commonmeta-ruby 3.3.14 → 3.3.16
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +2 -2
- data/bin/commonmeta +1 -1
- data/lib/commonmeta/cli.rb +5 -5
- data/lib/commonmeta/readers/json_feed_reader.rb +6 -5
- data/lib/commonmeta/utils.rb +15 -15
- data/lib/commonmeta/version.rb +1 -1
- data/spec/cli_spec.rb +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id.yml +62 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/{json_feed_unregistered/blog_post_uuid.yml → encode/by_id_unknown_uuid.yml} +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml +189 -1704
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_unregistered.yml +54 -1969
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id.yml +65 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id_specific_prefix.yml +62 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +210 -518
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +6 -1450
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +54 -8
- data/spec/readers/json_feed_reader_spec.rb +7 -7
- metadata +6 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post.yml +0 -360
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post_uuid.yml +0 -980
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presentations today at MTE14, and the papers that go with them\",\"summary\":\"BIG
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day today. The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota
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(MTE14) is taking place in Salt Lake City this week. Normally I’d be there
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in a heartbeat, but my son is graduating from high school next week and I’m
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far too busy to get away. Still, I’m an author on one poster and two talks
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that are running today, along with the three associated short papers that
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are published in the conference volume in The Anatomical Record. I will be
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blogging about these things, and shortly,...\",\"date_published\":\"2023-06-09T13:02:26Z\",\"date_modified\":\"2023-06-09T13:02:26Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Matt
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Wedel\"}],\"image\":null,\"content_html\":\"\\n<p><a href=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\\\"><img
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loading=\\\"lazy\\\" data-attachment-id=\\\"21001\\\" data-permalink=\\\"https://svpow.com/2023/06/09/three-presentations-today-at-mte14-and-the-papers-that-go-with-them/ripple-rock-in-the-oklahoma-morrison/\\\"
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data-orig-file=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\\\"
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data-orig-size=\\\"2000,2000\\\" data-comments-opened=\\\"1\\\" data-image-meta=\\\"{\\\"aperture\\\":\\\"1.8\\\",\\\"credit\\\":\\\"\\\",\\\"camera\\\":\\\"iPhone
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7\\\",\\\"caption\\\":\\\"\\\",\\\"created_timestamp\\\":\\\"1530009833\\\",\\\"copyright\\\":\\\"\\\",\\\"focal_length\\\":\\\"3.99\\\",\\\"iso\\\":\\\"20\\\",\\\"shutter_speed\\\":\\\"0.00051203277009729\\\",\\\"title\\\":\\\"\\\",\\\"orientation\\\":\\\"1\\\"}\\\"
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data-image-title=\\\"Ripple rock in the Oklahoma Morrison\\\" data-image-description=\\\"\\\"
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data-image-caption=\\\"\\\" data-medium-file=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=300\\\"
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class=\\\"size-large wp-image-21001 aligncenter\\\" src=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=480\\\"
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alt=\\\"\\\" width=\\\"480\\\" height=\\\"480\\\" srcset=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=480
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480w, https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=960
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768w\\\" sizes=\\\"(max-width: 480px) 100vw, 480px\\\" /></a></p>\\n<p>BIG
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day today. The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota
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(MTE14) is taking place in Salt Lake City this week. Normally I’d be
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there in a heartbeat, but my son is graduating from high school next week
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and I’m far too busy to get away. Still, I’m an author on one
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poster and two talks that are running today, along with the three associated
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short papers that are published in the conference volume in The Anatomical
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Record. </p>\\n<p>I will be blogging about these things, and shortly, but
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for now here are Wedel-related presentations and links to the papers, in chronological
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order. (The whole conference volume is available <a href=\\\"https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/ar.25219\\\">here</a>,
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I just extracted the papers I’m on as separate PDFs to post in the links
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below.)</p>\\n<p>1. Wedel and Atterholt on expanded neurocentral joints in
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sauropods — Jessie is presenting our poster, which should be up for
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most of the day. Citation and link to paper:</p>\\n<p style=\\\"padding-left:
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40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/wedel-and-atterholt-2023-expanded-neurocentral-joints-in-sauropods.pdf\\\">Wedel,
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M.J., and Atterholt, J. 2023. Expanded neurocentral joints in the vertebrae
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of sauropod dinosaurs. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
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(eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
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Record 306(S1):256-257.</a></p>\\n<p>2. Curtice et al. on the first material
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of <em>Haplocanthosaurus</em> from Dry Mesa — I believe Brian Curtice
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and Colin Boisvert are tag-teaming this talk at 2:00 pm MDT. </p>\\n<p style=\\\"padding-left:
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40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/curtice-et-al-2023-haplocanthosaurus-from-dry-mesa.pdf\\\">Curtice,
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B., Wedel, M.J., Wilhite, D.R., and Boisvert, C. 2023. New material of <em>Haplocanthosaurus</em>
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(Hatcher 1903) from the Dry Mesa Dinosaur Quarry and a comment on sauropod
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diversity. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A. (eds), 14th
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Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical Record
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306(S1):79-81.</a></p>\\n<p>3. Weil et al. on Morrison microvertebrates from
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the Oklahoma panhandle — Anne Weil is giving this talk at 2:15 pm MDT.</p>\\n<p
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style=\\\"padding-left: 40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/weil-et-al-2023-oklahoma-morrison-microvertebrates.pdf\\\">Weil,
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A., Hall, L., and Wedel, M.J. 2023. Microvertebrate expansion of known fauna
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of the Morrison Formation of Oklahoma will enable more meaningful comparisons
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with other regions. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
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(eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
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Record 306(S1):257-258.</a></p>\\n<p>Stand by for more info on all this stuff.
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And if you’re attending MTE14, go catch these presentations and say
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hi to all these excellent human beings!</p>\\n\",\"tags\":[\"#MTE14\",\"conferences\",\"navel
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blogging\",\"timely\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"dkvra02\",\"blog\":{\"id\":\"dkvra02\",\"title\":\"Sauropod
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Vertebra Picture of the Week\",\"description\":\"SV-POW! ... All sauropod
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vertebrae, except when we're talking about Open Access\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://svpow.com/feed/atom/\",\"home_page_url\":\"https://svpow.com\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T14:28:02+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
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(.com)\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-06-09T19:54:23+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/gybpr-7mq58\",\"uuid\":\"a3e4b240-26dd-486a-913a-325f697c6aef\",\"url\":\"https://svpow.com/2023/04/12/more-on-the-disturbing-plausibility-of-chatgpt/\",\"title\":\"More
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on the disturbing plausibility of ChatGPT\",\"summary\":\"Prompted by a post
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on Mastodon (which, like all Mastodon posts, I can no longer find), I asked
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ChatGPT to tell me about my own papers. The response started out well but
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quickly got much worse. I will indent my comments on its response. Q. What
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are some articles written by Michael P. Taylor? A. Michael P. Taylor is a
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vertebrate paleontologist and open science advocate. He has written numerous
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articles and papers on topics such as the taxonomy and systematics of sauropod
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dinosaurs, open access...\",\"date_published\":\"2023-04-12T22:40:38Z\",\"date_modified\":\"2023-04-12T22:40:38Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Mike
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Taylor\"}],\"image\":null,\"content_html\":\"<p>Prompted by a post on Mastodon
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(which, like all Mastodon posts, I can no longer find), <a href=\\\"https://chat.openai.com/chat/e3febb81-8cf4-47c5-bf2b-49dade1f6518\\\">I
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asked ChatGPT to tell me about my own papers</a>. The response started out
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well but quickly got much worse. I will indent my comments on its response.</p>\\n<hr
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/>\\n<p><strong>Q. What are some articles written by Michael P. Taylor?</strong></p>\\n<p>A.
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Michael P. Taylor is a vertebrate paleontologist and open science advocate.
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He has written numerous articles and papers on topics such as the taxonomy
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and systematics of sauropod dinosaurs, open access publishing, and scholarly
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communication.</p>\\n<blockquote><p>So far, so good. In general, LLMs seem
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to be good at synthesizing overviews. It’s specific facts that trip
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them up.</p></blockquote>\\n<p>Here are a few examples of his articles:</p>\\n<p>Taylor,
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M. P. (2009). A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria,
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Sauropoda) and its generic separation from Giraffatitan brancai (Janensch
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1914) (Dinosauria, Sauropoda). Journal of Vertebrate Paleontology, 29(3),
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787-806.</p>\\n<blockquote><p>The first one gives is pretty good. The only
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mistake is that it’s oddly appended “(Dinosauria, Sauropoda)”
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to the end of the article title. The journal, volume, issue and page-numbers
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are all correct.</p></blockquote>\\n<p>Taylor, M. P. (2011). Sauropod dinosaur
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research: a historical review. In A. W. A. Kellner, & D. A. S. Silva (Eds.),
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Vertebrate paleontology and sedimentology of the Jurassic-Cretaceous boundary
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in the northern and central parts of the Lusitanian Basin, Portugal (pp. 11-43).
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Sociedade de Geologia de Portugal.</p>\\n<blockquote><p>I did write a book-chapter
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titled “Sauropod dinosaur research: a historical review”. But
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it came out in 2010, not 2011. And it ran from pages 361–386, not 11-43. And
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it was in <em>Dinosaurs and Other Extinct Saurians: a Historical Perspective</em>,
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not <em>Vertebrate paleontology and sedimentology of the Jurassic-Cretaceous
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boundary in the northern and central parts of the Lusitanian Basin, Portugal</em>
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(which doesn’t exist). Which was edited by Richard T. J. Moody, Eric
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Buffetaut, Darren Naish and David M. Martill, not A. W. A. Kellner & D. A.
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S. Silva. And published by the Geological Society of London, not Sociedade
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de Geologia de Portugal.</p></blockquote>\\n<p>Taylor, M. P., & Wedel, M.
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J. (2018). Why sauropods had long necks; and why giraffes have short necks.
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PeerJ Preprints, 6, e27537v1.</p>\\n<blockquote><p>I and Matt did co-write
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a paper with a similar title in <em>PeerJ</em>. But it’s Why sauropods
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had long necks; and why giraffes have short necks, not the other way around.
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And it came out in 2013, not 2018. And it was in <em>PeerJ</em> proper, not
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<em>PeerJ Preprints</em>.</p></blockquote>\\n<p>Taylor, M. P. (2020). The
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open-access wars: How to free science from academic paywalls. Wired.</p>\\n<blockquote><p>I
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never wrote any such paper. <a href=\\\"https://www.vox.com/the-highlight/2019/6/3/18271538/open-access-elsevier-california-sci-hub-academic-paywalls\\\">There <em>is</em>
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an article out there</a> whose HTML title is the one given here, though the
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visible title is completely different: “The war to free science”.
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It’s in <em>Vox</em>, not <em>Wired;</em> it came out in 2019, not 2020.
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And it’s by Brian Resnick and Julia Belluz.</p></blockquote>\\n<p>Taylor,
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M. P., & Knope, M. L. (2021). The future of scholarly publishing is in our
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hands. The Conversation.</p>\\n<blockquote><p>As far as I recall, I never
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wrote anything for <em>The Conversation</em>. There seems to be no article
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named “The future of scholarly publishing is in our hands”. And
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I have never met or corresponded with, far less co-authored with, anyone with
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the surname Knope.</p></blockquote>\\n<hr />\\n<p>All in all, a pretty horrible
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performance — but, and this is the scary part, one that even someone pretty
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familiar with my work could very easily have swallowed.</p>\\n<p>I made a
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very similar point a few months ago in <a href=\\\"https://svpow.com/2023/01/15/these-new-artificial-intelligence-programs-dont-know-what-theyre-talking-about/\\\">These
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new “artificial intelligence” programs don’t know what they’re talking about.</a>
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If the responses were obviously wrong, there wouldn’t be too much of
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a problem here. But this is close enough to fool most people most of the time.</p>\\n<p>As
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more and more of what we read is likely to be written by LLMs in the next
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years, I am concerned that we’re going to be dealing with an awful lot
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of this kind of thing. The ability to pan gold out of the stream of lies is
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going to become really important.</p>\\n\",\"tags\":[\"Just Plain Wrong\",\"rants\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"dkvra02\",\"blog\":{\"id\":\"dkvra02\",\"title\":\"Sauropod
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Vertebra Picture of the Week\",\"description\":\"SV-POW! ... All sauropod
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vertebrae, except when we're talking about Open Access\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://svpow.com/feed/atom/\",\"home_page_url\":\"https://svpow.com\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T14:28:02+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
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(.com)\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-06-09T19:54:23+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/4d6s7-hve18\",\"uuid\":\"9ee85ccd-6e21-4e78-96dd-5123fc62afbc\",\"url\":\"https://tarleb.com/posts/quarto-sitemap/index.html\",\"title\":\"Generating
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must be put in quotes. You’ll find the sitemap.xml file in your _site...\",\"date_published\":\"2022-08-24T00:00:00Z\",\"date_modified\":null,\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Albert
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property:</p>\\n<div class=\\\"sourceCode\\\" id=\\\"cb1\\\" style=\\\"background:
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#f1f3f5;\\\"><pre class=\\\"sourceCode yaml code-with-copy\\\"><code class=\\\"sourceCode
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render</code>.</p>\\n\\n\\n\\n \",\"tags\":[\"quarto\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"7gyq558\",\"blog\":{\"id\":\"7gyq558\",\"title\":\"tarleb\",\"description\":\"tarleb's
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blog\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://tarleb.com/index.xml\",\"home_page_url\":\"https://tarleb.com/index.html\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:58:43+00:00\",\"indexed_at\":\"2023-04-20\",\"feed_format\":\"application/rss+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Quarto
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1.2.475\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-03-24T00:00:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":false,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/btxxm-sr025\",\"uuid\":\"6eb9a4e0-b8b4-4867-bcf0-5e6e0b84c9df\",\"url\":\"http://gigasciencejournal.com/blog/indexed-in-pubmed/\",\"title\":\"GigaByte
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now indexed in PubMed and PubMed Central (PMC)\",\"summary\":\"GigaScience
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Press is pleased to announce GigaByte journal is now indexed in PubMed and
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inclusion into PMC is also necessary for many researchers to meet their research
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funders policies...\",\"date_published\":\"2023-02-28T12:10:05Z\",\"date_modified\":\"2023-02-28T12:10:06Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"http://orcid.org/0000-0001-6444-1436\",\"name\":\"Scott
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Edmunds\"}],\"image\":null,\"content_html\":\"\\n<figure class=\\\"wp-block-image
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size-large is-resized\\\"><img decoding=\\\"async\\\" loading=\\\"lazy\\\"
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alt=\\\"indexed in pubmed\\\" class=\\\"wp-image-4831\\\" width=\\\"768\\\"
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1620w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>GigaScience
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Press is pleased to announce <em>GigaByte</em> journal is now indexed in PubMed
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and <a href=\\\"https://www.ncbi.nlm.nih.gov/pmc/journals/4281/\\\">PubMed
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Central (PMC)</a> databases run by the US National Library of Medicine. PubMed
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being a searchable database of biomedical citations and abstracts, and PMC
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being a free digital archive of the full-text of Open Access articles. While
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inclusion into PMC is also necessary for many researchers to meet their research
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funders policies and mandates on Open Access. As Open Access advocates, now
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this has been added to our publication workflow our authors do not need to
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worry about depositing their publications themselves. We <a href=\\\"https://clockss.org/clockss-announces-the-support-of-additional-libraries-and-publishers-2/\\\">use
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and archiving in PMC also provides an additional level of protection and survival
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of preserved digital content.</p>\\n\\n\\n\\n<p>PubMed and PMC join googlescholar,
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<a href=\\\"https://scholar.cnki.net/home/search?region=db&val=SQHE&resType=Journal\\\">CNKI</a>,
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<a href=\\\"https://jgateplus.com/home/j-gate/\\\">JGate</a> and the <a href=\\\"https://doaj.org/toc/2709-4715\\\">Directory
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of Open Access Journals (DOAJ)</a> as indexes to discover and browse our content.
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Our partners at River Valley Technologies have worked hard to produce the
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highest quality XML for our human and machine readers (see our <a href=\\\"https://gigabytejournal.com/text-and-data-mining\\\">text
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and data mining portal</a>), and this has made the process of indexing easier.
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PMC, <a href=\\\"https://doaj.org/toc/2709-4715\\\">DOAJ</a> and JGate using
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converted versions of our XML to mirror our Open Access content. The DOAJ
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awarding us their seal for journals that demonstrate best practice in open
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access publishing, and CrossRef giving us a near-100% score in their <a href=\\\"https://www.crossref.org/members/prep/23445\\\">Participation
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Reports</a> for the richness of our metadata (only being let down on the funding
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categories as our <a href=\\\"https://gigabytejournal.com/open-access-and-apc\\\">cost-effective
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APCs</a> and waivers mean we publish quite a lot of number of papers without
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external funding).</p>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<figure class=\\\"wp-block-image
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size-large is-resized\\\"><img decoding=\\\"async\\\" loading=\\\"lazy\\\"
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src=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-1024x972.png\\\"
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alt=\\\"indexing in PubMed\\\" class=\\\"wp-image-4833\\\" width=\\\"768\\\"
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height=\\\"729\\\" srcset=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-1024x972.png
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1342w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>Not
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only is our XML rich with this metadata, but we’ve been using it to capture
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<a href=\\\"http://gigasciencejournal.com/blog/how-to-publish-multilingual-articles/\\\">multilingual
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versions of our content</a>, and this also displays in the PMC versions of
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our papers (see our recent English/Spanish/Ukrainian paper in <em><a href=\\\"https://doi.org/10.46471/gigabyte.73\\\">GigaByte</a></em>
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and <a href=\\\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693923/\\\">PMC</a>).
