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       string: '{"id":"f3629c86-06e0-42c0-844a-266b03a91ef1","doi":"https://doi.org/10.59350/37y2z-gre70","url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","title":"Ten
         years and a million links","summary":"As trailed on a Twitter thread last
         week I’ve been working on a manuscript describing the efforts to map taxonomic
-        names to their original descriptions in the taxonomic literature. Putting
-        together a manuscript on linking taxonomic names to the primary literature,
-        basically “um, what, exactly, have you been doing all these years?”. TL;DR
-        Across fungi, plants, and animals approx 1.3 million names have been linked
-        to a persistent identifier for a publication.— Roderic Page (@rdmpage) May
-        25,...","published_at":1685553960,"updated_at":1685554180,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
-        Page"}],"image":null,"tags":[],"language":"en","reference":[],"blog_id":"tyfqw20","blog_name":"iPhylo","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
+        names to their original descriptions in the taxonomic literature.","content_html":"<p>As
+        trailed on a Twitter thread last week I’ve been working on a manuscript describing
+        the efforts to map taxonomic names to their original descriptions in the taxonomic
+        literature.</p>\n<blockquote><p>Putting together a manuscript on linking taxonomic
+        names to the primary literature, basically “um, what, exactly, have you been
+        doing all these years?”. TL;DR Across fungi, plants, and animals approx 1.3
+        million names have been linked to a persistent identifier for a publication.</p>—
+        Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
+        25, 2023</a></blockquote> \n<p>The preprint is on bioRxiv <a href=\"https://doi.org/10.1101/2023.05.29.542697\">doi:10.1101/2023.05.29.542697</a></p>\n<blockquote>\n<p>A
+        major gap in the biodiversity knowledge graph is a connection between taxonomic
+        names and the taxonomic literature. While both names and publications often
+        have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
+        or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
+        DOIs for publications. This article describes efforts to make those connections
+        across three large taxonomic databases: Index Fungorum, International Plant
+        Names Index (IPNI), and the Index of Organism Names (ION). Over a million
+        names have been matched to DOIs or other persistent identifiers for taxonomic
+        publications. This represents approximately 36% of names for which publication
+        data is available. The mappings between LSIDs and publication PIDs are made
+        available through ChecklistBank. Applications of this mapping are discussed,
+        including a web app to locate the citation of a taxonomic name, and a knowledge
+        graph that uses data on researcher’s ORCID ids to connect taxonomic names
+        and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
+        the work has been linking taxa to names, which still has huge gaps. There
+        are also interesting differences in coverage between plants, animals, and
+        fungi (see preprint for details).</p>\n\n<div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png\"
+        /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s320/fungi-coverage.png\"
+        /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s320/plants-coverage.png\"
+        /></a></div>\n\n\nThere is also a simple app to demonstrate these links, see
+        <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
+        with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","published_at":1685553960,"updated_at":1685554180,"indexed_at":1689933917,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png","tags":[],"language":"en","reference":[],"relationships":[],"blog_id":"tyfqw20","blog_name":"iPhylo","blog_slug":"iphylo","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
         raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
         and biodiversity informatics.  For more ranty and less considered opinions,
         see my <a href=\"https://twitter.com/rdmpage\">Twitter feed</a>.<br>ISSN 2051-8188.
