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I think this integration with #946 isn't working due to the json not yet being available post-merge. I'm going to hold off debugging in case it fixes itself. |
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agitter
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Apr 29, 2021
content/60.methods.md
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| While some of this information has been disseminated by traditional publishing mechanisms, in other cases, it is made public through preprint servers or even press releases. | ||
| With information being produced rapidly through both traditional publishing venues and preprint servers, some papers that are published face scrutiny after their initial release. | ||
| Concerns have been raised that the number of COVID-19 papers being retracted may be higher, or potentially much higher, than is typical, although a thorough investigation of this question will not be possible until more time has elapsed [@doi:10.1080/08989621.2020.1782203; @doi:10.1080/08989621.2020.1793675]. | ||
| Other papers are updated with corrections or expressions of concern [@doi:10.1080/08989621.2020.1793675; @url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers]. |
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URL citations to a website will probably not covert well when we translate the .json reference to .bib. We could add manual references to try to override the reference type in the bib file. Or we could add the URLs in the text instead of citing them.
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Oh yikes, I had a few URLs in this one! I'm happy to just manually fix things if that's the easiest way to do it.
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I'm not sure what the best approach is. Check the latest PDF build in #943 to see how these will render in the reference list. Considering our time crunch, this may be low priority. Let's take care of the other content first.
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| An additional four manuscripts are in preparation. | ||
| All seven will be submitted to _mSystems_ as part of a special issue that is providing support for evolving reviews, so that they will continue to be updated as more information becomes available. | ||
| These manuscripts cover a wide range of topics including the fundamental biology of SARS-CoV-2 (pathogenesis [@arxiv:2102.01521] and evolution [@individual-evolution]), biomedical advances in responding to the virus and COVID-19 (pharmaceutical therapeutics [@arxiv:2103.02723], nutraceutical therapeutics [@arxiv:2102.02250], vaccines [@individual-vaccines], and diagnostic technologies [@individual-diagnostics]), and biological and social factors influencing variable effects on patients [@individual-inequality].<!--To Do: add these additional individual citations--> | ||
| To date, [number] authors are associated with the consortium.<!--To Do: break down by undergrad, grad/med student, post-doc, jr faculty?--> |
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This could a place to cross-reference growth in the number of authors if we plot that.
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| #### Integration of COVID-19 Resources with Manubot | ||
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| Data were integrated into the manuscripts from a number of sources. | ||
| The workflow file is available from <https://github.com/greenelab/covid19-review/blob/master/.github/workflows/update-external-resources.yaml> and the scripts are available from <https://github.com/greenelab/covid19-review/tree/external-resources>. |
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I would stick our code availability in METHODS.
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Excellent, I'll move it up in my next commit!
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| The workflow file is available from <https://github.com/greenelab/covid19-review/blob/master/.github/workflows/update-external-resources.yaml> and the scripts are available from <https://github.com/greenelab/covid19-review/tree/external-resources>. | ||
| The Python package versions are available in <https://github.com/greenelab/covid19-review/blob/external-resources/environment.yml>. | ||
| <!-- To Do: These files are archived with [Zenodo?](...). --> | ||
| <!--To Do: Discussion of the absurd number of references?--> |
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Hopefully we can plot this! 🤞
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rando2
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Apr 29, 2021
content/60.methods.md
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| The plugin uses the [Scite](https://scite.ai/) service to display a badge below any citation with a DOI. | ||
| The badge contains a set of icons and numbers that indicate how many times that source has been mentioned, supported, or disputed, and whether there have been any important editorial notices, such as retractions or corrections. | ||
| Using this, we were able to quickly identify references that needed to be checked again since the time they had been added. | ||
| This was invaluable given the nature of the project, where we were disseminating rapidly evolving information of great consequence from over a thousand different sources. | ||
| The badges also allow readers to roughly evaluate the reliability of cited sources at a glance. | ||
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| Because in this implementation of Manubot, most collaborators were writing and editing text through the GitHub website rather than in a local text editor, we also needed to add spell-checking functionalities to Manubot. | ||
| <!--To Do: Describe--> | ||
| <!--To Do: Describe -- perhaps @agitter can lead this?--> |
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@agitter this is an area where I am super not knowledgeable, in case you're looking for a place to fill in text!