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Further increasing the accessibility and global reach of our papers.</p>\\n\\n\\n\\n<figure
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class=\\\"wp-block-image size-large is-resized\\\"><img decoding=\\\"async\\\"
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loading=\\\"lazy\\\" src=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-1024x704.png\\\"
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alt=\\\"\\\" class=\\\"wp-image-4834\\\" width=\\\"768\\\" height=\\\"528\\\"
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1644w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>Now
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we have sufficient quantity and quality of publishing data for many other
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indexes we are continuing the process of submitting to these databases, so
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watch this space for updates on how that process goes.</p>\\n<p>The post <a
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rel=\\\"nofollow\\\" href=\\\"http://gigasciencejournal.com/blog/indexed-in-pubmed/\\\">GigaByte
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now indexed in PubMed and PubMed Central (PMC)</a> appeared first on <a rel=\\\"nofollow\\\"
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href=\\\"http://gigasciencejournal.com/blog\\\">GigaBlog</a>.</p>\\n\",\"tags\":[\"Open
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Access\",\"GigaByte\",\"Indexing\",\"open access\",\"pubmed\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"3ffcd46\",\"blog\":{\"id\":\"3ffcd46\",\"title\":\"GigaBlog\",\"description\":\"Data
|
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driven blogging from the GigaScience editors\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"http://gigasciencejournal.com/blog/feed/atom/\",\"home_page_url\":\"http://gigasciencejournal.com/blog\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T13:42:00+00:00\",\"indexed_at\":\"2023-02-05\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
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6.2.2\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-24T20:01:37+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/ejtg5cm-mtt292s\",\"uuid\":\"4eb9ac30-9edc-4830-b2ad-25183fb1548a\",\"url\":\"https://syldavia-gazette.org/data-sharing-challenger-expedition-research-software/\",\"title\":\"Data
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Sharing, Challenger Expedition, Research Software, Adornment, Prostate Cancer\",\"summary\":\"Ten
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(not so) simple rules for clinical trial data-sharingThe authors propose 10
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(not so) simple rules for researchers wishing to share data, aligned on the
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clinical trial lifecycle.The Challenger Expedition - 1872Report of a BBC Radio
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episode about the 1872 four-year-long Challenger expedition to investigate
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the oceans of the earth.Defining the roles of research softwareWorkshop report
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that tries to define the various roles of research software.This 2,300-Year-Old
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Mummy Has a Heart (and...\",\"date_published\":\"2023-03-15T20:37:00Z\",\"date_modified\":\"2023-04-13T12:34:10Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
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Fenner\"}],\"image\":\"https://digitalpress.fra1.cdn.digitaloceanspaces.com/gtpg506/2023/04/journal.pcbi.1010879.g001.png\",\"content_html\":\"
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<h3 id=\\\"ten-not-so-simple-rules-for-clinical-trial-data-sharing\\\"><a
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href=\\\"https://doi.org/10.1371/journal.pcbi.1010879?ref=syldavia-gazette.org\\\">Ten
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(not so) simple rules for clinical trial data-sharing</a></h3><p>The authors
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propose 10 (not so) simple rules for researchers wishing to share data, aligned
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on the clinical trial lifecycle.</p><h3 id=\\\"the-challenger-expedition1872\\\"><a
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href=\\\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9?ref=syldavia-gazette.org\\\">The
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Challenger Expedition - 1872</a></h3><p>Report of a BBC Radio episode about
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the 1872 four-year-long Challenger expedition to investigate the oceans of
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the earth.</p><h3 id=\\\"defining-the-roles-of-research-software\\\"><a href=\\\"https://doi.org/10.54900/9akm9y5-5ject5y?ref=syldavia-gazette.org\\\">Defining
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the roles of research software</a></h3><p>Workshop report that tries to define
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the various roles of research software.</p><h3 id=\\\"this-2300-year-old-mummy-has-a-heart-and-tongue-of-gold\\\"><a
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href=\\\"https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold?ref=syldavia-gazette.org\\\">This
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2,300-Year-Old Mummy Has a Heart (and Tongue) of Gold</a></h3><p>To acquire
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additional insight into the practice of adornment in ancient Egypt, three
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researchers recently \\\"digitally unwrapped\\\" the mummified body of a wealthy
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teenage boy from 2,300 years ago.</p><h3 id=\\\"prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds\\\"><a
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href=\\\"https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds?ref=syldavia-gazette.org\\\">Prostate
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cancer treatments can be avoided or delayed in many cases, huge study finds</a></h3><p>Fifteen-year
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outcomes after monitoring, surgery, or radiotherapy for localized prostate
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cancer. Prostate cancer–specific mortality was low regardless of the treatment
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assigned.</p><hr><h3 id=\\\"references\\\">References</h3><ol><li>Pellen C,
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Louarn AL, Spurrier-Bernard G, et al. Ten (not so) simple rules for clinical
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trial data-sharing. <em>PLOS Computational Biology</em>. 2023;19(3):e1010879.
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doi:<a href=\\\"https://doi.org/10.1371/journal.pcbi.1010879?ref=syldavia-gazette.org\\\">10.1371/journal.pcbi.1010879</a></li><li>The
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Challenger Expedition - 1872. Accessed March 28, 2023. <a href=\\\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9?ref=syldavia-gazette.org\\\">https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9</a></li><li>Nieuwpoort
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R van, Katz DS. Defining the roles of research software. <em>Upstream</em>.
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Published online March 14, 2023. doi:<a href=\\\"https://doi.org/10.54900/9akm9y5-5ject5y?ref=syldavia-gazette.org\\\">10.54900/9akm9y5-5ject5y</a></li><li>This
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2,300-Year-Old Mummy Has a Heart (and Tongue) of Gold. Discover Magazine.
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Accessed March 28, 2023. <a href=\\\"https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold?ref=syldavia-gazette.org\\\">https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold</a></li><li>Prostate
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cancer treatments can be avoided or delayed in many cases, huge study finds
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| Live Science. Accessed March 28, 2023. <a href=\\\"https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds?ref=syldavia-gazette.org\\\">https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds</a></li></ol>
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\",\"tags\":[],\"language\":\"en\",\"references\":[{\"doi\":\"https://doi.org/10.1371/journal.pcbi.1010879\",\"key\":\"ref1\"},{\"key\":\"ref2\",\"url\":\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9\"},{\"doi\":\"https://doi.org/10.54900/9akm9y5-5ject5y\",\"key\":\"ref3\"},{\"key\":\"ref4\",\"url\":\"https://discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold\"},{\"key\":\"ref5\",\"url\":\"https://livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds\"}],\"blog_id\":\"f4wdg32\",\"blog\":{\"id\":\"f4wdg32\",\"title\":\"Syldavia
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Gazette\",\"description\":\"The Syldavia Gazette is a weekly newsletter that
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highlights interesting science stories from around the web.\",\"language\":\"en\",\"favicon\":\"https://syldavia-gazette.org/favicon.png\",\"feed_url\":\"https://syldavia-gazette.org/atom/\",\"home_page_url\":\"https://syldavia-gazette.org\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:54:04+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
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5.40\",\"category\":\"Humanities\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-03-15T20:37:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":false,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/ymc6x-rx659\",\"uuid\":\"0807f515-f31d-4e2c-9e6f-78c3a9668b9d\",\"url\":\"https://iphylo.blogspot.com/2022/09/dna-barcoding-as-intergenerational.html\",\"title\":\"DNA
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barcoding as intergenerational transfer of taxonomic knowledge\",\"summary\":\"I
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tweeted about this but want to bookmark it for later as well. The paper “A
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molecular-based identification resource for the arthropods of Finland” doi:10.1111/1755-0998.13510
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contains the following: …the annotated barcode records assembled by FinBOL
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participants represent a tremendous intergenerational transfer of taxonomic
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knowledge … the time contributed by current taxonomists in identifying and
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contributing voucher specimens represents a great gift to future generations
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who will benefit...\",\"date_published\":\"2022-09-14T10:12:00Z\",\"date_modified\":\"2022-09-29T13:57:30Z\",\"date_indexed\":\"1909-06-16T11:02:21+00:00\",\"authors\":[{\"url\":null,\"name\":\"Roderic
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Page\"}],\"image\":null,\"content_html\":\"<p>I <a href=\\\"https://twitter.com/rdmpage/status/1569738844416638981?s=21&t=9OVXuoUEwZtQt-Ldzlutfw\\\">tweeted
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about this</a> but want to bookmark it for later as well. The paper “A molecular-based
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identification resource for the arthropods of Finland” <a href=\\\"https://doi.org/10.1111/1755-0998.13510\\\">doi:10.1111/1755-0998.13510</a>
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contains the following:</p>\\n<blockquote>\\n<p>…the annotated barcode records
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assembled by FinBOL participants represent a tremendous <mark>intergenerational
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transfer of taxonomic knowledge</mark> … the time contributed by current taxonomists
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in identifying and contributing voucher specimens represents a great gift
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to future generations who will benefit from their expertise when they are
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no longer able to process new material.</p>\\n</blockquote>\\n<p>I think this
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is a very clever way to characterise the project. In an age of machine learning
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this may be commonest way to share knowledge , namely as expert-labelled training
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data used to build tools for others. Of course, this means the expertise itself
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may be lost, which has implications for updating the models if the data isn’t
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complete. But it speaks to Charles Godfrey’s theme of <a href=\\\"https://biostor.org/reference/250587\\\">“Taxonomy
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as information science”</a>.</p>\\n<p>Note that the knowledge is also transformed
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in the sense that the underlying expertise of interpreting morphology, ecology,
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behaviour, genomics, and the past literature is not what is being passed on.
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Instead it is probabilities that a DNA sequence belongs to a particular taxon.</p>\\n<p>This
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feels is different to, say iNaturalist, where there is a machine learning
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model to identify images. In that case, the model is built on something the
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community itself has created, and continues to create. Yes, the underlying
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idea is that same: “experts” have labelled the data, a model is trained, the
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model is used. But the benefits of the <a href=\\\"https://www.inaturalist.org\\\">iNaturalist</a>
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model are immediately applicable to the people whose data built the model.
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In the case of barcoding, because the technology itself is still not in the
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hands of many (relative to, say, digital imaging), the benefits are perhaps
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less tangible. Obviously researchers working with environmental DNA will find
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it very useful, but broader impact may await the arrival of citizen science
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DNA barcoding.</p>\\n<p>The other consideration is whether the barcoding helps
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taxonomists. Is it to be used to help prioritise future work (“we are getting
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lots of unknown sequences in these taxa, lets do some taxonomy there”), or
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is it simply capturing the knowledge of a generation that won’t be replaced:</p>\\n<blockquote>\\n<p>The
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need to capture such knowledge is essential because there are, for example,
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no young Finnish taxonomists who can critically identify species in many key
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groups of ar- thropods (e.g., aphids, chewing lice, chalcid wasps, gall midges,
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most mite lineages).</p>\\n</blockquote>\\n<p>The cycle of collect data, test
|
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and refine model, collect more data, rinse and repeat that happens with iNaturalist
|
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creates a feedback loop. It’s not clear that a similar cycle exists for DNA
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barcoding.</p>\\n<blockquote>\\n<p>Written with <a href=\\\"https://stackedit.io/\\\">StackEdit</a>.</p>\\n</blockquote>\",\"tags\":[],\"language\":\"en\",\"references\":[],\"blog_id\":\"tyfqw20\",\"blog\":{\"id\":\"tyfqw20\",\"title\":\"iPhylo\",\"description\":\"Rants,
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raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
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and biodiversity informatics. For more ranty and less considered opinions,
|
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see my <a href=\\\"https://twitter.com/rdmpage\\\">Twitter feed</a>.<br>ISSN
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2051-8188. Written content on this site is licensed under a <a href=\\\"https://creativecommons.org/licenses/by/4.0/\\\">Creative
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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\":\"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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7.00\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-31T17:26:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/e7b4h-2eh30\",\"uuid\":\"eeb9b865-9fbf-4a15-b156-5363b81060ae\",\"url\":\"https://larsgw.blogspot.com/2018/08/citationjs-showing-blogger-posts-on.html\",\"title\":\"Citation.js:
|
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Showing Blogger Posts on a Different Site\",\"summary\":\"Citation.js: Showing
|
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Blogger Posts on a Different Site I made a small client for Blogger that
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takes a tag and transforms it into its own little blog: citation.js.org/blog/?post=542….
|
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No metadata though, as it’s all client-side. — Lars Willighagen (@larswillighagen)
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\ August 6, 2018 I made a Material-themed page showing Citation.js blog posts
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from Blogger. It supports pagination, tags, search and linking individual
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posts. Since it’s a single, static page I can’t support meta and link...\",\"date_published\":\"2018-08-22T19:36:00Z\",\"date_modified\":\"2023-03-30T20:48:33Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
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Willighagen\"}],\"image\":null,\"content_html\":\"<!DOCTYPE html>\\n<html>\\n\\n<head>\\n
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\ <meta charset=\\\"utf-8\\\">\\n <meta name=\\\"viewport\\\" content=\\\"width=device-width,
|
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initial-scale=1.0\\\">\\n <title>Citation.js: Showing Blogger Posts on a
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Different Site</title>\\n <link rel=\\\"stylesheet\\\" href=\\\"https://stackedit.io/style.css\\\"
|
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|
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/>\\n</head>\\n\\n<body class=\\\"stackedit\\\">\\n <div class=\\\"stackedit__html\\\"><blockquote>\\n<p>I
|
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made a small client for Blogger that takes a tag and transforms it into its
|
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own little blog: <a href=\\\"https://t.co/CYoveVJIOE\\\">citation.js.org/blog/?post=542…</a>.