         Written content on this site is licensed under a <a href=\"https://creativecommons.org/licenses/by/4.0/\">Creative
-        Commons Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","home_page_url":"https://iphylo.blogspot.com/","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T08:03:14+00:00","indexed_at":"2023-02-06","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
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+        Commons Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","home_page_url":"https://iphylo.blogspot.com","user_id":"b98bb1b6-b96b-4e8a-94d3-4285ea715f5b","created_at":"2023-02-06","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
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         programs that will help jumpstart their careers by exposing them to mentorship
         and opportunities to conduct research. While the gold standard of academic
         productivity (for the time being) remains peer-reviewed publications, conference
+        posters and presentations are an important secondary metric.","content_html":"<p>Students
+        and residents aspiring for a career in academic surgery are looking for training
+        programs that will help jumpstart their careers by exposing them to mentorship
+        and opportunities to conduct research. While the gold standard of academic
+        productivity (for the time being) remains peer-reviewed publications, conference
         posters and presentations are an important secondary metric. In addition to
         feeding eventual papers, conference talks allow trainees to practice presentation
-        skills, build...","published_at":1685768070,"updated_at":1685768070,"indexed_at":1689006804,"authors":[{"url":null,"name":"Tejas
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+        skills, build their networks, and learn about the work being done at peer
+        institutions and the field more broadly. Residents pursuing professional development
+        are encouraged to apply to and attend conferences--though in the post-COVID
+        era the cost of conference attendance and travel are being re-evaluated. For
+        now, academic conference participation can serve as an important albeit limited
+        metric to evaluate an overall institution''s research power – especially as
+        it relates to trainees.</p><p>The <a href=\"https://www.academicsurgicalcongress.org/?ref=ideasurg.pub\">Academic
+        Surgical Congress</a> (ASC) is a joint surgical meeting co-hosted by the <a
+        href=\"https://www.aasurg.org/?ref=ideasurg.pub\">Association for Academic
+        Surgery</a> (AAS) and the <a href=\"https://www.susweb.org/?ref=ideasurg.pub\">Society
+        for University Surgeons</a> (SUS) and held annually in February. Anecdotally,
+        it is a popular conference for students and residents to attend. The ASC maintains
+        a public archive of all abstracts dating from 2015-2020. We obtained a machine
+        readable version of this public database through the webmaster (this version
+        of the data spans 2016 to 2023). Using number of accepted abstracts as a surrogate
+        for research productivity, we wanted to identify successful institutions.
+        Conceivably, by finding institutions who achieved high abstract numbers, we
+        could conduct interviews and focus groups among key stakeholders at these
+        programs to understand what they did, and how these actions can be replicated.
+        We were particularly interested in seeing which programs demonstrated a high
+        number of absolute accepted abstracts within the study period and also which
+        programs were able to improve their abstract performance from year to year.
+        </p><p>For each abstract, we looked at the year and primary institution at
+        which the work was conducted. In the dataset, all of the institutional affiliations
+        for each author are combined in one text string. To figure out the primary
+        institution, we searched the institution block string for the first presence
+        of \"university\", \"hospital\", \"institute\", or \"medical center\" or the
+        first expression to occur before a comma. This method was chosen as institutions’
+        names are written variably (Department of Surgery, University Hospital, New
+        York, NY vs. University Hospital, Division of Colorectal Surgery, Department
+        of Surgery, New York, NY). Next, we found that for several abstracts belonging
+        to the same institution in reality, the institution name was written in various
+        ways (e.g. University of Alabama vs. University of Alabama - Birmingham or
+        University of California - Los Angeles vs. David Geffen School of Medicine).
+        We attempted fuzzy string matching as well as some manual corrections to improve
+        this issue. While our efforts were not able to achieve perfect results, we
+        were able to resolve a majority of the mismatches.</p><p>In order to do a
+        primary survey of institutional trends in this dataset, we conducted the following
+        analyses. First, we measured the number of abstracts accepted each year from
+        2016 to 2023. Second, we looked at the number of accepted abstracts by institution
+        over the entire study period and identified the top twenty institutions. Then,
+        we looked at the number of abstract institutions by year for each of these
+        top twenty institutions to study changes in institutional trends over time.
+        Finally, we did a subset analysis on post-COVID data (2021 to 2023) to look
+        at absolute and per cent year-over-year changes in accepted abstracts to see
+        which institutions were able to significantly increase their abstract performance
+        in one year. </p><h3>Accepted Abstracts are increasing but down from peak</h3><p>There
+        were a total of 10,396 unique abstracts accepted at the Academic Surgical
+        Congress between 2016 and 2023 for which complete institutional data is available.</p><p>We
+        plotted the total number of abstracts accepted by year. The number of accepted
+        abstracts increased from 1125 in 2016 to an all-time high of 1742 in 2020
+        before declining to 922 and 848 in 2021 and 2022, respectively. Accepted abstracts
+        have since rebounded to 1469 in 2023, or roughly 84% of the maximum amount.
