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- 08:12, 2 November 2022 Has DOI::10.48550/arXiv.2209.07493 (hist | edit) [853 bytes] Jonny (talk | contribs) (→Discord: new section)
- 08:12, 2 November 2022 Linked Data (hist | edit) [3,222 bytes] Jonny (talk | contribs) (→Discord: new section)
- 08:12, 2 November 2022 ActivityPub (hist | edit) [3,842 bytes] Jonny (talk | contribs) (→Discord: new section)
- 08:12, 2 November 2022 Mastodon (hist | edit) [4,818 bytes] Jonny (talk | contribs) (→Discord: new section)
- 07:42, 2 November 2022 Testing Wikibot2 (hist | edit) [337 bytes] Jonny (talk | contribs) (→Discord: new section)
- 23:54, 31 October 2022 Testing Wikibot (hist | edit) [978 bytes] Jonny (talk | contribs) (→Discord: new section)
- 12:47, 29 October 2022 Cosma (hist | edit) [199 bytes] ArthurPerret (talk | contribs) (Created page with "Cosma is a document graph visualization tool. It modelizes interlinked Markdown files and renders them as an interactive network in a web interface. More information at https://cosma.graphlab.fr/en/.")
- 12:23, 29 October 2022 Translate Logseq Knowledge Graph to Systems Biology Network Diagrams (hist | edit) [3,542 bytes] AWY (talk | contribs) (Created page with "{{Project |Description=Looking at possibilities to generalized knowledge graph in Logseq based on Discourse Graph developed by Prof. Joel Chan and David Vargas for knowledge synthesis, with the possibility to export the information to Systems biology graphical notation markup language to create the network/graph. |Publications=https://doi.org/10.1515/jib-2020-0016, https://doi.org/10.1016/j.tplants.2010.03.005, https://doi.org/10.1002/psp4.12155 }}") originally created as "Building a knowledge graph in Logseq"
- 09:14, 29 October 2022 Reproducibility (hist | edit) [1,528 bytes] Khinsen (talk | contribs) (Created page with "Reproducibility is one of the cornerstones of the scientific method. If I say "here's what I have done and that's what I found", then someone else should be able to retrace my steps and arrive at the same outcome. Without reproducibility, it is very difficult to verify someone else's work, or to build on it in subsequent work. Over the last 10 to 20 years, many scientific disciplines have experienced a [https://en.wikipedia.org/wiki/Replication_crisis reproducibility cr...")
- 09:03, 29 October 2022 Leibniz (hist | edit) [500 bytes] Khinsen (talk | contribs) (Leibniz is an experimental digital scientific notation for computational physics and chemistry (and maybe more))
- 08:50, 29 October 2022 CNRS (hist | edit) [225 bytes] Khinsen (talk | contribs) (Created page with "The [https://www.cnrs.fr/ Centre National de la Recherche Scientifique] is the largest public research organization in France. It runs research laboratories all over the country, often in cooperation with a nearby university.")
- 18:00, 28 October 2022 Martin Karlsson (hist | edit) [283 bytes] Joelchan (talk | contribs) (Created page with "{{Participant |Timezone=CET (GMT+01:00/GMT+02:00) |Table Assignment=Table 4 }} {{Workshop Submission |Frame=Tool-builder |Materials=https://www.lateral.io/ https://graphlab.addpotion.com/ |Organizer Topics=Decentralization, Incentive Systems, Semantic Web }}")
- 17:58, 28 October 2022 Pooja Upadhyay (hist | edit) [2,504 bytes] Joelchan (talk | contribs) (add new participant)
- 07:41, 28 October 2022 Joel Chan (hist | edit) [240 bytes] Joelchan (talk | contribs) (Created page with "{{Participant |Timezone=America/New York (GMT−05:00/GMT−04:00) |Homepage=joelchan.me |Affiliation=University of Maryland |Interests=HCI, Synthesis, Social Systems, Transdisciplinarity, Discovery, Wikis, Search }} {{Workshop Submission}}")
- 23:24, 27 October 2022 Making New Pages (hist | edit) [1,332 bytes] Jonny (talk | contribs) (Created page with "All pages "already exist" in a wiki. You can replace the current page in the URL of any page, and if it doesn't exist, you will be prompted to create it. Typically pages are created by making links to them so they aren't "orphaned" pages without any means of finding them. tl;dr: Make a link to a new page. Save page. Click on link. Add to new page. Save! == Visual Editor == # Click the Edit button in the top right corner of any page # Insert a new link by clicking the...")
