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Interfaces: Difference between revisions
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== Workshop goals == | == Workshop goals == | ||
* Organization | * '''Organization''' | ||
** Jodi: what can we map (discourse) of this workshop? | ** 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 | ** 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 | *** 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 | **** Focus on one thing as a discipline and reach a “thorough” description of it | ||
* Questions for workshop | * '''Questions for workshop''' | ||
** What is needed to build …[missed this part] | ** What is needed to build …[missed this part] | ||
** What is missing from current set of tools | ** What is missing from current set of tools | ||
** Incentivizing more people to get involved in collaborations - social systems | ** Incentivizing more people to get involved in collaborations - social systems | ||
* Projected outcomes | * '''Projected outcomes''' | ||
** Diagram processes/ types | ** Diagram processes/ types | ||
** Needs and solutions for collaboration, first principles | ** Needs and solutions for collaboration, first principles | ||
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== What could a tool do for synthesis (wiki style topic page) == | == What could a tool do for synthesis (wiki style topic page) == | ||
* Processes within tool | * '''Processes within tool''' | ||
** - move towards stabilization, but could be never ending - always more things could be added | ** - move towards stabilization, but could be never ending - always more things could be added | ||
* Process (joseph) | * Process (joseph) | ||
** Individual level: | ** '''Individual level:''' | ||
** Discovery - finding right set of papers for literature review | ** Discovery - finding right set of papers for literature review | ||
** Sharing papers, notes on how papers were relevant | ** Sharing papers, notes on how papers were relevant | ||
** Collaborative: | ** '''Collaborative:''' | ||
** Shared document - shuffle around -organizing - Documents relevant! | ** Shared document - shuffle around -organizing - Documents relevant! | ||
*** Wiki | *** Wiki | ||
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** Identify gaps - subtopics | ** Identify gaps - subtopics | ||
** Pick out things central to paper | ** Pick out things central to paper | ||
** Iteration, slack communication - converge | ** '''Iteration''', slack communication - converge | ||
* Process (Jodi) | * Process (Jodi) | ||
** Individual level | ** '''Individual level''' | ||
** Asynchronous: Send people an email about papers to look at. | ** Asynchronous: Send people an email about papers to look at. | ||
*** Linear process - share title first, doi, then abstract. Maybe add ideas about it. | *** Linear process - share title first, doi, then abstract. Maybe add ideas about it. | ||
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** Early on - overview of the information landscape | ** Early on - overview of the information landscape | ||
*** “Keyword searching” inside Zotero -> Use of terms related to concept | *** “Keyword searching” inside Zotero -> Use of terms related to concept | ||
** Collaborative: Lab Zotero collection | ** '''Collaborative:''' Lab Zotero collection | ||
*** Literature at the field level | *** Literature at the field level | ||
*** Folders of different subtopics to make sure good coverage | *** Folders of different subtopics to make sure good coverage | ||
*** [triaging] Manual auditing process when you are looking at 30+ things | *** [triaging] Manual auditing process when you are looking at 30+ things | ||
** Individual level: Later - citation chasing (can sometimes become a rabbit hole) | ** '''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 | *** Citation context are very useful for this because they point to interesting aspects of a paper | ||
** Writing - one level of synthesis, identifying gaps | ** Writing - one level of synthesis, identifying gaps | ||
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** Formal scoping review (similar to medical systematic reviews / meta-analysis) | ** Formal scoping review (similar to medical systematic reviews / meta-analysis) | ||