rando2
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Apr 29, 2021
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| Manubot provides the advantage of allowing a manuscript to be rendered in several formats that serve different purposes, and the current project extended these options. | ||
| Docx is a necessary format for a biological collaboration where authors are typically not working in LaTeX. | ||
| <!--To Do: continue expanding to describe docx updates and possibly LaTeX updates--> | ||
| <!-- To Do: Also, if we end up automating anything to do with the Manubot-to-LaTeX or bibtex workflow while trying to submit this paper, we should describe that too, as well as the udpates for the Microsoft Word crowd to generating the complete review manuscript along with the individual manuscripts reviewing specific topics. <!-- To Do: reference individual manuscripts --> |
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I'm writing something for this
rando2
commented
Apr 29, 2021
content/60.methods.md
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| While some of this information has been disseminated by traditional publishing mechanisms, in other cases, it is made public through preprint servers or even press releases. | ||
| With information being produced rapidly through both traditional publishing venues and preprint servers, some papers that are published face scrutiny after their initial release. | ||
| Concerns have been raised that the number of COVID-19 papers being retracted may be higher, or potentially much higher, than is typical, although a thorough investigation of this question will not be possible until more time has elapsed [@doi:10.1080/08989621.2020.1782203; @doi:10.1080/08989621.2020.1793675]. | ||
| Other papers are updated with corrections or expressions of concern [@doi:10.1080/08989621.2020.1793675; @url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers]. |
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Oh yikes, I had a few URLs in this one! I'm happy to just manually fix things if that's the easiest way to do it.
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| #### Integration of COVID-19 Resources with Manubot | ||
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| Data were integrated into the manuscripts from a number of sources. | ||
| The workflow file is available from <https://github.com/greenelab/covid19-review/blob/master/.github/workflows/update-external-resources.yaml> and the scripts are available from <https://github.com/greenelab/covid19-review/tree/external-resources>. |
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Excellent, I'll move it up in my next commit!
rando2
commented
Apr 29, 2021
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| Using CI, Manubot now checks that the manuscript was built correctly, runs spellchecking, and cross-references the manuscripts cited in this review, as summarized in Appendix A and discussed in the project's issues and pull requests. | ||
| The new features required for the COVID-19 project are now included in Manubot's rootstock. | ||
| Manubot and Zotero now support citing clinical trial identifiers such as `clinicaltrials:NCT04292899` [@clinicaltrials:NCT04292899], and the scite integration and spell-checking functionalities have been integrated into the current release of Manubot <!--To Do: Link-->. | ||
| <!--To Do: have the individual builds been pushed up to rootstock?--> |
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A question for you @agitter!
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No, the individual manuscript modifications to build.sh are custom and only live in this repository. I feel like this is a pretty niche use case so we won't move it into rootstock unless someone requests it.
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rando2
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Apr 30, 2021
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| ### ABSTRACT | |||
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Does ACM have a word limit on abstracts? I couldn't find it. This is 363 words which seems too long, but if they don't say otherwise...
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The sample manuscript doesn't state a word limit either
covid19-review/build/assets/acmart-master/samples/sample-sigconf.tex
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rando2
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Apr 30, 2021
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| This development was necessary because the manuscript grew so large that it needed to be split into seven separate papers for submission. | ||
| Similarly, we expanded the range of possible export formats to include LaTeX. | ||
| Because LaTeX is used for manuscript submission in many fields, automating the process of converting markdown to a submission-friendly format is desirable. | ||
| <!-- To Do: Also, if we end up automating anything to do with the Manubot-to-LaTeX or bibtex workflow while trying to submit this paper, we should describe that too, as well as the udpates for the Microsoft Word crowd to generating the complete review manuscript along with the individual manuscripts reviewing specific topics. |
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rdvelazquez
approved these changes
Apr 30, 2021
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This looks great! Fantastic job summarizing the project.
A few random comments:
- The tense shifted around quite a bit. It would be too much to try to keep the tense consistent across the whole thing, and even within some paragraphs a tense shift seemed necessary, but if in the course of finalizing you see places to keep tense more consistent, it may help readability
- More mention of the potential downsides/limitations of this approach could actually strengthen the argument (address them ourselves rather than have the reader think of them); I'm thinking specifically of questions people may have around things like "what is the canonical version of the paper?" or "is it always kept up to date; how do I know if it's out of date?"