|
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No metadata though, as it’s all client-side.<br>\\n— Lars Willighagen (@larswillighagen)
|
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|
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\ <a href=\\\"https://twitter.com/larswillighagen/status/1026536137958072320?ref_src=twsrc%5Etfw\\\">August
|
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|
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6, 2018</a></p>\\n</blockquote>\\n<p>I made a <a href=\\\"https://getmdl.io\\\">Material-themed</a>
|
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page showing Citation.js blog posts from Blogger. It supports pagination,
|
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tags, search and linking individual posts. Since it’s a single, static page
|
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I can’t support <code>meta</code> and <code>link</code> tags for metadata,
|
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that would require JavaScript which indexers don’t run.</p>\\n<p>The great
|
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thing about the Blogger API is that you can generate feeds for single tags,
|
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like Citation.js for example, and search for tags and general queries within
|
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that tag. That’s what makes all this possible. The URL scheme is very simple:</p>\\n<pre
|
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class=\\\" language-bash\\\"><code class=\\\"prism language-bash\\\"><span
|
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class=\\\"token comment\\\"># Tag feed</span>\\nhttps://<span class=\\\"token
|
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variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span class=\\\"token
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variable\\\">$TAG</span>\\n\\n<span class=\\\"token comment\\\"># Tag-in-tag
|
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feed</span>\\nhttps://<span class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span
|
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class=\\\"token variable\\\">$TAG</span>/<span class=\\\"token variable\\\">$OTHER_TAG</span>\\n\\n<span
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class=\\\"token comment\\\"># Search-in-tag feed</span>\\n<span class=\\\"token
|
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comment\\\"># Note: don't copy this, there's a ZWS before ?q= for syntax highlighting</span>\\nhttps://<span
|
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class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span
|
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class=\\\"token variable\\\">$TAG</span>?q<span class=\\\"token operator\\\">=</span><span
|
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class=\\\"token variable\\\">$QUERY</span>\\n\\n<span class=\\\"token comment\\\">#
|
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Post</span>\\nhttps://<span class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/<span
|
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class=\\\"token variable\\\">$POST</span>\\n</code></pre>\\n<p>Pagination
|
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|
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and response formats complicate things a little, and are dealt with in the
|
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code below.</p>\\n<p>Apart from the Material theme, it only uses vanilla JavaScript
|
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to generate the pages. The search bar doesn’t even use JavaScript at all,
|
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just good ol’ <code>form</code> semantics. The JavaScript it does use is fairly
|
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simple. First, the query is parsed and an API URL is generated.</p>\\n<pre
|
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class=\\\" language-js\\\"><code class=\\\"prism language-js\\\">window<span
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class=\\\"token punctuation\\\">.</span><span class=\\\"token function-variable
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function\\\">onload</span> <span class=\\\"token operator\\\">=</span> <span
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class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span><span
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class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
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operator\\\">=</span> <span class=\\\"token punctuation\\\">{</span><span
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class=\\\"token punctuation\\\">}</span>\\n \\n location<span class=\\\"token
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punctuation\\\">.</span>search<span class=\\\"token punctuation\\\">.</span><span
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class=\\\"token function\\\">slice</span><span class=\\\"token punctuation\\\">(</span><span
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class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">)</span><span
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class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">split</span><span
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class=\\\"token punctuation\\\">)</span><span class=\\\"token punctuation\\\">.</span><span
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class=\\\"token function\\\">map</span><span class=\\\"token punctuation\\\">(</span><span
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class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
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\ pair <span class=\\\"token operator\\\">=</span> pair<span class=\\\"token
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punctuation\\\">.</span><span class=\\\"token function\\\">split</span><span
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class=\\\"token punctuation\\\">(</span><span class=\\\"token string\\\">'='</span><span
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class=\\\"token punctuation\\\">)</span>\\n params<span class=\\\"token
|
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punctuation\\\">[</span>pair<span class=\\\"token punctuation\\\">[</span><span
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class=\\\"token number\\\">0</span><span class=\\\"token punctuation\\\">]</span><span
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class=\\\"token punctuation\\\">]</span> <span class=\\\"token operator\\\">=</span>
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pair<span class=\\\"token punctuation\\\">[</span><span class=\\\"token number\\\">1</span><span
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class=\\\"token punctuation\\\">]</span>\\n <span class=\\\"token punctuation\\\">}</span><span
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class=\\\"token punctuation\\\">)</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
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url\\n\\n <span class=\\\"token keyword\\\">if</span> <span class=\\\"token
|
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punctuation\\\">(</span>params<span class=\\\"token punctuation\\\">.</span>post<span
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class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
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\ url <span class=\\\"token operator\\\">=</span> <span class=\\\"token
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string\\\">'https://larsgw.blogspot.com/feeds/posts/default/'</span> <span
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|
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<span class=\\\"token keyword\\\">if</span> <span class=\\\"token punctuation\\\">(</span>params<span
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class=\\\"token punctuation\\\">.</span>tag<span class=\\\"token punctuation\\\">)</span>
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<span class=\\\"token punctuation\\\">{</span>\\n url <span class=\\\"token
|
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|
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operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js/'</span>
|
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|
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class=\\\"token punctuation\\\">.</span>query<span class=\\\"token punctuation\\\">)</span>
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operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js/?q='</span>
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|
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<span class=\\\"token operator\\\">+</span> params<span class=\\\"token punctuation\\\">.</span>query
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|
|
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operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js?alt=json-in-script&callback=cb'</span>\\n
|
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\ <span class=\\\"token punctuation\\\">}</span>\\n\\n <span class=\\\"token
|
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|
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keyword\\\">var</span> startIndex <span class=\\\"token operator\\\">=</span>
|
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|
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location<span class=\\\"token punctuation\\\">.</span>href<span class=\\\"token
|
|
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|
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punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
|
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|
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class=\\\"token punctuation\\\">(</span><span class=\\\"token regex\\\">/start-index=(\\\\d+)/</span><span
|
|
487
|
-
class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
|
|
488
|
-
<span class=\\\"token punctuation\\\">(</span>startIndex<span class=\\\"token
|
|
489
|
-
punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
490
|
-
\ url <span class=\\\"token operator\\\">+=</span> <span class=\\\"token
|
|
491
|
-
string\\\">'&'</span> <span class=\\\"token operator\\\">+</span> startIndex<span
|
|
492
|
-
class=\\\"token punctuation\\\">[</span><span class=\\\"token number\\\">0</span><span
|
|
493
|
-
class=\\\"token punctuation\\\">]</span>\\n <span class=\\\"token punctuation\\\">}</span>\\n\\n
|
|
494
|
-
\ <span class=\\\"token function\\\">load</span><span class=\\\"token punctuation\\\">(</span>url<span
|
|
495
|
-
class=\\\"token punctuation\\\">)</span>\\n<span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>Since
|
|
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|
-
the only JSON API for Blogger is JSON-in-script, we append a script element
|
|
497
|
-
loading the resource. This then calls the callback, <code>cb</code>.</p>\\n<pre
|
|
498
|
-
class=\\\" language-js\\\"><code class=\\\"prism language-js\\\"><span class=\\\"token
|
|
499
|
-
keyword\\\">function</span> <span class=\\\"token function\\\">cb</span> <span
|
|
500
|
-
class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">)</span>
|
|
501
|
-
<span class=\\\"token punctuation\\\">{</span>\\n content<span class=\\\"token
|
|
502
|
-
punctuation\\\">.</span>innerHTML <span class=\\\"token operator\\\">=</span>
|
|
503
|
-
data<span class=\\\"token punctuation\\\">.</span>feed <span class=\\\"token
|
|
504
|
-
operator\\\">?</span> templates<span class=\\\"token punctuation\\\">.</span><span
|
|
505
|
-
class=\\\"token function\\\">feed</span><span class=\\\"token punctuation\\\">(</span>data<span
|
|
506
|
-
class=\\\"token punctuation\\\">.</span>feed<span class=\\\"token punctuation\\\">.</span>entry<span
|
|
507
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">:</span>
|
|
508
|
-
templates<span class=\\\"token punctuation\\\">.</span><span class=\\\"token
|
|
509
|
-
function\\\">feedItem</span><span class=\\\"token punctuation\\\">(</span>data<span
|
|
510
|
-
class=\\\"token punctuation\\\">.</span>entry<span class=\\\"token punctuation\\\">)</span>\\n\\n
|
|
511
|
-
\ <span class=\\\"token comment\\\">// pagination</span>\\n <span class=\\\"token
|
|
512
|
-
keyword\\\">if</span> <span class=\\\"token punctuation\\\">(</span>data<span
|
|
513
|
-
class=\\\"token punctuation\\\">.</span>feed<span class=\\\"token punctuation\\\">)</span>
|
|
514
|
-
<span class=\\\"token punctuation\\\">{</span>\\n <span class=\\\"token
|
|
515
|
-
keyword\\\">var</span> href <span class=\\\"token operator\\\">=</span> location<span
|
|
516
|
-
class=\\\"token punctuation\\\">.</span>href\\n <span class=\\\"token keyword\\\">var</span>
|
|
517
|
-
hasIndex <span class=\\\"token operator\\\">=</span> href<span class=\\\"token
|
|
518
|
-
punctuation\\\">.</span><span class=\\\"token function\\\">indexOf</span><span
|
|
519
|
-
class=\\\"token punctuation\\\">(</span><span class=\\\"token string\\\">'start-index'</span><span
|
|
520
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">></span>
|
|
521
|
-
<span class=\\\"token operator\\\">-</span><span class=\\\"token number\\\">1</span>\\n
|
|
522
|
-
\ <span class=\\\"token keyword\\\">var</span> hasParams <span class=\\\"token
|
|
523
|
-
operator\\\">=</span> href<span class=\\\"token punctuation\\\">.</span><span
|
|
524
|
-
class=\\\"token function\\\">indexOf</span><span class=\\\"token punctuation\\\">(</span><span
|
|
525
|
-
class=\\\"token string\\\">'?'</span><span class=\\\"token punctuation\\\">)</span>
|
|
526
|
-
<span class=\\\"token operator\\\">></span> <span class=\\\"token operator\\\">-</span><span
|
|
527
|
-
class=\\\"token number\\\">1</span>\\n <span class=\\\"token keyword\\\">var</span>
|
|
528
|
-
indexPattern <span class=\\\"token operator\\\">=</span> <span class=\\\"token
|
|
529
|
-
regex\\\">/start-index=(\\\\d+)/</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
|
|
530
|
-
prev <span class=\\\"token operator\\\">=</span> <span class=\\\"token function\\\">find</span><span
|
|
531
|
-
class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">.</span>feed<span
|
|
532
|
-
class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">,</span>
|
|
533
|
-
<span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>link<span
|
|
534
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
|
|
535
|
-
<span class=\\\"token keyword\\\">return</span> link<span class=\\\"token
|
|
536
|
-
punctuation\\\">.</span>rel <span class=\\\"token operator\\\">===</span>
|
|
537
|
-
<span class=\\\"token string\\\">'previous'</span> <span class=\\\"token punctuation\\\">}</span><span
|
|
538
|
-
class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
|
|
539
|
-
<span class=\\\"token punctuation\\\">(</span>prev<span class=\\\"token punctuation\\\">)</span>
|
|
540
|
-
<span class=\\\"token punctuation\\\">{</span>\\n prev <span class=\\\"token
|
|
541
|
-
operator\\\">=</span> <span class=\\\"token string\\\">'start-index='</span>
|
|
542
|
-
<span class=\\\"token operator\\\">+</span> prev<span class=\\\"token punctuation\\\">.</span>href<span
|
|
543
|
-
class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
|
|
544
|
-
class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
|
|
545
|
-
punctuation\\\">)</span><span class=\\\"token punctuation\\\">[</span><span
|
|
546
|
-
class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">]</span>\\n
|
|
547
|
-
\ <span class=\\\"token keyword\\\">var</span> url <span class=\\\"token
|
|
548
|
-
operator\\\">=</span> hasIndex <span class=\\\"token operator\\\">?</span>
|
|
549
|
-
href<span class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
|
|
550
|
-
class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
|
|
551
|
-
punctuation\\\">,</span> prev<span class=\\\"token punctuation\\\">)</span>
|
|
552
|
-
<span class=\\\"token punctuation\\\">:</span> href <span class=\\\"token
|
|
553
|
-
operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span>hasParams
|
|
554
|
-
<span class=\\\"token operator\\\">?</span> <span class=\\\"token string\\\">'?'</span>
|
|
555
|
-
<span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">''</span><span
|
|
556
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>
|
|
557
|
-
prev\\n paginatePrev<span class=\\\"token punctuation\\\">.</span><span
|
|
558
|
-
class=\\\"token function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
|
|
559
|
-
class=\\\"token string\\\">'href'</span><span class=\\\"token punctuation\\\">,</span>
|
|
560
|
-
url<span class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token
|
|
561
|
-
punctuation\\\">}</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
|
|
562
|
-
next <span class=\\\"token operator\\\">=</span> <span class=\\\"token function\\\">find</span><span
|
|
563
|
-
class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">.</span>feed<span
|
|
564
|
-
class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">,</span>
|
|
565
|
-
<span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>link<span
|
|
566
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
|
|
567
|
-
<span class=\\\"token keyword\\\">return</span> link<span class=\\\"token
|
|
568
|
-
punctuation\\\">.</span>rel <span class=\\\"token operator\\\">===</span>
|
|
569
|
-
<span class=\\\"token string\\\">'next'</span> <span class=\\\"token punctuation\\\">}</span><span
|
|
570
|
-
class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
|
|
571
|
-
<span class=\\\"token punctuation\\\">(</span>next<span class=\\\"token punctuation\\\">)</span>
|
|
572
|
-
<span class=\\\"token punctuation\\\">{</span>\\n next <span class=\\\"token
|
|
573
|
-
operator\\\">=</span> <span class=\\\"token string\\\">'start-index='</span>
|
|
574
|
-
<span class=\\\"token operator\\\">+</span> next<span class=\\\"token punctuation\\\">.</span>href<span
|
|
575
|
-
class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
|
|
576
|
-
class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
|
|
577
|
-
punctuation\\\">)</span><span class=\\\"token punctuation\\\">[</span><span
|
|
578
|
-
class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">]</span>\\n
|
|
579
|
-
\ <span class=\\\"token keyword\\\">var</span> url <span class=\\\"token
|
|
580
|
-
operator\\\">=</span> hasIndex <span class=\\\"token operator\\\">?</span>
|
|
581
|
-
href<span class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
|
|
582
|
-
class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
|
|
583
|
-
punctuation\\\">,</span> next<span class=\\\"token punctuation\\\">)</span>
|
|
584
|
-
<span class=\\\"token punctuation\\\">:</span> href <span class=\\\"token
|
|
585
|
-
operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span>hasParams
|
|
586
|
-
<span class=\\\"token operator\\\">?</span> <span class=\\\"token string\\\">'&'</span>
|
|
587
|
-
<span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">'?'</span><span
|
|
588
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>
|
|
589
|
-
next\\n paginateNext<span class=\\\"token punctuation\\\">.</span><span
|
|
590
|
-
class=\\\"token function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
|
|
591
|
-
class=\\\"token string\\\">'href'</span><span class=\\\"token punctuation\\\">,</span>
|
|
592
|
-
url<span class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token
|
|
593
|
-
punctuation\\\">}</span>\\n <span class=\\\"token punctuation\\\">}</span>\\n<span
|
|
594
|
-
class=\\\"token punctuation\\\">}</span>\\n\\n<span class=\\\"token keyword\\\">function</span>
|
|
595
|
-
<span class=\\\"token function\\\">load</span> <span class=\\\"token punctuation\\\">(</span>url<span
|
|
596
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
597
|
-
\ loader<span class=\\\"token punctuation\\\">.</span><span class=\\\"token
|
|
598
|
-
function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
|
|
599
|
-
class=\\\"token string\\\">'src'</span><span class=\\\"token punctuation\\\">,</span>
|
|
600
|
-
url<span class=\\\"token punctuation\\\">)</span>\\n<span class=\\\"token
|
|
601
|
-
punctuation\\\">}</span>\\n</code></pre>\\n<p>The callback then uses simple
|
|
602
|
-
templates, which are just JS functions taking in the API response and outputting
|
|
603
|
-
HTML to show the results on the page. Then, it figures out the pagination.