+        Of note, the 2021 and 2022 meetings were held virtually due to the COVID-19
+        pandemic. Conversely the 2020 meeting was held immediately prior to the institution
+        of lockdowns and other social distancing policies.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-2-1.png\"
+        loading=\"lazy\" width=\"2000\" height=\"1251\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-2-1.png
+        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-2-1.png
+        1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-2-1.png
+        1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-2-1.png
+        2400w\" /><figcaption>Number of accepted abstracts at the Academic Surgical
+        Congress by year from 2016-2023</figcaption></figure><h3>Alabama, Michigan
+        lead abstract acceptances during study period</h3><p>Next, we plotted the
+        total number of accepted abstracts by institution. The graph shows data for
+        the twenty leading institutions. The University of Alabama and the University
+        of Michigan lead in abstract acceptances during the study period (509 and
+        382, respectively). Given an eight year time-range, the top twenty institutions
+        reflect an average annual abstract acceptance ranging from roughly seventeen
+        to 63.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-1.png\"
+        loading=\"lazy\" width=\"2000\" height=\"1061\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-1.png
+        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-1.png
+        1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-1.png
+        1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-1.png
+        2400w\" /><figcaption>Number of accepted ASC abstracts for the top twenty
+        institutions from 2016-2023</figcaption></figure><p>We also plotted the number
+        of accepted abstracts by year using a separate line plot for each institution.
+        The University of Alabama surged from 15 to 58 abstracts from 2016 and 2017,
+        maintaining over 60 abstracts per year thereafter. The University of Michigan
+        maintained between 30 and 60 abstracts for each year and has ranked in the
+        top three for each year studied. Overall, there appears to be a general clustering
+        of the remaining institutions.</p><p>Of note, there is a noticeable dip from
+        2020 to 2022 seen at most institutions which starts to recover in 2023, consistent
+        with the aggregated data shown in the previous figure.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-3.png\"
+        loading=\"lazy\" width=\"2000\" height=\"1359\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-3.png
+        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-3.png
+        1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-3.png
+        1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-3.png
+        2400w\" /></figure><h3>MGH, Brigham lead absolute and per cent increase in
+        abstracts in 2023</h3><p>Next, we measured the absolute and percent change
+        between accepted abstracts in consecutive years for the top twenty institutions.
+        We restricted our analysis to 2021, 2022, and 2023. The greatest absolute
+        increases in accepted abstracts came from Massachusetts General Hospital in
+        2023 (28), The University of Pennsylvania (17), and Brigham and Women''s Hospital
+        (15), all in 2023. The greatest percentage increases in accepted abstracts
+        came from Brigham and Women''s Hospital (500%), Massachusetts General Hospital
+        (400%), and Yale Univeristy (275%), also all in 2023. Interestingly, University
+        of Alabama (+0 in 2022, +5 in 2023) and University of Michigan (+5 in 2022,
+        +8 in 2023)  - which rank at the top in all time and yearly abstracts - experienced
+        less extreme swings during the 2021-2023 time period. The greatest year-over-year
+        increase in the study period was University of Alabama''s increase of 43 abstracts
+        in 2017, but as it falls outside the time range of this subset analysis, that
+        data is not shown here.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-4--5-.png\"
+        loading=\"lazy\" width=\"2000\" height=\"903\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-4--5-.png
+        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-4--5-.png