- 23:19, 27 October 2022 Wiki Formatting (hist | edit) [2,141 bytes] Jonny (talk | contribs) (Created page with "== Official Documentation == * [https://www.mediawiki.org/wiki/Help:Formatting Basic Wiki Formatting] * [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Links Links] * [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Lists Lists] * [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Images Images] * [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Tables Tables] == Formatting Example == {| class="wikitable" ! You type !! You get |- | <pre> ==...")
- 23:18, 27 October 2022 How to Think in Wiki (hist | edit) [4,144 bytes] Jonny (talk | contribs) (Created page with "== Getting Started == * Make an account! - Editing is limited to those people with accounts. == Wiki Thinking == Wikis work differently than other types of communicative/collaborative media! * '''No Mistakes''' - Nothing is a mistake in a wiki! You cannot break it! You should feel empowered to play around with the wiki, try anything you want to, because any change can always be reverted! There is never any notion of "completeness" or what a...")
- 01:03, 27 October 2022 Code of Conduct (hist | edit) [658 bytes] Joelchan (talk | contribs) (add code of conduct) Tag: Visual edit
- 00:40, 27 October 2022 Organizers (hist | edit) [4,149 bytes] Joelchan (talk | contribs) (add organizers) Tag: Visual edit
- 20:28, 26 October 2022 Table 5 (hist | edit) [28 bytes] Jonny (talk | contribs) (Created page with "{{Table}} Category:Table")
- 20:28, 26 October 2022 Table 4 (hist | edit) [28 bytes] Jonny (talk | contribs) (Created page with "{{Table}} Category:Table")
- 20:28, 26 October 2022 Table 3 (hist | edit) [28 bytes] Jonny (talk | contribs) (Created page with "{{Table}} Category:Table")
- 20:28, 26 October 2022 Table 2 (hist | edit) [28 bytes] Jonny (talk | contribs) (Created page with "{{Table}} Category:Table")
- 20:26, 26 October 2022 Katherine Baney (hist | edit) [2,002 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=Invisible College }} {{Workshop Submission |Interest=The Invisible College was started in the 1600s by Robert Boyle, of "Boyle's Law". The Academy in Boyle's day had become corrupt; depending on authorities (often the Church) to determine truth, rather than evidence and experiment. Scientists instead convened in the Invisible College to discuss empirical approaches to understanding the wo...")
- 20:26, 26 October 2022 Raphael Walker (hist | edit) [2,169 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=Invisible College }} {{Workshop Submission |Interest=The Invisible College was started in the 1600s by Robert Boyle, of "Boyle's Law". The Academy in Boyle's day had become corrupt; depending on authorities (often the Church) to determine truth, rather than evidence and experiment. Scientists instead convened in the Invisible College to discuss empirical approaches to understanding the wo...")
- 20:25, 26 October 2022 Michael Toomim (hist | edit) [2,028 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=Invisible College }} {{Workshop Submission |Interest=The Invisible College was started in the 1600s by Robert Boyle, of "Boyle's Law". The Academy in Boyle's day had become corrupt; depending on authorities (often the Church) to determine truth, rather than evidence and experiment. Scientists instead convened in the Invisible College to discuss empirical approaches to understanding the wo...")
- 20:23, 26 October 2022 Eran Egmon (hist | edit) [2,069 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=University of Connecticut }} {{Workshop Submission |Interest=My new lab at the University of Washington combines biophysical modeling with experimental measurements to study how cells move their membranes. Our long-term goal is to identify some of the principles that govern the transition from nonliving proteins to living, adapting cells. Such an understanding requires a synthesis of dispa...")
- 20:23, 26 October 2022 Graham Johnson (hist | edit) [2,062 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=Allen Institute }} {{Workshop Submission |Interest=My new lab at the University of Washington combines biophysical modeling with experimental measurements to study how cells move their membranes. Our long-term goal is to identify some of the principles that govern the transition from nonliving proteins to living, adapting cells. Such an understanding requires a synthesis of disparate data...")