|
|
604
|
-
Below is an example template. It extracts the post id to make links and does
|
|
605
|
-
some preprocessing, removing stackedit metadata and styling and lowering each
|
|
606
|
-
heading two levels. Then, it puts together the HTML with some additional util
|
|
607
|
-
functions and subtemplates.</p>\\n<pre class=\\\" language-js\\\"><code class=\\\"prism
|
|
608
|
-
\ language-js\\\"> feedItem<span class=\\\"token punctuation\\\">:</span>
|
|
609
|
-
<span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>item<span
|
|
610
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
611
|
-
\ <span class=\\\"token keyword\\\">var</span> id <span class=\\\"token
|
|
612
|
-
operator\\\">=</span> item<span class=\\\"token punctuation\\\">.</span>id<span
|
|
613
|
-
class=\\\"token punctuation\\\">.</span>$t<span class=\\\"token punctuation\\\">.</span><span
|
|
614
|
-
class=\\\"token function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
|
|
615
|
-
class=\\\"token regex\\\">/^.*\\\\.post-(\\\\d+)$/</span><span class=\\\"token
|
|
616
|
-
punctuation\\\">,</span> <span class=\\\"token string\\\">'$1'</span><span
|
|
617
|
-
class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">var</span>
|
|
618
|
-
content <span class=\\\"token operator\\\">=</span> item<span class=\\\"token
|
|
619
|
-
punctuation\\\">.</span>content<span class=\\\"token punctuation\\\">.</span>$t\\n
|
|
620
|
-
\ <span class=\\\"token punctuation\\\">.</span><span class=\\\"token
|
|
621
|
-
function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
|
|
622
|
-
class=\\\"token regex\\\">/^[\\\\s\\\\S]*<div class=\\\"stackedit__html\\\">([\\\\s\\\\S]*)<\\\\/div>[\\\\s\\\\S]*$/</span><span
|
|
623
|
-
class=\\\"token punctuation\\\">,</span> <span class=\\\"token string\\\">'$1'</span><span
|
|
624
|
-
class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token punctuation\\\">.</span><span
|
|
625
|
-
class=\\\"token function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
|
|
626
|
-
class=\\\"token regex\\\">/<(\\\\/?)h([1-6])/g</span><span class=\\\"token
|
|
627
|
-
punctuation\\\">,</span> <span class=\\\"token keyword\\\">function</span>
|
|
628
|
-
<span class=\\\"token punctuation\\\">(</span>match<span class=\\\"token punctuation\\\">,</span>
|
|
629
|
-
slash<span class=\\\"token punctuation\\\">,</span> level<span class=\\\"token
|
|
630
|
-
punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
631
|
-
\ <span class=\\\"token keyword\\\">if</span> <span class=\\\"token
|
|
632
|
-
punctuation\\\">(</span><span class=\\\"token operator\\\">+</span>level <span
|
|
633
|
-
class=\\\"token operator\\\">></span> <span class=\\\"token number\\\">4</span><span
|
|
634
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
635
|
-
\ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
|
|
636
|
-
string\\\">'<'</span> <span class=\\\"token operator\\\">+</span> slash
|
|
637
|
-
<span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'b'</span>\\n
|
|
638
|
-
\ <span class=\\\"token punctuation\\\">}</span> <span class=\\\"token
|
|
639
|
-
keyword\\\">else</span> <span class=\\\"token punctuation\\\">{</span>\\n
|
|
640
|
-
\ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
|
|
641
|
-
string\\\">'<'</span> <span class=\\\"token operator\\\">+</span> slash
|
|
642
|
-
<span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'h'</span>
|
|
643
|
-
<span class=\\\"token operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span><span
|
|
644
|
-
class=\\\"token operator\\\">+</span>level <span class=\\\"token operator\\\">+</span>
|
|
645
|
-
<span class=\\\"token number\\\">2</span><span class=\\\"token punctuation\\\">)</span>\\n
|
|
646
|
-
\ <span class=\\\"token punctuation\\\">}</span>\\n <span class=\\\"token
|
|
647
|
-
punctuation\\\">}</span><span class=\\\"token punctuation\\\">)</span>\\n\\n
|
|
648
|
-
\ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
|
|
649
|
-
string\\\">'<div class=\\\"mdl-card mdl-shadow--2dp mdl-cell mdl-cell--12-col\\\">'</span>
|
|
650
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
651
|
-
string\\\">'<div class=\\\"mdl-card__title\\\">'</span> <span class=\\\"token
|
|
652
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'<h2 class=\\\"mdl-card__title-text\\\">'</span>
|
|
653
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
654
|
-
string\\\">'<a href=\\\"?post='</span> <span class=\\\"token operator\\\">+</span>
|
|
655
|
-
id <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'\\\">'</span>
|
|
656
|
-
<span class=\\\"token operator\\\">+</span> item<span class=\\\"token punctuation\\\">.</span>title<span
|
|
657
|
-
class=\\\"token punctuation\\\">.</span>$t <span class=\\\"token operator\\\">+</span>
|
|
658
|
-
<span class=\\\"token string\\\">'</a>'</span> <span class=\\\"token
|
|
659
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'</h2>'</span>
|
|
660
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
661
|
-
string\\\">'</div>'</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
662
|
-
\ <span class=\\\"token string\\\">'<div class=\\\"mdl-card__supporting-text
|
|
663
|
-
mdl-card--border\\\">'</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
664
|
-
\ <span class=\\\"token string\\\">'<p>'</span> <span class=\\\"token
|
|
665
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'<span><i
|
|
666
|
-
class=\\\"material-icons\\\">edit</i> '</span> <span class=\\\"token
|
|
667
|
-
operator\\\">+</span>\\n templates<span class=\\\"token punctuation\\\">.</span><span
|
|
668
|
-
class=\\\"token function\\\">author</span><span class=\\\"token punctuation\\\">(</span>item<span
|
|
669
|
-
class=\\\"token punctuation\\\">.</span>author<span class=\\\"token punctuation\\\">[</span><span
|
|
670
|
-
class=\\\"token number\\\">0</span><span class=\\\"token punctuation\\\">]</span><span
|
|
671
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
672
|
-
\ <span class=\\\"token string\\\">'</span>'</span> <span class=\\\"token
|
|
673
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'<span><i
|
|
674
|
-
class=\\\"material-icons\\\">access_time</i> '</span> <span class=\\\"token
|
|
675
|
-
operator\\\">+</span>\\n <span class=\\\"token function\\\">formatDate</span><span
|
|
676
|
-
class=\\\"token punctuation\\\">(</span>item<span class=\\\"token punctuation\\\">.</span>updated<span
|
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|
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class=\\\"token punctuation\\\">.</span>$t<span class=\\\"token punctuation\\\">)</span>
|
|
678
|
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<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
679
|
-
string\\\">'</span>'</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
680
|
-
\ <span class=\\\"token string\\\">'<span><i class=\\\"material-icons\\\">link</i>
|
|
681
|
-
<a href=\\\"'</span> <span class=\\\"token operator\\\">+</span>\\n <span
|
|
682
|
-
class=\\\"token function\\\">canonical</span><span class=\\\"token punctuation\\\">(</span>item<span
|
|
683
|
-
class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">)</span>
|
|
684
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
685
|
-
string\\\">'\\\">Original post</a></span>'</span> <span class=\\\"token
|
|
686
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'</p>'</span>
|
|
687
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
688
|
-
string\\\">'<p>'</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
689
|
-
\ <span class=\\\"token string\\\">'<span><i class=\\\"material-icons\\\">bookmark</i>
|
|
690
|
-
'</span> <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
691
|
-
function\\\">map</span><span class=\\\"token punctuation\\\">(</span>item<span
|
|
692
|
-
class=\\\"token punctuation\\\">.</span>category<span class=\\\"token punctuation\\\">,</span>
|
|
693
|
-
templates<span class=\\\"token punctuation\\\">.</span>tag<span class=\\\"token
|
|
694
|
-
punctuation\\\">)</span><span class=\\\"token punctuation\\\">.</span><span
|
|
695
|
-
class=\\\"token function\\\">join</span><span class=\\\"token punctuation\\\">(</span><span
|
|
696
|
-
class=\\\"token string\\\">' '</span><span class=\\\"token punctuation\\\">)</span>
|
|
697
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
698
|
-
string\\\">'</span>'</span> <span class=\\\"token operator\\\">+</span>\\n
|
|
699
|
-
\ <span class=\\\"token string\\\">'</p>'</span> <span class=\\\"token
|
|
700
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'</div>'</span>
|
|
701
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
|
|
702
|
-
string\\\">'<div class=\\\"mdl-card__supporting-text\\\">'</span> <span
|
|
703
|
-
class=\\\"token operator\\\">+</span>\\n content <span class=\\\"token
|
|
704
|
-
operator\\\">+</span>\\n <span class=\\\"token string\\\">'</div>'</span>
|
|
705
|
-
<span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token string\\\">'</div>'</span>\\n
|
|
706
|
-
\ <span class=\\\"token punctuation\\\">}</span><span class=\\\"token punctuation\\\">,</span>\\n</code></pre>\\n<p>The
|
|
707
|
-
full source is available at <a href=\\\"https://github.com/citation-js/site/blob/master/static/js/blog.js\\\">here</a>,
|
|
708
|
-
and the page can be viewed <a href=\\\"https://citation.js.org/blog/\\\">here</a>.</p>\\n<p><img
|
|
709
|
-
src=\\\"https://lh3.googleusercontent.com/Qd8EXpblQui1CSErr_BU1Os9Ykk-ximWT_hcTxGhtJBwY6JoM7jSxt7FlAwOSkAs57G4nZ64ccAtMg=s2000\\\"
|
|
710
|
-
alt=\\\"Blog screenshot\\\"><br>\\n<em>Blog screenshot</em></p>\\n</div>\\n</body>\\n\\n</html>\",\"tags\":[\"Citation.js\",\"programming\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
|
|
711
|
-
baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
|
|
712
|
-
statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
|
|
713
|
-
7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/m9fs5-nap05\",\"uuid\":\"fb7abef9-d035-47a0-bc31-b5b1240cac19\",\"url\":\"https://blog.front-matter.io/posts/starting-to-register-dois-for-all-blog-posts-included-in-the-rogue-scholar/\",\"title\":\"Starting
|
|
714
|
-
to register DOIs for all blog posts included in the Rogue Scholar\",\"summary\":\"The
|
|
715
|
-
Rogue Scholar archive of scholarly blogs has grown to 34 blogs with about
|
|
716
|
-
420 blog posts. In order to implement DOI registration for these blog posts,
|
|
717
|
-
I needed two things:Content and metadata, ideally without requiring blogs
|
|
718
|
-
to implement anything special.A way to track the DOIs that have been registeredInitial
|
|
719
|
-
work on DOI registration for blog posts focussed on exposing the relevant
|
|
720
|
-
metadata on the blog landing page, using schema.org and/or HTML meta tags.
|
|
721
|
-
While this approach worked well...\",\"date_published\":\"2023-06-05T13:18:24Z\",\"date_modified\":\"2023-06-05T13:18:24Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
|
|
722
|
-
Fenner\"}],\"image\":\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49-1.png\",\"content_html\":\"
|
|
723
|
-
<p><img src=\\\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49-1.png\\\"></p><p>The
|
|
724
|
-
<a href=\\\"https://rogue-scholar.org/\\\">Rogue Scholar</a> archive of scholarly
|
|
725
|
-
blogs has grown to 34 blogs with about 420 blog posts. In order to implement
|
|
726
|
-
DOI registration for these blog posts, I needed two things:</p><ul><li>Content
|
|
727
|
-
and metadata, ideally without requiring blogs to implement anything special.</li><li>A
|
|
728
|
-
way to track the DOIs that have been registered</li></ul><p>Initial work on
|
|
729
|
-
DOI registration for blog posts focussed on exposing the relevant metadata
|
|
730
|
-
on the blog landing page, using schema.org and/or HTML meta tags. While this
|
|
731
|
-
approach worked well for this and similar blogs, it was too complicated and
|
|
732
|
-
didn't scale well for the large and diverse number of blogs the Rogue Scholar
|
|
733
|
-
aims to cover. </p><p>Therefore I implemented a different workflow taking
|
|
734
|
-
advantage of the fact that all blogs come with RSS feeds that include content
|
|
735
|
-
and metadata. More work was needed because there are different formats for
|
|
736
|
-
these feeds (multiple flavors of RSS, as well as <a href=\\\"https://en.wikipedia.org/wiki/Atom_(web_standard)\\\">Atom</a>,
|
|
737
|
-
and the newer <a href=\\\"https://www.jsonfeed.org/\\\">JSON Feed</a>). Luckily,
|
|
738
|
-
libraries in multiple programming languages exist to simplify the parsing
|
|
739
|
-
of the various RSS Feed formats (I use the Javascript library <a href=\\\"https://www.npmjs.com/package/@extractus/feed-extractor\\\">feed-extractor</a>).</p><p>The
|
|
740
|
-
main challenge with metadata for blog posts – and with DOI metadata more general
|
|
741
|
-
– is author names. They might not be natural names (for example <strong>mfenner</strong>
|
|
742
|
-
instead of <strong>Martin Fenner</strong>), might be names for organizations
|
|
743
|
-
and not people, the blogging platform might not support multiple authors,
|
|
744
|
-
and some work is required to include the ORCID author identifier (or ROR institutional.
|
|
745
|
-
identifier). The Atom format supports an <strong>author URL</strong>, which
|
|
746
|
-
can hold the ORCID ID (or ROR ID), and Wordpress can be enhanced with the
|
|
747
|
-
popular <a href=\\\"https://wordpress.org/plugins/co-authors-plus/\\\">Co-Authors
|
|
748
|
-
Plus</a> plugin to support multiple authors. </p><p>The other challenge with
|
|
749
|
-
DOI registration is keeping track of the content that has already been registered,
|
|
750
|
-
and for this I launched a database, with one record for each post. I need
|
|
751
|
-
the database also to enable full-text search across all blog posts, something
|
|
752
|
-
I will implement in the coming weeks. </p><p>Will all the required pieces
|
|
753
|
-
coming together, I was finally able to start DOI registrations yesterday.
|
|
754
|
-
You will easily detect blog posts with a DOI on the Rogue Scholar website
|
|
755
|
-
(there is a DOI icon next to the title, and the underlying link to the blog
|
|
756
|
-
post is a DOI):</p><figure class=\\\"kg-card kg-image-card\\\"><img src=\\\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png\\\"
|
|
757
|
-
class=\\\"kg-image\\\" alt loading=\\\"lazy\\\" width=\\\"2000\\\" height=\\\"1046\\\"
|
|
758
|
-
srcset=\\\"https://blog.front-matter.io/content/images/size/w600/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
|
|
759
|
-
600w, https://blog.front-matter.io/content/images/size/w1000/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
|
|
760
|
-
1000w, https://blog.front-matter.io/content/images/size/w1600/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
|
|
761
|
-
1600w, https://blog.front-matter.io/content/images/size/w2400/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
|
|
762
|
-
2400w\\\" sizes=\\\"(min-width: 720px) 720px\\\"></figure><p>The process of
|
|
763
|
-
DOI registration for all included blog posts should be concluded by the end
|
|
764
|
-
of the month. There is more work needed to resolve issues with some author
|
|
765
|
-
names, and DOI registration can be further automated (I am currently using
|
|
766
|
-
GitHub Actions and a cronjob). </p><p>What also needs more work is getting
|
|
767
|
-
the DOIs displayed on the blogs (the DOIs resolve to the blog post and not
|
|
768
|
-
the Rogue Scholar archive). This is probably straightforward when using a
|
|
769
|
-
static site generator, but requires more work when a database is involved
|
|
770
|
-
(e.g. Wordpress). For Ghost blogs like this one, I found the <strong>canonical_url</strong>
|
|
771
|
-
field to be a good place to store the DOI.</p> \",\"tags\":[\"Feature\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"f0m0e38\",\"blog\":{\"id\":\"f0m0e38\",\"title\":\"Front
|
|
772
|
-
Matter\",\"description\":\"The Front Matter Blog covers the intersection of
|
|
773
|
-
science and technology since 2007.\",\"language\":\"en\",\"favicon\":\"https://blog.front-matter.io/favicon.png\",\"feed_url\":\"https://blog.front-matter.io/atom/\",\"home_page_url\":\"https://blog.front-matter.io\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T07:20:33+00:00\",\"indexed_at\":\"2023-01-02\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
|
|
774
|
-
5.52\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-06-05T13:18:24+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/z9v2s-bh329\",\"uuid\":\"2a6fb006-ecb2-45d0-9d73-ca8a0e7f559e\",\"url\":\"https://blog.front-matter.io/posts/rogue-scholar-open-for-business/\",\"title\":\"The
|
|
775
|
-
Rogue Scholar is now open for business\",\"summary\":\"The Rogue Scholar science
|
|
776
|
-
blog archive launched with limited functionality on April 3rd. Interested
|
|
777
|
-
science blogs can go to the sign-up page, provide some basic information via
|
|
778
|
-
the sign-up form, and then will be added to the Rogue Scholar archive within
|
|
779
|
-
two business days. To be included in the service, your blog needs to:be about
|
|
780
|
-
science or scholarship and written in English or German (more languages will
|
|
781
|
-
follow later, reach out to me if you can help),make the full-text content
|
|
782
|
-
available via...\",\"date_published\":\"2023-04-04T08:43:36Z\",\"date_modified\":\"2023-04-04T09:31:14Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
|
|
783
|
-
Fenner\"}],\"image\":\"https://images.unsplash.com/photo-1575663620136-5ebbfcc2c597?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=MnwxMTc3M3wwfDF8c2VhcmNofDR8fG9wZW4lMjBmb3IlMjBidXNpbmVzc3xlbnwwfHx8fDE2ODA1OTI3NTU&ixlib=rb-4.0.3&q=80&w=2000\",\"content_html\":\"
|
|
784
|
-
<p><img src=\\\"https://images.unsplash.com/photo-1575663620136-5ebbfcc2c597?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=MnwxMTc3M3wwfDF8c2VhcmNofDR8fG9wZW4lMjBmb3IlMjBidXNpbmVzc3xlbnwwfHx8fDE2ODA1OTI3NTU&ixlib=rb-4.0.3&q=80&w=2000\\\"></p><p>The
|
|
785
|
-
<a href=\\\"https://rogue-scholar.org/\\\">Rogue Scholar</a> science blog
|
|
786
|
-
archive launched with limited functionality on April 3rd. Interested science
|
|
787
|
-
blogs can go to the sign-up page, provide some basic information via the <a
|
|
788
|
-
href=\\\"https://jvinjjenjik.typeform.com/to/uxgAsHPl\\\">sign-up form</a>,
|
|
789
|
-
and then will be added to the Rogue Scholar archive within two business days.