*** Current tool “EPPI-Reviewer” | *** Current tool “EPPI-Reviewer” | ||
*** Comparable concepts, non-comparable but related, develop an evolving taxonomy (collaborative) | *** 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 | *** One person developing taxonomy, another commenting - linear - putting papers with concept types into categories | ||
*** Ontology collaboration - shared vocabulary | *** Ontology collaboration - shared vocabulary | ||
*** Becomes a shared mental model about topic at hand | *** Becomes a shared mental model about topic at hand | ||
** Highly iterative, not same across projects | ** '''Highly iterative, not same across projects''' | ||
** Sometimes use multi-modal formats (e.g. diagrams) for synthesis | ** Sometimes use multi-modal formats (e.g. diagrams) for synthesis | ||
** Concerns: diffuse topics, discussed differently across subdomains | ** Concerns: diffuse topics, discussed differently across subdomains | ||
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== Discussion about tools for synthesis == | == Discussion about tools for synthesis == | ||
* Maybe PDFs are not evil? | * '''Maybe PDFs are not evil?''' | ||
** MVP: moving beyond PDFs is hard, so using them as a starting point to gather insights may help (Jay). | ** 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) | ** E.g. claim extraction that users may do from scientific papers, may vary in different paper types (e..g theory) | ||
** Augmenting PDFs? | ** Augmenting PDFs? | ||
* People consume linearly | * '''People consume linearly''' | ||
** PDFs/pages/documents provide narratives that are easier to digest than graph | ** 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) | ** Sometimes with evidence maps/databases, it’s nonlinear (practitioner/policy maker searching for interventions) | ||
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*** Tradeoffs: clear & succinct claims + readability | *** Tradeoffs: clear & succinct claims + readability | ||
** Is the “best” way to write the “best” way to read? | ** Is the “best” way to write the “best” way to read? | ||
* The limitation of Wikipedia / large scale collaboration | * '''The limitation of Wikipedia / large scale collaboration''' | ||
** How do you deal with conflicts and disagreements? | ** How do you deal with conflicts and disagreements? | ||
*** The Wisdom of Polarized Crowds (Wikipedia) | *** [https://arxiv.org/pdf/1712.06414.pdf The Wisdom of Polarized Crowds] (Wikipedia) | ||
*** Argumentation frameworks (Computational Logic, Rhetoric) | *** Argumentation frameworks (Computational Logic, Rhetoric) | ||
*** Conflict resolution literature | *** Conflict resolution literature | ||
** How do you deal with higher coordination costs? | ** How do you deal with higher coordination costs? | ||
* How much support can we provide to scholarly and non-scholarly readers beyond PDFs? | * '''How much support can we provide to scholarly and non-scholarly readers beyond PDFs?''' | ||
** Distill.pub offers some example explorable essays for inspiration | ** Distill.pub offers some example explorable essays for inspiration | ||
*** Excellent guide: | *** Excellent guide: https://distill.pub/2020/communicating-with-interactive-articles/ | ||
** Jay did some prototyping of explorable essays for scholars with embedded interactive simulations and received (anecdotal) feedback (old software startup). | ** 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. | ** 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? | *** What are the low-hanging fruits? | ||
*** How can we speed up the process (because it’s time-consuming!) | *** How can we speed up the process (because it’s time-consuming!) | ||
**** Motivation to contribute? → Consider awarding credits/tokens with Rescognito ( | **** Motivation to contribute? → Consider awarding credits/tokens with Rescognito (https://rescognito.com/) to brag about. | ||
***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual) | ***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual) | ||
**** UI/UX process | **** UI/UX process | ||
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***** Human-generated summaries | ***** Human-generated summaries | ||
****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion. | ****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion. | ||
****** Metadata for information | ****** Metadata for information | ||
* Collaborative synthesis: what interfaces do we need? What solutions exist today? (written from the researcher’s perspective, focusing on digital tools) | * '''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? | ** '''What interfaces do we need for collaborative synthesis?''' | ||