- 20:23, 26 October 2022 Maggie Fuqua (hist | edit) [2,071 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=University of Washington }} {{Workshop Submission |Interest=My new lab at the University of Washington combines biophysical modeling with experimental measurements to study how cells move their membranes. Our long-term goal is to identify some of the principles that govern the transition from nonliving proteins to living, adapting cells. Such an understanding requires a synthesis of dispar...")
- 20:22, 26 October 2022 Michael Gartner (hist | edit) [2,072 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=University of Washington }} {{Workshop Submission |Interest=My new lab at the University of Washington combines biophysical modeling with experimental measurements to study how cells move their membranes. Our long-term goal is to identify some of the principles that govern the transition from nonliving proteins to living, adapting cells. Such an understanding requires a synthesis of dispar...")
- 20:22, 26 October 2022 Matthew Akamatsu (hist | edit) [2,071 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Los Angeles (GMT−08:00/GMT−07:00) |Affiliation=University of Washington }} {{Workshop Submission |Interest=My new lab at the University of Washington combines biophysical modeling with experimental measurements to study how cells move their membranes. Our long-term goal is to identify some of the principles that govern the transition from nonliving proteins to living, adapting cells. Such an understanding requires a synthesis of dispar...")
- 20:20, 26 October 2022 Deniz Aydemir (hist | edit) [2,567 bytes] Jonny (talk | contribs) (Created page with "{{Participant}} {{Workshop Submission |Interest=It is becoming increasingly important to create a standard for how knowledge graphs and ontologies can be made interoperable, and I propose solving this with what I am calling a "Discourse Protocol". More and more users are thinking about how best to structure their own research and writing using personal ontologies, and tools like Roam, Logseq, Obsidian, Notion, and now Tana (among others) are continuing to add more ways f...")
- 20:13, 26 October 2022 Arthur Perret (hist | edit) [2,074 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=CET (GMT+01:00/GMT+02:00) |Affiliation=Université Bordeaux Montaigne |Projects=Cosma }} {{Workshop Submission |Interest=I am a doctoral student in information science, I will be defending my thesis in December. I have spent the past few years studying personal documentation, document graphs and the use of hypertext for synthesizing individual knowledge. My findings relate to linking as a knowledge organization process; the epistemology of visuali...")
- 20:08, 26 October 2022 Patrice Lopez (hist | edit) [2,652 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Chicago (GMT−06:00/GMT−05:00) |Projects=SoftCite }} {{Workshop Submission |Interest=We are working to make software visible in the scholarly record, where it matters most to incentivizing high quality software work, and so that researchers, disciplines, and funders of science can all better discuss, analyze, coordinate, and improve our software dependent scientific work. I am interested in the workshop to explore understanding two asp...")
- 20:07, 26 October 2022 James Howison (hist | edit) [2,741 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=America/Chicago (GMT−06:00/GMT−05:00) |Projects=SoftCite }} {{Workshop Submission |Interest=We are working to make software visible in the scholarly record, where it matters most to incentivizing high quality software work, and so that researchers, disciplines, and funders of science can all better discuss, analyze, coordinate, and improve our software dependent scientific work. I am interested in the workshop to explore understanding two asp...")
- 20:04, 26 October 2022 Akila Wijerathna-Yapa (hist | edit) [1,989 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Affiliation=ARC Centre of Excellence for Plant Success, University of Queensland }} {{Workshop Submission |Interest=We use knowledge of networks, multidisciplinary hypothesis-driven mechanistic modeling, molecular plant physiology, genetics, and genomics approach to understand how plants regulate bud outgrowth and discover new network components that facilitate breeding. I am looking forward to learning how the community is using Computer-Supported tools...")
- 19:58, 26 October 2022 Dom Falcao (hist | edit) [1,986 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=CET (GMT+01:00/GMT+02:00) |Affiliation=Deep Science Ventures }} {{Workshop Submission |Interest=In recent years, systems that track knowledge across the sciences, such as knowledge graphs and AI-driven publishing search engines, have grown in popularity. These systems help us find scientific facts but they can't tell us the functions of scientific knowledge or align incentives between researchers, funders and entrepreneurs. This means we can’t k...")