|
|
790
|
-
</p><p>To be included in the service, your blog needs to:</p><ul><li>be about
|
|
791
|
-
science or scholarship and written in English or German (more languages will
|
|
792
|
-
follow later, reach out to me if you can help),</li><li>make the full-text
|
|
793
|
-
content available via RSS feed and distributed under the terms of the Creative
|
|
794
|
-
Commons Attribution license (<a href=\\\"https://creativecommons.org/licenses/by/4.0/legalcode\\\">CC-BY</a>).</li></ul><p>Blogs
|
|
795
|
-
that have signed up for the service (more than twenty so far) are listed in
|
|
796
|
-
the <a href=\\\"https://rogue-scholar.org/blogs\\\">Rogue Scholar catalog
|
|
797
|
-
of science blogs</a> that <a href=\\\"https://doi.org/10.53731/n7vvs-h6995\\\">launched
|
|
798
|
-
last week</a>. And since yesterday summaries of the latest fifteen blog posts
|
|
799
|
-
of each blog are also available.</p><figure class=\\\"kg-card kg-image-card
|
|
800
|
-
kg-card-hascaption\\\"><img src=\\\"https://blog.front-matter.io/content/images/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png\\\"
|
|
801
|
-
class=\\\"kg-image\\\" alt loading=\\\"lazy\\\" width=\\\"1882\\\" height=\\\"1428\\\"
|
|
802
|
-
srcset=\\\"https://blog.front-matter.io/content/images/size/w600/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
|
|
803
|
-
600w, https://blog.front-matter.io/content/images/size/w1000/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
|
|
804
|
-
1000w, https://blog.front-matter.io/content/images/size/w1600/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
|
|
805
|
-
1600w, https://blog.front-matter.io/content/images/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
|
|
806
|
-
1882w\\\" sizes=\\\"(min-width: 720px) 720px\\\"><figcaption><a href=\\\"https://rogue-scholar.org/blogs/pm0p222\\\">Blog
|
|
807
|
-
posts displayed at the Rogue Scholar</a></figcaption></figure><p>These summaries
|
|
808
|
-
(precisely the information you get in the RSS feed) serve two purposes:</p><ul><li>for
|
|
809
|
-
readers: learn more about that particular science blog. Reading the full-text
|
|
810
|
-
post or other blog posts is only one click away</li><li>for blog authors and
|
|
811
|
-
Rogue Scholar staff: tweak the blog and/or Rogue Scholar if there are issues
|
|
812
|
-
with archiving. </li></ul><p>The screenshot highlights several considerations
|
|
813
|
-
when using the RSS Feed to archive a science blog in the Rogue Scholar:</p><ul><li>optional
|
|
814
|
-
but desired metadata, e.g logo, description, and language for blogs or description,
|
|
815
|
-
tags, and feature image for blog posts</li><li>handling authors, including
|
|
816
|
-
full names instead of usernames, multiple authors, and author identifiers
|
|
817
|
-
(ORCID)</li><li>handling DOIs, including exposing them in the RSS feed, and
|
|
818
|
-
making sure no DOI exists for the post yet</li></ul><p>The Rogue Scholar is
|
|
819
|
-
now open for business, and I hope the limited functionality (or <a href=\\\"https://www.zentao.pm/blog/mvp-minimum-viable-product-965.html\\\">minimum
|
|
820
|
-
viable product</a>) launched this week makes it an attractive service for
|
|
821
|
-
blog readers and authors to try out. The next big milestone is the launch
|
|
822
|
-
of the full-text index for searching and archiving, and that is planned to
|
|
823
|
-
happen within the next three months. Followed by DOI registration for blog
|
|
824
|
-
posts.</p> \",\"tags\":[\"News\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"f0m0e38\",\"blog\":{\"id\":\"f0m0e38\",\"title\":\"Front
|
|
825
|
-
Matter\",\"description\":\"The Front Matter Blog covers the intersection of
|
|
826
|
-
science and technology since 2007.\",\"language\":\"en\",\"favicon\":\"https://blog.front-matter.io/favicon.png\",\"feed_url\":\"https://blog.front-matter.io/atom/\",\"home_page_url\":\"https://blog.front-matter.io\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T07:20:33+00:00\",\"indexed_at\":\"2023-01-02\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
|
|
827
|
-
5.52\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-06-05T13:18:24+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/d3dc0-7an69\",\"uuid\":\"545c177f-cea5-4b79-b554-3ccae9c789d7\",\"url\":\"https://iphylo.blogspot.com/2021/10/reflections-on-macroscope-tool-for-21st.html\",\"title\":\"Reflections
|
|
828
|
-
on \\\"The Macroscope\\\" - a tool for the 21st Century?\",\"summary\":\"This
|
|
829
|
-
is a guest post by Tony Rees. It would be difficult to encounter a scientist,
|
|
830
|
-
or anyone interested in science, who is not familiar with the microscope,
|
|
831
|
-
a tool for making objects visible that are otherwise too small to be properly
|
|
832
|
-
seen by the unaided eye, or to reveal otherwise invisible fine detail in larger
|
|
833
|
-
objects. A select few with a particular interest in microscopy may also have
|
|
834
|
-
encountered the Wild-Leica \\\"Macroscope\\\", a specialised type of benchtop
|
|
835
|
-
microscope optimised for...\",\"date_published\":\"2021-10-07T12:38:00Z\",\"date_modified\":\"2021-10-08T10:26:22Z\",\"date_indexed\":\"1909-06-16T10:02:25+00:00\",\"authors\":[{\"url\":null,\"name\":\"Roderic
|
|
836
|
-
Page\"}],\"image\":null,\"content_html\":\"<p><img src=\\\"https://lh3.googleusercontent.com/-A99btr6ERMs/Vl1Wvjp2OtI/AAAAAAAAEFI/7bKdRjNG5w0/ytNkVT2U.jpg?imgmax=800\\\"
|
|
837
|
-
alt=\\\"YtNkVT2U\\\" title=\\\"ytNkVT2U.jpg\\\" border=\\\"0\\\" width=\\\"128\\\"
|
|
838
|
-
height=\\\"128\\\" style=\\\"float:right;\\\" /> This is a guest post by <a
|
|
839
|
-
href=\\\"https://about.me/TonyRees\\\">Tony Rees</a>.</p>\\n\\n<p>It would
|
|
840
|
-
be difficult to encounter a scientist, or anyone interested in science, who
|
|
841
|
-
is not familiar with the microscope, a tool for making objects visible that
|
|
842
|
-
are otherwise too small to be properly seen by the unaided eye, or to reveal
|
|
843
|
-
otherwise invisible fine detail in larger objects. A select few with a particular
|
|
844
|
-
interest in microscopy may also have encountered the Wild-Leica \\\"Macroscope\\\",
|
|
845
|
-
a specialised type of benchtop microscope optimised for low-power macro-photography.
|
|
846
|
-
However in this overview I discuss the \\\"Macroscope\\\" in a different sense,
|
|
847
|
-
which is that of the antithesis to the microscope: namely a method for visualizing
|
|
848
|
-
subjects too large to be encompassed by a single field of vision, such as
|
|
849
|
-
the Earth or some subset of its phenomena (the biosphere, for example), or
|
|
850
|
-
conceptually, the universe.</p>\\n\\n<p><div class=\\\"separator\\\" style=\\\"clear:
|
|
851
|
-
both;\\\"><a href=\\\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s500/2020045672.jpg\\\"
|
|
852
|
-
style=\\\"display: block; padding: 1em 0; text-align: center; clear: right;
|
|
853
|
-
float: right;\\\"><img alt=\\\"\\\" border=\\\"0\\\" height=\\\"320\\\" data-original-height=\\\"500\\\"
|
|
854
|
-
data-original-width=\\\"303\\\" src=\\\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s320/2020045672.jpg\\\"/></a></div>My
|
|
855
|
-
introduction to the term was via addresses given by Jesse Ausubel in the formative
|
|
856
|
-
years of the 2001-2010 <a href=\\\"http://www.coml.org\\\">Census of Marine
|
|
857
|
-
Life</a>, for which he was a key proponent. In Ausubel's view, the Census
|
|
858
|
-
would perform the function of a macroscope, permitting a view of everything
|
|
859
|
-
that lives in the global ocean (or at least, that subset which could realistically
|
|
860
|
-
be sampled in the time frame available) as opposed to more limited subsets
|
|
861
|
-
available via previous data collection efforts. My view (which could, of course,
|
|
862
|
-
be wrong) was that his thinking had been informed by a work entitled \\\"Le
|
|
863
|
-
macroscope, vers une vision globale\\\" published in 1975 by the French thinker
|
|
864
|
-
Joël de Rosnay, who had expressed such a concept as being globally applicable
|
|
865
|
-
in many fields, including the physical and natural worlds but also extending
|
|
866
|
-
to human society, the growth of cities, and more. Yet again, some ecologists
|
|
867
|
-
may also have encountered the term, sometimes in the guise of \\\"Odum's macroscope\\\",
|
|
868
|
-
as an approach for obtaining \\\"big picture\\\" analyses of macroecological
|
|
869
|
-
processes suitable for mathematical modelling, typically by elimination of
|
|
870
|
-
fine detail so that only the larger patterns remain, as initially advocated
|
|
871
|
-
by Howard T. Odum in his 1971 book \\\"Environment, Power, and Society\\\".</p>\\n\\n<p>From
|
|
872
|
-
the standpoint of the 21st century, it seems that we are closer to achieving
|
|
873
|
-
a \\\"macroscope\\\" (or possibly, multiple such tools) than ever before,
|
|
874
|
-
based on the availability of existing and continuing new data streams, improved
|
|
875
|
-
technology for data assembly and storage, and advanced ways to query and combine
|
|
876
|
-
these large streams of data to produce new visualizations, data products,
|
|
877
|
-
and analytical findings. I devote the remainder of this article to examples
|
|
878
|
-
where either particular workers have employed \\\"macroscope\\\" terminology
|
|
879
|
-
to describe their activities, or where potentially equivalent actions are
|
|
880
|
-
taking place without the explicit \\\"macroscope\\\" association, but are
|
|
881
|
-
equally worthy of consideration. To save space here, references cited here
|
|
882
|
-
(most or all) can be found via a Wikipedia article entitled \\\"<a href=\\\"https://en.wikipedia.org/wiki/Macroscope_(science_concept)\\\">Macroscope
|
|
883
|
-
(science concept)</a>\\\" that I authored on the subject around a year ago,
|
|
884
|
-
and have continued to add to on occasion as new thoughts or information come
|
|
885
|
-
to hand (see <a href=\\\"https://en.wikipedia.org/w/index.php?title=Macroscope_(science_concept)&offset=&limit=500&action=history\\\">edit
|
|
886
|
-
history for the article</a>).</p>\\n\\n<p>First, one can ask, what constitutes
|
|
887
|
-
a macroscope, in the present context? In the Wikipedia article I point to
|
|
888
|
-
a book \\\"Big Data - Related Technologies, Challenges and Future Prospects\\\"
|
|
889
|
-
by Chen <em>et al.</em> (2014) (<a href=\\\"https://doi.org/10.1007/978-3-319-06245-7\\\">doi:10.1007/978-3-319-06245-7</a>),
|
|
890
|
-
in which the \\\"value chain of big data\\\" is characterised as divisible
|
|
891
|
-
into four phases, namely data generation, data acquisition (aka data assembly),
|
|
892
|
-
data storage, and data analysis. To my mind, data generation (which others
|
|
893
|
-
may term acquisition, differently from the usage by Chen <em>et al.</em>)
|
|
894
|
-
is obviously the first step, but does not in itself constitute the macroscope,
|
|
895
|
-
except in rare cases - such as Landsat imagery, perhaps - where on its own,
|
|
896
|
-
a single co-ordinated data stream is sufficient to meet the need for a particular
|
|
897
|
-
type of \\\"global view\\\". A variant of this might be a coordinated data
|
|
898
|
-
collection program - such as that of the ten year Census of Marine Life -
|
|
899
|
-
which might produce the data required for the desired global view; but again,
|
|
900
|
-
in reality, such data are collected in a series of discrete chunks, in many
|
|
901
|
-
and often disparate data formats, and must be \\\"wrangled\\\" into a more
|
|
902
|
-
coherent whole before any meaningful \\\"macroscope\\\" functionality becomes
|
|
903
|
-
available.</p>\\n\\n<p>Here we come to what, in my view, constitutes the heart
|
|
904
|
-
of the \\\"macroscope\\\": an intelligently organized (i.e. indexable and
|
|
905
|
-
searchable), coherent data store or repository (where \\\"data\\\" may include
|
|
906
|
-
imagery and other non numeric data forms, but much else besides). Taking the
|
|
907
|
-
Census of Marine Life example, the data repository for that project's data
|
|
908
|
-
(plus other available sources as inputs) is the <a href=\\\"https://obis.org\\\">Ocean
|
|
909
|
-
Biodiversity Information System</a> or OBIS (previously the Ocean Biogeographic
|
|
910
|
-
Information System), which according to this view forms the \\\"macroscope\\\"
|
|
911
|
-
for which the Census data is a feed. (For non habitat-specific biodiversity
|
|
912
|
-
data, <a href=\\\"https://www.gbif.org\\\">GBIF</a> is an equivalent, and
|
|
913
|
-
more extensive, operation). Other planetary scale \\\"macroscopes\\\", by
|
|
914
|
-
this definition (which may or may not have an explicit geographic, i.e. spatial,
|
|
915
|
-
component) would include inventories of biological taxa such as the <a href=\\\"https://www.catalogueoflife.org\\\">Catalogue
|
|
916
|
-
of Life</a> and so on, all the way back to the pioneering compendia published
|
|
917
|
-
by Linnaeus in the eighteenth century; while for cartography and topographic
|
|
918
|
-
imagery, the current \\\"blockbuster\\\" of <a href=\\\"http://earth.google.com\\\">Google
|
|
919
|
-
Earth</a> and its predecessors also come well into public consciousness.</p>\\n\\n<p>In
|
|
920
|
-
the view of some workers and/or operations, both of these phases are precursors
|
|
921
|
-
to the real \\\"work\\\" of the macroscope which is to reveal previously unseen
|
|
922
|
-
portions of the \\\"big picture\\\" by means either of the availability of
|
|
923
|
-
large, synoptic datasets, or fusion between different data streams to produce
|
|
924
|
-
novel insights. Companies such as IBM and Microsoft have used phraseology
|
|
925
|
-
such as:</p>\\n\\n<blockquote>By 2022 we will use machine-learning algorithms
|
|
926
|
-
and software to help us organize information about the physical world, helping
|
|
927
|
-
bring the vast and complex data gathered by billions of devices within the
|
|
928
|
-
range of our vision and understanding. We call this a \\\"macroscope\\\" –
|
|
929
|
-
but unlike the microscope to see the very small, or the telescope that can
|
|
930
|
-
see far away, it is a system of software and algorithms to bring all of Earth's
|
|
931
|
-
complex data together to analyze it by space and time for meaning.\\\" (IBM)</blockquote>\\n\\n<blockquote>As
|
|
932
|
-
the Earth becomes increasingly instrumented with low-cost, high-bandwidth
|
|
933
|
-
sensors, we will gain a better understanding of our environment via a virtual,
|
|
934
|
-
distributed whole-Earth \\\"macroscope\\\"... Massive-scale data analytics
|
|
935
|
-
will enable real-time tracking of disease and targeted responses to potential
|
|
936
|
-
pandemics. Our virtual \\\"macroscope\\\" can now be used on ourselves, as
|
|
937
|
-
well as on our planet.\\\" (Microsoft) (references available via the Wikipedia
|
|
938
|
-
article cited above).</blockquote>\\n\\n<p>Whether or not the analytical capabilities
|
|
939
|
-
described here are viewed as being an integral part of the \\\"macroscope\\\"
|
|
940
|
-
concept, or are maybe an add-on, is ultimately a question of semantics and
|
|
941
|
-
perhaps, personal opinion. Continuing the Census of Marine Life/OBIS example,
|
|
942
|
-
OBIS offers some (arguably rather basic) visualization and summary tools,
|
|
943
|
-
but also makes its data available for download to users wishing to analyse
|
|
944
|
-
it further according to their own particular interests; using OBIS data in
|
|
945
|
-
this manner, Mark Costello et al. in 2017 were able to demarcate a finite
|
|
946
|
-
number of data-supported marine biogeographic realms for the first time (Costello
|
|
947
|
-
et al. 2017: Nature Communications. 8: 1057. <a href=\\\"https://doi.org/10.1038/s41467-017-01121-2\\\">doi:10.1038/s41467-017-01121-2</a>),
|
|
948
|
-
a project which I was able to assist in a small way in an advisory capacity.