+        1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-4--5-.png
+        1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-4--5-.png
+        2400w\" /><figcaption>Year-over-year absolute change in ASC accepted abstracts
+        from 2021-2023</figcaption></figure><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-5--9-.png\"
+        loading=\"lazy\" width=\"2000\" height=\"884\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-5--9-.png
+        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-5--9-.png
+        1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-5--9-.png
+        1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-5--9-.png
+        2400w\" /><figcaption>Year-over-year percent change in ASC accepted abstracts
+        from 2021-2023</figcaption></figure><h3>Conclusions</h3><p>In this data exploration,
+        we analyzed abstract acceptance data for the Academic Surgical Congress between
+        2016 and 2023. We showed that the number of abstracts increased from 2016
+        to 2020, dipped in 2021 and 2022, and is recovering in 2023 - likely reflecting
+        the variability forced by COVID19 and the transition to virtual conferences
+        in 2021 and 2022. We also showed that the University of Alabama and the University
+        of Michigan have significantly led accepted abstracts throughout the study
+        period with University of Alabama maintaining a top position following an
+        impressive 287% percent increase in abstracts between 2016 and 2017. In 2023,
+        Massachusetts General Hospital and Brigham and Women''s Hospital rank in the
+        top three for both absolute and percent changes in year-over-year abstract
+        acceptances in 2023. </p><h3>Limitations and Future Directions</h3><p>This
+        data exploration has several limitations. First, our study is limited to one
+        conference, and conferences themselves are only a limited component of academic
+        productivity. However, the Academic Surgical Congress is an international
+        meeting that is well regarded, popular among trainees, and has consistent
+        multi-year data. We can improve the generalizability of our findings by bringing
+        in similar data from other large meetings – such as the American College of
+        Surgeons Clinical Congress and the Society of American Gastrointestinal and
+        Endoscopic Surgeons (SAGES). We can also use the PubMed API to perform similar
+        analyses in top surgical journals such as JAMA Surgery or the Annals of Surgery.</p><p>Furthermore,
+        there is renewed concern that the <a href=\"https://jamanetwork.com/journals/jamasurgery/article-abstract/2797087?ref=ideasurg.pub\">ever-increasing
+        number</a> of abstracts and papers required for trainees to progress academically
+        is leading to an unhealthy \"research treadmill\". While these concerns are
+        valid, research productivity remains an important component of academic development,
+        and number of abstract acceptances can serve as a meaningful metric in guaging
+        an institution''s research productivity and culture.</p><p>Another limitation
+        of our study is our assumption that the first institution listed in the author
+        block is the primary institution–a method which does not take into account
+        multi-institutional abstracts. However, we suspect this reflects the minority
+        of the abstracts. Finally, we have not fully optimized name-matching to correctly
+        combine terms like \"University of Alabama\" and \"University of Alabama Birmingham\".
+        One future direction to improve this analysis would be to optimize the fuzzy
+        string matching algorithm used in our code. Alternatively, more granular source
+        data could also help improve the accuracy of our findings.</p><p>With regards
+        to the data we have obtained, we can conduct survey-based studies or focus
+        groups with key stakeholders from institutions that have demonstrated strong
+        abstract performance during the study period as well as those who have shown
+        significant improvement. By talking to department chairs, program directors,
+        and research and education leaders we can understand what steps each institution
+        took to improve abstract acceptance (e.g. hiring a new research faculty, creating
+        a mentorship program, providing administrative support for IRBs/stats etc.).