- 19:57, 26 October 2022 Eirini Malliaraki (hist | edit) [1,986 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=CET (GMT+01:00/GMT+02:00) |Affiliation=Deep Science Ventures }} {{Workshop Submission |Interest=In recent years, systems that track knowledge across the sciences, such as knowledge graphs and AI-driven publishing search engines, have grown in popularity. These systems help us find scientific facts but they can't tell us the functions of scientific knowledge or align incentives between researchers, funders and entrepreneurs. This means we can’t k...")
- 06:58, 26 October 2022 Table Assignments (hist | edit) [71 bytes] Jonny (talk | contribs) (Created page with "{{#ask: Category:Table }}")
- 06:57, 26 October 2022 Table 1 (hist | edit) [28 bytes] Jonny (talk | contribs) (Created page with "Category:Table")
- 06:54, 26 October 2022 Konrad Hinsen (hist | edit) [4,310 bytes] Jonny (talk | contribs) (Created page with "{{Participant |Timezone=CET (GMT+01:00/GMT+02:00) |Affiliation=CNRS |Projects=Leibniz }} {{Workshop Submission |Interest=Ever since I started doing computational biophysics research 25 years ago, I have been unhappy with the state of the art in dealing with complex computational models. Then and still now, they are represented in two unconnected forms: a narrative providing the scientific background and a summary, and an optimized (and hence unreadable) piece of simulati...")
- 02:39, 26 October 2022 Workshop Agenda (hist | edit) [10,679 bytes] Joelchan (talk | contribs) (first draft of workshop agenda) Tag: Visual edit
- 02:06, 26 October 2022 Jodi Schneider (hist | edit) [318 bytes] Jodi.a.schneider (talk | contribs) (Created page with "{{Participant |Timezone=America/Chicago (GMT−06:00/GMT−05:00) |Homepage=http://jodischneider.com/jodi.html |Affiliation=University of Illinois at Urbana-Champaign }} {{Workshop Submission}}")
- 02:00, 26 October 2022 Wiki (hist | edit) [2,985 bytes] Jodi.a.schneider (talk | contribs) (initial edit) Tag: Visual edit: Switched
- 23:57, 25 October 2022 Resources (hist | edit) [765 bytes] Jonny (talk | contribs) (Created page with "Submit a new Resource And see Category:Resource for schema, form, and template details. == Documents == {{#ask: Category:Document |?Contributor=Contributor(s) |?Part of |?Topic=Topic(s) |?PDF |?Description |format=broadtable }} == Videos == {{#ask: Category:Document |?Contributor=Contributor(s) |?Part of |?Topic=Topic(s) |?Video |?Description |format=broadtable }} == Code == {{#ask: Category:Document |?Contributor...")
- 03:05, 25 October 2022 Semantic Wiki Guide (hist | edit) [3,322 bytes] Jonny (talk | contribs) (Created page with "This wiki runs [https://www.semantic-mediawiki.org/wiki/Semantic_MediaWiki Semantic Mediawiki] - an extension that lets you declare triplet links with the current page as the subject, a Property which serves as the predicate, and an object with a [https://www.semantic-mediawiki.org/wiki/Help:List_of_datatypes type] specified by the property. Semantic mediawiki lets you declare semantic/triplet links within text with a minor extension to wikilinks...")
- 02:30, 22 October 2022 Participant Onboarding Checklist (hist | edit) [2,618 bytes] Joelchan (talk | contribs) (Created page with "[TODO]")
- 08:54, 21 October 2022 Clustering/Graphing (hist | edit) [3,684 bytes] Jonny (talk | contribs) (Created page with "Up to: Clustering Idk some late night clustering. see ya tomorrow :) class="img-responsive" <syntaxhighlight lang="python"> from autopilot.utils import wiki import requests import graphviz import networkx as nx import pdb from matplotlib import pyplot as plt def unnest(entries:dict): unnested = [] for entry in entries: entry_name = list(entry.keys())[0] nested_entry = entry[entry_name] unnest_entry...")
- 06:41, 21 October 2022 Open Source Attention (hist | edit) [1,064 bytes] Jonny (talk | contribs) (Created page with "{{Project |Homepage= |Description= |Repository URL= }}")
- 06:24, 21 October 2022 Sci2sci (hist | edit) [2,028 bytes] Jonny (talk | contribs) (Created page with "{{Project |Homepage= |Description= |Repository URL= }}")
