest aspect of this manuscript?: Working + code and published artifacts + +5. What do you see as the weakest aspect of this manuscript?: Lack of + context in the field missing very relevant work that eliminates much, if + not all, of the novelty of this work. + +1. Does the manuscript contain title, abstract, and/or keywords?: Yes + +2. Are the title, abstract, and keywords appropriate? Please elaborate in + the Detailed Comments section.: Yes + +3. Does the manuscript contain sufficient and appropriate references + (maximum 12-unless the article is a survey or tutorial in scope)? Please + elaborate in the Detailed Comments section.: Important references are + missing; more references are needed + +4. Does the introduction clearly state a valid thesis? Please explain your + answer in the Detailed Comments section.: Could be improved + +5. How would you rate the organization of the manuscript? Please elaborate + in the Detailed Comments section.: Satisfactory + +6. Is the manuscript focused? Please elaborate in the Detailed Comments + section.: Could be improved + +7. Is the length of the manuscript appropriate for the topic? Please + elaborate in the Detailed Comments section.: Could be improved + +8. Please rate and comment on the readability of this manuscript in the + Detailed Comaments section.: Easy to read + +9. Please rate and comment on the timeliness and long term interest of this + manuscript to CiSE readers in the Detailed Comments section. Select all + that apply.: Topic and content are likely to be of growing interest to + CiSE readers over the next 12 months + +Please rate the manuscript. Explain your choice in the Detailed Comments +section.: Fair |