+        Following this, we can map individual interventions to improvements to understand
+        the contribution that each can have on increased academic productivity.</p><p>We
+        have also not yet mined the abstract text itself for themes. Using natural
+        language processing, we can understand how themes and trends of emergent research
+        change from year to year, and even develop models to predict which topics
+        will be of interest in future works. This will likely be the subject of a
+        future data exploration.</p><p>Overall, we hope to demonstrate that abstract
+        acceptance data from a single international meeting can provide interesting,
+        meaningful data on which programs have strong research infrastructure and
+        which programs are making strides to achieve it. By studying this data and
+        improving the inputs, we can better understand whose example to follow and
+        ultimately develop a playbook that all institutions can employ to maximize
+        the academic opportunities of students and trainees.</p><h3>See the Data</h3><p>You
+        can see the raw data as well as all of our code <a href=\"https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32?ref=ideasurg.pub\">here</a>,
+        and use this for your own studies with appropriate attribution.</p><h3>Acknowledgements</h3><p>Special
+        thanks to Ojas Sathe for assistance with the fuzzy string matching</p>","published_at":1685768070,"updated_at":1685768070,"indexed_at":1690923223,"authors":[{"url":"https://orcid.org/0000-0003-0449-4469","name":"Tejas
+        S. Sathe"}],"image":"https://www.ideasurg.pub/content/images/2023/06/Frame-2-1.png","tags":["Preprint"],"language":"en","reference":[],"relationships":[],"blog_id":"3cxcm20","blog_name":"I.D.E.A.S.","blog_slug":"ideas","blog":{"id":"3cxcm20","title":"I.D.E.A.S.","description":"Innovation
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         it compose?","summary":"One question I have increasingly asked myself in the
-        past few years. Meaning Can I run this open source software using Docker containers
-        and a Docker Compose file?As the Docker project turned ten this spring, it
-        has become standard practice to distribute open source software via Docker
-        images and to provide a Docker Compose file to run the software together with
-        other dependencies. The Awesome Compose project has collected many examples,
-        and all you need is a docker-compose.ymlfile and a...","published_at":1684237016,"updated_at":1687084066,"indexed_at":1689007007,"authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
-        Fenner"}],"image":"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib=rb-4.0.3&q=80&w=2000","tags":["News"],"language":"en","reference":[],"blog_id":"f0m0e38","blog_name":"Front
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-  recorded_at: Mon, 10 Jul 2023 21:04:49 GMT
+        past few years. Meaning Can I run this open source software  using Docker
+        containers and a Docker Compose file? As the Docker project turned ten this
+        spring, it has become standard practice to distribute open source software
+        via Docker images and to provide a Docker Compose file to run the software
+        together with other dependencies.","content_html":" <p><img src=\"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop=entropy&amp;cs=tinysrgb&amp;fit=max&amp;fm=jpg&amp;ixid=M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&amp;ixlib=rb-4.0.3&amp;q=80&amp;w=2000\"
+        /></p><p>One question I have increasingly asked myself in the past few years.
+        Meaning </p><blockquote>Can I run this open source software  using Docker
+        containers and a Docker Compose file?</blockquote><p>As the Docker project
+        <a href=\"https://snyk.io/blog/the-docker-project-turns-10/\">turned ten this
+        spring</a>, it has become standard practice to distribute open source software
+        via Docker images and to provide a <a href=\"https://docs.docker.com/compose/\">Docker
+        Compose</a> file to run the software together with other dependencies. The
+        <a href=\"https://github.com/docker/awesome-compose\">Awesome Compose</a>
+        project has collected many examples, and all you need is a <code>docker-compose.yml</code>file
+        and a recent installation of Docker, e.g. <a href=\"https://www.docker.com/products/docker-desktop/\">Docker
+        Desktop</a>. Be aware that Docker Compose has evolved over the years. It started
+        out as a dedicated Python application but was later integrated into the Docker
+        application (written in Go) as Compose V2.</p><p>Docker and Docker Compose
+        allow you to run pretty complex applications without first addressing a long
+        list of requirements (which might conflict with other software you have installed),
+        or needing a long and complex build step where many things can go wrong. For
+        example a self-hosted instance of Supabase (a hosted Postgres database with
+        additional features) that I installed last week following <a href=\"https://supabase.com/docs/guides/self-hosting/docker\">these
+        instructions</a>.</p><p>An important open source project that I am involved
+        in is <a href=\"https://inveniordm.docs.cern.ch/\">InvenioRDM</a>, the turn-key
+        research data management repository. InvenioRDM started in 2019, with a first
+        production-suitable version in August 2021, and the <a href=\"https://inveniosoftware.org/products/rdm/#status\">next
+        major goal </a>is to have the large and popular <a href=\"https://zenodo.org/\">Zenodo</a>
+        repository running on top of InvenioRDM. Zenodo <a href=\"https://blog.zenodo.org/2023/05/08/2023-05-08-10years/\">turned
+        ten last week</a>, a few weeks after Docker. Interestingly, my personal tenth
+        anniversary was last year in May as I became a full-time software developer
+        and left academic medicine as a medical doctor treating cancer patients in
+        <a href=\"https://doi.org/10.53731/r294649-6f79289-8cw2j\">May 2012</a>.</p><p>Unfortunately,
+        InvenioRDM \"doesn''t compose\" yet. It is very close, but there are no ready-made
+        Docker images to download, and the <a href=\"https://inveniordm.docs.cern.ch/install/\">installation
+        instructions</a> start with installing a Python command-line tool (invenio-cli).