|
|
949
|
-
In a case such as this, perhaps the final function of the macroscope, namely
|
|
950
|
-
data visualization and analysis, was outsourced to the authors' own research
|
|
951
|
-
institution. Similarly at an earlier phase, \\\"data aggregation\\\" can also
|
|
952
|
-
be virtual rather than actual, i.e. avoiding using a single physical system
|
|
953
|
-
to hold all the data, enabled by open web mapping standards WMS (web map service)
|
|
954
|
-
and WFS (web feature service) to access a set of distributed data stores,
|
|
955
|
-
e.g. as implemented on the portal for the <a href=\\\"https://portal.aodn.org.au/\\\">Australian
|
|
956
|
-
Ocean Data Network</a>.</p>\\n\\n<p>So, as we pass through the third decade
|
|
957
|
-
of the twenty first century, what developments await us in the \\\"macroscope\\\"
|
|
958
|
-
area\\\"? In the biodiversity space, one can reasonably presume that the existing
|
|
959
|
-
\\\"macroscopic\\\" data assembly projects such as OBIS and GBIF will continue,
|
|
960
|
-
and hopefully slowly fill current gaps in their coverage - although in the
|
|
961
|
-
marine area, strategic new data collection exercises may be required (Census
|
|
962
|
-
2020, or 2025, anyone?), while (again hopefully), the Catalogue of Life will
|
|
963
|
-
continue its progress towards a \\\"complete\\\" species inventory for the
|
|
964
|
-
biosphere. The Landsat project, with imagery dating back to 1972, continues
|
|
965
|
-
with the launch of its latest satellite Landsat 9 just this year (21 September
|
|
966
|
-
2021) with a planned mission duration for the next 5 years, so the \\\"macroscope\\\"
|
|
967
|
-
functionality of that project seems set to continue for the medium term at
|
|
968
|
-
least. Meanwhile the ongoing development of sensor networks, both on land
|
|
969
|
-
and in the ocean, offers an exciting new method of \\\"instrumenting the earth\\\"
|
|
970
|
-
to obtain much more real time data than has ever been available in the past,
|
|
971
|
-
offering scope for many more, use case-specific \\\"macroscopes\\\" to be
|
|
972
|
-
constructed that can fuse (e.g.) satellite imagery with much more that is
|
|
973
|
-
happening at a local level.</p>\\n\\n<p>So, the \\\"macroscope\\\" concept
|
|
974
|
-
appears to be alive and well, even though the nomenclature can change from
|
|
975
|
-
time to time (IBM's \\\"Macroscope\\\", foreshadowed in 2017, became the \\\"IBM
|
|
976
|
-
Pairs Geoscope\\\" on implementation, and is now simply the \\\"Geospatial
|
|
977
|
-
Analytics component within the IBM Environmental Intelligence Suite\\\" according
|
|
978
|
-
to available IBM publicity materials). In reality this illustrates a new dichotomy:
|
|
979
|
-
even if \\\"everyone\\\" in principle has access to huge quantities of publicly
|
|
980
|
-
available data, maybe only a few well funded entities now have the computational
|
|
981
|
-
ability to make sense of it, and can charge clients a good fee for their services...</p>\\n\\n<p>I
|
|
982
|
-
present this account partly to give a brief picture of \\\"macroscope\\\"
|
|
983
|
-
concepts today and in the past, for those who may be interested, and partly
|
|
984
|
-
to present a few personal views which would be out of scope in a \\\"neutral
|
|
985
|
-
point of view\\\" article such as is required on Wikipedia; also to see if
|
|
986
|
-
readers of this blog would like to contribute further to discussion of any
|
|
987
|
-
of the concepts traversed herein.</p>\",\"tags\":[\"guest post\",\"macroscope\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"tyfqw20\",\"blog\":{\"id\":\"tyfqw20\",\"title\":\"iPhylo\",\"description\":\"Rants,
|
|
988
|
-
raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
|
|
989
|
-
and biodiversity informatics. For more ranty and less considered opinions,
|
|
990
|
-
see my <a href=\\\"https://twitter.com/rdmpage\\\">Twitter feed</a>.<br>ISSN
|
|
991
|
-
2051-8188. Written content on this site is licensed under a <a href=\\\"https://creativecommons.org/licenses/by/4.0/\\\">Creative
|
|
992
|
-
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
|
|
993
|
-
7.00\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-31T17:26:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/k4bck-1me51\",\"uuid\":\"57878bca-6994-4e35-8350-4140326a7b28\",\"url\":\"https://larsgw.blogspot.com/2019/07/citationjs-ris-rework-pt-1.html\",\"title\":\"Citation.js:
|
|
994
|
-
RIS Rework Pt. 1\",\"summary\":\"Citation.js: RIS Rework Pt. 1 So a while
|
|
995
|
-
ago I was looking around for the RIS specification again. I had not found
|
|
996
|
-
it earlier, only a reference implementation from Zotero, a surprisingly complete
|
|
997
|
-
list of tags and types on Wikipedia and some examples from various websites
|
|
998
|
-
and programs exporting RIS files. They did not seem to go together well, however.
|
|
999
|
-
There were some slight differences in tags here and there, and a bunch of
|
|
1000
|
-
useful tags listed by Wikipedia were labelled “degenerate” in...\",\"date_published\":\"2019-07-30T21:16:00Z\",\"date_modified\":\"2023-03-30T20:47:44Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
|
|
1001
|
-
Willighagen\"}],\"image\":null,\"content_html\":\"<!DOCTYPE html>\\n<html>\\n\\n<head>\\n
|
|
1002
|
-
\ <meta charset=\\\"utf-8\\\">\\n <meta name=\\\"viewport\\\" content=\\\"width=device-width,
|
|
1003
|
-
initial-scale=1.0\\\">\\n <title>Citation.js: RIS Rework Pt. 1</title>\\n
|
|
1004
|
-
\ <link rel=\\\"stylesheet\\\" href=\\\"https://stackedit.io/style.css\\\"
|
|
1005
|
-
/>\\n</head>\\n\\n<body class=\\\"stackedit\\\">\\n <div class=\\\"stackedit__html\\\"><p>So
|
|
1006
|
-
a while ago I was looking around for the RIS specification again. I had not
|
|
1007
|
-
found it earlier, only a reference implementation from Zotero, a surprisingly
|
|
1008
|
-
complete list of tags and types on Wikipedia and some examples from various
|
|
1009
|
-
websites and programs exporting RIS files. They did not seem to go together
|
|
1010
|
-
well, however. There were some slight differences in tags here and there,
|
|
1011
|
-
and a bunch of useful tags listed by Wikipedia were labelled “degenerate”
|
|
1012
|
-
in the Zotero codebase, and only used for imports — implying some sort of
|
|
1013
|
-
problem.</p>\\n<p>What could be going on? Well, I checked out the references
|
|
1014
|
-
on the Wikipedia page again, to see if there really was no official specification
|
|
1015
|
-
or some other more reliable source where it got its information from. And,
|
|
1016
|
-
suddenly, there <em>was</em> an actual source this time. I do not know how
|
|
1017
|
-
I missed it earlier, but there was a page (<a href=\\\"https://web.archive.org/web/20120526103719/http://refman.com/support/risformat_intro.asp\\\">archived</a>)
|
|
1018
|
-
that linked to a zip file containing a PDF file with general specifications
|
|
1019
|
-
and an Excel file with sheets with property lists for all different types.</p>\\n<p>That
|
|
1020
|
-
sounded useful, so I spent <em>waaayy</em> to much time automating <a href=\\\"https://github.com/citation-js/ris-mappings\\\">a
|
|
1021
|
-
script</a> to turn those sheets — with a bunch of user input — into usable
|
|
1022
|
-
mappings for Citation.js. I just finished that today, apart from some… questionable
|
|
1023
|
-
mappings, but I wanted to at least test the final script with an example.
|
|
1024
|
-
As for the results, well, see for yourself. <a href=\\\"https://en.wikipedia.org/wiki/RIS_(file_format)#Example_multi-record_format\\\">The
|
|
1025
|
-
example</a>, from the Wikipedia page (CC-BY-SA 3.0 Unported) was</p>\\n<pre><code>TY
|
|
1026
|
-
\ - JOUR\\nT1 - On computable numbers, with an application to the Entscheidungsproblem\\nA1
|
|
1027
|
-
\ - Turing, Alan Mathison\\nJO - Proc. of London Mathematical Society\\nVL
|
|
1028
|
-
\ - 47\\nIS - 1\\nSP - 230\\nEP - 265\\nY1 - 1937\\nER -\\n</code></pre>\\n<p>and
|
|
1029
|
-
my results were</p>\\n<pre class=\\\" language-js\\\"><code class=\\\"prism
|
|
1030
|
-
\ language-js\\\"><span class=\\\"token punctuation\\\">{</span> issue<span
|
|
1031
|
-
class=\\\"token punctuation\\\">:</span> <span class=\\\"token number\\\">1</span><span
|
|
1032
|
-
class=\\\"token punctuation\\\">,</span> page<span class=\\\"token punctuation\\\">:</span>
|
|
1033
|
-
<span class=\\\"token number\\\">230</span><span class=\\\"token punctuation\\\">,</span>
|
|
1034
|
-
type<span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">'article-journal'</span><span
|
|
1035
|
-
class=\\\"token punctuation\\\">,</span> volume<span class=\\\"token punctuation\\\">:</span>
|
|
1036
|
-
<span class=\\\"token number\\\">47</span> <span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>That
|
|
1037
|
-
looked really weird and disappointing. Again, what could possibly be going
|
|
1038
|
-
on here? The example on Wikipedia is using <code>T1</code>, <code>A1</code>,
|
|
1039
|
-
<code>JO</code> and <code>Y1</code> while the specs say to use <code>TI</code>,
|
|
1040
|
-
<code>AU</code>, <code>T2</code> and <code>PY</code> here. Where are these
|
|
1041
|
-
differences coming from?</p>\\n<p>After some digging around on Wikipedia I
|
|
1042
|
-
found <a href=\\\"https://en.wikipedia.org/wiki/Talk:RIS_(file_format)#Versions_of_the_specification\\\">a
|
|
1043
|
-
comment</a> saying that there are in fact two specifications: one from 2011
|
|
1044
|
-
and one from before. The archived spec I checked out was from 2012 (as linked
|
|
1045
|
-
by Wikipedia!), while they use the version from before 2011; which luckily
|
|
1046
|
-
is <a href=\\\"https://web.archive.org/web/20110930172154/http://www.refman.com/support/risformat_intro.asp\\\">still
|
|
1047
|
-
available</a>. To be continued.</p>\\n</div>\\n</body>\\n\\n</html>\",\"tags\":[\"bibliography\",\"Citation.js\",\"programming\",\"RIS\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
|
|
1048
|
-
baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
|
|
1049
|
-
statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
|
|
1050
|
-
7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/det4g-prf93\",\"uuid\":\"d1c551e3-7371-4683-99d8-a9a62e11d2ae\",\"url\":\"https://larsgw.blogspot.com/2021/03/github-pages-404-redirection.html\",\"title\":\"GitHub
|
|
1051
|
-
pages 404 redirection\",\"summary\":\"Recently I moved the Citation.js API
|
|
1052
|
-
documentation from /api to /api/0.3, to put the new documentation on /api/0.5.
|
|
1053
|
-
I fixed all the links to the documentation, but I still got a issue request
|
|
1054
|
-
regarding a 404 error after just a few days. All in all, I had to redirect
|
|
1055
|
-
pages from /api/* to /api/0.3/* while all these pages are hosted as static
|
|
1056
|
-
files on GitHub Pages. There are three ways I found to do this: I make otherwise
|
|
1057
|
-
empty HTML files in /api/* that redirect to /api/0.3/* via JavaScript or...\",\"date_published\":\"2021-03-26T13:08:00Z\",\"date_modified\":\"2023-03-30T20:46:06Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
|
|
1058
|
-
Willighagen\"}],\"image\":null,\"content_html\":\"<p>Recently I moved the
|
|
1059
|
-
<a href=\\\"https://citation.js.org\\\">Citation.js</a> API documentation
|
|
1060
|
-
from <code>/api</code> to <code>/api/0.3</code>, to put the new documentation
|
|
1061
|
-
on <code>/api/0.5</code>. I fixed all the links to the documentation, but
|
|
1062
|
-
I still got a issue request regarding a 404 error after just a few days. All
|
|
1063
|
-
in all, I had to redirect pages from <code>/api/*</code> to <code>/api/0.3/*</code>
|
|
1064
|
-
while all these pages are hosted as static files on GitHub Pages.</p>\\n<p>There
|
|
1065
|
-
are three ways I found to do this:</p>\\n<ol>\\n<li>I make otherwise empty
|
|
1066
|
-
HTML files in <code>/api/*</code> that redirect to <code>/api/0.3/*</code>
|
|
1067
|
-
via JavaScript or a <code><meta></code> tag.</li>\\n<li>I make use of
|
|
1068
|
-
<a href=\\\"https://github.com/jekyll/jekyll-redirect-from\\\"><code>jekyll-redirect-from</code></a>.
|
|
1069
|
-
This is equivalent to option 1, I think.</li>\\n</ol>\\n<p>Option 1 seemed
|
|
1070
|
-
like a hassle and I do not use Jekyll so option 2 seemed out of the question
|
|
1071
|
-
as well. However, we still have option 3 to consider:</p>\\n<ol start=\\\"3\\\">\\n<li>I
|
|
1072
|
-
add a <code>404.html</code> to the repository which gets served automatically
|
|
1073
|
-
on a 404. It then redirects to <code>/api/0.3/*</code> with JavaScript, and
|
|
1074
|
-
gives guidance on how to find the new URL manually if JavaScript is disabled.</li>\\n</ol>\\n<p><code>404.html</code>
|
|
1075
|
-
is just a normal 404 page with 4 lines of JavaScript:</p>\\n<pre class=\\\"
|
|
1076
|
-
language-js\\\"><code class=\\\"prism language-js\\\"><span class=\\\"token
|
|
1077
|
-
keyword\\\">var</span> docsPattern <span class=\\\"token operator\\\">=</span>
|
|
1078
|
-
<span class=\\\"token regex\\\">/(\\\\/api)(\\\\/(?!0.[35]\\\\/)|$)/</span>
|
|
1079
|
-
\ \\n \\n<span class=\\\"token keyword\\\">if</span> <span class=\\\"token
|
|
1080
|
-
punctuation\\\">(</span>docsPattern<span class=\\\"token punctuation\\\">.</span><span
|
|
1081
|
-
class=\\\"token function\\\">test</span><span class=\\\"token punctuation\\\">(</span>location<span
|
|
1082
|
-
class=\\\"token punctuation\\\">.</span>pathname<span class=\\\"token punctuation\\\">)</span><span
|
|
1083
|
-
class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
|
|
1084
|
-
\ \\n location<span class=\\\"token punctuation\\\">.</span>pathname <span
|
|
1085
|
-
class=\\\"token operator\\\">=</span> location<span class=\\\"token punctuation\\\">.</span>pathname<span
|
|
1086
|
-
class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
|
|
1087
|
-
class=\\\"token punctuation\\\">(</span>docsPattern<span class=\\\"token punctuation\\\">,</span>
|
|
1088
|
-
<span class=\\\"token string\\\">'$1/0.3$2'</span><span class=\\\"token punctuation\\\">)</span>
|
|
1089
|
-
\ \\n<span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>Breaking
|
|
1090
|
-
down the RegExp pattern:</p>\\n<ul>\\n<li><code>(\\\\/api)</code> matches
|
|
1091
|
-
“/api” in the URL</li>\\n<li><code>(\\\\/(?!0.[35]\\\\/)|$)</code> matches
|
|
1092
|
-
one of two things, immediately after “/api”\\n<ul>\\n<li>Either <code>$</code>,
|
|
1093
|
-
the end of the string (like “<a href=\\\"https://citation.js.org/api\\\">https://citation.js.org/api</a>”
|
|
1094
|
-
without the trailing slash)</li>\\n<li>Or <code>\\\\/(?!0.[35]\\\\/)</code>,
|
|
1095
|
-
which matches a forward slash (\\\"/api/\\\") followed by anything except
|
|
1096
|
-
“0.3” or “0.5”. This is to avoid matching things like “/apical/” or “/api/0.3/does-not-exist”.</li>\\n</ul>\\n</li>\\n</ul>\\n<p>This
|
|
1097
|
-
is not the neatest solution but I like it conceptually. It shows a bit of
|
|
1098
|
-
potential for Single-Page Applications as well: you can serve the same HTML+JavaScript
|
|
1099
|
-
for every possible path without having to rely on URLs like <code>https://example.org/#/path/page</code>.
|
|
1100
|
-
The problem is that you still get the 404 HTTP status (as you should), so
|
|
1101
|
-
if a browser or search crawler decides to care you have a problem.</p>\\n<p>Try
|
|
1102
|
-
it out now: <a href=\\\"https://citation.js.org/api/\\\">https://citation.js.org/api/</a></p>\\n<p><img
|
|
1103
|
-
src=\\\"https://1.bp.blogspot.com/-srnQgvIYR1c/YF3aOogA3AI/AAAAAAAAuro/gVpFdn1m-Gk4JBh9Nsrw6Gd_bR-QKApEACLcBGAsYHQ/s0/citation.js.org_api_0.3_test.png\\\"
|
|
1104
|
-
alt=\\\"The new "Page not Found" page in the same style as the homepage.\\\"></p>\",\"tags\":[\"Citation.js\",\"programming\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
|
|
1105
|
-
baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
|
|
1106
|
-
statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
|
|
1107
|
-
7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/7dz35-q5185\",\"uuid\":\"d2b5f8f3-dde5-4944-a4e1-f9776c86b38b\",\"url\":\"http://sfmatheson.blogspot.com/2023/06/design-without-designer-explaining-and.html\",\"title\":\"Design
|
|
1108
|
-
without a designer: explaining and answering some questions\",\"summary\":\"I've
|
|
1109
|
-
been writing and thinking about design in biology since I started Quintessence
|
|
1110
|
-
of Dust. I want to write and think about it a lot more, so in my last post
|
|
1111
|
-
I introduced my view of the concept and pointed ahead to this post, which
|
|
1112
|
-
consists of edited excerpts from some conversations at a discussion forum
|
|
1113
|
-
at the Peaceful Science site. You will find links to those conversations in
|
|
1114
|
-
the previous post. I have removed people's names and lightly edited for clarity.
