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 * [[Related To::HCI]]
-== Notes ==
+== Workshop goals ==
+* Organization
+** Jodi: what can we map (discourse) of this workshop?
+** Jay: we could find a common problem to work on, engaging in cycles of collaboration and competition
+*** Similar to how early cognitive science pioneers proposed studying the mind/brain
+**** Focus on one thing as a discipline and reach a “thorough” description of it
+* Questions for workshop
+** What is needed to build …[missed this part]
+** What is missing from current set of tools
+** Incentivizing more people to get involved in collaborations - social systems
+* Projected outcomes
+** Diagram processes/ types
+** Needs and solutions for collaboration, first principles
+== What could a tool do for synthesis (wiki style topic page) ==
+* Processes within tool
+** - move towards stabilization, but could be never ending - always more things could be added
+* Process (joseph)
+** Individual level:
+** Discovery - finding right set of papers for literature review
+** Sharing papers, notes on how papers were relevant
+** Collaborative:
+** Shared document - shuffle around -organizing -  Documents relevant!
+*** Wiki
+*** Shared document Google doc - - commenting/open topics/prioritization topics to go check out
+**** Hyperlinks (may have scaling issue)
+*** Writing: related work section
+*** Synchronized Chat Room is used for syncing on ideas , coordination - works for small groups with similar background knowledge / shared understanding of concepts that may be implicit
+**** Might break down for larger groups
+**** More diversity of thought & backgrounds
+** Identify gaps - subtopics
+** Pick out things central to paper
+** Iteration,  slack communication - converge
+* Process (Jodi)
+** Individual level
+** Asynchronous: Send people an email about papers to look at.
+*** Linear process - share title first, doi, then abstract. Maybe add ideas about it.
+*** Copying and pasting a bunch of info is cumbersome
+** Early on - overview of the information landscape
+*** “Keyword searching” inside Zotero -> Use of terms related to concept
+** Collaborative: Lab Zotero collection
+*** Literature at the field level
+*** Folders of different subtopics to make sure good coverage
+*** [triaging] Manual auditing process when you are looking at 30+ things
+** Individual level: Later - citation chasing (can sometimes become a rabbit hole)
+*** Citation context are very useful for this because they point to interesting aspects of a paper
+** Writing - one level of synthesis, identifying gaps
+*** Sometimes help realize missing area that needs further exploration
+** Formal scoping review (similar to medical systematic reviews / meta-analysis)
+*** Current tool “EPPI-Reviewer”
+*** Comparable concepts, non-comparable but related, develop an evolving taxonomy (collaborative)
+*** One person developing taxonomy, another commenting - linear - putting papers with concept types into categories
+*** Ontology collaboration - shared vocabulary
+*** Becomes a shared mental model about topic at hand
+** Highly iterative, not same across projects
+** Sometimes use multi-modal formats (e.g. diagrams) for synthesis
+** Concerns: diffuse topics, discussed differently across subdomains
+*** Topics that are under-explored
+*** Empirical research (including case studies) Philosophical research would be out of scope
+== Discussion about tools for synthesis ==
+* Maybe PDFs are not evil?
+** MVP: moving beyond PDFs is hard, so using them as a starting point to gather insights may help (Jay).
+** E.g. claim extraction that users may do from scientific papers, may vary in different paper types (e..g theory)
+** Augmenting PDFs?
+* People consume linearly
+** PDFs/pages/documents provide narratives that are easier to digest than graph
+** Sometimes with evidence maps/databases, it’s nonlinear (practitioner/policy maker searching for interventions)
+** Users may have diverse strategies of sensemaking of narrative formats, bringing in background knowledge
+** What is the right granular level?
+*** Tradeoffs: clear & succinct claims + readability
+** Is the “best” way to write the “best” way to read?
+* The limitation of Wikipedia / large scale collaboration
+** How do you deal with conflicts and disagreements?
+*** The Wisdom of Polarized Crowds (Wikipedia)
+*** Argumentation frameworks (Computational Logic, Rhetoric)
+*** Conflict resolution literature
+** How do you deal with higher coordination costs?
+* How much support can we provide to scholarly and non-scholarly readers beyond PDFs?
+** Distill.pub offers some example explorable essays for inspiration
+*** Excellent guide: <nowiki>https://distill.pub/2020/communicating-with-interactive-articles/</nowiki>
+** Jay did some prototyping of explorable essays for scholars with embedded interactive simulations and received (anecdotal) feedback (old software startup).
+** Thomas is working on this issue (Jay would love to collaborate and chat long-term) with his educational psychology/tech background.
+*** What are the low-hanging fruits?
+*** How can we speed up the process (because it’s time-consuming!)
+**** Motivation to contribute? → Consider awarding credits/tokens with Rescognito (<nowiki>https://rescognito.com/</nowiki>) to brag about.
+***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual)
+**** UI/UX process
+**** Scaffolding
+***** Definitions
+***** Metaphors-analogies
+***** Math annotations
+***** Reillustrating figures and annotating them for clarity
+***** Multi-modal formats of information for sensemaking
+***** Linking to videos, simulations, extra resources for curation purposes
+***** Human-generated summaries
+****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion.