+        So if you have 1-2 hours to play with InvenioRDM and get a first impression,
+        there is no official solution from the InvenioRDM project yet. For this reason,
+        I started the <a href=\"https://github.com/front-matter/docker-invenio-rdm\">docker-invenio-rdm</a>
+        repository on Github. It contains a Docker Compose file that uses pre-built
+        Docker images, and using that file with a <code>docker compose up</code>command
+        on your local computer should give you a running InvenioRDM within 15 minutes:</p><figure><img
+        src=\"https://blog.front-matter.io/content/images/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png\"
+        loading=\"lazy\" width=\"2000\" height=\"1210\" srcset=\"https://blog.front-matter.io/content/images/size/w600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        600w, https://blog.front-matter.io/content/images/size/w1000/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        1000w, https://blog.front-matter.io/content/images/size/w1600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        1600w, https://blog.front-matter.io/content/images/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        2193w\" /></figure><p>I started this recently and obviously want to move forward
+        in two directions:</p><ul><li>fine-tune the initial configuration to provide
+        a great initial experience with InvenioRDM, e.g. making it easy to <a href=\"https://inveniordm.docs.cern.ch/develop/topics/theming/\">theme</a>
+        the InvenioRDM instance</li><li>make this an official part of the InvenioRDM
+        project, extending the <a href=\"https://github.com/inveniosoftware/docker-invenio\">docker-invenio</a>
+        GitHub repository that provides Docker base images for InvenioRDM and other
+        projects using the Invenio software.</li></ul><p>But of course, Docker Compose
+        is not the answer to all questions regarding running Docker-based infrastructure.
+        For production environments, most people shy away from using Docker Compose.
+        The reasons for that and the alternatives will be the topic of a future blog
+        post (spoiler: there is exciting news).</p><p>Docker Compose also needs more
+        work to be set up correctly for development environments. It is a common practice
+        and a workflow I used while working at DataCite (where we launched Docker-based
+        infrastructure in 2016), but for now, the easiest way to set up InvenioRDM
+        development environments is using the <a href=\"https://inveniordm.docs.cern.ch/install/\">invenio-cli
+        tool with a local development environment</a>.</p><p>Please reach out to me
+        with feedback on running Docker Compose for InvenioRDM (use the <a href=\"https://github.com/front-matter/docker-invenio-rdm/discussions\">discussions</a>
+        feature in the GitHub repo), or if you have questions about running InvenioRDM
+        in production.</p> ","published_at":1684237016,"updated_at":1687084066,"indexed_at":1689007007,"authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
+        Fenner"}],"image":"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop&#x3D;entropy&cs&#x3D;tinysrgb&fit&#x3D;max&fm&#x3D;jpg&ixid&#x3D;M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib&#x3D;rb-4.0.3&q&#x3D;80&w&#x3D;2000","tags":["News"],"language":"en","reference":[],"relationships":[],"blog_id":"f0m0e38","blog_name":"Front
+        Matter","blog_slug":"front_matter","blog":{"id":"f0m0e38","title":"Front Matter","description":"The
+        Front Matter Blog covers the intersection of science and technology since
+        2007.","language":"en","favicon":"https://blog.front-matter.io/favicon.png","feed_url":"https://blog.front-matter.io/atom-complete/","home_page_url":"https://blog.front-matter.io","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-01-02","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Ghost
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         a couple of years of working to support institutions implementing their OA
         policies, we''re so proud to see OA.Report, our development partner, and one