|
|
1115
|
-
Other people’s words are indented;...\",\"date_published\":\"2023-06-06T20:22:00Z\",\"date_modified\":\"2023-06-07T20:44:58Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Stephen
|
|
1116
|
-
Matheson\"}],\"image\":null,\"content_html\":\"I've been writing and thinking
|
|
1117
|
-
about design in biology since I started <i>Quintessence of Dust</i>. I want
|
|
1118
|
-
to write and think about it a lot more, so <a href=\\\"https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html\\\"
|
|
1119
|
-
target=\\\"_blank\\\">in my last post</a> I introduced my view of the concept
|
|
1120
|
-
and pointed ahead to this post, which consists of edited excerpts from some
|
|
1121
|
-
conversations at a discussion forum at the Peaceful Science site. You will
|
|
1122
|
-
find links to those conversations in the <a href=\\\"https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html\\\"
|
|
1123
|
-
target=\\\"_blank\\\">previous post</a>. I have removed people's names and
|
|
1124
|
-
lightly edited for clarity. Other people’s words are indented; the rest are
|
|
1125
|
-
mine.<div><hr /><br /><div><div><blockquote>I would like to understand better
|
|
1126
|
-
how you think about it because it seems quite different from the way I normally
|
|
1127
|
-
think about it. I would really like learn more about how you see it and expand
|
|
1128
|
-
my understanding of \\\"design\\\".</blockquote></div><div>This is a potentially
|
|
1129
|
-
big interesting deep conversation that is worthy of a dedicated thread with
|
|
1130
|
-
some clear goals. Someday I’ll propose that, since I believe that we can improve
|
|
1131
|
-
the quality and tone of conversations about biological design by getting at
|
|
1132
|
-
least some unbelievers to agree that design in biology is an interesting and
|
|
1133
|
-
worthy question that need not and should not have inherent religious overtones.</div><div><br
|
|
1134
|
-
/></div><div>I guess my first question for you as you compare your conception
|
|
1135
|
-
of 'design' to mine is this: do you think design is something that is <i>done</i>
|
|
1136
|
-
(by a designer) or do you think it is something that <i>exists</i> and can
|
|
1137
|
-
be detected by humans? Obviously both can be true, but as long as a person
|
|
1138
|
-
believes that 'design' necessitates a 'designer', then they won’t see design
|
|
1139
|
-
the way I do. Because my view is that design exists whether or not it is linked
|
|
1140
|
-
to a designer. To me, it is axiomatic that a mindless process can generate
|
|
1141
|
-
design, not only because we have seen it happen but because there is no good
|
|
1142
|
-
argument to the contrary. It is instructive, IMO, that the \\\"argument\\\"
|
|
1143
|
-
offered to the contrary is something like \\\"all of our examples of design
|
|
1144
|
-
can be traced back to a mind.\\\" This is not even an argument.</div><div><br
|
|
1145
|
-
/></div><div>But what do we mean by 'design'? Here I think we can look at
|
|
1146
|
-
some of the definitions and conceptions offered by the ID movement. I think
|
|
1147
|
-
Behe’s \\\"purposeful arrangement of parts\\\" is a nice start, because it
|
|
1148
|
-
captures something that we all detect when we consider (for example) a molecular
|
|
1149
|
-
machine. Was a bacterial flagellum designed by a designer? I don’t know. Does
|
|
1150
|
-
a bacterial flagellum evince design? To me, the answer is obviously yes. <span><a
|
|
1151
|
-
name='more'></a></span>So, I disagree with many fellow unbelievers (materialists
|
|
1152
|
-
for the most part) who use phrases like \\\"apparent design\\\" or words like
|
|
1153
|
-
'designoid' to describe the biological world. My view is that design is design.
|
|
1154
|
-
If I see it, I should call it design. This doesn’t imply a designer. That
|
|
1155
|
-
simply doesn’t follow.</div><div><blockquote>How do you manage the distinction
|
|
1156
|
-
between design as a \\\"process of making\\\" vs. \\\"plan or schematic\\\"
|
|
1157
|
-
vs. \\\"product of a designing process\\\"?</blockquote></div><div>I don’t
|
|
1158
|
-
manage that. Those are all conceptions of design, but they’re not what we
|
|
1159
|
-
see when we look at ATP synthase or a flagellum. I think those things are
|
|
1160
|
-
all distractions away from what I (personally) care about, especially since
|
|
1161
|
-
they all assume the presence of a designer.</div><div><blockquote>Is that
|
|
1162
|
-
last one even rightly called design?</blockquote></div><div>Sure, why not?
|
|
1163
|
-
Anyone who believes otherwise would have to claim that the sentence \\\"I
|
|
1164
|
-
see design in this thing\\\" is linguistically incorrect. I can respect that,
|
|
1165
|
-
but then it ends the conversation.</div><div><blockquote>So you are trying
|
|
1166
|
-
to legitimize one understanding of design in its own right, separate from
|
|
1167
|
-
other definitions.</blockquote></div><div>Yes, though I think the work of
|
|
1168
|
-
\\\"legitimizing\\\" this understanding is already done. To reject this use
|
|
1169
|
-
of the word/concept is defensible in principle, but there’s nothing revolutionary
|
|
1170
|
-
about saying \\\"design is detectable without knowledge of a designer.\\\"</div><div><blockquote>Seems
|
|
1171
|
-
like the same thing would have to be done with the term \\\"purpose.\\\"</blockquote></div><div>Maybe.
|
|
1172
|
-
[shrug]</div><div><blockquote>I don’t think science recognizes design without
|
|
1173
|
-
a model of a designer. So this would be pretty revolutionary.</blockquote></div><div>Science
|
|
1174
|
-
has never spoken on this, since it can’t do that. But scientists have. Here
|
|
1175
|
-
are just a few examples from places I know well.</div><div><a href=\\\"https://www.cell.com/molecular-cell/fulltext/S1097-2765(13)00004-X\\\"
|
|
1176
|
-
target=\\\"_blank\\\">Design Principles of Regulatory Networks: Searching
|
|
1177
|
-
for the Molecular Algorithms of the Cell</a></div><div><a href=\\\"https://www.cell.com/cell/fulltext/S0092-8674(20)30277-4\\\"
|
|
1178
|
-
target=\\\"_blank\\\">Defining the Design Principles of Skin Epidermis Postnatal
|
|
1179
|
-
Growth</a></div><div><a href=\\\"https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30188-8\\\"
|
|
1180
|
-
target=\\\"_blank\\\">Quantitative Operating Principles of Yeast Metabolism
|
|
1181
|
-
during Adaptation to Heat Stress</a></div><div><blockquote>I tend towards
|
|
1182
|
-
notion of \\\"appearance of design,\\\" and trying to make sense of what defines
|
|
1183
|
-
that appearance. That is, I think, closely aligned with what you are after.</blockquote></div><div>I
|
|
1184
|
-
don’t see that as closely aligned, because I don’t assume that design requires
|
|
1185
|
-
a designer. \\\"Appearance of design\\\" downgrades ATP synthase to an \\\"appearance\\\"
|
|
1186
|
-
of something I consider obvious. I understand why people do this, and especially
|
|
1187
|
-
why naturalism leads people to do it (that infamous quote about a \\\"divine
|
|
1188
|
-
foot in the door\\\") but I’m with Dan Dennett here. The biological world
|
|
1189
|
-
is overflowing with design. Calling it \\\"apparent\\\" just encourages the
|
|
1190
|
-
madness of attempting to find the \\\"real\\\" design that isn’t just \\\"apparent\\\"
|
|
1191
|
-
design. Does this give some kind of comfort to ID creationists and their propaganda
|
|
1192
|
-
machines? Maybe, but that just means that they didn’t read to the end of the
|
|
1193
|
-
sentence: \\\"…without a designer.\\\"</div><div><br /></div><div>But here’s
|
|
1194
|
-
the thought experiment. Suppose I sit down at my supercomputer to predict
|
|
1195
|
-
ways to build a much better version of enzyme Z; let’s even say that my enzyme
|
|
1196
|
-
has a new substrate specificity and is orders of magnitude more stable than
|
|
1197
|
-
enzyme Z. I synthesize the gene and insert it into bacteria. Does this enzyme
|
|
1198
|
-
evince design? Or only apparent design? Is there any way to tell the difference,
|
|
1199
|
-
without knowing that I designed the new enzyme on my supercomputer? Are we
|
|
1200
|
-
going to actually say, \\\"well I can’t tell whether this is design or apparent
|
|
1201
|
-
design until I investigate supercomputer user patterns?\\\"</div><div><br
|
|
1202
|
-
/></div><div>Just a couple of quick thoughts at this point.</div><div style=\\\"text-align:
|
|
1203
|
-
left;\\\">\U0001F335In a universe that includes one or more omnipotent gods,
|
|
1204
|
-
it is impossible to argue persuasively that <i>anything</i> came about without
|
|
1205
|
-
a designer, for the straightforward reason that such beings can make anything
|
|
1206
|
-
they want, and make it look any way they want.<br />\U0001F332To me, the fundamental
|
|
1207
|
-
first question is not \\\"can we have design without a designer?\\\" but \\\"does
|
|
1208
|
-
design detection imply knowledge or assumptions about possible designers?\\\"
|
|
1209
|
-
I am saying an emphatic ‘no’ to that question, but one can coherently circumscribe
|
|
1210
|
-
‘design’ to essentially require the answer to be ‘yes.’ I think that creates
|
|
1211
|
-
problems, which I’ve mentioned above, but it’s coherent and defensible to
|
|
1212
|
-
limit ‘design’ in that way. I will grant that once you answer ‘no’ to the
|
|
1213
|
-
fundamental question then it’s hard (maybe impossible) to answer ‘no’ to the
|
|
1214
|
-
first question.</div><div><blockquote>What would you suggest as terminology
|
|
1215
|
-
for the two cases?</blockquote></div><div>I don’t need any new words and I
|
|
1216
|
-
don’t share the premise of \\\"design implies a designer\\\" with you. I have
|
|
1217
|
-
tried to document the fact that design is a pretty integrated concept in biology,
|
|
1218
|
-
such that many biologists talk about design and design principles with no
|
|
1219
|
-
worry that they will be misunderstood. I’m afraid I don’t see how the concept
|
|
1220
|
-
of design without a designer is either hard to grasp (conceptually) or hard
|
|
1221
|
-
to understand (linguistically).</div><div><br /></div><div>People have tried
|
|
1222
|
-
words like 'designoid' and phrases like 'apparent design.' The subtitle of
|
|
1223
|
-
Dawkins’ <i>The Blind Watchmaker</i> is \\\"Why the Evidence of Evolution
|
|
1224
|
-
Reveals a Universe without Design.\\\" I’m well aware that many believers
|
|
1225
|
-
and unbelievers alike are stuck with the word 'design' linked to 'designer'.
|
|
1226
|
-
I have seen only one argument for this approach so far, which is the dictionary.
|
|
1227
|
-
Maybe there are other things going on. But here is Dennett (from <a href=\\\"https://www.edge.org/conversation/the-false-allure-of-group-selection#dd\\\"
|
|
1228
|
-
target=\\\"_blank\\\">this piece</a>) on one reason why it might not be a
|
|
1229
|
-
good idea to refuse to give ATP synthase the honor of showing design:</div><div><br
|
|
1230
|
-
/></div><div><blockquote>The second misplaced emphasis is Pinker’s phrase
|
|
1231
|
-
'the illusion of design in the natural world.\\\" Richard Dawkins, in a similar
|
|
1232
|
-
vein, says \\\"the illusion of design conjured by Darwinian natural selection
|
|
1233
|
-
is so breathtakingly powerful\\\" in <i>The Ancestors’ Tale</i> (p 457), and
|
|
1234
|
-
elsewhere proposes to speak of \\\"designoid\\\" features of the natural world
|
|
1235
|
-
(eg., <i>Climbing Mount Improbable</i>, p 4). I disagree with this policy,
|
|
1236
|
-
which can backfire badly. I recently overheard a conversation among some young
|
|
1237
|
-
people in a bar about the marvels of the nano-machinery discovered inside
|
|
1238
|
-
all cells. \\\"When you see all those fantastic little robots working away,
|
|
1239
|
-
how can you possibly believe in evolution!\\\" one exclaimed, and another
|
|
1240
|
-
nodded wisely. Somehow these folks had gotten the impression that evolutionary
|
|
1241
|
-
biologists thought that the intricacies and ingenuities of life’s processes
|
|
1242
|
-
weren’t all that wonderful. These evolution-doubters were not rednecks; they
|
|
1243
|
-
were Harvard Medical students! They hugely underestimated the power of natural
|
|
1244
|
-
selection because they had been told by evolutionary biologists, again and
|
|
1245
|
-
again, that there is no actual design in nature, only the appearance of design.
|
|
1246
|
-
This episode strongly suggested to me that one of the themes that has been
|
|
1247
|
-
gaining ground in \\\"common knowledge\\\" is that evolutionary biologists
|
|
1248
|
-
are reluctant to \\\"admit\\\" or \\\"acknowledge\\\" the manifest design
|
|
1249
|
-
in nature. I recommend instead the expository policy of calling nature’s marvels
|
|
1250
|
-
design, as real as any design in the universe, but just not the products of
|
|
1251
|
-
an intelligent designer.</blockquote></div><div>You can read how Dennett describes
|
|
1252
|
-
design <a href=\\\"https://books.google.com/books?id=PEp8DAAAQBAJ&lpg=PP1&pg=PT46#v=onepage&q&f=false\\\"
|
|
1253
|
-
target=\\\"_blank\\\">here</a>, in his recent cool book <i>From Bacteria to
|
|
1254
|
-
Bach and Back</i>.</div><div><br /></div><div>Biology shows design. I don’t
|
|
1255
|
-
think that’s confusing or unclear, and I think it’s a mistake to make distinctions
|
|
1256
|
-
based on old dictionaries. YMMV.</div><div><br /></div></div></div>\",\"tags\":[\"Design\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"5764g49\",\"blog\":{\"id\":\"5764g49\",\"title\":\"Quintessence
|
|
1257
|
-
of Dust\",\"description\":\"<i>Quintessence of Dust</i> explores science,
|
|
1258
|
-
society, and human nature, focusing on genetics, development, evolution, neuroscience,
|
|
1259
|
-
systems biology, and topics related to scientific literacy. I occasionally
|
|
1260
|
-
discuss intelligent design, creationism, science denial, and other political/social
|
|
1261
|
-
influences on scientific literacy. Additional topics: philosophy, baseball,
|
|
1262
|
-
scientific culture, and Shakespeare. My main theme is <b><u>scientific explanation</u></b>.\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"http://sfmatheson.blogspot.com/feeds/posts/default\",\"home_page_url\":\"http://sfmatheson.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T14:21:27+00:00\",\"indexed_at\":\"2023-04-18\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
|
|
1263
|
-
7.00\",\"category\":\"Social Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-06-06T20:22:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/stsb5-45v78\",\"uuid\":\"5fc2c7d7-082a-4994-aa33-d94d1e474c4c\",\"url\":\"https://jabberwocky.weecology.org/2020/04/27/supporting-and-managing-academic-labs-during-a-pandemic-some-thoughts/\",\"title\":\"Supporting
|
|
1264
|
-
and managing academic labs during a pandemic, some thoughts\",\"summary\":\"Adjust
|
|
1265
|
-
expectations, be flexible, support your groups Research will be different
|
|
1266
|
-
from normal for a while and even in the best cases it will also be slower.