+****** Metadata for information
+* Collaborative synthesis: what interfaces do we need? What solutions exist today? (written from the researcher’s perspective, focusing on digital tools)
+** What interfaces do we need for collaborative synthesis?
+*** We need ways to work with materials.
+**** This includes:
+***** Gathering things (collecting)
+***** Breaking them down (analyzing)
+***** Organizing them (classifying, tagging, linking)
+***** Combining them to create new things (synthesizing)
+***** … ?
+**** This can be done with:
+***** Specialized software (e.g. reference management software for references)
+***** Relational databases, graph databases
+***** Outlining, mind mapping
+***** Hypertext (e.g. wikis, plain text files with wikilinks…)
+***** … ?
+*** We need collaborative writing interfaces that meet our scientific writing needs, which are:
+**** Writing citations, math, footnotes, figures, code, mixing different languages/scripts…
+**** Producing structured output
+**** Automation (e.g. processing citations and generating bibliographies, cross-referencing figure labels, indexes…)
+**** Choice of synchronous/asynchronous editing
+**** Editorial workflow management
+**** … ?
+*** We need ways to navigate and share what we're creating
+**** Lists
+**** Tables
+**** Document views
+**** Graph views
+**** Backlinks
+**** … ?
+** What are our options if we want to do this right now?
+*** Multiple interoperable tools. This can be:
+**** Web applications exchanging data via API?
+***** Any examples?
+**** Decentralized plain text-based solutions, with collaboration enabled by version control software (e.g. Git). Like Manubot but not document/publication centric.
+***** Any examples?
+**** …?
+*** All-in-one solution
+**** Are there existing examples?
+***** Semantic software:
+****** Semantic MediaWiki
+****** Omeka-S
+****** …?
+**** Are there solutions that could be adapted or expanded to meet our needs?
+***** …?
+== Bibliography ==
+=== Useful links ===
+* <nowiki>https://zettlr.com</nowiki>
+** (a little about it)
+* <nowiki>http://www.kialo.com</nowiki>
+** (a little about it)
+* Polymath (link????)
+** Collaborative problem-solving in mathematics.
+* Rescognito (<nowiki>https://rescognito.com/</nowiki>)
+** (a little about it)
+* <nowiki>https://distill.pub/2020/communicating-with-interactive-articles/</nowiki>
+** Excellent guide to Distill.pub
+=== Collaborative writing systems ===
+* Manubot: <nowiki>https://manubot.org</nowiki> (see also related papers below)
+=== Problems/solutions ===
+* Citing often requires page numbers, especially in fields with long documents. HTML does not natively have page numbers or paragraph numbers.
+** Project MUSE papers often have page numbers in the HTML: <nowiki>https://muse.jhu.edu</nowiki> For example:  [End Page 316] here: <nowiki>https://muse.jhu.edu/pub/50/article/781390</nowiki>
+=== Papers and research ===
+Beyond the PDF
+Utopia Docs: <nowiki>https://doi.org/10.1093/bioinformatics/btq383</nowiki>
+Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. <nowiki>https://doi.org/10.1371/journal.pcbi.0010034</nowiki>
+Collaborative writing
+Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. <nowiki>https://doi.org/10.1038/d41586-020-00916-6</nowiki>
+Collaborative writing using Manubot
+Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, et al. (2019) Open collaborative writing with Manubot. PLOS Computational Biology 15(6): e1007128. <nowiki>https://doi.org/10.1371/journal.pcbi.1007128</nowiki>
+Rando, Halie M., Simina M. Boca, Lucy D’Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, and Anthony Gitter. "An open-publishing response to the COVID-19 infodemic." In DISCO2021 at JCDL 2021. CEUR workshop proceedings, vol. 2976. <nowiki>https://ceur-ws.org/Vol-2976/paper-2.pdf</nowiki>
+Collaborative writing using other systems
+Ei Pa Pa Pe-Than, Laura Dabbish, and James D. Herbsleb. 2018. Collaborative Writing on GitHub: A Case Study of a Book Project. In Companion of the 2018 ACM Conference on Computer Supported Cooperative Work and Social Computing (CSCW '18). Association for Computing Machinery, New York, NY, USA, 305–308. <nowiki>https://doi.org/10.1145/3272973.3274083</nowiki>
+Textbook written:
+<nowiki>https://github.com/HoTT/book/</nowiki>
+=== Citation ===
+Trigg on hypertext - typing
+Bluebook citation
+=== Provenance ===
+(sometimes using provenance vocabularies/ontologies)
+On including different points of view: Europeana 1914-1918: <nowiki>http://www.europeana1914-1918.eu/en/explore</nowiki>
+Polarization
+Shi, Feng, Misha Teplitskiy, Eamon Duede, and James A. Evans. "The wisdom of polarized crowds." Nature human behaviour 3, no. 4 (2019): 329-336.  <nowiki>https://doi.org/10.1038/s41562-019-0541-6</nowiki>
+== Original notes ==
 * https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit#

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Revision as of 17:58, 12 November 2022