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| Manubot uses Zotero [@url:https://www.zotero.org] to extract metadata for some types of citations, but Zotero did not support clinical trial identifiers. | ||
| In order to enable Manubot to pull metadata associated with clinical trials based on their identifiers, we needed to develop Zotero support for these identifiers. | ||
| The need for this feature to be enabled in Zotero had also been identified by other researchers [@url:https://forums.zotero.org/discussion/74933/import-from-clinical-trials-registry; @url:https://forums.zotero.org/discussion/77721/add-reference-from-clinical-trials-org]. | ||
| This update was achieved through the implementation of a query of clinicaltrials.gov to retrieve XML metadata associated with each identifier using JavaScript [@url:https://github.com/zotero/translators/pull/2153]. |
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This looks good. Thanks for summarizing that!
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@rdvelazquez I pushed a little more detail to this paragraph. If you have time, could you please double-check it again?
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cgreene
approved these changes
Apr 30, 2021
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I have some suggestions and comments but nothing breaking. My biggest takeaway though for this venue is: "why is this an ACM-BCB paper?" What should a computational biologist or bioinformaticist take away from this? Is it the power of manubot, the opportunity for the science of science, something about education? I think a summary (or intro paragraph) that helps a reviewer understand why this is a fit for the venue (I think it's a story that is a combo of the above items) by explicitly stating it might go a long way to helping get reviewers excited.
| The first release, on March 16, 2020, contained 28,000 manuscripts on topics relevant to SARS-CoV-2 and related coronaviruses [@arxiv:2004.10706]. | ||
| Since then, these articles have continued to proliferate (left), with both traditionally published and preprint manuscripts in the corpus (right). | ||
| At present, it contains {{cord19_total_preprints}} preprints from _arXiv_, _bioRxiv_, and _medRxiv_. | ||
| While not all of the manuscripts are focused explicitly on SARS-CoV-2 or COVID-19, this corpus is likely to contain all or most manuscripts relevant to writing a literature review, which requires assessing both emerging and prior research. |
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In the future, one could imagine examining the fraction of papers that we cite that are in CORD.
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Yes! I think this would be a cool analysis!
| A new plugin was added to Manubot to support "smart citations" in the HTML build of manuscripts. | ||
| The plugin uses the [Scite](https://scite.ai/) [@doi:10.1101/2021.03.15.435418] service to display a badge below any citation with a DOI. | ||
| The badge contains a set of icons and numbers that indicate how many times that source has been mentioned, supported, or disputed and whether there have been any important editorial notices, such as retractions or corrections. | ||
| Using this, we were able to identify references that needed to be reevaluated. |
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In the idea world, we'd cite a retracted paper here so that folks could see the rendering but that won't work with ACM's template. What about citing a retracted paper and then putting a link to the instance in the manubot html? Maybe this is too self referential.
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I think we could put a screengrab if we have room? But we have a lot of figs so I'm not sure if we'll have room!
| Similarly, the clinical trials statistics and figure were generated based on data from the University of Oxford Evidence-Based Medicine Data Lab's COVID-19 TrialsTracker [@doi:10.5281/zenodo.3732709]. | ||
| The evolution of this figure over time is shown in Figure @fig:ebm-trials. | ||
| Information about vaccine distribution was extracted from Our World In Data [@url:https://github.com/owid/covid-19-data]. | ||
| Figure 1 (above) also uses this approach to dynamically integrate data directly from the CORD-19 dataset [@arxiv:2004.10706].<!--To Do: Flow chart of data integration? We could have a summary figure showing all of the external data sources that are integrated into the manuscript. We have icons for MSSM reviews, JHU data, etc. at the top. That flows into a GitHub repo, which also takes input from all the contributors. Then the output of the repo is the manuscript and other CI artifacts.--> |
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Time probably doesn't exist, but I do like this figure idea. It should definitely be in a presentation if accepted at the conference.
rando2
commented
Apr 30, 2021
| The first release, on March 16, 2020, contained 28,000 manuscripts on topics relevant to SARS-CoV-2 and related coronaviruses [@arxiv:2004.10706]. | ||
| Since then, these articles have continued to proliferate (left), with both traditionally published and preprint manuscripts in the corpus (right). | ||
| At present, it contains {{cord19_total_preprints}} preprints from _arXiv_, _bioRxiv_, and _medRxiv_. | ||
| While not all of the manuscripts are focused explicitly on SARS-CoV-2 or COVID-19, this corpus is likely to contain all or most manuscripts relevant to writing a literature review, which requires assessing both emerging and prior research. |
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Yes! I think this would be a cool analysis!