*** We need ways to work with materials. | *** We need ways to work with materials. | ||
**** This includes: | **** This includes: | ||
***** Gathering things (collecting) | ***** Gathering things (collecting) | ||
***** Breaking them down (analyzing) | ***** Breaking them down ('''analyzing''') | ||
***** Organizing them (classifying, tagging, linking) | ***** Organizing them (classifying, tagging, linking) | ||
***** Combining them to create new things (synthesizing) | ***** Combining them to create new things ('''synthesizing''') | ||
***** … ? | ***** … ? | ||
**** This can be done with: | **** This can be done with: | ||
***** Specialized software (e.g. reference management software for references) | ***** Specialized software (e.g. reference management software for references) | ||
***** Relational databases, graph databases | ***** Relational databases, '''graph databases''' | ||
***** Outlining, mind mapping | ***** Outlining, mind mapping | ||
***** Hypertext (e.g. wikis, plain text files with wikilinks…) | ***** '''Hypertext''' (e.g. wikis, plain text files with wikilinks…) | ||
***** … ? | ***** … ? | ||
*** We need collaborative writing interfaces that meet our scientific writing needs, which are: | *** We need collaborative writing interfaces that meet our scientific writing needs, which are: | ||
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**** Backlinks | **** Backlinks | ||
**** … ? | **** … ? | ||
** What are our options if we want to do this right now? | ** '''What are our options if we want to do this right now?''' | ||
*** Multiple interoperable tools. This can be: | *** Multiple interoperable tools. This can be: | ||
**** Web applications exchanging data via API? | **** Web applications exchanging data via API? | ||
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=== Useful links === | === Useful links === | ||
* | * https://zettlr.com | ||
** (a little about it) | ** (a little about it) | ||
* | * http://www.kialo.com | ||
** (a little about it) | ** (a little about it) | ||
* Polymath (link????) | * Polymath (link????) | ||
** Collaborative problem-solving in mathematics. | ** Collaborative problem-solving in mathematics. | ||
* Rescognito ( | * Rescognito (https://rescognito.com/) | ||
** (a little about it) | ** (a little about it) | ||
* | * https://distill.pub/2020/communicating-with-interactive-articles/ | ||
** Excellent guide to Distill.pub | ** Excellent guide to Distill.pub | ||
=== Collaborative writing systems === | === Collaborative writing systems === | ||
* Manubot: | * Manubot: https://manubot.org (see also related papers below) | ||
=== Problems/solutions === | === Problems/solutions === | ||
* Citing often requires page numbers, especially in fields with long documents. HTML does not natively have page numbers or paragraph numbers. | * 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: | ** Project MUSE papers often have page numbers in the HTML: https://muse.jhu.edu For example: [End Page 316] here: https://muse.jhu.edu/pub/50/article/781390 | ||
=== Papers and research === | === Papers and research === | ||
Beyond the PDF | '''Beyond the PDF''' | ||
Utopia Docs: | Utopia Docs: [https://doi.org/10.1371/journal.pcbi.0010034 https://doi.org/10.1093/bioinformatics/btq383] | ||
Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. | Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. https://doi.org/10.1371/journal.pcbi.0010034 | ||
Collaborative writing | '''Collaborative writing''' | ||
Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. | Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. https://doi.org/10.1038/d41586-020-00916-6 | ||
Collaborative writing using Manubot | '''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. | Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, et al. (2019) Open collaborative writing with Manubot. PLOS Computational Biology 15(6): e1007128. https://doi.org/10.1371/journal.pcbi.1007128 | ||
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. | 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. https://ceur-ws.org/Vol-2976/paper-2.pdf | ||
Collaborative writing using other systems | '''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. | 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. https://doi.org/10.1145/3272973.3274083 | ||
Textbook written: | '''Textbook written:''' | ||
https://github.com/HoTT/book/ | |||
=== Citation === | === Citation === | ||
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(sometimes using provenance vocabularies/ontologies) | (sometimes using provenance vocabularies/ontologies) | ||
On including different points of view: Europeana 1914-1918: | On including different points of view: Europeana 1914-1918: http://www.europeana1914-1918.eu/en/explore | ||
Polarization | [http://www.europeana1914-1918.eu/en/explore 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. | Shi, Feng, Misha Teplitskiy, Eamon Duede, and James A. Evans. "The wisdom of polarized crowds." Nature human behaviour 3, no. 4 (2019): 329-336. https://doi.org/10.1038/s41562-019-0541-6 | ||
== Original notes == | == Original notes == | ||
* https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit# | * https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit# | ||