         of our collaborators featured in Nature. We appreciate Nature bringing attention
-        to the progress being made in more effectively implementing OA policies.Read
-        the full story on Nature''s website.Screenshot of the story on the Nature
-        websiteFind out more about how OA.Report can help your organization on our
-        website or in our recent...","published_at":1674558707,"updated_at":1674558707,"indexed_at":1688982864,"authors":[{"url":null,"name":"OA.Works"}],"image":"https://blog.oa.works/content/images/2023/01/nature-website-v2.png","tags":["OA.Report"],"language":"en","reference":[],"blog_id":"h7bpg11","blog_name":"OA.Works
-        Blog","blog":{"id":"h7bpg11","title":"OA.Works Blog","description":"OA.Works
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+        to the progress being made in more effectively implementing OA policies.","content_html":"<img
+        src=\"https://blog.oa.works/content/images/2023/01/nature-website-v2.png\"
+        alt=\"Nature features OA.Report''s work putting OA policy into practice!\"
+        /><p>After a couple of years of working to support institutions implementing
+        their OA policies, we''re so proud to see <a href=\"https://oa.report/?ref=blog.oa.works\">OA.Report</a>,
+        <a href=\"https://blog.oa.works/grant-to-bolster-oa-policies-from-bmgf/\">our
+        development partner</a>, and <a href=\"https://dataseer.ai/?ref=blog.oa.works\">one
+        of our collaborators</a> <a href=\"https://www.nature.com/articles/d41586-023-00175-1?ref=blog.oa.works\">featured
+        in Nature</a>. We appreciate Nature bringing attention to the progress being
+        made in more effectively implementing OA policies.</p><p>Read the full story
+        on <a href=\"https://www.nature.com/articles/d41586-023-00175-1?ref=blog.oa.works\">Nature''s
+        website</a>.</p><figure><a href=\"https://www.nature.com/articles/d41586-023-00175-1?ref=blog.oa.works\"><img
+        src=\"https://blog.oa.works/content/images/2023/01/nature-website-v2-1.png\"
+        alt=\"Nature features OA.Report''s work putting OA policy into practice!\"
+        loading=\"lazy\" width=\"1520\" height=\"1584\" srcset=\"https://blog.oa.works/content/images/size/w600/2023/01/nature-website-v2-1.png
+        600w, https://blog.oa.works/content/images/size/w1000/2023/01/nature-website-v2-1.png
+        1000w, https://blog.oa.works/content/images/2023/01/nature-website-v2-1.png
+        1520w\" /></a><figcaption>Screenshot of the story on the Nature website</figcaption></figure><p>Find
+        out more about how OA.Report can help your organization <a href=\"https://oa.report/?ref=blog.oa.works\">on
+        our website</a> or <a href=\"https://blog.oa.works/oa-report-helps-funders-measure-and-increase-oa-policy-compliance-and-their-investments-impact/\">in
+        our recent update</a>.</p><hr /><p>Grant support for this work was provided
+        in part by the Bill and Melinda Gates Foundation and the Robert Wood Johnson
+        Foundation. The views expressed here do not necessarily reflect the views
+        of either foundation.</p>","published_at":1674558707,"updated_at":1674558707,"indexed_at":1688982864,"authors":[{"url":null,"name":"OA.Works"}],"image":"https://blog.oa.works/content/images/2023/01/nature-website-v2.png","tags":["OA
+        Report"],"language":"en","reference":[],"relationships":[],"blog_id":"h7bpg11","blog_name":"OA.Works
+        Blog","blog_slug":"oa_works","blog":{"id":"h7bpg11","title":"OA.Works Blog","description":"OA.Works
+        Blog","language":"en","favicon":"https://blog.oa.works/favicon.png","feed_url":"https://blog.oa.works/rss/","home_page_url":"https://blog.oa.works","user_id":"dead81b3-8a8b-45c9-85fe-f01bb3948c77","created_at":"2023-01-04","feed_format":"application/rss+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Ghost
+        5.61","category":"computerAndInformationSciences","prefix":"10.59350","modified_at":"2023-07-31T10:36:26+00:00","version":"https://jsonfeed.org/version/1.1","current_feed_url":null,"status":"active","issn":null,"backlog":165,"authors":null,"plan":"Starter","slug":"oa_works","use_mastodon":false}}'
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