| A new plugin was added to Manubot to support "smart citations" in the HTML build of manuscripts. | ||
| The plugin uses the [Scite](https://scite.ai/) [@doi:10.1101/2021.03.15.435418] service to display a badge below any citation with a DOI. | ||
| The badge contains a set of icons and numbers that indicate how many times that source has been mentioned, supported, or disputed and whether there have been any important editorial notices, such as retractions or corrections. | ||
| Using this, we were able to identify references that needed to be reevaluated. |
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I think we could put a screengrab if we have room? But we have a lot of figs so I'm not sure if we'll have room!
Great job! I have pretty minor comments. Also added a couple of "To Do" comments so they're easier to pick out.
Co-authored-by: Casey Greene <cgreene@users.noreply.github.com>
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cbrueffer
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May 1, 2021
| The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures presents unique challenges to collaborative science. | ||
| We sought to apply a massive online open publishing approach to this problem using Manubot. | ||
| Through GitHub, collaborators contributed summaries and critiques of literature via issue templates and contributed literature summaries as pull requests. | ||
| Manubot rendered the manuscript content into pdf, HTML, and docx outputs, and an up-to-date version was always available online. |
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| Manubot rendered the manuscript content into pdf, HTML, and docx outputs, and an up-to-date version was always available online. | |
| Manubot rendered the manuscript content into PDF, HTML, and DOCX outputs, and an up-to-date version was always available online. |
| We adapted Manubot's figure generation workflow to retrieve up-to-date data from online sources nightly. | ||
| Additionally, we integrated scite, a tool for checking the status of references, including retractions, into the HTML build to simplify the process of monitoring changes to publications after their release. | ||
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| Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1000 sources and authored seven literature reviews. |
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| Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1000 sources and authored seven literature reviews. | |
| Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,000 sources and authored seven literature reviews. |
| However, any static review is likely to quickly become dated as new research is released or existing research is retracted or superseded, and the explosive rate of publication made localized efforts to curate new publications increasingly difficult. | ||
| Additionally, the complex nature of COVID-19 means that significant advantages can be gained from examining the virus and disease in a multidisciplinary context. | ||
| The downsides of "excessive publication" have been recognized for over forty years, as it was raised as a major concern about the move towards electronic, rather than print, publishing at the turn of the millennium [@doi:10/d3bmnv]. | ||
| The contents of the COVID-19 Open Research Dataset (CORD-19) [@arxiv:2004.10706], which was developed in part to assist in efforts to train machine learning algorithms on COVID-19-related text, illustrates the volume of publication relevant to understanding this virus (Figure @fig:cord19-growth). |
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| The contents of the COVID-19 Open Research Dataset (CORD-19) [@arxiv:2004.10706], which was developed in part to assist in efforts to train machine learning algorithms on COVID-19-related text, illustrates the volume of publication relevant to understanding this virus (Figure @fig:cord19-growth). | |
| The contents of the COVID-19 Open Research Dataset (CORD-19) [@arxiv:2004.10706], which was developed in part to assist in efforts to train machine learning algorithms on COVID-19-related text, illustrates the volume of publications relevant to understanding this virus (Figure @fig:cord19-growth). |
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Perhaps "scholarly literature" instead of publications, since it includes preprints? At least to me, perhaps falsely, publication suggests peer review.