|
|
1267
|
-
The shift to working remotely will limit the kinds of work we can do and everyone
|
|
1268
|
-
doing research is experiencing a dramatic disturbance to their lives. This
|
|
1269
|
-
means the people in our labs will need flexibility and support. Talk to your
|
|
1270
|
-
lab members to understand their needs: Recognize that these needs will be
|
|
1271
|
-
different for different people....\",\"date_published\":\"2020-04-27T13:19:27Z\",\"date_modified\":\"2020-04-27T13:19:27Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0001-6728-7745\",\"name\":\"Ethan
|
|
1272
|
-
White\"}],\"image\":null,\"content_html\":\"<h2>Adjust expectations, be flexible,
|
|
1273
|
-
support your groups</h2>\\n<p>Research will be different from normal for a
|
|
1274
|
-
while and even in the best cases it will also be slower. The shift to working
|
|
1275
|
-
remotely will limit the kinds of work we can do and everyone doing research
|
|
1276
|
-
is experiencing a dramatic disturbance to their lives. This means the people
|
|
1277
|
-
in our labs will need flexibility and support.</p>\\n<p><b>Talk to your lab
|
|
1278
|
-
members to understand their needs: </b>Recognize that these needs will be
|
|
1279
|
-
different for different people. Many will have new responsibilities and stresses
|
|
1280
|
-
that preclude working normally, but some may use work as a coping mechanism.</p>\\n<p><b>Make
|
|
1281
|
-
it clear that moving more slowly and delaying things is expected and 100%
|
|
1282
|
-
OK.</b> Push back project timelines, understand that some folks will make
|
|
1283
|
-
little to no progress for a while, consider delaying stressful graduate activities
|
|
1284
|
-
like qualifying exams.</p>\\n<p><b>Provide financial reassurance:</b> If true,
|
|
1285
|
-
ensure your team that their current funding won’t be cut. If possible, offer
|
|
1286
|
-
extensions on funding. This will help alleviate stress and uncertainty.</p>\\n<p><b>Recognize
|
|
1287
|
-
power dynamics when offering flexibility:</b> Make sure that team members
|
|
1288
|
-
are comfortable opting-out of “optional” choices and don’t
|
|
1289
|
-
feel pressured to be productive, to work on-campus, or work at certain times.</p>\\n<p><b>Provide
|
|
1290
|
-
access to university resources:</b> Inform group members about university
|
|
1291
|
-
programs related to mental health, expanded sick leave, and other forms of
|
|
1292
|
-
support for well being.</p>\\n<p><b>Give your team the resources they need
|
|
1293
|
-
to work from home: </b>Encourage your group to move things from campus that
|
|
1294
|
-
they need to work at home including computers, books, and chairs. Universities
|
|
1295
|
-
typically allow this for remote work (there may be a form to fill out). If
|
|
1296
|
-
possible, purchase additional supplies needed for remote work (e.g., headsets).</p>\\n<h2>Adopt
|
|
1297
|
-
& adapt tools and approaches for managing remote teams</h2>\\n<p>Remote management
|
|
1298
|
-
recommendations focus on good communication, breaking projects into manageable
|
|
1299
|
-
pieces, keeping everyone on the same page with clear next steps, and tracking
|
|
1300
|
-
progress. This will make your group more efficient and inclusive when working
|
|
1301
|
-
remotely.</p>\\n<p><b>Use video conferencing to replace in-person interactions:</b>
|
|
1302
|
-
Do this for any regular meetings you have (e.g., one-on-one meetings, lab
|
|
1303
|
-
group meetings) and also informal interactions (like popping into an advisors
|
|
1304
|
-
office or chatting science with labmates). Communicate your availability and
|
|
1305
|
-
how to set up meetings.</p>\\n<p><b>Use a group-based discussion tool (e.g.,
|
|
1306
|
-
Slack or Microsoft Teams) : </b>This supports asking questions and working
|
|
1307
|
-
on group projects and facilitates interactions among lab members with different
|
|
1308
|
-
work hours (important for those with responsibilities like child care). It
|
|
1309
|
-
can also provide an outlet for social interactions. Text does lose subtle
|
|
1310
|
-
social cues so video or audio is still best for delicate conversations. Check
|
|
1311
|
-
out the getting started documentation for <a href=\\\"https://slack.com/help/categories/360000049043-Getting-started\\\">Slack</a>
|
|
1312
|
-
or <a href=\\\"https://docs.microsoft.com/en-us/MicrosoftTeams/get-started-with-teams-quick-start\\\">Microsoft
|
|
1313
|
-
Teams</a>.</p>\\n<p><b>Read up on managing remote teams:</b> There are some
|
|
1314
|
-
unique skills to remote management, but there is lots of information on how
|
|
1315
|
-
to do this including: <a href=\\\"https://www.askamanager.org/2016/10/how-to-overcome-your-worries-about-letting-people-work-remotely.html\\\">How
|
|
1316
|
-
to overcome your worries about letting people work remotely</a>, <a href=\\\"https://www.askamanager.org/2015/05/how-to-oversee-a-remote-teams-work.html\\\">How
|
|
1317
|
-
to oversee a remote team’s work</a>, <a href=\\\"https://doi.org/10.7287/peerj.preprints.27907v1\\\">Ten
|
|
1318
|
-
simple rules for a successful remote postdoc</a>.</p>\\n<p><b>Use project
|
|
1319
|
-
management and collaboration tools: </b>These tools help you use good remote
|
|
1320
|
-
management practices. Most labs will benefit from a tool for writing and a
|
|
1321
|
-
tool for project management. Labs that write code (including for analyzing
|
|
1322
|
-
data) will also benefit from a code collaboration platform. Check out getting
|
|
1323
|
-
started guides for <a href=\\\"https://www.howtogeek.com/420971/the-beginners-guide-to-google-docs/\\\">Google
|
|
1324
|
-
Docs (for writing)</a> and <a href=\\\"https://trello.com/guide/trello-101\\\">Trello
|
|
1325
|
-
(for project management)</a>. Learning version control for managing code is
|
|
1326
|
-
a bigger commitment, but the <a href=\\\"http://swcarpentry.github.io/git-novice/\\\">Software
|
|
1327
|
-
Carpentry lessons</a> are a good starting point.</p>\\n<h3>Help identify research
|
|
1328
|
-
that can be done remotely, but understand the limits</h3>\\n<p>It’s important
|
|
1329
|
-
to prioritize the safety of your team over research. This may mean changing
|
|
1330
|
-
your research plans to support social distancing and reduce or eliminate travel.</p>\\n<p><b>Focus
|
|
1331
|
-
on analyzing and writing up existing data and ideas: </b>This is the easiest
|
|
1332
|
-
adjustment because it minimizes shifts in research area and need for new skills.
|
|
1333
|
-
Existing data isn’t just what a specific student has already collected, but
|
|
1334
|
-
can include previous data collection from your lab.</p>\\n<p><b>Synthesize
|
|
1335
|
-
existing knowledge: </b>Writing reviews lets your team use their expertise
|
|
1336
|
-
to synthesize existing knowledge.</p>\\n<p><b>Conduct research on open data:</b>
|
|
1337
|
-
There are increasingly large amounts of openly available data in many fields.
|
|
1338
|
-
There may be data that can be used to address questions similar to those you
|
|
1339
|
-
are studying using field or lab based approaches.</p>\\n<p><b>Collaborate
|
|
1340
|
-
when extending into new research areas: </b>Computational research, working
|
|
1341
|
-
with large datasets, systematic reviews and metaanalyses all take expertise.
|
|
1342
|
-
To pivot into new methods or topics consider finding someone with the associated
|
|
1343
|
-
expertise to collaborate with. There may well be experts on your students’
|
|
1344
|
-
committees or in your department or university.</p>\\n<p><b>Develop new skills/expertise
|
|
1345
|
-
to expand your groups’ research horizons:</b> Instead of jumping into
|
|
1346
|
-
a new project requiring new skills support your team taking this time to learn
|
|
1347
|
-
new skills (e.g., computing methods or statistical approaches) or develop
|
|
1348
|
-
new expertise (reading up on new areas of the literature) to serve as the
|
|
1349
|
-
foundation for future research.</p>\\n<p><i>Initially prepared for the UF/IFAS
|
|
1350
|
-
Faculty Forum: Living, Working, and Adapting to the New Normal of COVID-19.
|
|
1351
|
-
Led by </i><a href=\\\"https://twitter.com/ethanwhite\\\"><i>Ethan White (@ethanwhite)</i></a><i>
|
|
1352
|
-
(who is responsible for anything bad) with contributions from </i><a href=\\\"https://twitter.com/skmorgane\\\"><i>SK
|
|
1353
|
-
Morgan Ernest (@skmorgane)</i></a><i>, </i><a href=\\\"https://twitter.com/Hao_and_Y\\\"><i>Hao
|
|
1354
|
-
Ye (@Hao_and_Y)</i></a><i>, </i><a href=\\\"https://twitter.com/brandonscooper\\\"><i>Brandon
|
|
1355
|
-
S. Cooper (@brandonscooper)</i></a><i>, </i><a href=\\\"https://twitter.com/JJ_Emerson\\\"><i>JJ
|
|
1356
|
-
Emerson (@JJ_Emerson)</i></a><i>, </i><a href=\\\"https://twitter.com/katyhuff\\\"><i>Katy
|
|
1357
|
-
Huff (@katyhuff)</i></a><i>, </i><a href=\\\"https://twitter.com/ryneches\\\"><i>Russell
|
|
1358
|
-
Neches (@ryneches)</i></a><i>, </i><a href=\\\"https://twitter.com/RallidaeRule\\\"><i>Auriel
|
|
1359
|
-
Fournier (@RallidaeRule)</i></a><i>, </i><a href=\\\"https://twitter.com/TrashBirdEcol\\\"><i>Jessica
|
|
1360
|
-
Burnett (@TrashBirdEcol)</i></a><i>, </i><a href=\\\"https://twitter.com/mlrethlefsen\\\"><i>Melissa
|
|
1361
|
-
Rethlefsen (@mlrethlefsen)</i></a><i>, </i><a href=\\\"https://twitter.com/LeafyEricScott\\\"><i>Eric
|
|
1362
|
-
Scott (@LeafyEricScott)</i></a><i>, </i><a href=\\\"https://twitter.com/KatheMathBio\\\"><i>Kathe
|
|
1363
|
-
Todd-Brown (@KatheMathBio)</i></a><i>, </i><a href=\\\"https://twitter.com/itatiVCS\\\"><i>itati
|
|
1364
|
-
en casa (@itatiVCS)</i></a><i>, </i><a href=\\\"https://twitter.com/ashiklom711\\\"><i>Alexey
|
|
1365
|
-
Shiklomanov (@ashiklom711)</i></a><i> (who are responsible for anything awesome).
|
|
1366
|
-
A lot of the thinking in “Adopt & adapt tools and approaches for managing
|
|
1367
|
-
remote teams” was influenced by “<a href=\\\"https://doi.org/10.7287/peerj.preprints.27907v1\\\">Ten
|
|
1368
|
-
simple rules for a successful remote postdoc</a>” by <a href=\\\"https://twitter.com/KRBurgio\\\">Kevin
|
|
1369
|
-
Burgio</a>, <a href=\\\"https://twitter.com/CaitlinInMaine\\\">Caitlin McDonough
|
|
1370
|
-
MacKenzie</a>, <a href=\\\"https://twitter.com/PetrelStation\\\">Stephanie
|
|
1371
|
-
Borrelle</a>, <a href=\\\"https://twitter.com/skmorgane\\\">Morgan Ernest</a>,
|
|
1372
|
-
<a href=\\\"https://twitter.com/JacquelynGill\\\">Jacquelyn Gill</a>, <a href=\\\"https://twitter.com/kurtingeman\\\">Kurt
|
|
1373
|
-
Ingeman</a>, <a href=\\\"https://twitter.com/tefferfish\\\">Amy Teffer</a>,
|
|
1374
|
-
and me.<br />\\n</i></p>\\n\",\"tags\":[\"science\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"h56tk29\",\"blog\":{\"id\":\"h56tk29\",\"title\":\"Jabberwocky
|
|
1375
|
-
Ecology\",\"description\":\"Ethan White and Morgan Ernest's blog for
|
|
1376
|
-
discussing issues and ideas related to ecology and academia.\",\"language\":\"en\",\"favicon\":\"https://secure.gravatar.com/blavatar/805953466a80fcabef50a73dfb96d52b?s=96&d=https%3A%2F%2Fs0.wp.com%2Fi%2Fbuttonw-com.png\",\"feed_url\":\"https://jabberwocky.weecology.org/feed/atom/\",\"home_page_url\":\"https://jabberwocky.weecology.org\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T13:55:58+00:00\",\"indexed_at\":\"2023-01-04\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
|
|
1377
|
-
(.com)\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-03-13T12:16:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/fearkb7-7wz03w9\",\"uuid\":\"7291350e-4828-429a-a188-5bf77c96efda\",\"url\":\"https://syldavia-gazette.org/planetary-defense-healthy-food-slime/\",\"title\":\"Planetary
|
|
1378
|
-
Defense, Healthy Food, Slime, Software Citation, Parthenon Marbles\",\"summary\":\"The
|
|
1379
|
-
Era of Planetary Defense Has BegunIn their textbook Modern Principles of Economics,
|
|
1380
|
-
Tyler and Tabarrok use asteroid defense as an example of a public good.Food
|
|
1381
|
-
fight: FDA is redefining ‘healthy’ and food industry is pushing backLess saturated
|
|
1382
|
-
fat, less sodium, less added sugar; manufacturers say almost no packaged foods
|
|
1383
|
-
would qualify under the agency’s new rules.From Ghostbusters to H.P. Lovecraft:
|
|
1384
|
-
A Cultural History of SlimeA short cultural history of slime.Advancing Software
|
|
1385
|
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Citation...\",\"date_published\":\"2023-03-08T21:30:00Z\",\"date_modified\":\"2023-04-13T13:58:33Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
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Fenner\"}],\"image\":\"https://digitalpress.fra1.cdn.digitaloceanspaces.com/gtpg506/2023/04/Elgin_Marbles_east_pediment.jpg\",\"content_html\":\"
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<h3 id=\\\"the-era-of-planetary-defense-has-begun\\\"><a href=\\\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html?ref=syldavia-gazette.org\\\">The
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Era of Planetary Defense Has Begun</a></h3><p>In their textbook <em>Modern
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Principles of Economics</em>, Tyler and Tabarrok use asteroid defense as an
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example of a public good.</p><h3 id=\\\"food-fight-fda-is-redefining-%E2%80%98healthy%E2%80%99-and-food-industry-is-pushing-back\\\"><a
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href=\\\"https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/?ref=syldavia-gazette.org\\\">Food
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fight: FDA is redefining ‘healthy’ and food industry is pushing back</a></h3><p>Less
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saturated fat, less sodium, less added sugar; manufacturers say almost no
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packaged foods would qualify under the agency’s new rules.</p><h3 id=\\\"from-ghostbusters-to-hp-lovecraft-a-cultural-history-of-slime\\\"><a
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href=\\\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/?ref=syldavia-gazette.org\\\">From
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Ghostbusters to H.P. Lovecraft: A Cultural History of Slime</a></h3><p>A short
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cultural history of slime.</p><h3 id=\\\"advancing-software-citation-implementation-software-citation-workshop-2022\\\"><a
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href=\\\"https://doi.org/10.48550/arXiv.2302.07500?ref=syldavia-gazette.org\\\">Advancing
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Software Citation Implementation (Software Citation Workshop 2022)</a></h3><p>This
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report outlines a series of collaborative discussions that brought together
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an international group of stakeholders and experts. </p><h3 id=\\\"the-strange-journey-of-the-parthenon-marbles-to-the-british-museum\\\"><a
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href=\\\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum?ref=syldavia-gazette.org\\\">The
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strange journey of the Parthenon Marbles to the British Museum</a></h3><p>Short
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video telling the story of how the Parthenon Marbles were moved from Athens
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to London 200 years ago.</p><hr><h3 id=\\\"references\\\">References</h3><ol><li>Tabarrok
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A. The Era of Planetary Defense Has Begun. Marginal REVOLUTION. Published
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March 8, 2023. Accessed March 28, 2023. <a href=\\\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html?ref=syldavia-gazette.org\\\">https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html</a></li><li>Reiley
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1408
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L. Food fight: FDA is redefining ‘healthy’ and food industry is pushing back.
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<em>Washington Post</em>. <a href=\\\"https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/?ref=syldavia-gazette.org\\\">https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/</a>.
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Published March 6, 2023. Accessed March 28, 2023.</li><li>From Ghostbusters
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to H.P. Lovecraft: A Cultural History of Slime ‹ Literary Hub. Accessed March
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28, 2023. <a href=\\\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/?ref=syldavia-gazette.org\\\">https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/</a></li><li>Bouquin
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D, Trisovic A, Bertuch O, Colón-Marrero E. Advancing Software Citation Implementation
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(Software Citation Workshop 2022). Published online February 15, 2023. doi:<a
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href=\\\"https://doi.org/10.48550/arXiv.2302.07500?ref=syldavia-gazette.org\\\">10.48550/arXiv.2302.07500</a></li><li>The
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strange journey of the Parthenon Marbles to the British Museum | Aeon Videos.
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Aeon. Accessed March 28, 2023. <a href=\\\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum?ref=syldavia-gazette.org\\\">https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum</a></li></ol>
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\",\"tags\":[],\"language\":\"en\",\"references\":[{\"key\":\"ref1\",\"url\":\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html\"},{\"key\":\"ref2\",\"url\":\"https://washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar\"},{\"key\":\"ref3\",\"url\":\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime\"},{\"doi\":\"https://doi.org/10.48550/arxiv.2302.07500\",\"key\":\"ref4\"},{\"key\":\"ref5\",\"url\":\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum\"}],\"blog_id\":\"f4wdg32\",\"blog\":{\"id\":\"f4wdg32\",\"title\":\"Syldavia
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Gazette\",\"description\":\"The Syldavia Gazette is a weekly newsletter that
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re3data.org – the Registry of Research Data Repositories – officially launched.
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The registry is nicely described in a preprint also published this week.re3data.org
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offers researchers, funding organizations, libraries and publishers and overview
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of the heterogeneous research data repository landscape. Information icons
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Fenner"}],"image":"https://blog.front-matter.io/content/images/2022/08/figure2.png","tags":["News"],"language":"en","references":[{"doi":"https://doi.org/10.7287/peerj.preprints.21v1","key":"ref1"},{"doi":"https://doi.org/10.2312/re3.002","key":"ref2"}],"blog_id":"f0m0e38","blog":{"id":"f0m0e38","title":"Front
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cancer risk following computed tomography scans","summary":"Two papers (this
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examine the cancer risks associated with the use of computed tomography (CT)
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