| Concerns have been raised that the number of COVID-19 papers being retracted may be higher, or potentially much higher, than is typical, although a thorough investigation of this question will not be possible until more time has elapsed [@doi:10.1080/08989621.2020.1782203; @doi:10.1080/08989621.2020.1793675]. | ||
| Other papers are updated with corrections or expressions of concern [@doi:10.1080/08989621.2020.1793675;url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers]. | ||
| These include both preprints and papers published in more traditional venues [@url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers; @url:https://asapbio.org/preprints-and-covid-19]. | ||
| Preprints provide a venue for scientists to release findings rapidly but have both the advantage and disadvantage of making research available before it has undergone the peer-review process. |
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| Preprints provide a venue for scientists to release findings rapidly but have both the advantage and disadvantage of making research available before it has undergone the peer-review process. | |
| Preprints provide a venue for scientists to release findings rapidly but have both the advantage and disadvantage of making research available before it has undergone the peer review process. |
| Manubot is an ideal platform for analyzing COVID-19 literature because it facilitates the automatic integration of new data through CI. | ||
| However, the Manubot workflow can appear intimidating to contributors who are not well-versed in git [@doi:10.5334/kula.63]. | ||
| The synthesis and discussion of the emerging literature by biomedical scientists and clinicians is imperative to a robust interpretation of COVID-19 research, but in biology, such efforts often rely on What You See Is What You Get tools such as Google Docs, despite the significant limitations of these platforms in the face of excessive publication. | ||
| Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot present a significant technical barrier to domain experts. |
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| Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot present a significant technical barrier to domain experts. | |
| Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot presents a significant technical barrier to domain experts. |
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| With the worldwide scientific community uniting during 2020 to investigate SARS-CoV-2 and COVID-19 from a wide range of perspectives, findings from many disciplines are relevant on a rapid timescale to a broad scientific audience. | ||
| While Manubot manuscripts are written in markdown, they can be rendered in several formats that provide different advantages. | ||
| For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, docx, and now, LaTeX. |
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| For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, docx, and now, LaTeX. | |
| For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, DOCX, and now, LaTeX. |
| While Manubot manuscripts are written in markdown, they can be rendered in several formats that provide different advantages. | ||
| For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, docx, and now, LaTeX. | ||
| The HTML manuscript format offers several advantages over a static PDF to harmonize available resources that we were able to apply to specific problems of COVID-19. | ||
| The integration of scite into the HTML build makes references more manageable by visually representing whether their results are contested or whether they have been corrected or retracted. |
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| The integration of scite into the HTML build makes references more manageable by visually representing whether their results are contested or whether they have been corrected or retracted. | |
| The integration of Scite into the HTML build makes references more manageable by visually representing whether their results are contested or whether they have been corrected or retracted. |
| The HTML manuscript format offers several advantages over a static PDF to harmonize available resources that we were able to apply to specific problems of COVID-19. | ||
| The integration of scite into the HTML build makes references more manageable by visually representing whether their results are contested or whether they have been corrected or retracted. | ||
| Cross-referencing different pieces of the manuscript, such as cited preprints with reviews stored in an appendix, is another dynamic option presented by HTML. | ||
| Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate docx outputs was expanded to allow users to generate docx files containing only a section of the manuscript. |
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| Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate docx outputs was expanded to allow users to generate docx files containing only a section of the manuscript. | |
| Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate DOCX outputs was expanded to allow users to generate DOCX files containing only a section of the manuscript. |
| Cross-referencing different pieces of the manuscript, such as cited preprints with reviews stored in an appendix, is another dynamic option presented by HTML. | ||
| Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate docx outputs was expanded to allow users to generate docx files containing only a section of the manuscript. | ||
| In our case, where the full project is nearly 100,000 words, this allows individual pieces to be shared widely. | ||
| Finally, the addition of LaTeX output is useful for researchers from computational fields who submit papers in tex format and removes the step of reformatting markdown prior to submission. |
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| Finally, the addition of LaTeX output is useful for researchers from computational fields who submit papers in tex format and removes the step of reformatting markdown prior to submission. | |
| Finally, the addition of LaTeX output is useful for researchers from computational fields who submit papers in TeX format and removes the step of reformatting Markdown prior to submission. |
| @@ -917,6 +923,7 @@ dimorphism | |||
| disaggregate | |||
| dl | |||
| docosahexaenoic | |||
| docx | |||
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| docx | |
| DOCX |
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Thanks for these suggestions @cbrueffer. We can accept all of these proposed changes, but I want to make a plan with @rando2 about the order of operations. We submitted the first version of this manuscript to the ACM-BCB conference last Friday to meet their deadline. @rando2 what do you think of the following order for updates to this methods manuscript:
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[ci skip] This build is based on 33b6023. This commit was created by the following CI build and job: https://github.com/greenelab/covid19-review/commit/33b6023bbcf9be6c97c694f1788ff1cde0057727/checks https://github.com/greenelab/covid19-review/runs/833119364
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Original review #947 (review) Co-authored-by: Christian Brueffer <christian.brueffer@med.lu.se>
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I'm currently doing a pass through the manuscript to make some updates. I know others might do this, so figured I should do it section by section. Here is a second pass through on the intro.
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